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Journal articles on the topic 'Peptide conformation'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 September 2023

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1

Bierzyński, A. "Methods of peptide conformation studies." Acta Biochimica Polonica 48, no. 4 (2001): 1091–99. http://dx.doi.org/10.18388/abp.2001_3870.

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In solution most of the peptides assume multiple flexible conformations. Determination of the dominant conformers and evaluation of their populations is the aim of peptide conformation studies, in which theoretical and experimental methods play complementary roles. Molecular dynamics or Monte Carlo methods are quite effective in searching the conformational space accessible to a peptide but they are not able to estimate, precisely enough, the populations of various conformations. Therefore, they must be supplemented by experimental data. In this paper, a short review of the experimental method

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2

Żyłka, Romuald, Justyna Kupiec, and Stanislaw Przestalski. "Peptides conformational changes of the erythrocyte membrane induced by organometallic tin compounds." Current Topics in Biophysics 34, no. 1 (2011): 31–35. http://dx.doi.org/10.2478/v10214-011-0005-2.

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Peptides conformational changes of the erythrocyte membrane induced by organometallic tin compoundsThe paper presents the results of a study on the effect of selected organic chlorides of tin on peptide conformations of erythrocyte ghosts from pig blood. The following compounds were used: dibutyltin dichloride (DBT), tributyltin chloride (TBT), diphenyltin dichloride (DPhT) and triphenyltin chloride (TPhT). Peptide conformation changes were determined on the basis of measurements done with the ATR FTIR technique. This method made it possible to measure the percent share of a peptide with speci

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3

Smith, K. D., B. E. Mace, A. Valenzuela, et al. "Probing HLA-B7 conformational shifts induced by peptide-binding groove mutations and bound peptide with anti-HLA monoclonal antibodies." Journal of Immunology 157, no. 6 (1996): 2470–78. http://dx.doi.org/10.4049/jimmunol.157.6.2470.

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Abstract To determine the influence of peptide-binding groove residues and MHC-bound peptide on HLA-B7 conformation, we investigated the binding sites of nine locus- or allele-specific mAbs using a panel of 82 HLA-B7 variants. The functional mAb epitopes encircle the HLA-B7 peptide-binding groove. Three mAbs are affected by mutations at solvent-accessible peptide-binding groove mutations. Mutations in peptide-binding groove residues 45, 63, and 150 affect multiple nonoverlapping mAb epitopes, probably by interaction with other MHC residues or bound peptide. However, 18 of 24 peptide-binding gr

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4

Kotovych, George, John R. Cann, John M. Stewart, and Hitoshi Yamamoto. "NMR and CD conformational studies of bradykinin and its agonists and antagonists: application to receptor binding." Biochemistry and Cell Biology 76, no. 2-3 (1998): 257–66. http://dx.doi.org/10.1139/o98-028.

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Most physiological processes are regulated by peptides that perform their functions by interacting with specific receptors on cells. Specific conformations of the peptides are required for correct interactions to take place, and a knowledge of the biologically important conformation is vital for the understanding of biological function. Over the last few years extensive studies using nuclear magnetic resonance and circular dichroism have been carried out on bradykinin (Arg1-Pro2-Pro3-Gly4-Phe5-Ser6-Pro7-Phe8-Arg9) and its antagonists with the objective of developing new drugs to combat severe

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5

LEE, HO-JIN, HYUN-MEE PARK, and KANG-BONG LEE. "CONFORMATIONAL PREFERENCES OF N-ACETYL–GLYCINE–GLYCINE–N′-METHYLAMIDE: A THEORETICAL STUDY." Journal of Theoretical and Computational Chemistry 08, no. 05 (2009): 799–811. http://dx.doi.org/10.1142/s0219633609005118.

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The conformational preferences of peptide models have been investigated to understand the protein folding mechanism and to develop the force field. Here, we report the minimum energy conformations for a model peptide, N-acetyl–glycine–glycine–N′-methylamide ( Ac–1Gly–2Gly–NHMe(I) ) at the HF/3-21G, HF/6-31G*, and the B3LYP/6-31G* level of theory. At the B3LYP/6-31G* level, the 31 minima were identified and the 10 β-turn structures among the minima were observed in gas-phase. The conformational preferences of Gly residue in the model peptide, I depend on its relative position and conformation o

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6

Wolfe, Saul, Kiyull Yang, and Maged Khalil. "Conformation–activity relationships and the mechanism of action of penicillin." Canadian Journal of Chemistry 66, no. 11 (1988): 2733–50. http://dx.doi.org/10.1139/v88-424.

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Using the MMPEN parameters of Allinger's MMP2(85) force field, a conformational analysis has been performed on four biologically active penicillins; D-ampicillin, L-α-phenoxyethylpenicillin, penicillin G, and penicillin V, and on five biologically inactive or much less active penicillins: L-ampicillin, D-α-phenoxyethylpenicillin, N-methylpenicillin G, 6α-methylpenicillin G, and bisnorpenicillin G. Antibacterial activity is found to be associated with the existence of a global minimum having a compact structure, whose convex face is accessible to a penicillin binding protein (PBP), with the C3-

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7

Solopova, O. N., L. P. Pozdnyakova, N. E. Varlamov, et al. "Conformational Differences between Active Angiotensins and Their Inactive Precursors." Acta Naturae 4, no. 1 (2012): 74–77. http://dx.doi.org/10.32607/20758251-2012-4-1-74-77.

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The peptide conformation in the context of a protein polypeptide chain is influenced by proximal amino acid residues. However, the mechanisms of this interference remain poorly understood. We studied the conformation of angiotensins 1, 2 and 3, which are produced naturally in a sequential fashion from a precursor protein angiotensinogen and contain an identical peptide core structure. Using the example of angiotensins 1, 2 and 3, it was shown that similar amino acid sequences may have significant conformational differences in various molecules. In order to assess the conformational changes, we

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Frič, Ivo, Michal Lebl, and Victor J. Hruby. "Melanin Concentrating Hormone Analogs: Contraction of the Cyclic Structure. III. CD Spectroscopic Study." Collection of Czechoslovak Chemical Communications 57, no. 3 (1992): 614–20. http://dx.doi.org/10.1135/cccc19920614.

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A comparison of the CD spectra of MCH analogs differing in length but containing a heterodetic ring of the same size (compounds I, IV and VII or III, VI and IX) reveals that a conformational change occurs upon elongating the peptide chain from thirteen to seventeen amino-acid residues. The 5-17 fragments appear to prefer a β-turn conformation, whereas the 1-17 full-sequence peptides prefer α-helical conformation. Peptides containing seventeen-membered ring exhibit greater conformational adaptability (the incorporation of their cyclic moiety into an ordered conformation being easier) than those

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9

Boggs, J. M., G. A. Hashim, E. D. Day, and M. A. Moscarello. "Lipid-induced recognition of a conformational determinant (residues 65 to 83) in myelin basic protein." Journal of Immunology 135, no. 4 (1985): 2617–22. http://dx.doi.org/10.4049/jimmunol.135.4.2617.

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Abstract The precipitation by antibodies to intact myelin basic protein (BP) and to synthetic peptides containing a sequence based on the region 65 to 83 of bovine BP, S82, S81, S79, and S24, of intact BP in solution or bound to lipid vesicles was compared, using 125I-BP or 14C-DPPC-labeled lipid-BP vesicles. The antipeptide antibodies were shown earlier to recognize conformational determinants which are not expressed in the intact protein in solution. Several anti-BP antibodies precipitated more of the BP free in solution than when bound to lipid vesicles, suggesting that some of the determin

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10

Chen, Y., J. Sidney, S. Southwood, et al. "Naturally processed peptides longer than nine amino acid residues bind to the class I MHC molecule HLA-A2.1 with high affinity and in different conformations." Journal of Immunology 152, no. 6 (1994): 2874–81. http://dx.doi.org/10.4049/jimmunol.152.6.2874.

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Abstract An equilibrium binding assay was used to directly measure the relative affinities of naturally processed 9-mer, 10-mer, and 12-mer peptides for the human class I MHC molecule HLA-A2.1. The peptides exhibited a range of affinities with IC50 values of 11 to 214 nM. The mode of interaction between these peptides and HLA-A2.1 was examined using peptides in which Asp had been substituted for suspected anchor residues. Regardless of length, the previously identified Leu at position 2 relative to the amino terminus was critical for peptide binding. While the carboxyl terminal residue was als

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Natarajan, Sateesh K., Masoumeh Assadi, and Scheherazade Sadegh-Nasseri. "Stable Peptide Binding to MHC Class II Molecule Is Rapid and Is Determined by a Receptive Conformation Shaped by Prior Association with Low Affinity Peptides." Journal of Immunology 162, no. 7 (1999): 4030–36. http://dx.doi.org/10.4049/jimmunol.162.7.4030.

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Abstract Formation of stable class II MHC/peptide complex involves conformational changes and proceeds via an intermediate. Although this intermediate complex forms and dissociates in minutes, its conversion to a stable complex is a very slow process, taking up to a few days to reach completion. Here, we investigate the different steps of this binding and demonstrate that the conformational changes necessary to generate a receptive molecule is the rate-determining slow step in the process, while formation of the stable MHC/peptide complex is very rapid. With HLA-DR1 as our model class II molec

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12

KESSLER, HORST, MECHTILD KLEIN, and KLAUS WAGNER. "Peptide conformation." International Journal of Peptide and Protein Research 31, no. 5 (2009): 481–98. http://dx.doi.org/10.1111/j.1399-3011.1988.tb00907.x.

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13

Alaofi, Ahmed L. "The Glu143 Residue Might Play a Significant Role in T20 Peptide Binding to HIV-1 Receptor gp41: An In Silico Study." Molecules 27, no. 12 (2022): 3936. http://dx.doi.org/10.3390/molecules27123936.

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Despite the enormous efforts made to develop other fusion inhibitors for HIV, the enfuvirtide (known as T20) peptide is the only approved HIV-1 inhibitory drug so far. Investigating the role of potential residues of the T20 peptide’s conformational dynamics could help us to understand the role of potential residues of the T20 peptide. We investigated T20 peptide conformation and binding interactions with the HIV-1 receptor (i.e., gp41) using MD simulations and docking techniques, respectively. Although the mutation of E143 into alanine decreased the flexibility of the E143A mutant, the conform

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14

Peng, Zhenghong. "NMR conformational analysis on cyclic decapeptide template molecule." Canadian Journal of Chemistry 77, no. 8 (1999): 1394–404. http://dx.doi.org/10.1139/v99-128.

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We report the synthesis and conformational analysis of a series of cyclic and bicyclic decapeptide templates for combinatorial chemistry. The peptides were synthesized via solid phase synthesis and followed by solution cyclization. The conformation of the peptides was studied by proton NMR spectroscopy in DMSO and in TFE-water. The structure of the peptide template was calculated with the program DIANA and followed by SA from the NMR experimental constraints. The peptide adopts a fold comprising two β-strands and two type II β-turns. The design of such a restained cyclic decapeptide template w

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15

Terness, P., I. Kohl, G. Hübener, et al. "The natural human IgG anti-F(ab')2 antibody recognizes a conformational IgG1 hinge epitope." Journal of Immunology 154, no. 12 (1995): 6446–52. http://dx.doi.org/10.4049/jimmunol.154.12.6446.

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Abstract Natural IgG anti-F(ab')2 Abs are part of the physiologic immune repertoire and have important immunoregulatory functions. Although previous work suggested that some of these Abs recognize epitopes located in the constant region of the F(ab')2 molecule, an exact epitope mapping has not been performed. We found that the anti-F(ab')2 Ab binds strongly to F(ab')2 but only weakly to Fab fragments. Fab fragments are lacking the core and lower hinge region. In our experiments, we show that the IgG anti-F(ab')2 Ab binds strongly to a synthetic double chain peptide (225-237/225'-237') comprisi

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16

Kindahl, Lill, Corine Sandström, A. Grey Craig, Thomas Norberg, and Lennart Kenne. "1H NMR studies on the solution conformation of contulakin-G and analogues." Canadian Journal of Chemistry 80, no. 8 (2002): 1022–31. http://dx.doi.org/10.1139/v02-115.

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The conformation of contulakin-G, a bioactive 16 amino acid O-linked glycopeptide (ZSEEGGSNAT*KKPYIL) with the disaccharide β-D-Gal(1[Formula: see text]3)α-D-GalNAc attached to the threonine residue in position 10, has been investigated by 1H NMR spectroscopy. The 1H NMR data for the non-glycosylated peptide and for two glycopeptide analogues, one with the monosaccharide α-D-GalNAc at Thr10 and one with the disaccharide β-D-Gal(1–>3)α-D-GalNAc at Ser7, all of lower bioactivity than contulakin-G, have also been collected. The chemical shifts, NOEs, temperature coefficients of amide protons,

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17

Tarjányi, Tamás, Ferenc Bogár, Janos Minarovits, Márió Gajdács, and Zsolt Tóth. "Interaction of KRSR Peptide with Titanium Dioxide Anatase (100) Surface: A Molecular Dynamics Simulation Study." International Journal of Molecular Sciences 22, no. 24 (2021): 13251. http://dx.doi.org/10.3390/ijms222413251.

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Due to its tensile strength and excellent biocompatibility, titanium (Ti) is commonly used as an implant material in medicine and dentistry. The success of dental implants depends on the formation of a contact between the oxidized surface of Ti implant and the surrounding bone tissue. The adsorption of proteins and peptides to the implant surface allows the bone-forming osteoblast cells to adhere to such modified surfaces. Recently, it has been observed that tetrapeptide KRSR (Lys-Arg-Ser-Arg) functionalization could promote osteoblast adhesion to implant surfaces. This may facilitate the esta

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18

Bharathikumar, V. M., Kris Barreto, Marciano D. Reis, John F. Decoteau, and C. Ronald Geyer. "Genetic Screen to Isolate “Lariat” Peptides for Characterizing ABL Kinase Activity and Conformation." Blood 116, no. 21 (2010): 438. http://dx.doi.org/10.1182/blood.v116.21.438.438.

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Abstract Abstract 438 Type II Abl kinase inhibitors such as imatinib achieve high selectivity by specifically targeting the inactive Abl/c-Kit conformation. However, these inhibitors are prone to inactivation by resistance mutations that cause conformational changes. A better understanding of mutant Abl conformations would provide information to design inhibitors that recognize multiple states of Abl with lower rates of resistance. To more easily examine Abl kinase conformations, conformer specific reagents are needed that are (i) easily generated against a given Abl conformation, (ii) compati

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Yu, Jingxian, John R. Horsley, and Andrew D. Abell. "The Influence of Secondary Structure on Electron Transfer in Peptides." Australian Journal of Chemistry 66, no. 8 (2013): 848. http://dx.doi.org/10.1071/ch13276.

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A series of synthetic peptides containing 0–5 α-aminoisobutyric acid (Aib) residues and a C-terminal redox-active ferrocene was synthesised and their conformations defined by NMR and circular dichroism. Each peptide was separately attached to an electrode for subsequent electrochemical analysis in order to investigate the effect of peptide chain length (distance dependence) and secondary structure on the mechanism of intramolecular electron transfer. While the shorter peptides (0–2 residues) do not adopt a well defined secondary structure, the longer peptides (3–5 residues) adopt a helical con

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Hatami, Asa, Sanaz Monjazeb, Saskia Milton та Charles G. Glabe. "Familial Alzheimer's Disease Mutations within the Amyloid Precursor Protein Alter the Aggregation and Conformation of the Amyloid-β Peptide". Journal of Biological Chemistry 292, № 8 (2017): 3172–85. http://dx.doi.org/10.1074/jbc.m116.755264.

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Most cases of Alzheimer's disease (AD) are sporadic, but a small percentage of AD cases, called familial AD (FAD), are associated with mutations in presenilin 1, presenilin 2, or the amyloid precursor protein. Amyloid precursor protein mutations falling within the amyloid-β (Aβ) sequence lead to a wide range of disease phenotypes. There is increasing evidence that distinct amyloid structures distinguished by amyloid conformation-dependent monoclonal antibodies have similarly distinct roles in pathology. It is possible that this phenotypic diversity of FAD associated with mutations within the A

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Bremer, J., and GL Mendz. "Conformational Energy Calculations on the Eosinophil Chemotactic Peptide Analog Val-Gly-Ala-Glu: Comparison of Theory and Experiment." Australian Journal of Chemistry 41, no. 12 (1988): 1841. http://dx.doi.org/10.1071/ch9881841.

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Conformational energy calculations have been employed to obtain minimum energy conformations of the peptide Val- Gly-Ala-Glu , an analogue of eosinophil chemotactic tetrapeptides. The calculated conformations of the peptide can be described as an ensemble of structures in which the C-terminal and N-terminal regions of the molecule are in close proximity. The charge state of the peptide showed a marked effect on the calculated conformation, and the results were also sensitive to the electrostatic environment. The calculations performed on the dianionic form of the molecule showed good agreement

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Sambasivam, Dhandayuthapani, Senthilkumar Sivanesan, Sayeeda Sultana та Jayakumar Rajadas. "Conformational Preferences of Aβ25-35 and Aβ35-25 in Membrane Mimicking Environments". Protein & Peptide Letters 26, № 5 (2019): 386–90. http://dx.doi.org/10.2174/0929866526666190228122849.

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Background: The structural transition of aggregating Abeta peptides is the key event in the progression of Alzheimer’s Disease (AD). Objective: In the present work, the structural modifications of toxic Aβ25-35 and the scrambled Aβ35-25 were studied in Trifluoroethanol (TFE) and in aqueous SDS micelles. Methods: Using CD spectroscopic investigations, the conformational transition of Aβ25-35 and Aβ35-25 peptides were determined in different membrane mimicking environments such as TFE and SDS. An interval scan CD of the peptides on evaporation of TFE was performed. TFE titrations were carried ou

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Xiong, Qinsi, Ziye Liu, and Wei Han. "Sequence-Dependent Nanofiber Structures of Phenylalanine and Isoleucine Tripeptides." International Journal of Molecular Sciences 21, no. 22 (2020): 8431. http://dx.doi.org/10.3390/ijms21228431.

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The molecular design of short peptides to achieve a tailor-made functional architecture has attracted attention during the past decade but remains challenging as a result of insufficient understanding of the relationship between peptide sequence and assembled supramolecular structures. We report a hybrid-resolution model to computationally explore the sequence–structure relationship of self-assembly for tripeptides containing only phenylalanine and isoleucine. We found that all these tripeptides have a tendency to assemble into nanofibers composed of laterally associated filaments. Molecular a

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Northfield, Susan E., Simon J. Mountford, Jerome Wielens, et al. "Propargyloxyproline Regio- and Stereoisomers for Click-Conjugation of Peptides: Synthesis and Application in Linear and Cyclic Peptides." Australian Journal of Chemistry 68, no. 9 (2015): 1365. http://dx.doi.org/10.1071/ch15146.

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The use of the click reaction for the introduction of conjugate groups, such as affinity or fluorescent labels, to a peptide for the study of peptide biochemistry and pharmacology is widespread. However, the nature and location of substituted 1,2,3-triazoles in peptide sequences may markedly affect conformation or binding as compared with native sequences. We have examined the preparation and application of propargyloxyproline (Pop) residues as a precursor to such peptide conjugates. Pop residues are available in a range of regio- and stereoisomers from hydroxyproline precursors and are readil

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Nousiainen, Marjaana, Pirjo Vainiotalo, Peter J. Derrick, et al. "Calcium and Peptide Binding to Folded and Unfolded Conformations of Cardiac Troponin C. Electrospray Ionization and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." European Journal of Mass Spectrometry 8, no. 6 (2002): 471–81. http://dx.doi.org/10.1255/ejms.523.

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The binding of Ca2+ and of a peptide (N-TnC) to human cardiac troponin C (TnC) and its isolated N- and C-terminal domains has been characterized by electrospray ionization Fourier transform ion cyclotron resonance (ESI FT-ICR) mass spectrometry. The peptide N-TnI corresponds to residues 1–29 of the cardiac-specific N-terminal extension of human cardiac troponin I (TnI). The binding of Ca2+ to intact TnC in the absence of the peptide was found to take a bimodal form with preferred stoichiometries of 1:1 TnC: Ca2+ and 1:3 TnC: Ca2+. It is concluded that TnC existed in two conformational isomers

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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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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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Egorov, Vladimir, Natalia Grudinina, Andrey Vasin, and Dmitry Lebedev. "Peptide-Induced Amyloid-Like Conformational Transitions in Proteins." International Journal of Peptides 2015 (September 8, 2015): 1–5. http://dx.doi.org/10.1155/2015/723186.

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Changes in protein conformation can occur both as part of normal protein functioning and during disease pathogenesis. The most common conformational diseases are amyloidoses. Sometimes the development of a number of diseases which are not traditionally related to amyloidoses is associated with amyloid-like conformational transitions of proteins. Also, amyloid-like aggregates take part in normal physiological processes such as memorization and cell signaling. Several primary structural features of a protein are involved in conformational transitions. Also the protein proteolytic fragments can c

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Fakih, Taufik Muhammad, and Mentari Luthfika Dewi. "The design of bioactive marine peptides as a HIV-1 protease inhibitor." Jurnal Ilmiah Farmasi 17, no. 2 (2021): 160–71. http://dx.doi.org/10.20885/jif.vol17.iss2.art6.

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Background: Human immunodeficiency virus/acquired immunodeficiency syndrome (HIV or AIDS) is a disease related to the human immune system. Given its important role in viral replication, HIV1 protease (HIV1 PR) becomes the major therapeutic target in the treatment of AIDS. In this case, we need a dynamic aspect of molecular interactions that can demonstrate the important role of conformational variability in the design of HIV1 PR inhibitors. There are several inhibitor candidates from marine organisms, such as the LLEYSL and LLEYSI bioactive peptides produced by oysters (Crassostrea gigas). Obj

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Elghobashi-Meinhardt, Nadia. "Exploring Peptide–Solvent Interactions: A Computational Study." Molecules 23, no. 9 (2018): 2355. http://dx.doi.org/10.3390/molecules23092355.

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The dilemma of reconciling the contradictory evidence regarding the conformation of long solvated peptide chains is the so-called “reconciliation problem”. Clues regarding the stability of certain conformations likely lie in the electronic structure at the peptide–solvent interface, but the peptide–solvent interaction is not fully understood. Here, we study the influence of aqueous solvent on peptide conformations by using classical molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) energy calculations. The model systems include an 11-residue peptide, X 2 A 7 O 2 (XAO)

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Feng, Lei, Yong-Yu Gao, Mingwei Sun, et al. "The Parallel Presentation of Two Functional CTL Epitopes Derived from the O and Asia 1 Serotypes of Foot-and-Mouth Disease Virus and Swine SLA-2*HB01: Implications for Universal Vaccine Development." Cells 11, no. 24 (2022): 4017. http://dx.doi.org/10.3390/cells11244017.

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Foot-and-mouth disease virus (FMDV) poses a significant threat to the livestock industry. Through their recognition of the conserved epitopes presented by the swine leukocyte antigen (SLA), T cells play a pivotal role in the antiviral immunity of pigs. Herein, based on the peptide binding motif of SLA-2*HB01, from an original SLA-2 allele, a series of functional T-cell epitopes derived from the dominant antigen VP1 of FMDV with high binding capacity to SLA-2 were identified. Two parallel peptides, Hu64 and As64, from the O and Asia I serotypes, respectively, were both crystallized with SLA-2*H

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Diharce, Julien, Mickaël Cueto, Massimiliano Beltramo, Vincent Aucagne, and Pascal Bonnet. "In Silico Peptide Ligation: Iterative Residue Docking and Linking as a New Approach to Predict Protein-Peptide Interactions." Molecules 24, no. 7 (2019): 1351. http://dx.doi.org/10.3390/molecules24071351.

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Peptide–protein interactions are corner-stones of living functions involved in essential mechanisms, such as cell signaling. Given the difficulty of obtaining direct experimental structural biology data, prediction of those interactions is of crucial interest for the rational development of new drugs, notably to fight diseases, such as cancer or Alzheimer’s disease. Because of the high flexibility of natural unconstrained linear peptides, prediction of their binding mode in a protein cavity remains challenging. Several theoretical approaches have been developed in the last decade to address th

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Catipović, B., G. Talluri, J. Oh, et al. "Analysis of the structure of empty and peptide-loaded major histocompatibility complex molecules at the cell surface." Journal of Experimental Medicine 180, no. 5 (1994): 1753–61. http://dx.doi.org/10.1084/jem.180.5.1753.

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We compared the conformation of empty and peptide-loaded class I major histocompatibility complex (MHC) molecules at the cell surface. Molecular conformations were analyzed by fluorescence resonance energy transfer (FRET) between fluorescent-labeled Fab fragments bound to the alpha 2 domain of the MHC heavy chain and fluorescent-labeled Fab fragments bound to beta 2-microglobulin. No FRET was found between Fab fragments bound to empty H-2Kb, but FRET was detected when empty H-2Kb molecules were loaded with peptide. The magnitude of FRET depended on the sequence of the peptide used. The results

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Dobrovolska, Olena, Øyvind Strømland, Ørjan Sele Handegård, et al. "Investigating the Disordered and Membrane-Active Peptide A-Cage-C Using Conformational Ensembles." Molecules 26, no. 12 (2021): 3607. http://dx.doi.org/10.3390/molecules26123607.

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The driving forces and conformational pathways leading to amphitropic protein-membrane binding and in some cases also to protein misfolding and aggregation is the subject of intensive research. In this study, a chimeric polypeptide, A-Cage-C, derived from α-Lactalbumin is investigated with the aim of elucidating conformational changes promoting interaction with bilayers. From previous studies, it is known that A-Cage-C causes membrane leakages associated with the sporadic formation of amorphous aggregates on solid-supported bilayers. Here we express and purify double-labelled A-Cage-C and prep

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Mohan, Madhan Kumar, Nikita Abraham, Rajesh R P та ін. "Structure and allosteric activity of a single-disulfide conopeptide from Conus zonatus at human α3β4 and α7 nicotinic acetylcholine receptors". Journal of Biological Chemistry 295, № 20 (2020): 7096–112. http://dx.doi.org/10.1074/jbc.ra119.012098.

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Conopeptides are neurotoxic peptides in the venom of marine cone snails and have broad therapeutic potential for managing pain and other conditions. Here, we identified the single-disulfide peptides Czon1107 and Cca1669 from the venoms of Conus zonatus and Conus caracteristicus, respectively. We observed that Czon1107 strongly inhibits the human α3β4 (IC50 15.7 ± 3.0 μm) and α7 (IC50 77.1 ± 0.05 μm) nicotinic acetylcholine receptor (nAChR) subtypes, but the activity of Cca1669 remains to be identified. Czon1107 acted at a site distinct from the orthosteric receptor site. Solution NMR experimen

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Solheim, J. C., B. M. Carreno, J. D. Smith, et al. "Binding of peptides lacking consensus anchor residue alters H-2Ld serologic recognition." Journal of Immunology 151, no. 10 (1993): 5387–97. http://dx.doi.org/10.4049/jimmunol.151.10.5387.

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Abstract CTL recognize class I MHC/peptide complexes on the surface of target cells. Crystallographic and serologic data have indicated that peptide ligands can influence the conformation of class I molecules and hence T cell recognition. How the binding of peptides with disparate sequence motifs affects the conformation of distinct regions within a class I molecule remains unknown. A series of site-directed mutants of the murine class I molecule H-2Ld was studied to address this question. These mutants were generated by in vitro mutagenesis and used to map the serologic epitopes recognized by

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Negroni, Maria, and Lawrence Stern. "Unexpected side reaction of lysine and arginine side chains preceding a photocleavable group in MHC-II UV-cleavable peptides. (P5028)." Journal of Immunology 190, no. 1_Supplement (2013): 41.15. http://dx.doi.org/10.4049/jimmunol.190.supp.41.15.

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Abstract MHC class II molecules (MHCII) present peptides to CD4+ T cells, and HLA-DM (DM) catalyzes peptide exchange favoring binding of high affinity peptides. The effects of DM on peptide association and dissociation kinetics are not yet clear. In the absence of peptide, DR1 (a MHCII) is in equilibrium between inactive and active conformations. In order to understand the kinetics of this process and how it is affected by DM, we wanted to generate DR1 in the active conformation using a peptide carrying the photocleavable 3-amino-3-(2-nitrophenyl)-propionic acid residue, an approach previously

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Tresnoningtias, Mutiara Anisa, Andre Sasongko Nurwarrohman, Ihyar Kurnia, Christian Rinaldy, Asy’ari Mukhammad, and Siahaan Parsaoran. "Computational Study: Noncovalent Interaction of Cys-Ala Peptide with Alkaline Earth Metal Ions and its Conformation Changes." Key Engineering Materials 874 (January 2021): 128–35. http://dx.doi.org/10.4028/www.scientific.net/kem.874.128.

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The study of the intermolecular interactions is important to explain the phenomenon occurred on the human body. One of the most important processes that can be studied is the interaction of the peptide with metal ions. In this study, a computational approach was harnessed to predict the interaction and the changes in peptide’s conformation between Cys-Ala peptide which is one of the important amino acids in e-cadherin with some of alkaline earth metal ions. Cys-Ala peptide (Ac-CA-NH2) was used as a molecular model in this calculation. All the molecular structure involved in the interaction was

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Chou, Chih-Ling, and Scheherazade Sadegh-Nasseri. "Hla-Dm Recognizes the Flexible Conformation of Major Histocompatibility Complex Class II." Journal of Experimental Medicine 192, no. 12 (2000): 1697–706. http://dx.doi.org/10.1084/jem.192.12.1697.

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DM facilitates formation of high affinity complexes of peptide–major histocompatibility complex (MHC) by release of class II MHC–associated invariant chain peptide (CLIP). This has been proposed to occur through discrimination of complex stability. By probing kinetic and conformational intermediates of the wild-type and mutant human histocompatibility leukocyte antigen (HLA)-DR1–peptide complexes, and examining their reactivities with DM, we propose that DM interacts with the flexible hydrophobic pocket 1 of DR1 and converts the molecule into a conformation that is highly peptide receptive. A

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Maize, Kimberly M., Elbek K. Kurbanov, Teresa De La Mora-Rey, et al. "Anthrax toxin lethal factor domain 3 is highly mobile and responsive to ligand binding." Acta Crystallographica Section D Biological Crystallography 70, no. 11 (2014): 2813–22. http://dx.doi.org/10.1107/s1399004714018161.

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The secreted anthrax toxin consists of three components: the protective antigen (PA), edema factor (EF) and lethal factor (LF). LF, a zinc metalloproteinase, compromises the host immune system primarily by targeting mitogen-activated protein kinase kinases in macrophages. Peptide substrates and small-molecule inhibitors bind LF in the space between domains 3 and 4 of the hydrolase. Domain 3 is attached on a hinge to domain 2viaresidues Ile300 and Pro385, and can move through an angular arc of greater than 35° in response to the binding of different ligands. Here, multiple LF structures includi

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Hlaváček, Jan, Ivo Frič, Petr Maloň, Karel Jošt, and Karel Bláha. "Three cyclohexapeptides modelling the oxytocin ring moiety: Synthesis and circular dichroism." Collection of Czechoslovak Chemical Communications 52, no. 7 (1987): 1841–56. http://dx.doi.org/10.1135/cccc19871841.

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A series of cyclic disulfides cysteinyl-triglycyl-asparaginyl-cysteine (Ib), cysteinyl-diglycyl-glutaminyl-asparaginyl-cysteine (Ic), and cysteinyl-glycyl-isoleucyl-glutaminyl-asparaginyl-cysteine (Id) has been prepared. The effect of gradual attachment of side chains to the ring on the peptide backbone and the disulfide group conformation has been studied using circular dichroism. Introduction of side chains reduces substantially the conformational mobility of the backbone , but not enough to let any conformational β-turn type predominate (in polar solvents). Conformation of the disulfide gro

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Sergeyev, O. V., and I. F. Barinsky. "Synthetic peptide vaccines." Problems of Virology 61, no. 1 (2016): 5–8. http://dx.doi.org/10.18821/0507-4088-2016-61-1-5-8.

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An update on the development and trials of synthetic peptide vaccines is reviewed. The review considers the successful examples of specific protection as a result of immunization with synthetic peptides using various protocols. The importance of conformation for the immunogenicity of the peptide is pointed out. An alternative strategy of the protection of the organism against the infection using synthetic peptides is suggested.

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Dyall, R., D. H. Fremont, S. C. Jameson, and J. Nikolić-Zugić. "T cell receptor (TCR) recognition of MHC class I variants: intermolecular second-site reversion provides evidence for peptide/MHC conformational variation." Journal of Experimental Medicine 184, no. 1 (1996): 253–58. http://dx.doi.org/10.1084/jem.184.1.253.

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We investigated mechanistic differences in antigen presentation between murine MHC class I variants H-2K(b) and H-2K(bm)8. H-2K(bm)8 differs from H-2K(b) by four residues at the floor of the peptide-binding site, affecting its B pocket which interacts with the second (P2) residue of the peptide. The rest of the molecule, including the T cell receptor (TCR)-contacting residues, is identical to H-2K(b). Due to this variation, CTLs that recognize the ovalbumin 257-264 and HSV gB 498-505 peptides on H-2K(b) cannot recognize them on H-2K(bm)8. This could be due to impaired peptide binding or an alt

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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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Negroni, Maria Pia, and Lawrence J. Stern. "The length of the N-terminal region of a photocleavable peptide bound to DR1 determines the kinetics of photocleavable peptide fragment release." Journal of Immunology 196, no. 1_Supplement (2016): 185.1. http://dx.doi.org/10.4049/jimmunol.196.supp.185.1.

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Abstract MHC class II molecules (MHCII) bind peptides and present them to CD4+ T cells. As prepared as a recombinant protein, DR1 (a MHCII) is in equilibrium between peptide-receptive and peptide-averse conformations. In order to dissect which step of the peptide binding reaction is being affected in DR1 mutants with altered peptide affinity, we wanted to generate DR1 fully in the peptide-receptive conformation. To generate this form, we used a peptide carrying the photocleavable 3-amino-3-(2-nitrophenyl)-propionic acid residue, an approach previously used for other MHCI and MHCII proteins. We

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YAŞAR, FATİH. "THE EQUILIBRIUM THERMODYNAMICS OF VARIOUS PEPTIDE SEQUENCES." International Journal of Modern Physics C 15, no. 04 (2004): 583–93. http://dx.doi.org/10.1142/s0129183104006066.

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The equilibrium thermodynamic properties of two peptide sequences of β-casein in the α-helix regions were studied by three-dimensional molecular modeling in vacuum. All the three-dimensional conformations of each peptide sequences were obtained by multicanonical simulations using ECEPP/2 force field and each simulation was started from completely random initial conformation. No a-priori information about ground-state is used in the simulations. In the present study, we calculated the average values of total energy, specific heat, fourth-order cumulant for two peptide sequences of β-casein as a

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Fanelli, Ilaria, Paolo Rovero, Paul Robert Hansen, Jette Frederiksen, Gunnar Houen та Nicole Hartwig Trier. "Specificity of Anti-Citrullinated Protein Antibodies to Citrullinated α-Enolase Peptides as a Function of Epitope Structure and Composition". Antibodies 10, № 3 (2021): 27. http://dx.doi.org/10.3390/antib10030027.

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Rheumatoid arthritis (RA) is an autoimmune disease affecting approximately 1–2% of the world population. In addition to the first discovered serologic markers for RA, the rheumatoid factors (RFs), anti-citrullinated protein antibodies (ACPAs) are even more specific for the disease compared to RFs and are found in 70–80% of RA patient sera. RA etiopathogenesis still needs to be elucidated, as different factors are proposed to be involved, such as Epstein–Barr virus infection. Hence, understanding the interaction between ACPAs and their citrullinated peptide targets is relevant for a better know

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Matt, Alexander, Björn Kuttich, Isabelle Grillo, Susann Weißheit, Christina M. Thiele, and Bernd Stühn. "Temperature induced conformational changes in the elastin-like peptide GVG(VPGVG)3." Soft Matter 15, no. 20 (2019): 4192–99. http://dx.doi.org/10.1039/c9sm00583h.

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Yin, Liusong, Peter Trenh, and Lawrence Stern. "MHC II-peptide complex conformation constrained by interactions throughout the peptide binding groove determines HLA-DM susceptibility (P5014)." Journal of Immunology 190, no. 1_Supplement (2013): 41.8. http://dx.doi.org/10.4049/jimmunol.190.supp.41.8.

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Abstract HLA-DM (DM) mediates the exchange of peptides loaded onto MHC II. However, the determinants of DM-mediated peptide release remain unclear and controversial. In this study, we synthesized a series of peptides derived from HLA-A2104-117 and measured their kinetic stabilities when bound to HLA-DR1 (DR1) in the absence or presence of DM. As expected from previous work, we found that peptides with non-optimal pocket 1 residues were highly DM susceptible. Surprisingly we found that substitution of the pocket 9 residue can counteract the low binding affinity, low kinetic stability and high D

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Hoffmann, Silke, Esther Jonas, Simone König, Andrea Preusser-Kunze, and Dieter Willbold. "Nef protein of human immunodeficiency virus type 1 binds its own myristoylated N-terminus." Biological Chemistry 388, no. 2 (2007): 181–83. http://dx.doi.org/10.1515/bc.2007.020.

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AbstractHIV-1 Nef is a small protein (approx. 25 kDa) that is posttranslationally modified by myristoylation. To explain its complex activities, a ‘Nef-cycle’ is discussed, which postulates different molecular conformations of Nef. Using recombinant full-length non-myristoylated Nef and synthetic peptides, we demonstrate by fluorescence titration experiments that a peptide representing the myristoylated N-terminus of Nef is specifically bound by Nef. A non-myristoylated N-terminal fragment of Nef or a myristoylated control peptide does not bind to Nef. These results are the first direct experi

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