Journal articles: 'Chemical Shift Perturbations'

1

Stark, Jaime, and Robert Powers. "Rapid Protein−Ligand Costructures Using Chemical Shift Perturbations." Journal of the American Chemical Society 130, no. 2 (January 2008): 535–45. http://dx.doi.org/10.1021/ja0737974.

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2

Kukic, Predrag, Damien Farrell, Lawrence P. McIntosh, Bertrand García-Moreno E., Kristine Steen Jensen, Zigmantas Toleikis, Kaare Teilum, and Jens Erik Nielsen. "Protein Dielectric Constants Determined from NMR Chemical Shift Perturbations." Journal of the American Chemical Society 135, no. 45 (October 31, 2013): 16968–76. http://dx.doi.org/10.1021/ja406995j.

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Artikis, Efrosini, and Charles L. Brooks. "Modeling pH-Dependent NMR Chemical Shift Perturbations in Peptides." Biophysical Journal 117, no. 2 (July 2019): 258–68. http://dx.doi.org/10.1016/j.bpj.2019.06.003.

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4

ten Brink, Tim, Clémentine Aguirre, Thomas E. Exner, and Isabelle Krimm. "Performance of Protein–Ligand Docking with Simulated Chemical Shift Perturbations." Journal of Chemical Information and Modeling 55, no. 2 (October 30, 2014): 275–83. http://dx.doi.org/10.1021/ci500446s.

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González-Ruiz, Domingo, and Holger Gohlke. "Steering Protein−Ligand Docking with Quantitative NMR Chemical Shift Perturbations." Journal of Chemical Information and Modeling 49, no. 10 (October 2, 2009): 2260–71. http://dx.doi.org/10.1021/ci900188r.

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Xu, Yunyao, Dongyu Zhang, Rivkah Rogawski, Crina M. Nimigean, and Ann E. McDermott. "Identifying coupled clusters of allostery participants through chemical shift perturbations." Proceedings of the National Academy of Sciences 116, no. 6 (January 24, 2019): 2078–85. http://dx.doi.org/10.1073/pnas.1811168116.

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Allosteric couplings underlie many cellular signaling processes and provide an exciting avenue for development of new diagnostics and therapeutics. A general method for identifying important residues in allosteric mechanisms would be very useful, but remains elusive due to the complexity of long-range phenomena. Here, we introduce an NMR method to identify residues involved in allosteric coupling between two ligand-binding sites in a protein, which we call chemical shift detection of allostery participants (CAP). Networks of functional groups responding to each ligand are defined through correlated NMR perturbations. In this process, we also identify allostery participants, groups that respond to both binding events and likely play a role in the coupling between the binding sites. Such residues exhibit multiple functional states with distinct NMR chemical shifts, depending on binding status at both binding sites. Such a strategy was applied to the prototypical ion channel KcsA. We had previously shown that the potassium affinity at the extracellular selectivity filter is strongly dependent on proton binding at the intracellular pH sensor. Here, we analyzed proton and potassium binding networks and identified groups that depend on both proton and potassium binding (allostery participants). These groups are viewed as candidates for transmitting information between functional units. The vital role of one such identified amino acid was validated through site-specific mutagenesis, electrophysiology functional studies, and NMR-detected thermodynamic analysis of allosteric coupling. This strategy for identifying allostery participants is likely to have applications for many other systems.

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Yu, Zhuoqin, Pengfei Li, and Kenneth M. Merz. "Using Ligand-Induced Protein Chemical Shift Perturbations To Determine Protein–Ligand Structures." Biochemistry 56, no. 18 (April 27, 2017): 2349–62. http://dx.doi.org/10.1021/acs.biochem.7b00170.

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8

Aguirre, Clémentine, Tim ten Brink, Olivier Cala, Jean-François Guichou, and Isabelle Krimm. "Protein–ligand structure guided by backbone and side-chain proton chemical shift perturbations." Journal of Biomolecular NMR 60, no. 2-3 (September 26, 2014): 147–56. http://dx.doi.org/10.1007/s10858-014-9864-9.

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9

Ju, Dapeng, Wei Zhang, Jiawei Yan, Haijiao Zhao, Wei Li, Jiawen Wang, Meimei Liao, et al. "Chemical perturbations reveal that RUVBL2 regulates the circadian phase in mammals." Science Translational Medicine 12, no. 542 (May 6, 2020): eaba0769. http://dx.doi.org/10.1126/scitranslmed.aba0769.

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Transcriptional regulation lies at the core of the circadian clockwork, but how the clock-related transcription machinery controls the circadian phase is not understood. Here, we show both in human cells and in mice that RuvB-like ATPase 2 (RUVBL2) interacts with other known clock proteins on chromatin to regulate the circadian phase. Pharmacological perturbation of RUVBL2 with the adenosine analog compound cordycepin resulted in a rapid-onset 12-hour clock phase-shift phenotype at human cell, mouse tissue, and whole-animal live imaging levels. Using simple peripheral injection treatment, we found that cordycepin penetrated the blood-brain barrier and caused rapid entrainment of the circadian phase, facilitating reduced duration of recovery in a mouse jet-lag model. We solved a crystal structure for human RUVBL2 in complex with a physiological metabolite of cordycepin, and biochemical assays showed that cordycepin treatment caused disassembly of an interaction between RUVBL2 and the core clock component BMAL1. Moreover, we showed with spike-in ChIP-seq analysis and binding assays that cordycepin treatment caused disassembly of the circadian super-complex, which normally resides at E-box chromatin loci such as PER1, PER2, DBP, and NR1D1. Mathematical modeling supported that the observed type 0 phase shifts resulted from derepression of E-box clock gene transcription.

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Kharche, Shalmali, Manali Joshi, Amitabha Chattopadhyay, and Durba Sengupta. "Conformational plasticity and dynamic interactions of the N-terminal domain of the chemokine receptor CXCR1." PLOS Computational Biology 17, no. 5 (May 20, 2021): e1008593. http://dx.doi.org/10.1371/journal.pcbi.1008593.

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The dynamic interactions between G protein-coupled receptors (GPCRs) and their cognate protein partners are central to several cell signaling pathways. For example, the association of CXC chemokine receptor 1 (CXCR1) with its cognate chemokine, interleukin-8 (IL8 or CXCL8) initiates pathways leading to neutrophil-mediated immune responses. The N-terminal domain of chemokine receptors confers ligand selectivity, but unfortunately the conformational dynamics of this intrinsically disordered region remains unresolved. In this work, we have explored the interaction of CXCR1 with IL8 by microsecond time scale coarse-grain simulations, complemented by atomistic models and NMR chemical shift predictions. We show that the conformational plasticity of the apo-receptor N-terminal domain is restricted upon ligand binding, driving it to an open C-shaped conformation. Importantly, we corroborated the dynamic complex sampled in our simulations against chemical shift perturbations reported by previous NMR studies and show that the trends are similar. Our results indicate that chemical shift perturbation is often not a reporter of residue contacts in such dynamic associations. We believe our results represent a step forward in devising a strategy to understand intrinsically disordered regions in GPCRs and how they acquire functionally important conformational ensembles in dynamic protein-protein interfaces.

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11

Lehmann, Teresa, Claudio Luchinat, and Mario Piccioli. "Redox-Related Chemical Shift Perturbations on Backbone Nuclei of High-Potential Iron−Sulfur Proteins." Inorganic Chemistry 41, no. 6 (March 2002): 1679–83. http://dx.doi.org/10.1021/ic010761i.

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12

Piazza, Michael, J. Guy Guillemette, and Thorsten Dieckmann. "Chemical shift perturbations induced by residue specific mutations of CaM interacting with NOS peptides." Biomolecular NMR Assignments 9, no. 2 (January 21, 2015): 299–302. http://dx.doi.org/10.1007/s12104-015-9596-0.

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13

SOLAZ-PORTOLÉS, Joan Josep, and Carlos CAURIN. "METHODOLOGY FOR PREDICTING CHEMICAL EQUILIBRIA SHIFT: CHANGING SYSTEM COMPOSITION AT CONSTANT TEMPERATURE." Periódico Tchê Química 09, no. 18 (August 20, 2012): 6–12. http://dx.doi.org/10.52571/ptq.v9.n18.2012.6_periodico18_pgs_6_12.pdf.

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The subject of perturbations of an equilibrium system and the direction in which it shifts as it moves towards a new equilibrium is an important aspect of general and physical chemistry courses. Of particular importance is students' ability to predict the effects of changing conditions on the position of chemical equilibrium. On a teaching context, the Le Chatelier's principle is still used as an infallible principle without showing its limitations which can lead to very important misconceptions. In this paper it is presented a teaching methodology to avoid the Le Chatelier’s qualitative rule. This methodology is based on extent of reaction, affinity of reaction, and thermodynamic potentials. Focusing on the effects of adding more reactants or products on chemical equilibrium (at constant temperature), our proposal gives the mathematical expression of the variation of the extent of reaction with the infinitesimal variation in the number of moles, and it allows to make exact predictions about the evolution of a perturbed chemical equilibrium system.

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14

Creutznacher, Robert, Eric Schulze, Georg Wallmann, Thomas Peters, Matthias Stein, and Alvaro Mallagaray. "Chemical‐Shift Perturbations Reflect Bile Acid Binding to Norovirus Coat Protein: Recognition Comes in Different Flavors." ChemBioChem 21, no. 7 (April 2020): 1007–21. http://dx.doi.org/10.1002/cbic.201900572.

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15

Moriya, Jun, Masayoshi Sakakura, Yuji Tokunaga, R. Scott Prosser, and Ichio Shimada. "An NMR method for the determination of protein binding interfaces using TEMPOL-induced chemical shift perturbations." Biochimica et Biophysica Acta (BBA) - General Subjects 1790, no. 10 (October 2009): 1368–76. http://dx.doi.org/10.1016/j.bbagen.2009.06.001.

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16

Harris, Robin K., Edwin D. Becker, Sonia M. Cabral de Menezes, Pierre Granger, Roy E. Hoffman, and Kurt W. Zilm. "Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008)." Pure and Applied Chemistry 80, no. 1 (January 1, 2008): 59–84. http://dx.doi.org/10.1351/pac200880010059.

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IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem.73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the 1H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3-(trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a parts per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating 13C NMR chemical shifts in solids to the scales used for high-resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids is reviewed in some detail, and recommendations are given for best practice.

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17

McCoy, Mark A., and Daniel F. Wyss. "Spatial Localization of Ligand Binding Sites from Electron Current Density Surfaces Calculated from NMR Chemical Shift Perturbations." Journal of the American Chemical Society 124, no. 39 (October 2002): 11758–63. http://dx.doi.org/10.1021/ja026166c.

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18

Wang, Bing, Lance M. Westerhoff, and Kenneth M. Merz. "A Critical Assessment of the Performance of Protein−Ligand Scoring Functions Based on NMR Chemical Shift Perturbations." Journal of Medicinal Chemistry 50, no. 21 (October 2007): 5128–34. http://dx.doi.org/10.1021/jm070484a.

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19

Lecoq, Lauriane, Catherine Bougault, Sébastien Triboulet, Vincent Dubée, Jean-Emmanuel Hugonnet, Michel Arthur, and Jean-Pierre Simorre. "Chemical shift perturbations induced by the acylation of Enterococcus faecium l,d-transpeptidase catalytic cysteine with ertapenem." Biomolecular NMR Assignments 8, no. 2 (August 2, 2013): 339–43. http://dx.doi.org/10.1007/s12104-013-9513-3.

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20

Liu, Yu-Nan, Yen-Ting Lai, Wei-I. Chou, Margaret Dah-Tsyr Chang, and Ping-Chiang Lyu. "Solution structure of family 21 carbohydrate-binding module from Rhizopus oryzae glucoamylase." Biochemical Journal 403, no. 1 (March 13, 2007): 21–30. http://dx.doi.org/10.1042/bj20061312.

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CBMs (carbohydrate-binding modules) function independently to assist carbohydrate-active enzymes. Family 21 CBMs contain approx. 100 amino acid residues, and some members have starchbinding functions or glycogen-binding activities. We report here the first structure of a family 21 CBM from the SBD (starch-binding domain) of Rhizopus oryzae glucoamylase (RoCBM21) determined by NMR spectroscopy. This CBM has a β-sandwich fold with an immunoglobulin-like structure. Ligand-binding properties of RoCBM21 were analysed by chemical-shift perturbations and automated docking. Structural comparisons with previously reported SBDs revealed two types of topologies, namely type I and type II, with CBM20, CBM25, CBM26 and CBM41 showing type I topology, with CBM21 and CBM34 showing type II topology. According to the chemical-shift perturbations, RoCBM21 contains two ligand-binding sites. Residues in site II are similar to those found in the family 20 CBM from Aspergillus niger glucoamylase (AnCBM20). Site I, however, is embedded in a region with unique sequence motifs only found in some members of CBM21s. Additionally, docking of β-cyclodextrin and malto-oligosaccharides highlights that side chains of Y83 and W47 (one-letter amino acid code) form the central part of the conserved binding platform in the SBD. The structure of RoCBM21 provides the first direct evidence of the structural features and the basis for protein–carbohydrate recognition from an SBD of CBM21.

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21

Sergeyev, Ivan V., and Ann E. McDermott. "ACCEPT-NMR: A New Tool for the Analysis of Crystal Contacts and Their Links to NMR Chemical Shift Perturbations." Journal of Crystallization Process and Technology 03, no. 01 (2013): 12–27. http://dx.doi.org/10.4236/jcpt.2013.31003.

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22

McCoy, Mark A., and Daniel F. Wyss. "Structures of Protein−Protein Complexes Are Docked Using Only NMR Restraints from Residual Dipolar Coupling and Chemical Shift Perturbations." Journal of the American Chemical Society 124, no. 10 (March 2002): 2104–5. http://dx.doi.org/10.1021/ja017242z.

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23

Wang, Bing, and Kenneth M. Merz. "Validation of the Binding Site Structure of the Cellular Retinol-Binding Protein (CRBP) by Ligand NMR Chemical Shift Perturbations." Journal of the American Chemical Society 127, no. 15 (April 2005): 5310–11. http://dx.doi.org/10.1021/ja042616k.

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24

Gardiennet, Carole, Thomas Wiegand, Alexandre Bazin, Riccardo Cadalbert, Britta Kunert, Denis Lacabanne, Irina Gutsche, Laurent Terradot, Beat H. Meier, and Anja Böckmann. "Solid-state NMR chemical-shift perturbations indicate domain reorientation of the DnaG primase in the primosome of Helicobacter pylori." Journal of Biomolecular NMR 64, no. 3 (March 2016): 189–95. http://dx.doi.org/10.1007/s10858-016-0018-0.

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25

Sixl, F., R. W. King, M. Bracken, and J. Feeney. "19F-n.m.r. studies of ligand binding to 5-fluorotryptophan- and 3-fluorotyrosine-containing cyclic AMP receptor protein from Escherichia coli." Biochemical Journal 266, no. 2 (March 1, 1990): 545–52. http://dx.doi.org/10.1042/bj2660545.

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Two fluorine-containing analogues of the cyclic AMP receptor protein (CRP) from Escherichia coli were prepared by biosynthetic incorporation of 5-fluorotryptophan (5-F-Trp) and 3-fluorotyrosine (3-F-Tyr). The 19F-n.m.r. spectrum of the [5-F-Trp]CRP showed two signals corresponding to the two tryptophan residues, and that of the [3-F-Tyr]CRP showed six signals (two overlapping) corresponding to the six tyrosine residues: these results are as expected for a symmetrical dimer. A comparison of the 19F-n.m.r. spectra of the CRP analogues in the presence and in the absence of cyclic AMP reveals that the chemical shifts of both tryptophan residues and of two of the six tyrosine residues show differences. Since none of these residues is in direct contact with the bound nucleotide (although Trp-85 is fairly close), these shift changes must arise from induced conformational effects. The 19F-n.m.r. spectra of complexes with cyclic GMP showed chemical-shift perturbations different from those caused by cyclic AMP, indicating that different conformational changes are induced by the binding of cyclic GMP. The 19F-n.m.r. spectrum of the complex of [3-F-Tyr]CRP with tubercidin 3′,5′-(cyclic)monophosphate (which can activate transcription) showed essentially the same chemical-shift changes as seen for the cyclic AMP complex, indicating that similar conformational changes have been induced by the nucleotide binding. [3-F-Tyr]CRP in the presence of an equimolar amount of the 20 bp self-complementary DNA oligomer 5′-AATGTGAGTTAACTCACATT-3′ and excess cyclic AMP gave an 19F-n.m.r. spectrum that was almost identical with that for the [3-F-Tyr]CRP-cyclic AMP complex, indicating that the binding of DNA does not induce significant conformational changes involving the tyrosine residues. Proteolysis of [3-F-Tyr]CRP with chymotrypsin produced a 31 kDa fragment that is a dimer containing the cyclic AMP-binding domain. This fragment contains five of the six tyrosine residues, and its 19F-n.m.r. chemical shifts were essentially the same as those of the intact protein except for one missing signal (signal F): this signal could be assigned to Tyr-206 and shown to be unperturbed by the binding of cyclic nucleotide to the intact [3-F-Tyr]CRP. The similarity of the 19F-n.m.r. chemical shifts in the alpha-fragment and the intact CRP indicates that the alpha-fragment retains the same structure as found in the intact protein.(ABSTRACT TRUNCATED AT 400 WORDS)

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26

Le Hir, G., Y. Goddéris, Y. Donnadieu, and G. Ramstein. "A geochemical modelling study of the evolution of the chemical composition of seawater linked to a "snowball" glaciation." Biogeosciences 5, no. 1 (February 21, 2008): 253–67. http://dx.doi.org/10.5194/bg-5-253-2008.

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Abstract. The Snowball Earth theory initially proposed by Kirschvink (1992) to explain the Neoproterozoic glacial episodes, suggested that the Earth was fully ice-covered at 720 Ma (Sturtian episode) and 640 Ma (Marinoan episode). This succession of extreme climatic crises induced environmental perturbations which are considered as a strong selective pressure on the evolution of life (Hoffman et al., 1998). Using a numerical model of carbon-alkalinity global cycles, we quantify environmental stresses caused by a global glaciation. According to our results, we suggest that during global glaciations, the ocean becomes acidic (pH~6), and undersaturated with respect to carbonate minerals. Moreover the quick transition from ice-house to greenhouse conditions implies an abrupt and large shift of the oceanic surface temperature which causes an extended hypoxia. The intense continental weathering, in the aftermath of the glaciation, deeply affects the seawater composition inducing rapid changes in terms of pH and alkalinity. We also propose a new timing for post glacial perturbations and for the cap carbonates deposition, ~2 Myr instead of 200 kyr as suggested in a previous modelling study. In terms of Precambrian life sustainability, seawater pH modifications appear drastic all along the glaciation, but we suggest that the buffering action of the oceanic crust dissolution avoids a total collapse of biological productivity. But short-lived and large post-glacial perturbations are more critical and may have played the role of an environmental filter proposed in the classic snowball Earth theory. Although the link between environmental changes and life sustainability cannot be modelled accurately, we suggest that only a permissive life (Knoll, 2003) may explain the relative continuity in microfossils diversity observed before, during and after Neoproterozoic glaciation events.

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27

Peroza, Carlos A., Fu Chen, Dale E. Wurster, and Santhana Mariappan Velupillai. "Solubilization of organics I: 1 H NMR chemical shift perturbations, diffusometry, and NOESY indicate biphenyls internalize in micelles formed by cetyltrimethylammonium bromide." Magnetic Resonance in Chemistry 57, no. 12 (June 20, 2019): 1097–106. http://dx.doi.org/10.1002/mrc.4891.

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28

Braesicke, P., J. Keeble, X. Yang, G. Stiller, S. Kellmann, N. L. Abraham, A. Archibald, P. Telford, and J. A. Pyle. "Circulation anomalies in the Southern Hemisphere and ozone changes." Atmospheric Chemistry and Physics 13, no. 21 (November 4, 2013): 10677–88. http://dx.doi.org/10.5194/acp-13-10677-2013.

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Abstract. We report results from two pairs of chemistry-climate model simulations using the same climate model but different chemical perturbations. In each pair of experiments an ozone change was triggered by a simple change in the chemistry. One pair of model experiments looked at the impact of polar stratospheric clouds (PSCs) and the other pair at the impact of short-lived halogenated species on composition and circulation. The model response is complex with both positive and negative changes in ozone concentration, depending on location. These changes result from coupling between composition, temperature and circulation. Even though the causes of the modelled ozone changes are different, the high latitude Southern Hemisphere response in the lower stratosphere is similar. In both pairs of experiments the high-latitude circulation changes, as evidenced by N2O differences, are suggesting a slightly longer-lasting/stronger stratospheric descent in runs with higher ozone destruction (a manifestation of a seasonal shift in the circulation). We contrast the idealised model behaviour with interannual variability in ozone and N2O as observed by the MIPAS instrument on ENVISAT, highlighting similarities of the modelled climate equilibrium changes to the year 2006–2007 in observations. We conclude that the climate system can respond quite sensitively in its seasonal evolution to small chemical perturbations, that circulation adjustments seen in the model can occur in reality, and that coupled chemistry-climate models allow a better assessment of future ozone and climate change than recent CMIP-type models with prescribed ozone fields.

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29

Serrano, Pedro, Margaret A. Johnson, Marcius S. Almeida, Reto Horst, Torsten Herrmann, Jeremiah S. Joseph, Benjamin W. Neuman, et al. "Nuclear Magnetic Resonance Structure of the N-Terminal Domain of Nonstructural Protein 3 from the Severe Acute Respiratory Syndrome Coronavirus." Journal of Virology 81, no. 21 (August 29, 2007): 12049–60. http://dx.doi.org/10.1128/jvi.00969-07.

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ABSTRACT This paper describes the structure determination of nsp3a, the N-terminal domain of the severe acute respiratory syndrome coronavirus (SARS-CoV) nonstructural protein 3. nsp3a exhibits a ubiquitin-like globular fold of residues 1 to 112 and a flexibly extended glutamic acid-rich domain of residues 113 to 183. In addition to the four β-strands and two α-helices that are common to ubiquitin-like folds, the globular domain of nsp3a contains two short helices representing a feature that has not previously been observed in these proteins. Nuclear magnetic resonance chemical shift perturbations showed that these unique structural elements are involved in interactions with single-stranded RNA. Structural similarities with proteins involved in various cell-signaling pathways indicate possible roles of nsp3a in viral infection and persistence.

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30

Fernandes, Ana P., Tiago C. Nunes, Catarina M. Paquete, and Carlos A. Salgueiro. "Interaction studies between periplasmic cytochromes provide insights into extracellular electron transfer pathways of Geobacter sulfurreducens." Biochemical Journal 474, no. 5 (February 20, 2017): 797–808. http://dx.doi.org/10.1042/bcj20161022.

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Geobacter bacteria usually prevail among other microorganisms in soils and sediments where Fe(III) reduction has a central role. This reduction is achieved by extracellular electron transfer (EET), where the electrons are exported from the interior of the cell to the surrounding environment. Periplasmic cytochromes play an important role in establishing an interface between inner and outer membrane electron transfer components. In addition, periplasmic cytochromes, in particular nanowire cytochromes that contain at least 12 haem groups, have been proposed to play a role in electron storage in conditions of an environmental lack of electron acceptors. Up to date, no redox partners have been identified in Geobacter sulfurreducens, and concomitantly, the EET and electron storage mechanisms remain unclear. In this work, NMR chemical shift perturbation measurements were used to probe for an interaction between the most abundant periplasmic cytochrome PpcA and the dodecahaem cytochrome GSU1996, one of the proposed nanowire cytochromes in G. sulfurreducens. The perturbations on the haem methyl signals of GSU1996 and PpcA showed that the proteins form a transient redox complex in an interface that involves haem groups from two different domains located at the C-terminal of GSU1996. Overall, the present study provides for the first time a clear evidence for an interaction between periplasmic cytochromes that might be relevant for the EET and electron storage pathways in G. sulfurreducens.

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31

Park, Sang Ho, Haley Siddiqi, Daniela V. Castro, Anna A. De Angelis, Aaron L. Oom, Charlotte A. Stoneham, Mary K. Lewinski, et al. "Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity." PLOS Pathogens 17, no. 5 (May 18, 2021): e1009519. http://dx.doi.org/10.1371/journal.ppat.1009519.

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SARS-CoV-2 is the novel coronavirus that is the causative agent of COVID-19, a sometimes-lethal respiratory infection responsible for a world-wide pandemic. The envelope (E) protein, one of four structural proteins encoded in the viral genome, is a 75-residue integral membrane protein whose transmembrane domain exhibits ion channel activity and whose cytoplasmic domain participates in protein-protein interactions. These activities contribute to several aspects of the viral replication-cycle, including virion assembly, budding, release, and pathogenesis. Here, we describe the structure and dynamics of full-length SARS-CoV-2 E protein in hexadecylphosphocholine micelles by NMR spectroscopy. We also characterized its interactions with four putative ion channel inhibitors. The chemical shift index and dipolar wave plots establish that E protein consists of a long transmembrane helix (residues 8–43) and a short cytoplasmic helix (residues 53–60) connected by a complex linker that exhibits some internal mobility. The conformations of the N-terminal transmembrane domain and the C-terminal cytoplasmic domain are unaffected by truncation from the intact protein. The chemical shift perturbations of E protein spectra induced by the addition of the inhibitors demonstrate that the N-terminal region (residues 6–18) is the principal binding site. The binding affinity of the inhibitors to E protein in micelles correlates with their antiviral potency in Vero E6 cells: HMA ≈ EIPA > DMA >> Amiloride, suggesting that bulky hydrophobic groups in the 5’ position of the amiloride pyrazine ring play essential roles in binding to E protein and in antiviral activity. An N15A mutation increased the production of virus-like particles, induced significant chemical shift changes from residues in the inhibitor binding site, and abolished HMA binding, suggesting that Asn15 plays a key role in maintaining the protein conformation near the binding site. These studies provide the foundation for complete structure determination of E protein and for structure-based drug discovery targeting this protein.

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32

Nygren, Patrik, Lisa M. Span, David T. Moore, Hong Cheng, Heinrich Roder, William F. DeGrado, and Joel S. Bennett. "Analysis of β3 Binding to the c-Src SH3 Domain." Blood 120, no. 21 (November 16, 2012): 383. http://dx.doi.org/10.1182/blood.v120.21.383.383.

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Abstract Abstract 383 An essential component of αIIbβ3-mediated outside-in signaling is activation of the tyrosine kinase c-Src, some of which is constitutively bound via its SH3 domain to the C-terminal Arg759-Gly760-Thr761 (RGT) sequence of the β3 cytoplasmic tail. RGT is quite different from the canonical polyproline sequence recognized by SH3 domains in which a polyproline helix packs against a shallow groove composed of aromatic residues (Tyr93, Tyr95, Tyr139 in c-Src). A specificity pocket located at the end of the groove and composed of residues from the n-Src- and RT-loops affects substrate specificity. Because of the obvious difference between RGT and polyproline sequences, we asked how RGT binds to the c-Src SH3 domain and what implications this has for c-Src regulation by αIIbβ3. Initially, we employed CD spectroscopy and tryptophan (Trp) fluorescence because these techniques are sensitive to changes in the local environment surrounding aromatic residues. However, there were no differences in the CD spectrum of the SH3 domain in absence or presence of the β3 peptide NITYRGT, whereas there was a clear shift in the presence of the core polyproline peptide RPLPPLP. Polyproline binding to Trp in the SH3 specificity pocket also results in a blue shift in Trp fluorescence from 355 nm to 347 nm; however, the fluorescence spectrum was essentially unchanged in the presence of NITYRGT. These experiments suggest that either the interaction of NITYRGT with SH3 is extremely weak and not observed at the concentrations used or occurs outside of the aromatic groove and the specificity pocket. Accordingly, we turned to NMR, a method able to detect weak protein-protein interactions. Two dimensional 1H-15N HSQC spectra of the SH3 domain in the presence of NITYRGT exhibited a number of changes in chemical shift compared to the spectrum in the absence of ligand. Sixteen residues located in the n-Src and RT-loops, grouped around the specificity pocket, had chemical shift changes > 0.05 ppm. The largest changes occurred in residues in or adjacent to the RT-loop, especially residues Arg98, Glu100, and Asp102. Of the resides forming the aromatic groove, only Tyr95 which is adjacent to the specificity pocket was perturbed by NITYRGT. Plots of the chemical shift changes for NH groups in SH3 vs. NITYRGT concentration were linear, indicating that the majority of SH3 domain was unbound. Further, a Kd for NITYRGT binding to SH3, estimated from these experiments, was between 175–350 mM. Next, we obtained HSQC spectra for SH3 in the presence of either RPLPPLP or a negative control peptide NITYEGK. Major perturbations due to RPLPPLP occurred in three regions: residues 98–103 (RT-loop), 116–122 (n-Src loop and specificity pocket), and residues 134–138; residues in the aromatic cluster were unaffected by the ligand. By contrast, only a handful of residues showed small perturbations in the presence of NITYEGK and there was no overlap between the affected residues and those affected by RPLPPLP. In conclusion, our results indicate that compared to polyproline sequences, the C-terminus of the β3 cytoplasmic tail binds to the c-Src SH3 domain in the region of the SH3 specificity pocket. Because chemical shifts for acidic residues located in the RT-loop were particularly sensitive to the presence of NITYRGT, it is likely that Arg759 in β3 makes an important contribution to the interaction. Moreover, we found that the interaction between NITYRGT and the c-Src SH3 domain is substantially weaker than was previously reported for the interaction of β3 with c-Src. This suggest the possibility that a third component is required for this interaction to occur under biological conditions. Recently we found that the β3 cytoplasmic tail in solution has weak affinity for the talin-1 FERM domain, but appending the tail to acidic phospholipids increased its affinity by three orders of magnitude. Since the c-Src SH3 domain contains a conserved patch of basic residues that are necessary for binding to acidic phospholipids, it is possible that the interaction of c-Src with β3 is also a ternary interaction in which protein-lipid interactions play an important role. Disclosures: No relevant conflicts of interest to declare.

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Le Hir, G., Y. Goddéris, Y. Donnadieu, and G. Ramstein. "A geochemical modelling study of the evolution of the chemical composition of seawater linked to a global glaciation: implications for life sustainability." Biogeosciences Discussions 4, no. 3 (June 20, 2007): 1839–76. http://dx.doi.org/10.5194/bgd-4-1839-2007.

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Abstract. The Snowball Earth theory initially proposed by Kirschvink (Kirschvink, 1992) to explain the Neoproterozoic glacial episodes, suggested that the Earth was fully ice-covered at 720 My (Sturtian episode) and 640 My (Marinoan episode). This succession of extreme climatic crises induced a stress which is considered as a strong selective pressure on the evolution of life (Hoffman et al., 1998). However recent biological records (Corsetti, 2006) do not support this theory as little change is observed in the diversity of microfossils outcrops before and after the Marinoan glacial interval. In this contribution we address this apparent paradox. Using a numerical model of carbon-alkalinity global cycles, we quantify several environmental stresses caused by a global glaciation. We suggest that during global glaciations, the ocean becomes acidic (pH~6), and unsaturated with respect to carbonate minerals. Moreover the quick transition from ice-house to greenhouse conditions implies an abrupt and large shift of the oceanic surface temperature which causes an extended hypoxia. The intense continental weathering, in the aftermath of the glaciation, deeply affects the seawater composition inducing rapid changes in terms of pH and alkalinity. We also propose a new timing for post glacial perturbations and for the cap carbonates deposition, ~2 Myr instead of 200 kyr as suggested in a previous modelling study. In terms of Precambrian life sustainability, seawater pH modifications appear drastic all along the glaciation, but we show that the buffering action of the oceanic crust dissolution processes avoids a total collapse of biological productivity. In opposite short-lived and large post-glacial perturbations are more critical and may have played a role of environmental filter suggested in the classic snowball Earth theory. Only a permissive life (prokaryotes or simple eukaryotes) may explain the relative continuity in microfossils diversity observed before, during and after Neoproterozoic glaciation events.

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Danhart, Eric M., Marina Bakhtina, William A. Cantara, Alexandra B. Kuzmishin, Xiao Ma, Brianne L. Sanford, Oscar Vargas-Rodriguez, et al. "Conformational and chemical selection by a trans-acting editing domain." Proceedings of the National Academy of Sciences 114, no. 33 (August 2, 2017): E6774—E6783. http://dx.doi.org/10.1073/pnas.1703925114.

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Molecular sieves ensure proper pairing of tRNAs and amino acids during aminoacyl-tRNA biosynthesis, thereby avoiding detrimental effects of mistranslation on cell growth and viability. Mischarging errors are often corrected through the activity of specialized editing domains present in some aminoacyl-tRNA synthetases or via single-domain trans-editing proteins. ProXp-ala is a ubiquitous trans-editing enzyme that edits Ala-tRNAPro, the product of Ala mischarging by prolyl-tRNA synthetase, although the structural basis for discrimination between correctly charged Pro-tRNAPro and mischarged Ala-tRNAAla is unclear. Deacylation assays using substrate analogs reveal that size discrimination is only one component of selectivity. We used NMR spectroscopy and sequence conservation to guide extensive site-directed mutagenesis of Caulobacter crescentus ProXp-ala, along with binding and deacylation assays to map specificity determinants. Chemical shift perturbations induced by an uncharged tRNAPro acceptor stem mimic, microhelixPro, or a nonhydrolyzable mischarged Ala-microhelixPro substrate analog identified residues important for binding and deacylation. Backbone 15N NMR relaxation experiments revealed dynamics for a helix flanking the substrate binding site in free ProXp-ala, likely reflecting sampling of open and closed conformations. Dynamics persist on binding to the uncharged microhelix, but are attenuated when the stably mischarged analog is bound. Computational docking and molecular dynamics simulations provide structural context for these findings and predict a role for the substrate primary α-amine group in substrate recognition. Overall, our results illuminate strategies used by a trans-editing domain to ensure acceptance of only mischarged Ala-tRNAPro, including conformational selection by a dynamic helix, size-based exclusion, and optimal positioning of substrate chemical groups.

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35

Sergeyev, Ivan V., Boris Itin, Rivkah Rogawski, Loren A. Day, and Ann E. McDermott. "Efficient assignment and NMR analysis of an intact virus using sequential side-chain correlations and DNP sensitization." Proceedings of the National Academy of Sciences 114, no. 20 (May 1, 2017): 5171–76. http://dx.doi.org/10.1073/pnas.1701484114.

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An experimental strategy has been developed to increase the efficiency of dynamic nuclear polarization (DNP) in solid-state NMR studies. The method makes assignments simpler, faster, and more reliable via sequential correlations of both side-chain and Cα resonances. The approach is particularly suited to complex biomolecules and systems with significant chemical-shift degeneracy. It was designed to overcome the spectral congestion and line broadening that occur due to sample freezing at the cryogenic temperatures required for DNP. Nonuniform sampling (NUS) is incorporated to achieve time-efficient collection of multidimensional data. Additionally, fast (25 kHz) magic-angle spinning (MAS) provides optimal sensitivity and resolution. Data collected in <1 wk produced a virtually complete de novo assignment of the coat protein of Pf1 virus. The peak positions and linewidths for samples near 100 K are perturbed relative to those near 273 K. These temperature-induced perturbations are strongly correlated with hydration surfaces.

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36

Hibbert, Richard G., Peter Teriete, Gabrielle J. Grundy, Rebecca L. Beavil, Rajko Reljić, V. Michael Holers, Jonathan P. Hannan, Brian J. Sutton, Hannah J. Gould, and James M. McDonnell. "The structure of human CD23 and its interactions with IgE and CD21." Journal of Experimental Medicine 202, no. 6 (September 19, 2005): 751–60. http://dx.doi.org/10.1084/jem.20050811.

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The low-affinity immunoglobulin E (IgE) receptor, CD23 (FcεRII), binds both IgE and CD21 and, through these interactions, regulates the synthesis of IgE, the antibody isotype that mediates the allergic response. We have determined the three-dimensional structure of the C-type lectin domain of CD23 in solution by nuclear magnetic resonance spectroscopy. An analysis of concentration-dependent chemical shift perturbations have allowed us to identify the residues engaged in self-association to the trimeric state, whereas ligand-induced changes have defined the binding sites for IgE and CD21. The results further reveal that CD23 can bind both ligands simultaneously. Despite the C-type lectin domain structure, none of the interactions require calcium. We also find that IgE and CD23 can interact to form high molecular mass multimeric complexes. The interactions that we have described provide a solution to the paradox that CD23 is involved in both up- and down-regulation of IgE and provide a structural basis for the development of inhibitors of allergic disease.

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Chhabra, Sandeep, Olan Dolezal, Meghan Hattarki, Thomas S. Peat, Jamie S. Simpson, and James D. Swarbrick. "Fragment Screening on Staphylococcus aureus HPPK – a Folate Pathway Target." Australian Journal of Chemistry 66, no. 12 (2013): 1537. http://dx.doi.org/10.1071/ch13298.

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An NMR-based screen of a commercially available fragment library was performed on the folate pathway antimicrobial target, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase from Staphylococcus aureus (SaHPPK). Initial 1D saturation transfer difference-NMR screening resulted in an impractically high hit rate (43 %), which advocated the use of a strategy based on 2D (SOFAST) 15N HMQC NMR experiments. Chemical shift perturbations were used to identify, validate, and map the location of 16 initial binders (hit rate of 2 %). Fourteen compounds were purchased based on an identified thioamide pharmacophore. Binding affinities (Kd) were measured by surface plasmon resonance, revealing a modest improvement in potency over the initial 16 hits, with the best fragment found to bind to the apo enzyme with a Kd of 420 µM, corresponding to a ligand efficiency of 1.8 kJ/heavy atom. Four fragments identified represent useful starting points for the generation of leads that may ultimately be developed into new antimicrobial agents.

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38

Madejová, J., J. Bujdák, S. Petit, and P. Komadel. "Effects of chemical composition and temperature of heating on the infrared spectra of Li-saturated dioctahedral smectites. (I) Mid-infrared region." Clay Minerals 35, no. 5 (December 2000): 739–51. http://dx.doi.org/10.1180/000985500547160.

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AbstractInfrared spectroscopy in the mid-IR region was used to follow the structural changes occurring in five Li-saturated dioctahedral smectites upon heating. The smectites included three montmorillonites, an Fe-beidellite and a ferruginous smectite. Fixation of Li+ ions in the structure even upon heating at 120°C caused the appearance of an AlMgLiOH-stretching band near 3670 cm–1 in the spectra of all three montmorillonites. This band confirmed the presence of Li(I) in the previously vacant octahedral positions in montmorillonites. No similar band was observed in the spectra of ferruginous heated smectites with prevailing tetrahedral charge. A gradual upward frequency shift and decrease in intensity of the AlAlOH-bending band showed that Li(I) present in the hexagonal cavities causes pronouncedperturbation of this OH-bending mode. The Li(I) present in the octahedral sheets causes small perturbations of the OH-bending mode near 850 cm–1 and activation of a new OH-bending mode near 803 cm–1. Reversible changes in the positions of the stretching Si–O and bending OH bands in the spectra of Fe-beidellite and a ferruginous smectite proved that Li was present in these minerals primarily in the hexagonal holes of the tetrahedral sheets.

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Amero, C. D., J. J. Arnold, I. M. Moustafa, C. E. Cameron, and M. P. Foster. "Identification of the oriI-Binding Site of Poliovirus 3C Protein by Nuclear Magnetic Resonance Spectroscopy." Journal of Virology 82, no. 9 (February 27, 2008): 4363–70. http://dx.doi.org/10.1128/jvi.02087-07.

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ABSTRACT Replication of picornaviral genomes requires recognition of at least three cis-acting replication elements: oriL, oriI, and oriR. Although these elements lack an obvious consensus sequence or structure, they are all recognized by the virus-encoded 3C protein. We have studied the poliovirus 3C-oriI interaction in order to begin to decipher the code of RNA recognition by picornaviral 3C proteins. oriI is a stem-loop structure that serves as the template for uridylylation of the peptide primer VPg by the viral RNA-dependent RNA polymerase. In this report, we have used nuclear magnetic resonance (NMR) techniques to study 3C alone and in complex with two single-stranded RNA oligonucleotides derived from the oriI stem. The 1H-15N spectra of 3C recorded in the presence of these RNAs revealed site-specific chemical shift perturbations. Residues that exhibit significant perturbations are primarily localized in the amino terminus and in a highly conserved loop between residues 81 and 89. In general, the RNA-binding site defined in this study is consistent with predictions based on biochemical and mutagenesis studies. Although some residues implicated in RNA binding by previous studies are perturbed in the 3C-RNA complex reported here, many are unique. These studies provide unique site-specific insight into residues of 3C that interact with RNA and set the stage for detailed structural investigation of the 3C-RNA complex by NMR. Interpretation of our results in the context of an intact oriI provides insight into the architecture of the picornavirus VPg uridylylation complex.

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40

Carrick, F. E., M. G. Hinds, K. A. McNeil, J. C. Wallace, B. E. Forbes, and R. S. Norton. "Interaction of insulin-like growth factor (IGF)-I and -II with IGF binding protein-2: mapping the binding surfaces by nuclear magnetic resonance." Journal of Molecular Endocrinology 34, no. 3 (June 2005): 685–98. http://dx.doi.org/10.1677/jme.1.01756.

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The interaction of IGF binding protein-2 (IGFBP-2) with IGF-I and -II has been investigated in solution using nuclear magnetic resonance (NMR) spectroscopy. Chemical shift perturbations in 15N- and 2H/15N-labelled IGF-I or -II upon binding to unlabelled thioredoxin-tagged bovine IGFBP-2 (Trx1–279IGFBP-2) have been monitored to identify residues involved directly in the binding interaction as well as any affected by conformational changes associated with the interaction. A key step in obtaining high-quality spectra of the complexes was the use of transverse relaxation optimised spectroscopy (TROSY) methods with partially deuterated ligands. Indeed, because the effects of conformational averaging and aggregation are eliminated in IGF-I and -II bound to IGFBP-2, the spectra of the complexes are actually superior to those of the free ligands. Comparison of our results with the crystal structure of the complex between IGF-I and an N-terminal fragment of IGFBP-5 allowed identification of those residues perturbed by the C-domain of IGFBP-2. Other perturbations, such as those of Gly19 and Asp20 of IGF-I (and the corresponding residues in IGF-II) – which are located in a reverse turn linking N-domain and C-domain interactive surfaces – are due to local conformational changes in the IGF-I and -II. Our results confirm that the C-domain of IGFBP-2 plays a key role in binding regions of IGF-I and -II that are also involved in binding to the type-1 IGF receptor and thereby blocking ligand binding to this receptor.

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41

Song, Yi, Geoffrey J. Gilleaudeau, Thomas J. Algeo, D. Jeffrey Over, Timothy W. Lyons, Ariel D. Anbar, and Shucheng Xie. "Biomarker evidence of algal-microbial community changes linked to redox and salinity variation, Upper Devonian Chattanooga Shale (Tennessee, USA)." GSA Bulletin 133, no. 1-2 (June 29, 2020): 409–24. http://dx.doi.org/10.1130/b35543.1.

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Abstract Late Devonian marine systems were characterized by major environmental perturbations and associated biotic community changes linked to climate change and widespread oceanic anoxia. Here, we provide high-resolution lipid biomarker chemostratigraphic records from the Upper Devonian Chattanooga Shale (Tennessee, USA) to investigate algal-microbial community changes in the southern Illinois Basin that were related to contemporaneous shifts in marine redox (as proxied by trace metals, Fe-species, and Corg/P) and salinity conditions (as proxied by B/Ga, Sr/Ba, and S/total organic carbon). The Frasnian was characterized by dominantly bacterial lipids (high hopane/sterane), near-marine salinity, and a shift from oxic to increasingly reducing conditions in response to increasing organic carbon sinking fluxes. Aryl isoprenoids and aryl isoprenoid ratios reveal that the O2-H2S chemocline was unstable and intermittently shallow (i.e., within the photic zone). The Frasnian-Famennian boundary was marked by a shift in microalgal community composition toward green algal (e.g., prasinophyte) dominance (lower C27 and higher C28 and C29 steranes), a sharp reduction in watermass salinity, and a stable O2-H2S chemocline below the photic zone, conditions that persisted until nearly the end of the Famennian. We infer that changing watermass conditions, especially a sharp reduction in salinity to possibly low-brackish conditions (<10 psu), were the primary cause of concurrent changes in the microalgal community, reflecting tolerance of low-salinity conditions by green algae. Transient spikes in moretane/hopane (M/H) ratios may record enhanced terrestrial weathering at the Frasnian-Famennian and Devonian–Carboniferous boundaries, triggered by coeval glacio-eustatic falls and increased inputs of soil organic matter. High M/H and pristane/phytane, in combination with low chemical index of alteration and K/Al, record a decrease in chemical weathering intensity during the Famennian that may have been due to contemporaneous climatic cooling, and a concurrent reduction in silt content may reflect stabilization of land surfaces by vascular plants and resulting reduced sediment yields. This study demonstrates the effectiveness of combining organic and inorganic geochemical proxies (including novel paleosalinity indices) for determination of environmental controls on the composition and productivity of plankton communities in paleomarine systems.

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42

See, Yee Chee, and Matthias Ihme. "Effects of finite-rate chemistry and detailed transport on the instability of jet diffusion flames." Journal of Fluid Mechanics 745 (March 25, 2014): 647–81. http://dx.doi.org/10.1017/jfm.2014.95.

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AbstractLocal linear stability analysis has been shown to provide valuable information about the response of jet diffusion flames to flow-field perturbations. However, this analysis commonly relies on several modelling assumptions about the mean flow prescription, the thermo-viscous-diffusive transport properties, and the complexity and representation of the chemical reaction mechanisms. In this work, the effects of these modelling assumptions on the stability behaviour of a jet diffusion flame are systematically investigated. A flamelet formulation is combined with linear stability theory to fully account for the effects of complex transport properties and the detailed reaction chemistry on the perturbation dynamics. The model is applied to a methane–air jet diffusion flame that was experimentally investigated by Füriet al.(Proc. Combust. Inst., vol. 29, 2002, pp. 1653–1661). Detailed simulations are performed to obtain mean flow quantities, about which the stability analysis is performed. Simulation results show that the growth rate of the inviscid instability mode is insensitive to the representation of the transport properties at low frequencies, and exhibits a stronger dependence on the mean flow representation. The effects of the complexity of the reaction chemistry on the stability behaviour are investigated in the context of an adiabatic jet flame configuration. Comparisons with a detailed chemical-kinetics model show that the use of a one-step chemistry representation in combination with a simplified viscous-diffusive transport model can affect the mean flow representation and heat release location, thereby modifying the instability behaviour. This is attributed to the shift in the flame structure predicted by the one-step chemistry model, and is further exacerbated by the representation of the transport properties. A pinch-point analysis is performed to investigate the stability behaviour; it is shown that the shear-layer instability is convectively unstable, while the outer buoyancy-driven instability mode transitions from absolutely to convectively unstable in the nozzle near field, and this transition point is dependent on the Froude number.

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Nshogoza, Gilbert, Yaqian Liu, Jia Gao, Mingqing Liu, Sayed Ala Moududee, Rongsheng Ma, Fudong Li, et al. "NMR Fragment-Based Screening against Tandem RNA Recognition Motifs of TDP-43." International Journal of Molecular Sciences 20, no. 13 (June 30, 2019): 3230. http://dx.doi.org/10.3390/ijms20133230.

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The TDP-43 is originally a nuclear protein but translocates to the cytoplasm in the pathological condition. TDP-43, as an RNA-binding protein, consists of two RNA Recognition Motifs (RRM1 and RRM2). RRMs are known to involve both protein-nucleotide and protein-protein interactions and mediate the formation of stress granules. Thus, they assist the entire TDP-43 protein with participating in neurodegenerative and cancer diseases. Consequently, they are potential therapeutic targets. Protein-observed and ligand-observed nuclear magnetic resonance (NMR) spectroscopy were used to uncover the small molecule inhibitors against the tandem RRM of TDP-43. We identified three hits weakly binding the tandem RRMs using the ligand-observed NMR fragment-based screening. The binding topology of these hits is then depicted by chemical shift perturbations (CSP) of the 15N-labeled tandem RRM and RRM2, respectively, and modeled by the CSP-guided High Ambiguity Driven biomolecular DOCKing (HADDOCK). These hits mainly bind to the RRM2 domain, which suggests the druggability of the RRM2 domain of TDP-43. These hits also facilitate further studies regarding the hit-to-lead evolution against the TDP-43 RRM domain.

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Crowe, Brandon L., Christopher J. Bohlen, Ross C. Wilson, Venkat Gopalan, and Mark P. Foster. "Assembly of the Complex between Archaeal RNase P Proteins RPP30 and Pop5." Archaea 2011 (2011): 1–12. http://dx.doi.org/10.1155/2011/891531.

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RNase P is a highly conserved ribonucleoprotein enzyme that represents a model complex for understanding macromolecular RNA-protein interactions. Archaeal RNase P consists of one RNA and up to five proteins (Pop5, RPP30, RPP21, RPP29, and RPP38/L7Ae). Four of these proteins function in pairs (Pop5-RPP30 and RPP21–RPP29). We have used nuclear magnetic resonance (NMR) spectroscopy and isothermal titration calorimetry (ITC) to characterize the interaction between Pop5 and RPP30 from the hyperthermophilic archaeonPyrococcus furiosus(Pfu). NMR backbone resonance assignments of free RPP30 (25 kDa) indicate that the protein is well structured in solution, with a secondary structure matching that observed in a closely related crystal structure. Chemical shift perturbations upon the addition of Pop5 (14 kDa) reveal its binding surface on RPP30. ITC experiments confirm a net 1 : 1 stoichiometry for this tight protein-protein interaction and exhibit complex isotherms, indicative of higher-order binding. Indeed, light scattering and size exclusion chromatography data reveal the complex to exist as a 78 kDa heterotetramer with two copies each of Pop5 and RPP30. These results will inform future efforts to elucidate the functional role of the Pop5-RPP30 complex in RNase P assembly and catalysis.

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45

Salmone, R. J., and E. Van Lunteren. "Effects of hypoxia and hypercapnia on geniohyoid contractility and endurance." Journal of Applied Physiology 71, no. 2 (August 1, 1991): 709–15. http://dx.doi.org/10.1152/jappl.1991.71.2.709.

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Sleep apnea and other respiratory diseases produce hypoxemia and hypercapnia, factors that adversely affect skeletal muscle performance. To examine the effects of these chemical alterations on force production by an upper airway dilator muscle, the contractile and endurance characteristics of the geniohyoid muscle were examined in situ during severe hypoxia (arterial PO2 less than 40 Torr), mild hypoxia (PO2 45–65 Torr), and hypercapnia (PCO2 55–80 Torr) and compared with hyperoxic-normocapnic conditions in anesthetized cats. Muscles were studied at optimal length, and contractile force was assessed in response to supramaximal electrical stimulation of the hypoglossal nerve (n = 7 cats) or geniohyoid muscle (n = 2 cats). There were no significant changes in the twitch kinetics or force-frequency curve of the geniohyoid muscle during hypoxia or hypercapnia. However, the endurance of the geniohyoid, as reflected in the fatigue index (ratio of force at 2 min to initial force in response to 40-Hz stimulation at a duty cycle 0.33), was significantly reduced by severe hypoxia but not by hypercapnia or mild hypoxia. In addition, the downward shift in the force-frequency curve after the repetitive stimulation protocol was greater during hypoxia than hyperoxia, especially at higher frequencies. In conclusion, the ability of the geniohyoid muscle to maintain force output during high levels of activation is adversely affected by severe hypoxia but not mild hypoxia or hypercapnia. However, none of these chemical perturbations affected muscle contractility acutely.

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46

Sieng, Monita, Michael P. Hayes, Joseph B. O'Brien, C. Andrew Fowler, Jon C. Houtman, David L. Roman, and Angeline M. Lyon. "High-resolution structure of RGS17 suggests a role for Ca2+ in promoting the GTPase-activating protein activity by RZ subfamily members." Journal of Biological Chemistry 294, no. 20 (April 2, 2019): 8148–60. http://dx.doi.org/10.1074/jbc.ra118.006059.

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Regulator of G protein signaling (RGS) proteins are negative regulators of G protein–coupled receptor (GPCR) signaling through their ability to act as GTPase-activating proteins (GAPs) for activated Gα subunits. Members of the RZ subfamily of RGS proteins bind to activated Gαo, Gαz, and Gαi1–3 proteins in the nervous system and thereby inhibit downstream pathways, including those involved in Ca2+-dependent signaling. In contrast to other RGS proteins, little is known about RZ subfamily structure and regulation. Herein, we present the 1.5-Å crystal structure of RGS17, the most complete and highest-resolution structure of an RZ subfamily member to date. RGS17 cocrystallized with Ca2+ bound to conserved positions on the predicted Gα-binding surface of the protein. Using NMR chemical shift perturbations, we confirmed that Ca2+ binds in solution to the same site. Furthermore, RGS17 had greater than 55-fold higher affinity for Ca2+ than for Mg2+. Finally, we found that Ca2+ promotes interactions between RGS17 and activated Gα and decreases the Km for GTP hydrolysis, potentially by altering the binding mechanism between these proteins. Taken together, these findings suggest that Ca2+ positively regulates RGS17, which may represent a general mechanism by which increased Ca2+ concentration promotes the GAP activity of the RZ subfamily, leading to RZ-mediated inhibition of Ca2+ signaling.

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Zheng, Y., N. Unger, A. Hodzic, L. Emmons, C. Knote, S. Tilmes, J. F. Lamarque, and P. Yu. "Limited effect of anthropogenic nitrogen oxides on secondary organic aerosol formation." Atmospheric Chemistry and Physics 15, no. 23 (December 8, 2015): 13487–506. http://dx.doi.org/10.5194/acp-15-13487-2015.

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Abstract. Globally, secondary organic aerosol (SOA) is mostly formed from emissions of biogenic volatile organic compounds (VOCs) by vegetation, but it can be modified by human activities as demonstrated in recent research. Specifically, nitrogen oxides (NOx = NO + NO2) have been shown to play a critical role in the chemical formation of low volatility compounds. We have updated the SOA scheme in the global NCAR (National Center for Atmospheric Research) Community Atmospheric Model version 4 with chemistry (CAM4-chem) by implementing a 4-product volatility basis set (VBS) scheme, including NOx-dependent SOA yields and aging parameterizations. Small differences are found for the no-aging VBS and 2-product schemes; large increases in SOA production and the SOA-to-OA ratio are found for the aging scheme. The predicted organic aerosol amounts capture both the magnitude and distribution of US surface annual mean measurements from the Interagency Monitoring of Protected Visual Environments (IMPROVE) network by 50 %, and the simulated vertical profiles are within a factor of 2 compared to aerosol mass spectrometer (AMS) measurements from 13 aircraft-based field campaigns across different regions and seasons. We then perform sensitivity experiments to examine how the SOA loading responds to a 50 % reduction in anthropogenic nitric oxide (NO) emissions in different regions. We find limited SOA reductions of 0.9–5.6, 6.4–12.0 and 0.9–2.8 % for global, southeast US and Amazon NOx perturbations, respectively. The fact that SOA formation is almost unaffected by changes in NOx can be largely attributed to a limited shift in chemical regime, to buffering in chemical pathways (low- and high-NOx pathways, O3 versus NO3-initiated oxidation) and to offsetting tendencies in the biogenic versus anthropogenic SOA responses.

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Alag, Reema, Asha Manikkoth Balakrishna, Sreekanth Rajan, Insaf A. Qureshi, Joon Shin, Julien Lescar, Gerhard Grüber, and Ho Sup Yoon. "Structural Insights into Substrate Binding by Pv FKBP35, a Peptidylprolyl cis-trans Isomerase from the Human Malarial Parasite Plasmodium vivax." Eukaryotic Cell 12, no. 4 (February 22, 2013): 627–34. http://dx.doi.org/10.1128/ec.00016-13.

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ABSTRACT The immunosuppressive drug FK506 binding proteins (FKBPs), an immunophilin family with the immunosuppressive drug FK506 binding property, exhibit peptidylprolyl cis-trans isomerase (PPIase) activity. While the cyclophilin-catalyzed peptidylprolyl isomerization of X-Pro peptide bonds has been extensively studied, the mechanism of the FKBP-mediated peptidylprolyl isomerization remains uncharacterized. Thus, to investigate the binding of FKBP with its substrate and the underlying catalytic mechanism of the FKBP-mediated proline isomerization, here we employed the FK506 binding domain (FKBD) of the human malarial parasite Plasmodium vivax FK506 binding protein 35 ( Pv FKBP35) and examined the details of the molecular interaction between the isomerase and a peptide substrate. The crystallographic structures of apo Pv FKBD35 and its complex with the tetrapeptide substrate succinyl-Ala-Leu-Pro-Phe- p -nitroanilide (sALPFp) determined at 1.4 Å and 1.65 Å resolutions, respectively, showed that the substrate binds to Pv FKBD35 in a cis conformation. Nuclear magnetic resonance (NMR) studies demonstrated the chemical shift perturbations of D55, H67, V73, and I74 residues upon the substrate binding. In addition, the X-ray crystal structure, along with the mutational studies, shows that Y100 is a key residue for the catalytic activity. Taken together, our results provide insights into the catalytic mechanism of Pv FKBP35-mediated cis-trans isomerization of substrate and ultimately might aid designing substrate mimetic inhibitors targeting the malarial parasite FKBPs.

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Reddy, E. Premkumar, Sai Krishna Divakar, Rodrigo Vasquez-Del Carpio, Kaushik Dutta, Stacey J. Baker, Ramana Reddy, and Aneel K. Aggarwal. "Rigosertib Blocks RAS Signaling By Acting As a Small Molecule RAS Mimetic That Binds to the RAS-Binding Domains of RAS Effector Proteins." Blood 124, no. 21 (December 6, 2014): 5616. http://dx.doi.org/10.1182/blood.v124.21.5616.5616.

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Abstract Oncogenic activation of RAS via point mutations occurs in more than 30% of all human cancers, including hematopoietic malignancies such as myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Investigations to understand the critical biochemical and biological mechanisms of RAS function are at the forefront of cancer research. Studies have shown that RAS interacts with a large number of effector proteins by a highly conserved mechanism that involves the switch region of RAS and the RAS-binding domains (RBDs) of its effector proteins. Because these interactions play an essential role in oncogenic RAS function, inhibiting them constitutes an attractive and important therapeutic approach for myeloid neoplasias and other cancers. Rigosertib is a novel styryl benzyl sulfone, which is in a Phase III clinical trial (ONTIME) for MDS. Here, we delineate the way rigosertib interacts with the RBDs of several RAS effector proteins: RAF, the PI3K family of proteins and RalGDS. To identify residues in the B-RAF RBD that interact with rigosertib, we recorded a series of 15N-1H HSQC spectra of 15N-labeled B-RAF RBD with increasing concentration of rigosertib. Strikingly, the chemical shift perturbations caused by addition of rigosertib are localized to the very region of the B-RAF-RBD implicated in RAS binding, namely the beta1 and beta2 strands and alpha3 helix (Fig 1). Additionally, this cluster of residues with largest chemical shift perturbation contains many of the same residues involved in RAS binding, namely Ile156, Lys164, Arg166, Thr167, Val168, Ala184 and Met187. These key residues are conserved within RAF RBDs, suggesting that rigosertib would bind to similar regions of the A- and c-RAF RBDs. Next, we examined the binding of rigosertib and GTP-RAS to wild type and mutant forms of c-RAF RBD that harbor mutations in residues that mediate binding to rigosertib. Our studies show that all mutations that cause dissociation of GTP-RAS binding also inhibit rigosertib binding to these mutant proteins. Taken together, the chemical shift data and mutagenesis data provide powerful evidence that rigosertib binds the B-RAF RBD at the same location as the RAS switch I region. A consequence of inhibiting RAS binding to RAF appears to be a block in growth factor-induced activation of RAF kinase activity. We also show that a result of this block in RAS/RAF interactions is an inability of RAF proteins to form dimers and activate MEK and ERK. This block in the activation of MEK/ERK pathways can be seen in cells that express wild-type RAS and RAF proteins (HeLa), in cells that express a constitutively active form of oncogenic RAS (HeLa-N-RAS-G12D), and in cells that exhibit amplification of EGF receptors (A431). Rigosertib also inhibits the phosphorylation of c-RAF serine 338, which has been shown to be essential for the activation of its kinase activity and for its association with and activation of PLK-1. Our results showing rigosertib-mediated inhibition of the PLK-1/RAF interaction might help explain the ability of this compound to induce mitotic arrest of human tumor cells and the ability of rigosertib to reduce blast counts in MDS patients (Seetharam et al, Leuk Res 2012). We have also demonstrated the binding of rigosertib to the RBDs of the PI3K family of kinases and RalGDS, both of which constitute important effectors of RAS. A consequence of the interaction of rigosertib with the RBD domains of PI3Ks appears to be a block in growth factor-induced AKT activation. These studies suggest that the disruption of multiple RAS-driven signaling pathways by rigosertib is mediated via rigosertib’s binding to RBDs of RAS effector proteins, leading to their inactivation. Figure 1 Figure 1. Disclosures Reddy: Onconova Therapeutics Inc: Research Funding. Divakar:Onconova Therapeutics Inc: Research Funding. Vasquez-Del Carpio:Onconova Therapeutics Inc: Research Funding. Dutta:Onconova Therapeutics Inc: Research Funding. Baker:Onconova Therapeautics Inc: Consultancy. Reddy:Onconova Therapeutics Inc: Consultancy. Aggarwal:Onconova Therapeutics Inc: Research Funding.

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Bassenden, Angelia, Dmitry Rodionov, Nilu Sabet-Kassouf, Tahereh Haji, Kun Shi, and Albert Berghuis. ""Structural characterization of aminoglycoside modifying enzyme ANT(2"")-Ia"." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C702. http://dx.doi.org/10.1107/s2053273314092973.

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Aminoglycosides are a class of broad-spectrum antibiotics used in the treatment of serious Gram-negative bacterial infections, they target the 16S RNA subunit and upon binding cause errors in translation, eventually inducing a bactericidal effect [1]. Aminoglycoside nucleotidyltransferase (2")-Ia (ANT(2")-Ia) is an aminoglycoside modifying enzyme that prevents aminoglycosides from binding to the ribosomal subunit, making this enzyme a principle candidate structure-based drug design [2]. Characterization of ANT(2")-Ia has been proven to be difficult due to the low stability and solubility of overexpressed protein, where 95% of the protein being expressed is in the form of inclusion bodies [3]. We describe a protocol that has lead to successful expression and purification of ANT(2")-Ia. A successful enzymatic assay has also been adapted and the protein is active and stable under these conditions with a specific activity of 0.14 U/mg. Furthermore, nuclear magnetic resonance (NMR) studies have allowed for the assignment of 144 of the 176 non-proline backbone residues. Substrate binding NMR experiments have shown unique global chemical shift perturbations upon binding ATP and tobramycin, suggesting unique binding sites for each substrate. Structural determination of ANT(2")-Ia using NMR in conjunction with x-ray crystallography can be utilized in order to develop small molecules that will act as more effective aminoglycosides in order to inhibit ANT(2")-Ia from binding and modifying these antibiotics.

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Journal articles on the topic 'Chemical Shift Perturbations'

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