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Journal articles on the topic 'Conformational characterization'

Author: Grafiati

Published: 14 March 2023

Last updated: 31 July 2025

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1

Seidler, Clarissa A., Janik Kokot, Monica L. Fernández-Quintero, and Klaus R. Liedl. "Structural Characterization of Nanobodies during Germline Maturation." Biomolecules 13, no. 2 (2023): 380. http://dx.doi.org/10.3390/biom13020380.

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Camelid heavy-chain antibody variable domains (VHH), nanobodies, are the smallest-known functional antibody fragments with high therapeutic potential. In this study, we investigate a VHH binding to hen egg-white lysozyme (HEL). We structurally and dynamically characterized the conformational diversity of four VHH variants to elucidate the antigen-binding process. For two of these antibodies, not only are the dissociation constants known, but also the experimentally determined crystal structures of the VHH in complex with HEL are available. We performed well-tempered metadynamics simulations in

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2

Raich, Ivan, Karel Pauk, Ales Imramovsky, and Josef Jampílek. "Conformational and Chiroptical Properties of Salicylamide-Based Peptidomimetics." Symmetry 16, no. 2 (2024): 138. http://dx.doi.org/10.3390/sym16020138.

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Optical rotation (OR), the most frequently used chiroptical method, is used for the characterization of newly synthesized or isolated compounds. Computational predictions of OR are, however, mainly used for the determination of the absolute configurations of chiral compounds, but they may also be used for the verification of conformational analysis results if the experimental values are known. Our computational study deals with the conformational analysis of flexible salicylamide-based peptidomimetics, starting with a conformation search, then a low-level ab initio preoptimization of the hundr

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3

Paz, Aviv, Derek P. Claxton, Jay Prakash Kumar, et al. "Conformational transitions of the sodium-dependent sugar transporter, vSGLT." Proceedings of the National Academy of Sciences 115, no. 12 (2018): E2742—E2751. http://dx.doi.org/10.1073/pnas.1718451115.

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Sodium-dependent transporters couple the flow of Na+ ions down their electrochemical potential gradient to the uphill transport of various ligands. Many of these transporters share a common core structure composed of a five-helix inverted repeat and deliver their cargo utilizing an alternating-access mechanism. A detailed characterization of inward-facing conformations of the Na+-dependent sugar transporter from Vibrio parahaemolyticus (vSGLT) has previously been reported, but structural details on additional conformations and on how Na+ and ligand influence the equilibrium between other state

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4

Dong, Qiwen, Kai Wang, Bin Liu, and Xuan Liu. "Characterization and Prediction of Protein Flexibility Based on Structural Alphabets." BioMed Research International 2016 (2016): 1–7. http://dx.doi.org/10.1155/2016/4628025.

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Motivation.To assist efforts in determining and exploring the functional properties of proteins, it is desirable to characterize and predict protein flexibilities.Results.In this study, the conformational entropy is used as an indicator of the protein flexibility. We first explore whether the conformational change can capture the protein flexibility. The well-defined decoy structures are converted into one-dimensional series of letters from a structural alphabet. Four different structure alphabets, including the secondary structure in 3-class and 8-class, the PB structure alphabet (16-letter),

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SENGE, MATHIAS O., INES BISCHOFF, NORA Y. NELSON, and KEVIN M. SMITH. "Synthesis, Reactivity and Structural Chemistry of 5,10,15,20-Tetraalkylporphyrins." Journal of Porphyrins and Phthalocyanines 03, no. 02 (1999): 99–116. http://dx.doi.org/10.1002/(sici)1099-1409(199902)3:2<99::aid-jpp109>3.0.co;2-6.

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The synthesis, reactivity and full characterization of a series of meso-tetraalkyl porphyrins and metalloporphyrins with R ≡ n-butyl (6), 2-methyl-propyl (7), isopropyl (8), l-ethyl-propyl (10) and tert-butyl (11) groups are reported. Derivatives of the last of these show considerably bathochromically shifted absorption bands and the crystal structure of Zn ( II )11(pyr) exhibits a severely ruffled macrocycle conformation. Systematic crystallographic studies of the porphyrins showed that the free base porphyrins with R ≡ n-butyl ( H 26), 2-methyl-propyl ( H 27) and 1-ethyl-propyl ( H 210) are

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6

Raisinghani, Nishank, Vedant Parikh, Brandon Foley, and Gennady Verkhivker. "AlphaFold2-Based Characterization of Apo and Holo Protein Structures and Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics and Ligand-Induced Conformational Changes." International Journal of Molecular Sciences 25, no. 23 (2024): 12968. https://doi.org/10.3390/ijms252312968.

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Proteins often exist in multiple conformational states, influenced by the binding of ligands or substrates. The study of these states, particularly the apo (unbound) and holo (ligand-bound) forms, is crucial for understanding protein function, dynamics, and interactions. In the current study, we use AlphaFold2, which combines randomized alanine sequence masking with shallow multiple sequence alignment subsampling to expand the conformational diversity of the predicted structural ensembles and capture conformational changes between apo and holo protein forms. Using several well-established data

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7

Moutusi, Manna, та K. Murarka Rajesh. "Characterization of conformational ensemble of C-terminally truncated α-synuclein in aqueous solution by atomistic molecular dynamics simulations". Journal of Indian Chemical Society Vol. 96, Jul 2019 (2019): 991–1002. https://doi.org/10.5281/zenodo.5644801.

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Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal-462 066, Madhya Pradesh, India <em>E-mail:</em> moutusi.manna.chem@gmail.com, rkm@iiserb.ac.in <em>Manuscript received online 30 April 2019, revised and accepted 28 May 2019</em> α-Synuclein is an intrinsically disordered protein, whose aggregation into amyloid fibril is involved in the pathology of Parkinson’s disease. C-terminally truncated α-synuclein variants, which are naturally generated from the full-length α-synuclein, are enriched in the pathological &

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8

Siddiqui, Mahtab Z. "Dehydrophenylalanine analogues: conformational characterization." International Journal of Biological Macromolecules 26, no. 1 (1999): 17–21. http://dx.doi.org/10.1016/s0141-8130(99)00063-x.

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9

Dluhy, R. A., D. Moffatt, D. G. Cameron, R. Mendelsohn, and H. H. Mantsch. "Characterization of cooperative conformational transitions by Fourier transform infrared spectroscopy: application to phospholipid binary mixtures." Canadian Journal of Chemistry 63, no. 7 (1985): 1925–32. http://dx.doi.org/10.1139/v85-319.

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Temperature-induced cooperative conformational transitions in biopolymers may be examined in aqueous solution by the use of Fourier transform infrared spectroscopy. The transition is described in terms of a two-state model with a fractional population parameter (which describes the degree of transition at various values intermediate between the two limiting cases) that can be generated by a least-squares technique. This procedure allows for calculation of a conformational index without assuming a linear dependence of the infrared parameter on the extent of transition. Calculations based on the

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10

Mountassif, Driss, Lucien Fabre, Kaustuv Basu, Mihnea Bostina, Slavica Jonic, and Isabelle Rouiller. "Conformational heterogeneity of the AAA ATPase p97 characterized by single particle cryo-EM." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C853. http://dx.doi.org/10.1107/s2053273314091463.

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p97, a member of the AAA (ATPase Associated with various Activities) ATPase family, is essential and centrally involved in a wide variety of cellular processes. Single amino-acid substitutions in p97 have been associated with the severe degenerative disorder of Inclusion Body Myopathy associated with Paget disease of bone and Frontotemporal Dementia (IBMPFD) as well as amytropic leteral sclerosis (ALS). Current models propose that p97 acts as a motor transmitting the energy from the ATPase cycle to conformational changes of substrate protein complexes causing segregation, remodeling or translo

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11

Yuan, Wen, Jessica Bazick, and Joseph Sodroski. "Characterization of the Multiple Conformational States of Free Monomeric and Trimeric Human Immunodeficiency Virus Envelope Glycoproteins after Fixation by Cross-Linker." Journal of Virology 80, no. 14 (2006): 6725–37. http://dx.doi.org/10.1128/jvi.00118-06.

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ABSTRACT The human immunodeficiency virus type 1 (HIV-1) gp120 exterior and gp41 transmembrane envelope glycoproteins assemble into trimers on the virus surface that represent potential targets for antibodies. Potent neutralizing antibodies bind the monomeric gp120 glycoprotein with small changes in entropy, whereas unusually large decreases in entropy accompany gp120 binding by soluble CD4 and less potent neutralizing antibodies. The high degree of conformational flexibility in the free gp120 molecule implied by these observations has been suggested to contribute to masking the trimer from an

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12

Polêto, Marcelo D., Bruno I. Grisci, Marcio Dorn, and Hugo Verli. "ConfID: an analytical method for conformational characterization of small molecules using molecular dynamics trajectories." Bioinformatics 36, no. 11 (2020): 3576–77. http://dx.doi.org/10.1093/bioinformatics/btaa130.

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Abstract Motivation The conformational space of small molecules can be vast and difficult to assess. Molecular dynamics (MD) simulations of free ligands in solution have been applied to predict conformational populations, but their characterization is often based on clustering algorithms or manual efforts. Results Here, we introduce ConfID, an analytical tool for conformational characterization of small molecules using MD trajectories. The evolution of conformational sampling and population frequencies throughout trajectories is calculated to check for sampling convergence while allowing to ma

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13

Appendino, G., M. Calleri, G. Chiari, P. Ugliengo, and D. Viterbo. "Conformational characterization of shiromodiol derivatives." Acta Crystallographica Section A Foundations of Crystallography 43, a1 (1987): C63. http://dx.doi.org/10.1107/s0108767387083806.

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14

Takahashi, Ken-ichi, Tosiyuki Noguti, Hironobu Hojo, Tadayasu Ohkubo, and Mitiko G? "Conformational characterization of designed minibarnase." Biopolymers 58, no. 3 (2001): 260–67. http://dx.doi.org/10.1002/1097-0282(200103)58:3<260::aid-bip1003>3.0.co;2-j.

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15

Tucker, David F., Jonathan T. Sullivan, Kimberly-Anne Mattia, et al. "Isolation of state-dependent monoclonal antibodies against the 12-transmembrane domain glucose transporter 4 using virus-like particles." Proceedings of the National Academy of Sciences 115, no. 22 (2018): E4990—E4999. http://dx.doi.org/10.1073/pnas.1716788115.

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The insulin-responsive 12-transmembrane transporter GLUT4 changes conformation between an inward-open state and an outward-open state to actively facilitate cellular glucose uptake. Because of the difficulties of generating conformational mAbs against complex and highly conserved membrane proteins, no reliable tools exist to measure GLUT4 at the cell surface, follow its trafficking, or detect the conformational state of the protein. Here we report the isolation and characterization of conformational mAbs that recognize the extracellular and intracellular domains of GLUT4, including mAbs that a

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16

Qi, Bo, Luran Jiang, Sai An, Wei Chen, and Yu-Fei Song. "Detecting the Subtle Photo-Responsive Conformational Bistability of Monomeric Azobenzene Functionalized Keggin Polyoxometalates by Using Ion-Mobility Mass Spectrometry." Molecules 27, no. 12 (2022): 3927. http://dx.doi.org/10.3390/molecules27123927.

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Accurately characterizing the conformational variation of novel molecular assemblies is important but often ignored due to limited characterization methods. Herein, we reported the use of ion-mobility mass spectrometry (IMS/MS) to investigate the conformational changes of four azobenzene covalently functionalized Keggin hybrids (azo-Keggins, compounds 1–4). The as-prepared azo-Keggins showed the general molecular formula of [C16H36N]4[SiW11O40(Si(CH2)3NH–CO(CH2)nO–C6H4N=NC6H4–R)2] (R = H, n = 0 (1); R = NO2, n = 0 (2); R = H, n = 5 (3); R = H, n = 10 (4)). The resultant azo-Keggins maintained

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17

Saxena, Sarika, Satoru Nagatoishi, Daisuke Miyoshi, and Naoki Sugimoto. "Structural and Functional Characterization of RecG Helicase under Dilute and Molecular Crowding Conditions." Journal of Nucleic Acids 2012 (2012): 1–8. http://dx.doi.org/10.1155/2012/392039.

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In an ATP-dependent reaction, theEscherichia coliRecG helicase unwinds DNA junctionsin vitro. We present evidence of a unique protein conformational change in the RecG helicase from anα-helix to aβ-strand upon an ATP binding under dilute conditions using circular dichroism (CD) spectroscopy. In contrast, under molecular crowding conditions, theα-helical conformation was stable even upon an ATP binding. These distinct conformational behaviors were observed to be independent of Na+and Mg2+. Interestingly, CD measurements demonstrated that the spectra of a frayed duplex decreased with increasing

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18

Watanabe, Tokio, Hirokazu Yagi, Saeko Yanaka, Takumi Yamaguchi, and Koichi Kato. "Comprehensive characterization of oligosaccharide conformational ensembles with conformer classification by free-energy landscape via reproductive kernel Hilbert space." Physical Chemistry Chemical Physics 23, no. 16 (2021): 9753–60. http://dx.doi.org/10.1039/d0cp06448c.

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19

Jablonski, Chet R., та Zhongxin Zhou. "Synthesis, multinuclear NMR, and solution conformation of (η5-indenyl)CoIRfL complexes (L = CO, P-donor)". Canadian Journal of Chemistry 70, № 10 (1992): 2544–51. http://dx.doi.org/10.1139/v92-322.

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The preparation, spectroscopic characterization, and conformational analysis of a series of Co(III) indenyl complexes, (C9H7)CoIRfL (Rf = C3F7, C6F13, L = CO, P-donor), 2–8, are described. I3C and 1H NMR parameters are consistent with a slightly distorted -η5-C9H7 coordination. 1H nuclear Overhauser effect difference (nOed) spectra indicate a preferred solution conformation in which the perfluoroalkyl group is trans to the C3a—C7a ring junction.

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20

Qu, Kun, Qiuluan Chen, Katarzyna A. Ciazynska, et al. "Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike." PLOS Pathogens 18, no. 7 (2022): e1010583. http://dx.doi.org/10.1371/journal.ppat.1010583.

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The spike (S) protein of SARS-CoV-2 has been observed in three distinct pre-fusion conformations: locked, closed and open. Of these, the function of the locked conformation remains poorly understood. Here we engineered a SARS-CoV-2 S protein construct “S-R/x3” to arrest SARS-CoV-2 spikes in the locked conformation by a disulfide bond. Using this construct we determined high-resolution structures confirming that the x3 disulfide bond has the ability to stabilize the otherwise transient locked conformations. Structural analyses reveal that wild-type SARS-CoV-2 spike can adopt two distinct locked

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21

Campos-Escamilla, Camila, Dritan Siliqi, Luis A. Gonzalez-Ramirez, Carmen Lopez-Sanchez, Jose Antonio Gavira, and Abel Moreno. "X-ray Characterization of Conformational Changes of Human Apo- and Holo-Transferrin." International Journal of Molecular Sciences 22, no. 24 (2021): 13392. http://dx.doi.org/10.3390/ijms222413392.

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Human serum transferrin (Tf) is a bilobed glycoprotein whose function is to transport iron through receptor-mediated endocytosis. The mechanism for iron release is pH-dependent and involves conformational changes in the protein, thus making it an attractive system for possible biomedical applications. In this contribution, two powerful X-ray techniques, namely Macromolecular X-ray Crystallography (MX) and Small Angle X-ray Scattering (SAXS), were used to study the conformational changes of iron-free (apo) and iron-loaded (holo) transferrin in crystal and solution states, respectively, at three

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22

Verkhivker, Gennady, Mohammed Alshahrani, and Grace Gupta. "Exploring Conformational Landscapes and Cryptic Binding Pockets in Distinct Functional States of the SARS-CoV-2 Omicron BA.1 and BA.2 Trimers: Mutation-Induced Modulation of Protein Dynamics and Network-Guided Prediction of Variant-Specific Allosteric Binding Sites." Viruses 15, no. 10 (2023): 2009. http://dx.doi.org/10.3390/v15102009.

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A significant body of experimental structures of SARS-CoV-2 spike trimers for the BA.1 and BA.2 variants revealed a considerable plasticity of the spike protein and the emergence of druggable binding pockets. Understanding the interplay of conformational dynamics changes induced by the Omicron variants and the identification of cryptic dynamic binding pockets in the S protein is of paramount importance as exploring broad-spectrum antiviral agents to combat the emerging variants is imperative. In the current study, we explore conformational landscapes and characterize the universe of binding po

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23

Yang, Jinhong, Na Sun, Xuelai Xie, et al. "Structure Characterization and Mechanical Properties of Acidity-Induced Helix of Alginate and Fibers." Materials 18, no. 11 (2025): 2619. https://doi.org/10.3390/ma18112619.

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The brittleness of alginate fibers has limited their biological applications. Enhancing fiber toughness without sacrificing fracture tensile strength is challenging. Herein, an acidity-triggered helical conformational change in alginate is demonstrated to improve fiber toughness. During fiber formation by Ca2+ crosslinking, HCl triggers 21-helical and antiparallel twofold helical conformational changes in sodium alginate. The helical structures were confirmed using circular dichroism and X-ray diffraction. Rheological analysis revealed that the helical conformation was flexible and could exten

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Násztor, Zoltán, János Horváth, and Balázs Leitgeb. "In Silico Conformational Analysis of the Short-Sequence Hypomurocin A Peptides." International Journal of Peptides 2015 (January 28, 2015): 1–6. http://dx.doi.org/10.1155/2015/281065.

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In this theoretical study, a conformational analysis was performed on short-sequence hypomurocin A peptides, in order to identify their characteristic structural properties. For each hypomurocin A molecule, not only the backbone conformations, but also the side-chain conformations were examined. The results indicated that certain tetrapeptide units could be characterized by types I and III β-turn structures, and considering the helical conformations, it could be concluded that the hypomurocin A peptides showed a preference for the 310-helical structure over the α-helical structure. Beside the

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25

SU, XIAODI. "SURFACE PLASMON RESONANCE SPECTROSCOPY AND QUARTZ CRYSTAL MICROBALANCE STUDY OF PROTEIN-DNA INTERACTIONS IN HORMONE RECEPTOR BIOLOGY." COSMOS 05, no. 01 (2009): 79–95. http://dx.doi.org/10.1142/s0219607709000415.

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Surface plasmon resonance (SPR) spectroscopy and quartz crystal microbalance (QCM) are surface sensitive analytical techniques capable of real-time monitoring of biomolecular interactions. In this article we review our past work on the use of these two techniques for studying protein–DNA interactions, exemplified with estrogen receptors (ER) and their response elements (ERE). Various assay schemes have been developed for a comprehensive characterization of ER–ERE interactions in terms of sequence specificity, binding affinity, stoichiometry, ligand effects on binding dynamics and conformationa

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OLSON, BRIAN, KEVIN MOLLOY, S. FARID HENDI, and AMARDA SHEHU. "GUIDING PROBABILISTIC SEARCH OF THE PROTEIN CONFORMATIONAL SPACE WITH STRUCTURAL PROFILES." Journal of Bioinformatics and Computational Biology 10, no. 03 (2012): 1242005. http://dx.doi.org/10.1142/s021972001242005x.

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The roughness of the protein energy surface poses a significant challenge to search algorithms that seek to obtain a structural characterization of the native state. Recent research seeks to bias search toward near-native conformations through one-dimensional structural profiles of the protein native state. Here we investigate the effectiveness of such profiles in a structure prediction setting for proteins of various sizes and folds. We pursue two directions. We first investigate the contribution of structural profiles in comparison to or in conjunction with physics-based energy functions in

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Shehu, Amarda, Lydia E. Kavraki, and Cecilia Clementi. "Multiscale characterization of protein conformational ensembles." Proteins: Structure, Function, and Bioinformatics 76, no. 4 (2009): 837–51. http://dx.doi.org/10.1002/prot.22390.

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28

Paiz, Elisia A., Karen A. Lewis, and Steven T. Whitten. "Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins." Molecules 26, no. 3 (2021): 634. http://dx.doi.org/10.3390/molecules26030634.

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The α and polyproline II (PPII) basins are the two most populated regions of the Ramachandran map when constructed from the protein coil library, a widely used denatured state model built from the segments of irregular structure found in the Protein Data Bank. This indicates the α and PPII conformations are dominant components of the ensembles of denatured structures that exist in solution for biological proteins, an observation supported in part by structural studies of short, and thus unfolded, peptides. Although intrinsic conformational propensities have been determined experimentally for t

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Xie, Tao, Tamjeed Saleh, Paolo Rossi, and Charalampos G. Kalodimos. "Conformational states dynamically populated by a kinase determine its function." Science 370, no. 6513 (2020): eabc2754. http://dx.doi.org/10.1126/science.abc2754.

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Protein kinases intrinsically sample a number of conformational states with distinct catalytic and binding activities. We used nuclear magnetic resonance spectroscopy to describe in atomic-level detail how Abl kinase interconverts between an active and two discrete inactive structures. Extensive differences in key structural elements between the conformational states give rise to multiple intrinsic regulatory mechanisms. The findings explain how oncogenic mutants can counteract inhibitory mechanisms to constitutively activate the kinase. Energetic dissection revealed the contributions of the a

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30

Palermo, Giulia, Yinglong Miao, Ross C. Walker, Martin Jinek, and J. Andrew McCammon. "CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations." Proceedings of the National Academy of Sciences 114, no. 28 (2017): 7260–65. http://dx.doi.org/10.1073/pnas.1707645114.

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CRISPR-Cas9 has become a facile genome editing technology, yet the structural and mechanistic features underlying its function are unclear. Here, we perform extensive molecular simulations in an enhanced sampling regime, using a Gaussian-accelerated molecular dynamics (GaMD) methodology, which probes displacements over hundreds of microseconds to milliseconds, to reveal the conformational dynamics of the endonuclease Cas9 during its activation toward catalysis. We disclose the conformational transition of Cas9 from its apo form to the RNA-bound form, suggesting a mechanism for RNA recruitment

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Sui, Ming-Yue, Yun Geng, Guang-Yan Sun, and Jian-Ping Wang. "Construction of a 9,9′-bifluorenylidene-based small molecule acceptor materials by screening conformation, steric configuration and repeating unit number: a theoretical design and characterization." J. Mater. Chem. C 5, no. 39 (2017): 10343–52. http://dx.doi.org/10.1039/c7tc03496b.

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The effects of molecular conformations, steric configurations and repeat units on the 99BF-based on photovoltaic properties were designed and compared at the molecular level. As a result, thep-conformational linear of the 4-unit molecule may be a high-performance 99′BF derivative.

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Lima, Igor, Ambuja Navalkar, Samir K. Maji, Jerson L. Silva, Guilherme A. P. de Oliveira, and Elio A. Cino. "Biophysical characterization of p53 core domain aggregates." Biochemical Journal 477, no. 1 (2020): 111–20. http://dx.doi.org/10.1042/bcj20190778.

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Aggregation is the cause of numerous protein conformation diseases. A common facet of these maladies is the transition of a protein from its functional native state into higher order forms, such as oligomers and amyloid fibrils. p53 is an essential tumor suppressor that is prone to such conformational transitions, resulting in its compromised ability to avert cancer. This work explores the biophysical properties of early-, mid-, and late-stage p53 core domain (p53C) aggregates. Atomistic and coarse-grained molecular dynamics (MD) simulations suggest that early- and mid-stage p53C aggregates ha

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Bingle, Wade H., James L. Doran, and William J. Page. "Characterization of the surface layer protein from Azotobacter vinelandii." Canadian Journal of Microbiology 32, no. 2 (1986): 112–20. http://dx.doi.org/10.1139/m86-023.

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The regular surface array protein (S protein) of Azotobacter vinelandii was extracted from outer membrane fragments with distilled water and further purified by gel filtration chromatography. The protein was shown to behave anomalously on sodium dodecyl sulfate polyacrylamide gels producing a number of conformational isomers. The amino acid composition of S protein was similar to that of other surface array proteins, particularly in its lack of cysteine. The theoretical monomelic molecular weight of S protein was calculated to be 60 218 based on the total amino acid composition and the apparen

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34

Gao, Rong, Aindrila Mukhopadhyay, Fang Fang, and David G. Lynn. "Constitutive Activation of Two-Component Response Regulators: Characterization of VirG Activation in Agrobacterium tumefaciens." Journal of Bacteriology 188, no. 14 (2006): 5204–11. http://dx.doi.org/10.1128/jb.00387-06.

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ABSTRACT Response regulators are the ultimate modulators in two-component signal transduction pathways. The N-terminal receiver domains generally accept phosphates from cognate histidine kinases to control output. VirG for example, the response regulator of the VirA/VirG two-component system in Agrobacterium tumefaciens, mediates the expression of virulence genes in response to plant host signals. Response regulators have a highly conserved structure and share a similar conformational activation upon phosphorylation, yet the sequence and structural features that determine or perturb the cooper

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Villain-Simonnet, Agnès, Michel Milas, and Marguerite Rinaudo. "A new bacterial polysaccharide (YAS34). I. Characterization of the conformations and conformational transition." International Journal of Biological Macromolecules 27, no. 1 (2000): 65–75. http://dx.doi.org/10.1016/s0141-8130(99)00120-8.

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Chen, Kun-Lin, Deng Li, Ting-Xuan Lu, and Shu-Wei Chang. "Structural Characterization of the CD44 Stem Region for Standard and Cancer-Associated Isoforms." International Journal of Molecular Sciences 21, no. 1 (2020): 336. http://dx.doi.org/10.3390/ijms21010336.

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CD44 is widely expressed in most vertebrate cells, whereas the expression of CD44v6 is restricted to only a few tissues and has been considered to be associated with tumor progression and metastasis. Thus, CD44v6 has been recognized as a promising prognostic biomarker and therapeutic target for various cancers for more than a decade. However, despite many experimental studies, the structural dynamics and differences between CD44s and CD44v6, particularly in their stem region, still remain elusive. Here, a computational study was conducted to address these problems. We found that the stem of CD

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Angulo-Cornejo, Jorge R., Ketty Ayala-León, Gabriel García Herbosa, et al. "Synthesis and Structural Characterization of N-[4-(2-Hydroxyethyl)-1,2,4-oxathiazinan-3-ylidene]-benzamide and its Mercury(II) Chloride Adduct." Zeitschrift für Naturforschung B 60, no. 9 (2005): 945–50. http://dx.doi.org/10.1515/znb-2005-0906.

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The synthesis of N-[4-(2-hydroxyethyl)-1,2,4-oxathiazinan-3-ylidene]-benzamide (2a) and N-[4- (2-hydroxyethyl)-1,2,4-oxathiazinan-3-ylidene]-2-fluorobenzamide (2b) by oxidation of the corresponding 1,1-bis(2-hydroxyethyl)-3-aroylthioureas with potassium iodate in aqueous solution is reported. Variable temperature 1H NMR spectra of 2a prove that the heterocyclic 1,2,4-(O, S,N) sixmembered ring is involved in a dynamic chair-boat conformational interconversion. Molecular mechanic calculations show that the chair conformation is more stable than the boat conformation by 3.0 kcal/mol. The synthesi

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Houde, Damian, Joseph Arndt, Wayne Domeier, Steven Berkowitz, and John R. Engen. "Characterization of IgG1 Conformation and Conformational Dynamics by Hydrogen/Deuterium Exchange Mass Spectrometry." Analytical Chemistry 81, no. 7 (2009): 2644–51. http://dx.doi.org/10.1021/ac802575y.

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Houde, Damian, Joseph Arndt, Wayne Domeier, Steven Berkowitz, and John R. Engen. "Characterization of IgG1 Conformation and Conformational Dynamics by Hydrogen/Deuterium Exchange Mass Spectrometry." Analytical Chemistry 81, no. 14 (2009): 5966. http://dx.doi.org/10.1021/ac9009287.

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Asakura, Tetsuo, Masanori Endo, Rina Fukuhara, and Yugo Tasei. "13C NMR characterization of hydrated 13C labeled Bombyx mori silk fibroin sponges prepared using glycerin, poly(ethylene glycol diglycidyl ether) and poly(ethylene glycol) as porogens." Journal of Materials Chemistry B 5, no. 11 (2017): 2152–60. http://dx.doi.org/10.1039/c7tb00323d.

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Pinto, B. Mario, Blair D. Johnston, Raymond J. Batchelor, Frederick W. B. Einstein, and Ian D. Gay. "Selenium coronands. A novel conformational pair." Canadian Journal of Chemistry 66, no. 11 (1988): 2956–58. http://dx.doi.org/10.1139/v88-457.

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The synthesis and characterization of the novel selenium coronands, 1,3,7,9-tetraselenacyclododecane 1a, 1,3,7,9,13,15-hexaselenacyclooctadecane 2a, the corresponding β-gem-dimethyl derivatives 1b, 2b, and 1,5,9,13-tetraselenacyclohexadecane 3, and 1,5,9,13,17,21-hexaselenacyclotetracosane 4 are described. X-ray crystallographic analysis of 1a reveals three independent molecules that exist in two distinct conformations, one molecule having approximate two-fold symmetry together with two molecules (of similar conformation) each having crystallographic [Formula: see text] symmetry. The conformat

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Zhang, Dapeng, and Naoki Kishimoto. "Theoretical Investigation of Interconversion Pathways and Intermediates in Hydride/Silyl Exchange of Niobocene Hydride–Silyl Complexes: A DFT Study Incorporating Conformational Search and Interaction Region Indicator (IRI) Analysis." Molecules 29, no. 21 (2024): 5075. http://dx.doi.org/10.3390/molecules29215075.

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Niobocene hydride–silyl complexes exhibit intriguing structural characteristics with the potential for direct hydride/silyl exchange, where hydride migration plays a crucial role during conformational interconversion. In this study, quantum chemical calculations were utilized to investigate the transformation pathways involved in hydride/silyl exchange in niobocene trihydride complexes with various dichlorosilanes, including SiCl2Me2, SiCl2iPr2, and SiCl2MePh ligands. The conformational changes and hydride shifts within these niobocene hydride–silyl complexes were examined, and key intermediat

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Price, Nicholas C. "Conformational issues in the characterization of proteins." Biotechnology and Applied Biochemistry 31, no. 1 (2000): 29. http://dx.doi.org/10.1042/ba19990102.

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Kamenik, Anna S., Uta Lessel, Julian E. Fuchs, Thomas Fox, and Klaus R. Liedl. "Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization." Journal of Chemical Information and Modeling 58, no. 5 (2018): 982–92. http://dx.doi.org/10.1021/acs.jcim.8b00097.

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da Silva, J. E. Pereira, S. I. Córdoba de Torresi, D. L. A. de Faria, and M. L. A. Temperini. "Raman characterization of polyaniline induced conformational changes." Synthetic Metals 101, no. 1-3 (1999): 834–35. http://dx.doi.org/10.1016/s0379-6779(98)01300-9.

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Lundblad, Roger L. "Conformational issues in the characterization of proteins." Biotechnology and Applied Biochemistry 31, no. 1 (2000): 69. http://dx.doi.org/10.1111/j.1470-8744.2000.tb00568.x.

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Signorelli, Sara, Salvatore Cannistraro, and Anna Rita Bizzarri. "Structural Characterization of the Intrinsically Disordered Protein p53 Using Raman Spectroscopy." Applied Spectroscopy 71, no. 5 (2016): 823–32. http://dx.doi.org/10.1177/0003702816651891.

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The intrinsically disordered protein p53 has attracted a strong interest for its important role in genome safeguarding and potential therapeutic applications. However, its disordered character makes difficult a full characterization of p53 structural architecture. A deep knowledge of p53 structural motifs could significantly help the understanding of its functional properties, in connection with its complex binding network. We have applied Raman spectroscopy to investigate the structural composition and the conformational heterogeneity of both full-length p53 and its DNA binding domain (DBD),

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Musavizadeh, Zahra, Alessandro Grottesi, Giulia Guarguaglini, and Alessandro Paiardini. "Phosphorylation, Mg-ADP, and Inhibitors Differentially Shape the Conformational Dynamics of the A-Loop of Aurora-A." Biomolecules 11, no. 4 (2021): 567. http://dx.doi.org/10.3390/biom11040567.

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The conformational state of the activation loop (A-loop) is pivotal for the activity of most protein kinases. Hence, the characterization of the conformational dynamics of the A-loop is important to increase our understanding of the molecular processes related to diseases and to support the discovery of small molecule kinase inhibitors. Here, we carry out a combination of molecular dynamics (MD) and essential dynamics (ED) analyses to fully map the effects of phosphorylation, ADP, and conformation disrupting (CD) inhibitors (i.e., CD532 and MLN8054) on the dynamics of the A-loop of Aurora-A. M

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Abou Assi, Hala, Atul K. Rangadurai, Honglue Shi, et al. "2′-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states." Nucleic Acids Research 48, no. 21 (2020): 12365–79. http://dx.doi.org/10.1093/nar/gkaa928.

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Abstract 2′-O-Methyl (Nm) is a highly abundant post-transcriptional RNA modification that plays important biological roles through mechanisms that are not entirely understood. There is evidence that Nm can alter the biological activities of RNAs by biasing the ribose sugar pucker equilibrium toward the C3′-endo conformation formed in canonical duplexes. However, little is known about how Nm might more broadly alter the dynamic ensembles of flexible RNAs containing bulges and internal loops. Here, using NMR and the HIV-1 transactivation response (TAR) element as a model system, we show that Nm

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Bouvier, Marlene, Xubiao Peng, and Lenong Li. "Visualization and characterization of the elusive MHC I intermediate states by x-ray crystallography and in silicostudies." Journal of Immunology 210, no. 1_Supplement (2023): 221.29. http://dx.doi.org/10.4049/jimmunol.210.supp.221.29.

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Abstract Background: Studies have suggested that MHC class I (MHC I) molecules fluctuate rapidly between conformational states as they sample peptides for potential ligands. It is the molecular features of these intermediates that are recognized by tapasin and TAPBPR at the C-terminus of the groove. To date, however, MHC I intermediates remain elusive molecules due to their transient nature. Moreover, whether the N-terminus of the groove has a role in MHC I maturation, and if it also serves as a conformationally sensing region, is not well characterized. Methods: We designed the HLA-B8-restric

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