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Journal articles on the topic 'Peptide in solution NMR study'

Author: Grafiati

Published: 4 June 2021

Last updated: 5 February 2022

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1

Kim, Minseon, Jinyoung Son, and Yongae Kim. "Structural and Mechanismic Studies of Lactophoricin Analog, Novel Antibacterial Peptide." International Journal of Molecular Sciences 22, no. 7 (2021): 3734. http://dx.doi.org/10.3390/ijms22073734.

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Naturally derived antibacterial peptides exhibit excellent pharmacological action without the risk of resistance, suggesting a potential role as biologicals. Lactophoricin-I (LPcin-I), found in the proteose peptone component-3 (PP3; lactophorin) of bovine milk, is known to exhibit antibiotic activity against Gram-positive and Gram-negative bacteria. Accordingly, we derived a new antibacterial peptide and investigated its structure–function relationship. This study was initiated by designing antibacterial peptide analogs with better antibacterial activity, less cytotoxicity, and shorter amino a

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2

Karas, John A., David W. Keizer, and Marc-Antoine Sani. "Nuclear Magnetic Resonance Study of the Peptide FRANCESSEPAROVIC." Australian Journal of Chemistry 73, no. 3 (2020): 158. http://dx.doi.org/10.1071/ch19357.

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As an eminent ambassador of STEM and renowned NMR spectroscopist, Frances Separovic is an internationally famous name, but could it also be a valuable membrane-active peptide sequence? Her name has been used as an amino acid sequence (FS), successfully synthesised, oxidised, and put into contact with membrane models to investigate any serendipitous activity. The 3D structure of the cyclic FS was determined in dodecylphosphocholine (DPC) micelles by solution NMR spectroscopy. FS displayed a twisted bend separating a helical stretch and an unstructured segment. Using solid-state NMR spectroscopy

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3

Kindahl, Lill, Lennart Kenne, and Corine Sandström. "1H NMR studies on the solution conformation of the [L-Ser10] and [D-Ser10] analogues of contulakin-G." Canadian Journal of Chemistry 83, no. 2 (2005): 156–65. http://dx.doi.org/10.1139/v04-176.

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The synthesis of the O-glycosylated serine-10 analogue of contulakin-G yielded both the [L-] and the [D-Ser10] analogues. The 1H NMR study indicated that the sugars of the two Ser10-glycosylated peptides lacked the hydrogen bond to the peptide backbone that exists in contulakin-G. NOEs showed that the glycan part of the [D-Ser10] analogue had a different orientation to the peptide backbone than that of the [L-Ser10] analogue. The peptide backbones in the two compounds were found to exist mainly in random coil conformations, with transient turns at the site of glycosylation. A transient turn wa

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4

Carver, John A. "A two dimensional 1H NMR study of the solution conformation of gastrin releasing peptide." Biochemical and Biophysical Research Communications 150, no. 2 (1988): 552–60. http://dx.doi.org/10.1016/0006-291x(88)90429-9.

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5

Thornton, S. E., and S. Fraga. "Theoretical studies of peptidic structures. Conformation of the tetrapeptide N-acetyl-Asp-Glu-Lys-Ser-NH-CH3." Canadian Journal of Chemistry 69, no. 11 (1991): 1636–38. http://dx.doi.org/10.1139/v91-239.

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The peptide Asp-Glu-Lys-Ser has been studied using the software package ALTA:maPS, with simulation of the pH conditions and the influence of the solvent, in order to investigate the possible stabilization of its structure by a hydrogen bond and a salt-bridge. The theoretical results confirm the existence of a salt-bridge, between the side chains of the Glu and Lys residues, in aqueous solution at neutral pH but not at acid pH, in agreement with the observation from NMR studies. On the other hand the calculations indicate that no hydrogen bond exists in aqueous solution at either pH. The fact t

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6

Santoro, Angelo, Manuela Grimaldi, Michela Buonocore, Ilaria Stillitano та Anna Maria D’Ursi. "Exploring the Early Stages of the Amyloid Aβ(1–42) Peptide Aggregation Process: An NMR Study". Pharmaceuticals 14, № 8 (2021): 732. http://dx.doi.org/10.3390/ph14080732.

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Alzheimer’s disease (AD) is a neurodegenerative pathology characterized by the presence of neurofibrillary tangles and amyloid plaques, the latter mainly composed of Aβ(1–40) and Aβ(1–42) peptides. The control of the Aβ aggregation process as a therapeutic strategy for AD has prompted the interest to investigate the conformation of the Aβ peptides, taking advantage of computational and experimental techniques. Mixtures composed of systematically different proportions of HFIP and water have been used to monitor, by NMR, the conformational transition of the Aβ(1–42) from soluble α-helical struct

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7

TANG, LIDA, JIANGWU WANG, WEIREN XU, and CHENG-LUNG CHEN. "SIMULATION STUDY OF THE EFFECTS OF LIGAND ON THE ACTIVE ZONE OF THE PEPTIDE DEFORMYLASE." Journal of Theoretical and Computational Chemistry 05, no. 01 (2006): 99–110. http://dx.doi.org/10.1142/s021963360600209x.

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Molecular Dynamics (MD) simulation was carried out to study the conformation changes of the active zone of a Peptide Deformylase. Both the simulation with and without ligand were initialed from the crystal structure (1bs8). The tripeptide, Met-Ala-Ser (MAS), was used as the ligand in simulation. After thermal equilibrium, trajectories of one nanosecond MD run was collected and analyzed. The simulation result was compared with the NMR and crystal observed structures. The simulation shows that within one nanosecond time domain, only local deformation of protein occurred. The active zone was defi

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Anastasiadis, Aphrodite, and Frances Separovic. "Solid-State NMR Structural Determination of Components in an Ion Channel Switch Biosensor." Australian Journal of Chemistry 56, no. 3 (2003): 163. http://dx.doi.org/10.1071/ch02195.

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High-resolution structural analysis of membrane proteins is difficult to achieve with the commonly used methods of structural biology, X-ray diffraction, and solution-state NMR spectroscopy. By combining solid-state NMR studies of membrane peptides in powder and oriented samples, with solution-state studies in detergent micelles, three dimensional molecular structures can be obtained. We have used solid-state NMR methods to study the antibiotic, gramicidin A (gA), a peptide that forms ion channels in bilayer lipid membranes (BLMs). Receptor groups have been linked to gA channels embedded in a

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9

Laussac, J. P., M. T. Cung, M. Pasdeloup, et al. "NMR study of thymulin, a lymphocyte differentiating thymic nonapeptide. Conformational states of free peptide in solution." Journal of Biological Chemistry 261, no. 17 (1986): 7784–90. http://dx.doi.org/10.1016/s0021-9258(19)57469-5.

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10

Sherman, Patrick J., Rebecca J. Jackway, John D. Gehman, et al. "Solution Structure and Membrane Interactions of the Antimicrobial Peptide Fallaxidin 4.1a: An NMR and QCM Study." Biochemistry 48, no. 50 (2009): 11892–901. http://dx.doi.org/10.1021/bi901668y.

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11

Castiglia, Francesca, Fabrizia Zevolini, Giulia Riolo, et al. "NMR Study of the Secondary Structure and Biopharmaceutical Formulation of an Active Branched Antimicrobial Peptide." Molecules 24, no. 23 (2019): 4290. http://dx.doi.org/10.3390/molecules24234290.

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The synthetic antimicrobial peptide SET-M33 is being developed as a possible new antibacterial candidate for the treatment of multi-drug resistant bacteria. SET-M33 is a branched peptide featuring higher resistance and bioavailability than its linear analogues. SET-M33 shows antimicrobial activity against different species of multi-resistant Gram-negative bacteria, including clinically isolated strains of Pseudomonas aeruginosa, Klebsiella pneumoniae, Acinetobacter baumanii and Escherichia coli. The secondary structure of this 40 amino acid peptide was investigated by NMR to fully characterize

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12

Skelton, Nicholas J., Tamas Blandl, Stephen J. Russell, Melissa A. Starovasnik та Andrea G. Cochran. "β‒hairpin polypeptides by design and selection". Spectroscopy 17, № 2-3 (2003): 213–30. http://dx.doi.org/10.1155/2003/148024.

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We have developed polypeptide scaffolds that readily adopt aβ‒hairpin conformation (a pair of antiparallel strands connected by a turn) in solution. The study of such peptides allows us to understand the factors that govern stability and folding of these motifs in proteins, and permits mimicry of functionally important regions of proteins. Spectroscopic and biophysical methods have been used to characterize the conformational preferences and stability of these peptides, with a strong emphasis on using restraints generated from1H NMR spectroscopy to determine their three‒dimensional structure.

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Zheng, Gang, Allan M. Torres, Marina Ali, Nicholas Manolios, and William S. Price. "NMR study of the structure and self-association of core peptide in aqueous solution and DPC micelles." Biopolymers 96, no. 2 (2011): 177–80. http://dx.doi.org/10.1002/bip.21423.

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14

Clemente, Joyce S., Edward G. Gregorich, André J. Simpson, Rajeev Kumar, Denis Courtier-Murias, and Myrna J. Simpson. "Comparison of nuclear magnetic resonance methods for the analysis of organic matter composition from soil density and particle fractions." Environmental Chemistry 9, no. 1 (2012): 97. http://dx.doi.org/10.1071/en11096.

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Environmental contextThe association of specific organic matter (OM) compounds with clay mineral surfaces is believed to protect these compounds from degradation and thus result in long-term protection in soil. The molecular-level composition of soil OM associated with soil fractions was measured and compared using solid-state 13C nuclear magnetic resonance (NMR) and solution-state 1H NMR methods. Combining these methods allowed more detailed characterisation of OM associated with different soil fractions and will improve the understanding of OM dynamics in soil. AbstractOrganic matter (OM) as

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15

DINGS, Ruud P. M., Monica M. ARROYO, Nathan A. LOCKWOOD, et al. "beta-Sheet is the bioactive conformation of the anti-angiogenic anginex peptide." Biochemical Journal 373, no. 1 (2003): 281–88. http://dx.doi.org/10.1042/bj20030295.

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Anginex is a designed peptide 33mer that functions as a cytokine-like agent to inhibit angiogenesis. Although this short linear peptide has been shown by NMR and CD to form a nascent β-sheet conformation in solution, the actual bioactive structure formed upon binding to its receptor on the surface of endothelial cells could be quite different. By using a series of double-cysteine disulphide-bridged analogues, we provide evidence in the present study that the β-sheet is in fact the bioactive conformation of anginex. CD and NMR spectral analysis of the analogues indicate formation of a β-sheet c

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Bernard, Guy M., Mark Miskolzie, George Kotovych, and Roderick E. Wasylishen. "A solid-state NMR investigation of orexin-B." Canadian Journal of Chemistry 82, no. 10 (2004): 1554–63. http://dx.doi.org/10.1139/v04-131.

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Some key aspects of the secondary structure of solid orexin-B, a 28 amino-acid peptide, have been investigated by solid-state NMR spectroscopy. The 13C15N dipolar coupling between the carbonyl carbon of Leu11 and the nitrogen of Leu15, as determined by rotational echo double resonance (REDOR) experiments, is 35 Hz, indicating that these nuclei are separated by approximately 4.5 Å. This distance is consistent with the α-helical structure determined for this segment of orexin-B by solution NMR measurements. REDOR measurements of the dipolar coupling between the carbonyl carbon of Ala17 and the

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17

Burade, Sachin S., Sushil V. Pawar, Tanmoy Saha та ін. "Sugar-derived oxazolone pseudotetrapeptide as γ-turn inducer and anion-selective transporter". Beilstein Journal of Organic Chemistry 15 (14 жовтня 2019): 2419–27. http://dx.doi.org/10.3762/bjoc.15.234.

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The intramolecular cyclization of a C-3-tetrasubstituted furanoid sugar amino acid-derived linear tetrapeptide afforded an oxazolone pseudo-peptide with the formation of an oxazole ring at the C-terminus. A conformational study of the oxazolone pseudo-peptide showed intramolecular C=O···HN(II) hydrogen bonding in a seven-membered ring leading to a γ-turn conformation. This fact was supported by a solution-state NMR and molecular modeling studies. The oxazolone pseudotetrapeptide was found to be a better Cl−-selective transporter for which an anion–anion antiport mechanism was established.

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18

Glisic, Biljana, Zorka Stanic, Snezana Rajkovic, Vesna Kojic, Gordana Bogdanovic, and Milos Djuran. "Solution study under physiological conditions and cytotoxic activity of the gold(III) complexes with L-histidine-containing peptides." Journal of the Serbian Chemical Society 78, no. 12 (2013): 1911–24. http://dx.doi.org/10.2298/jsc130920105g.

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Proton NMR spectroscopy and cyclic voltammetry have been applied to study the stability of three gold(III) complexes with L-histidine-containing peptides, [Au(Gly-L-His-N,N?,N??)Cl]NO3.1.25H2O (Au1), [Au(L-Ala-L-His-N,N?,N??)Cl]NO3.2.5H2O (Au2) and [Au(Gly-Gly-L-His-N,N?,N??,N???)]Cl.H2O (Au3) under physiologically relevant conditions. It was found that tridentate coordination of Gly-L-His and L-Ala-L-His dipeptides, as well as tetradentate coordination of Gly-Gly-L-His tripeptide in Au1, Au2 and Au3 complexes, respectively, stabilized +3 oxidation state of gold and prevented its reduction to

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19

Wang, Guangshun, Paul A. Keifer, and Alan Peterkofsky. "Short‒chain diacyl phosphatidylglycerols: which one to choose for the NMR structural determination of a membrane‒associated peptide fromEscherichia coli?" Spectroscopy 18, no. 2 (2004): 257–64. http://dx.doi.org/10.1155/2004/719137.

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Diacyl phosphatidylglycerols (PG) are the major anionic lipids in theEscherichia colimembrane. Short‒chain dihexanoyl phosphatidylglycerol (DHPG) was previously utilized for the structural determination, by NMR spectroscopy, of the peptide corresponding to the N-terminal membrane anchor of the glucose‒specific enzyme IIA (IIAGlc) fromE. coli. This study explores the possible use of lipid micelles of dioctanoyl phosphatidylglycerol (DOPG) and didecanoyl phosphatidylglycerol (DDPG) as alternatives to DHPG. At a peptide concentration of 1 mM, the minimum peptide/lipid molar ratios required for th

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20

Idress, Mohannad, Bruce F. Milne, Gary S. Thompson, Laurent Trembleau, Marcel Jaspars та Wael E. Houssen. "Structure-Based Design, Synthesis and Bioactivity of a New Anti-TNFα Cyclopeptide". Molecules 25, № 4 (2020): 922. http://dx.doi.org/10.3390/molecules25040922.

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As opposed to small molecules, macrocyclic peptides possess a large surface area and are recognised as promising candidates to selectively treat diseases by disrupting specific protein–protein interactions (PPIs). Due to the difficulty in predicting cyclopeptide conformations in solution, the de novo design of bioactive cyclopeptides remains significantly challenging. In this study, we used the combination of conformational analyses and molecular docking studies to design a new cyclopeptide inhibitor of the interaction between the human tumour necrosis factor alpha (TNFα) and its receptor TNFR

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21

Chittoor, Balasubramanyam, Bankala Krishnarjuna, Rodrigo A. V. Morales та Raymond S. Norton. "The Single Disulfide-Directed β-Hairpin Fold: Role of Disulfide Bond in Folding and Effect of an Additional Disulfide Bond on Stability". Australian Journal of Chemistry 73, № 4 (2020): 312. http://dx.doi.org/10.1071/ch19386.

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Disulfide bonds play a key role in the oxidative folding, conformational stability, and functional activity of many peptides. A few disulfide-rich peptides with privileged architecture such as the inhibitor cystine knot motif have garnered attention as templates in drug design. The single disulfide-directed β-hairpin (SDH), a novel fold identified more recently in contryphan-Vc1, has been shown to possess remarkable thermal, conformational, and chemical stability and can accept a short bioactive epitope without compromising the core structure of the peptide. In this study, we demonstrated that

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Zvi, Anat, Reuben Hiller, and Jacob Anglister. "Solution conformation of a peptide corresponding to the principal neutralizing determinant of HIV-1IIIB: a two-dimensional NMR study." Biochemistry 31, no. 30 (1992): 6972–79. http://dx.doi.org/10.1021/bi00145a015.

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23

Deraos, George, Eftichia Kritsi, Minos-Timotheos Matsoukas, et al. "Design of Linear and Cyclic Mutant Analogues of Dirucotide Peptide (MBP82–98) against Multiple Sclerosis: Conformational and Binding Studies to MHC Class II." Brain Sciences 8, no. 12 (2018): 213. http://dx.doi.org/10.3390/brainsci8120213.

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Background: Multiple sclerosis (MS) is an autoimmune disorder of the central nervous system. MS is a T cell-mediated disease characterized by the proliferation, infiltration, and attack of the myelin sheath by immune cells. Previous studies have shown that cyclization provides molecules with strict conformation that could modulate the immune system. Methods: In this study, we synthesized peptide analogues derived from the myelin basic protein (MBP)82–98 encephalitogenic sequence (dirucotide), the linear altered peptide ligand MBP82–98 (Ala91), and their cyclic counterparts. Results: The synthe

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Panteleev, Pavel V., Andrey V. Tsarev, Victoria N. Safronova та ін. "Structure Elucidation and Functional Studies of a Novel β-hairpin Antimicrobial Peptide from the Marine Polychaeta Capitella teleta". Marine Drugs 18, № 12 (2020): 620. http://dx.doi.org/10.3390/md18120620.

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Endogenous antimicrobial peptides (AMPs) are evolutionary ancient molecular factors of innate immunity that play a key role in host defense. Among the most active and stable under physiological conditions AMPs are the peptides of animal origin that adopt a β-hairpin conformation stabilized by disulfide bridges. In this study, a novel BRICHOS-domain related AMP from the marine polychaeta Capitella teleta, named capitellacin, was produced as the recombinant analogue and investigated. The mature capitellacin exhibits high homology with the known β-hairpin AMP family—tachyplesins and polyphemusins

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Haugaard-Jönsson, Linda M., Mohammed Akhter Hossain, Norelle L. Daly, David J. Craik, John D. Wade, and K. Johan Rosengren. "Structure of human insulin-like peptide 5 and characterization of conserved hydrogen bonds and electrostatic interactions within the relaxin framework." Biochemical Journal 419, no. 3 (2009): 619–27. http://dx.doi.org/10.1042/bj20082353.

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INSL5 (insulin-like peptide 5) is a two-chain peptide hormone related to insulin and relaxin. It was recently discovered through searches of expressed sequence tag databases and, although the full biological significance of INSL5 is still being elucidated, high expression in peripheral tissues such as the colon, as well as in the brain and hypothalamus, suggests roles in gut contractility and neuroendocrine signalling. INSL5 activates the relaxin family peptide receptor 4 with high potency and appears to be the endogenous ligand for this receptor, on the basis of overlapping expression profile

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26

Schmitz, Thomas, Ajay Abisheck Paul George, Britta Nubbemeyer, et al. "NMR-Based Structural Characterization of a Two-Disulfide-Bonded Analogue of the FXIIIa Inhibitor Tridegin: New Insights into Structure–Activity Relationships." International Journal of Molecular Sciences 22, no. 2 (2021): 880. http://dx.doi.org/10.3390/ijms22020880.

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The saliva of blood-sucking leeches contains a plethora of anticoagulant substances. One of these compounds derived from Haementeria ghilianii, the 66mer three-disulfide-bonded peptide tridegin, specifically inhibits the blood coagulation factor FXIIIa. Tridegin represents a potential tool for antithrombotic and thrombolytic therapy. We recently synthesized two-disulfide-bonded tridegin variants, which retained their inhibitory potential. For further lead optimization, however, structure information is required. We thus analyzed the structure of a two-disulfide-bonded tridegin isomer by soluti

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Trzepałka, Emilia, Marta Oleszczuk, Maciej Maciejczyk, and Bernard Lammek. "Solution structure of conformationally restricted vasopressin analogues." Acta Biochimica Polonica 51, no. 1 (2004): 33–49. http://dx.doi.org/10.18388/abp.2004_3594.

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In recent years, a massive effort has been directed towards designing potent and selective antagonists of neurohypophyseal hormones substituted at position 3. Modification of vasopressin at position 3 with 4,4'-biphenylalanine results in pharmacologically inactive analogues. Chemically, this substitution appears to vary only slightly from those previously made by us (1-Nal or 2-Nal), which afforded potent agonists of V(2) receptors. In this situation, it seemed worthwhile to study the structure of the analogues with 4,4'-biphenylalanine (BPhe) at position 3 in aqueous solution using NMR spectr

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28

BERTOLA, Françoise, Claude MANIGAND, Philippe PICARD, Maya BELGHAZI, and Gilles PRECIGOUX. "Human T-lymphotrophic virus type I nucleocapsid protein NCp15: structural study and stability of the N-terminal zinc-finger." Biochemical Journal 352, no. 2 (2000): 293–300. http://dx.doi.org/10.1042/bj3520293.

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An 18-residue peptide, corresponding to the minimum sequence of the N-terminal zinc-finger domain in the nucleocapsid of human T-lymphotrophic virus type I, was synthesized by a solid-phase method and fully characterized. Its ability to complex metal ions (Co2+ and Zn2+) was clearly established by UV–visible spectroscopy and MS. The stability of these complexes was investigated by an original method with HPLC chromatography. Our results show that, even in the presence of air, the Zn2+ complex is highly stable. In contrast, the Co2+ complex undergoes a relatively fast degradation due to an intr

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29

Deshmukh, Lalit, Rodolfo Ghirlando, and G. Marius Clore. "Conformation and dynamics of the Gag polyprotein of the human immunodeficiency virus 1 studied by NMR spectroscopy." Proceedings of the National Academy of Sciences 112, no. 11 (2015): 3374–79. http://dx.doi.org/10.1073/pnas.1501985112.

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Assembly and maturation of the human immunodeficiency virus type 1 (HIV-1) are governed by the Gag polyprotein. Here we study the conformation and dynamics of a large HIV-1 Gag fragment comprising the matrix, capsid, spacer peptide 1 and nucleocapsid domains (referred to as ΔGag) by heteronuclear multidimensional NMR spectroscopy. In solution, ΔGag exists in a dynamic equilibrium between monomeric and dimeric states. In the presence of nucleic acids and at low ionic strength ΔGag assembles into immature virus-like particles. The structured domains of ΔGag (matrix, the N- and C-terminal domains

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30

Daura, Xavier, Karl Gademann, Heiko Schäfer, Bernhard Jaun, Dieter Seebach та Wilfred F. van Gunsteren. "Τhe β-Peptide Hairpin in Solution: Conformational Study of a β-Hexapeptide in Methanol by NMR Spectroscopy and MD Simulation". Journal of the American Chemical Society 123, № 10 (2001): 2393–404. http://dx.doi.org/10.1021/ja003689g.

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Chiou, Aih-Jing, Geok-Toh Ong, Kung-Tsung Wang, Shyh-Horng Chiou, and Shih-Hsiung Wu. "Conformational Study of Two Linear Hexapeptides by Two-Dimensional NMR and Computer-Simulated Modeling: Implication for Peptide Cyclization in Solution." Biochemical and Biophysical Research Communications 219, no. 2 (1996): 572–79. http://dx.doi.org/10.1006/bbrc.1996.0275.

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Eaton, H. L., R. E. Austin, S. W. Fesik, and S. F. Martin. "NMR study of the possible interaction in solution of angiotensin II with a peptide encoded by angiotensin II complementary RNA." Proceedings of the National Academy of Sciences 86, no. 24 (1989): 9767–69. http://dx.doi.org/10.1073/pnas.86.24.9767.

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Harvey, Peta, Nyoman Kurniawan, Rocio Finol-Urdaneta та ін. "NMR Structure of μ-Conotoxin GIIIC: Leucine 18 Induces Local Repacking of the N-Terminus Resulting in Reduced NaV Channel Potency". Molecules 23, № 10 (2018): 2715. http://dx.doi.org/10.3390/molecules23102715.

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μ-Conotoxins are potent and highly specific peptide blockers of voltage-gated sodium channels. In this study, the solution structure of μ-conotoxin GIIIC was determined using 2D NMR spectroscopy and simulated annealing calculations. Despite high sequence similarity, GIIIC adopts a three-dimensional structure that differs from the previously observed conformation of μ-conotoxins GIIIA and GIIIB due to the presence of a bulky, non-polar leucine residue at position 18. The side chain of L18 is oriented towards the core of the molecule and consequently the N-terminus is re-modeled and located clos

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Liu, Xiaohong, Serafin Fraga, Albin Otter, George Kotovych та Paul G. Scott. "Effect of a hydrophobic amino acid at position (i −1) on the stability of β-turns in hydrophilic pentapeptides as studied by NMR and molecular mechanics". Canadian Journal of Chemistry 73, № 7 (1995): 972–80. http://dx.doi.org/10.1139/v95-120.

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A detailed NMR study of the peptide NAc-FDEKA-NH2 in aqueous and in CD3OH/H2O solutions as well as the N-acetylpentapeptide amides YDEKA, VDEKA, GDEKA, and the protected tetrapeptide NAc-DEKA-NH2 in methanolic solutions indicates the importance of the first amino acid (at i −1) on stabilizing the type I β-turn. The data illustrate the hydrophobic stabilization of this turn, which is present in FDEKA, YDEKA, and VDEKA. For GDEKA and DEKA, the NMR data indicate that this turn is not present. Molecular mechanics calculations support this conclusion and indicate that for FDEKA and GDEKA the type I

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Prosser, R. Scott, V. B. Volkov, and I. V. Shiyanovskaya. "Solid-state NMR studies of magnetically aligned phospholipid membranes: taming lanthanides for membrane protein studies." Biochemistry and Cell Biology 76, no. 2-3 (1998): 443–51. http://dx.doi.org/10.1139/o98-058.

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The addition of lanthanides (Tm3+, Yb3+, Er3+, or Eu3+) to a solution of long-chain phospholipids such as dimyristoylphosphatidylcholine (DMPC) and short-chain phospholipids such as dihexanoylphosphatidylcholine (DHPC) is known to result in a bilayer phase in which the average bilayer normal aligns parallel to an applied magnetic field. Lanthanide-doped bilayers have enormous potential for the study of membrane proteins by solid-state NMR, low-angle diffraction, and a variety of optical spectroscopic techniques. However, the addition of lanthanides poses certain challenges to the NMR spectrosc

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Campbell, A. Patricia, Daisy L. Bautista, Brian Tripet, et al. "Solution Secondary Structure of a Bacterially Expressed Peptide from the Receptor Binding Domain ofPseudomonas aeruginosaPili Strain PAK: A Heteronuclear Multidimensional NMR Study†." Biochemistry 36, no. 42 (1997): 12791–801. http://dx.doi.org/10.1021/bi9709304.

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Gaggelli, Elena, Nicola D'Amelio, Nicola Gaggelli, and Gianni Valensin. "Calcium Ions Affect the Exchange Network but not the Structure of a Small Peptide (Melanostatin) in Solution: A1H and13C NMR Spectroscopic Study." European Journal of Inorganic Chemistry 2000, no. 8 (2000): 1699–706. http://dx.doi.org/10.1002/1099-0682(200008)2000:8<1699::aid-ejic1699>3.0.co;2-g.

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PADILLA, ANDRÉ, JENNIFER A. HAUER, IGOR TSIGELNY, JOSEPH PARELLO, and SUSAN S. TAYLOR. "Solution structure of synthetic peptide inhibitor and substrate of cAMP-dependent protein kinase. A study by 2D 1H NMR and molecular dynamics." Journal of Peptide Research 49, no. 3 (2009): 210–20. http://dx.doi.org/10.1111/j.1399-3011.1997.tb00880.x.

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Andrieux, Marc, Eric Leroy, Eric Guittet, et al. "Transferred Nuclear Overhauser Effect Study of the C-Terminal Helix of Yeast Phosphoglycerate Kinase: NMR Solution Structure of the C-Terminal Bound Peptide." Biochemistry 34, no. 3 (1995): 842–46. http://dx.doi.org/10.1021/bi00003a018.

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VANHAVERBEKE, Cécile, Jean-Pierre SIMORRE, Rabia SADIR, Pierre GANS та Hugues LORTAT-JACOB. "NMR characterization of the interaction between the C-terminal domain of interferon-γ and heparin-derived oligosaccharides". Biochemical Journal 384, № 1 (2004): 93–99. http://dx.doi.org/10.1042/bj20040757.

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Interferons are cytokines that play a complex role in the resistance of mammalian hosts to pathogens. IFNγ (interferon-γ) is secreted by activated T-cells and natural killer cells. IFNγ is involved in a wide range of physiological processes, including antiviral activity, immune response, cell proliferation and apoptosis, as well as the stimulation and repression of a variety of genes. IFNγ activity is modulated by the binding of its C-terminal domain to HS (heparan sulphate), a glycosaminoglycan found in the extracellular matrix and at the cell surface. In the present study, we analysed the in

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Nagy, Tamás Milán, Krisztina Knapp, Eszter Illyés, et al. "Photochemical and Structural Studies on Cyclic Peptide Models." Molecules 23, no. 9 (2018): 2196. http://dx.doi.org/10.3390/molecules23092196.

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Ultra-violet (UV) irradiation has a significant impact on the structure and function of proteins that is supposed to be in relationship with the tryptophan-mediated photolysis of disulfide bonds. To investigate the correlation between the photoexcitation of Trp residues in polypeptides and the associated reduction of disulfide bridges, a series of small, cyclic oligopeptide models were analyzed in this work. Average distances between the aromatic side chains and the disulfide bridge were determined following molecular mechanics (MM) geometry optimizations. In this way, the possibility of catio

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Zhao, Ruiming, Hui Dai, Netanel Mendelman, Jordan H. Chill, and Steve A. N. Goldstein. "Tethered peptide neurotoxins display two blocking mechanisms in the K+ channel pore as do their untethered analogs." Science Advances 6, no. 10 (2020): eaaz3439. http://dx.doi.org/10.1126/sciadv.aaz3439.

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We show here that membrane-tethered toxins facilitate the biophysical study of the roles of toxin residues in K+ channel blockade to reveal two blocking mechanisms in the K+ channel pore. The structure of the sea anemone type I (SAK1) toxin HmK is determined by NMR. T-HmK residues are scanned by point mutation to map the toxin surface, and seven residues are identified to be critical to occlusion of the KcsA channel pore. T-HmK–Lys22 is shown to interact with K+ ions traversing the KcsA pore from the cytoplasm conferring voltage dependence on the toxin off rate, a classic mechanism that we obs

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Marion, Dominique. "Rotating frame nuclear overhauser effect: a practical tool for the 1 H NMR study of peptides in solution." FEBS Letters 192, no. 1 (1985): 99–103. http://dx.doi.org/10.1016/0014-5793(85)80051-x.

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Bereiter, Raphael, Maximilian Himmelstoß, Eva Renard, et al. "Impact of 3-deazapurine nucleobases on RNA properties." Nucleic Acids Research 49, no. 8 (2021): 4281–93. http://dx.doi.org/10.1093/nar/gkab256.

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Abstract Deazapurine nucleosides such as 3-deazaadenosine (c3A) are crucial for atomic mutagenesis studies of functional RNAs. They were the key for our current mechanistic understanding of ribosomal peptide bond formation and of phosphodiester cleavage in recently discovered small ribozymes, such as twister and pistol RNAs. Here, we present a comprehensive study on the impact of c3A and the thus far underinvestigated 3-deazaguanosine (c3G) on RNA properties. We found that these nucleosides can decrease thermodynamic stability of base pairing to a significant extent. The effects are much more

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Jackson, Graham E., Elumalai Pavadai, Gerd Gäde, and Niels H. Andersen. "The adipokinetic hormones and their cognate receptor from the desert locust, Schistocerca gregaria: solution structure of endogenous peptides and models of their binding to the receptor." PeerJ 7 (August 30, 2019): e7514. http://dx.doi.org/10.7717/peerj.7514.

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Background Neuropeptides exert their activity through binding to G protein-coupled receptors (GPCRs). GPCRs are well-known drug targets in the pharmaceutical industry and are currently discussed as targets to control pest insects. Here, we investigate the neuropeptide adipokinetic hormone (AKH) system of the desert locust Schistocerca gregaria. The desert locust is known for its high reproduction, and for forming devastating swarms consisting of billions of individual insects. It is also known that S. gregaria produces three different AKHs as ligands but has only one AKH receptor (AKHR). The A

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Gaggelli, Elena, Nicola D'Amelio, Nicola Gaggelli, and Gianni Valensin. "Metal Ion Effects on the cis/trans Isomerization Equilibrium of Proline in Short-Chain Peptides: A Solution NMR Study." ChemBioChem 2, no. 7-8 (2001): 524–29. http://dx.doi.org/10.1002/1439-7633(20010803)2:7/8<524::aid-cbic524>3.0.co;2-p.

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Stepanyuk, Galina A., Pedro Serrano, Eigen Peralta, et al. "UHM–ULM interactions in the RBM39–U2AF65 splicing-factor complex." Acta Crystallographica Section D Structural Biology 72, no. 4 (2016): 497–511. http://dx.doi.org/10.1107/s2059798316001248.

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RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional co-activator of estrogen receptors and Jun/AP-1, and its function has been associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belongs to the U2AF homology motif family (UHM), which mediate protein–protein interactions through a short tryptophan-containing peptide known as the UHM-ligand motif (ULM). Here, crystal and solution NMR structures of the RBM39-UHM domain, and the crystal structure of its complex with U2AF65-ULM, are reported. The RBM39–U2AF65 interaction was confirm

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Ozsváth, Bíró, Nagy, Buglyó, Sanna, and Farkas. "Trends and Exceptions in the Interaction of Hydroxamic Acid Derivatives of Common Di- and Tripeptides with Some 3d and 4d Metal Ions in Aqueous Solution." Molecules 24, no. 21 (2019): 3941. http://dx.doi.org/10.3390/molecules24213941.

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By using various techniques (pH-potentiometry, UV-Visible spectrophotometry, 1H and 17O-NMR, EPR, ESI-MS), first time in the literature, solution equilibrium study has been performed on complexes of dipeptide and tripeptide hydroxamic acids—AlaAlaNHOH, AlaAlaN(Me)OH, AlaGlyGlyNHOH, and AlaGlyGlyN(Me)OH—with 4d metals: the essential Mo(VI) and two half-sandwich type cations, [(η6-p-cym)Ru(H2O)3]2+ as well as [(η5-Cp*)Rh(H2O)3]2+, the latter two having potential importance in cancer therapy. The tripeptide derivatives have also been studied with some biologically important 3d metals, such as Fe(

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Abbassi, Feten, Cécile Galanth, Mohamed Amiche, et al. "Solution Structure and Model Membrane Interactions of Temporins-SH, Antimicrobial Peptides from Amphibian Skin. A NMR Spectroscopy and Differential Scanning Calorimetry Study†." Biochemistry 47, no. 40 (2008): 10513–25. http://dx.doi.org/10.1021/bi8006884.

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Tőke, Orsolya, Kitti Koprivanacz, László Radnai, et al. "Solution NMR Structure of the SH3 Domain of Human Caskin1 Validates the Lack of a Typical Peptide Binding Groove and Supports a Role in Lipid Mediator Binding." Cells 10, no. 1 (2021): 173. http://dx.doi.org/10.3390/cells10010173.

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SH3 domains constitute an important class of protein modules involved in a variety of cellular functions. They participate in protein-protein interactions via their canonical ligand binding interfaces composed of several evolutionarily conserved aromatic residues forming binding grooves for typical (PxxP) and atypical (PxxxPR, RxxK, RKxxY) binding motifs. The calcium/calmodulin-dependent serine protein kinase (CASK)-interacting protein 1, or Caskin1, a multidomain scaffold protein regulating the cortical actin filaments, is enriched in neural synapses in mammals. Based on its known interaction

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