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Relevant bibliographies by topics / Peptide structure analysis

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Journal articles

Academic literature on the topic 'Peptide structure analysis'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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Journal articles on the topic "Peptide structure analysis"

1

Baek, Mihwa, Masakatsu Kamiya, Taichi Nakazumi, et al. "3P011 Structural analysis of antimicrobial peptide CP1 with LPS by NMR(01A. Protein: Structure,Poster)." Seibutsu Butsuri 53, supplement1-2 (2013): S213. http://dx.doi.org/10.2142/biophys.53.s213_5.

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Syvitski, Raymond T., Xiao-Lin Tian, Kamal Sampara, et al. "Structure-Activity Analysis of Quorum-Sensing Signaling Peptides from Streptococcus mutans." Journal of Bacteriology 189, no. 4 (2006): 1441–50. http://dx.doi.org/10.1128/jb.00832-06.

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ABSTRACT Streptococcus mutans secretes and utilizes a 21-amino-acid signaling peptide pheromone to initiate quorum sensing for genetic competence, biofilm formation, stress responses, and bacteriocin production. In this study, we designed and synthesized a series of truncated peptides and peptides with amino acid substitutions to investigate their structure-activity relationships based on the three-dimensional structures of S. mutans wild-type signaling peptide UA159sp and C-terminally truncated peptide TPC3 from mutant JH1005 defective in genetic competence. By analyzing these peptides, we de

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3

Ma, Menglin, Jihong Li, and Bruce A. McClane. "Structure-Function Analysis of Peptide Signaling in the Clostridium perfringens Agr-Like Quorum Sensing System." Journal of Bacteriology 197, no. 10 (2015): 1807–18. http://dx.doi.org/10.1128/jb.02614-14.

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ABSTRACTThe accessory growth regulator (Agr)-like quorum sensing (QS) system ofClostridium perfringenscontrols the production of many toxins, including beta toxin (CPB). We previously showed (J. E. Vidal, M. Ma, J. Saputo, J. Garcia, F. A. Uzal, and B. A. McClane, Mol Microbiol 83:179–194, 2012,http://dx.doi.org/10.1111/j.1365-2958.2011.07925.x) that an 8-amino-acid, AgrD-derived peptide named 8-R upregulates CPB production by this QS system. The current study synthesized a series of small signaling peptides corresponding to sequences within theC. perfringensAgrD polypeptide to investigate the

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Rainey, Jan K., Larry Fliegel, and Brian D. Sykes. "Strategies for dealing with conformational sampling in structural calculations of flexible or kinked transmembrane peptidesThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Membrane Proteins in Health and Disease." Biochemistry and Cell Biology 84, no. 6 (2006): 918–29. http://dx.doi.org/10.1139/o06-178.

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Peptides corresponding to transmembrane (TM) segments from membrane proteins provide a potential route for the determination of membrane protein structure. We have determined that 2 functionally critical TM segments from the mammalian Na+/H+ exchanger display well converged structure in regions separated by break points. The flexibility of these break points results in conformational sampling in solution. A brief review of available NMR structures of helical membrane proteins demonstrates that there are a number of published structures showing similar properties. Such flexibility is likely ind

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Pan, Borlan, and Wayne J. Fairbrother. "NMR structural analysis of vascular endothelial growth factor in complex with a phage-derived peptide antagonist." Spectroscopy 17, no. 2-3 (2003): 169–81. http://dx.doi.org/10.1155/2003/364613.

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Vascular endothelial growth factor (VEGF) is a covalently linked homodimeric protein that functions as an endothelial cell-specific mitogen, and is an important mediator of pathological angiogenesis. Phage display has been used to select three different classes of novel disulfide-constrained peptides that bind to VEGF and disrupt receptor binding with IC50values between 0.2–10 µM. Mapping of peptide induced nuclear magnetic resonance (NMR) chemical shift changes shows that they target a region of the VEGF receptor-binding domain that overlaps with the contact surfaces of the receptors, Flt-1 a

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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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7

BRAZIER, Stephen P., Bala RAMESH, Parvez I. HARIS, David C. LEE, and Surjit K. S. SRAI. "Secondary structure analysis of the putative membrane-associated domains of the inward rectifier K+ channel ROMK1." Biochemical Journal 335, no. 2 (1998): 375–80. http://dx.doi.org/10.1042/bj3350375.

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The inward rectifier K+ channels contain two putative membrane-spanning domains per subunit (M1, M2) and a ‘pore ’ (P) region, which is similar to the H5 domain of voltage-gated K+ channels. Here we have used Fourier transform infrared (FTIR) and CD spectroscopy to analyse the secondary structures of synthetic peptides corresponding to the M1, M2 and P regions of ROMK1 in aqueous solution, in organic solvents and in phospholipid membranes. A previous CD study was unable to provide any structural data on a similar P peptide [Ben-Efraim and Shai (1997) Biophys. J. 72, 85–96]. However, our FTIR a

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Анисимов, Д. С., and D. S. Tikhonov. "for Peptides Microarray Data Analysis." Mathematical Biology and Bioinformatics 12, no. 2 (2017): 446—??? http://dx.doi.org/10.17537/2017.12.446.

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To find energetically advantageous variants of the structure of the peptide ligand complexing with the proteins of the major histocompatibility complex and the T-cell receptor (SwissProt ID: 2Z31), the binding energy of hexamers, which are fragments of the native ligand structure, was compared. To form a set of investigated hexamers, the Taguchi method was used. In total, 53 variants of the structure of the complex were constructed and investigated using molecular dynamics. Calculations were carried out both for complete complexes and for free structures - receptors and ligands. On the basis o

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Yates, John R., Edwin Carmack, Lara Hays, and Jimmy Eng. "High Throughput Analysis of Tandem Mass Spectrometry Data for Peptides." Laboratory Automation News 2, no. 2 (1997): 28–31. http://dx.doi.org/10.1177/221106829700200206.

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In recent years tandem mass spectrometry has made a substantial impact on the sequence analysis of peptides ( 1 ). In this process peptide ions are dissociated in a collision cell to produce a collection of fragment ions. The m/z values of the fragment ions are determined in the second mass analyzer. Fortuitously, peptide ions fragment primarily around the amide linkages or peptide bonds in a manner that produces a ladder of sequence ions. This method of analysis for peptides has several advantages; high throughput and sensitivity, the ability to analyze peptides contained in mixtures, and las

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Ochoa, Rodrigo, and Pilar Cossio. "PepFun: Open Source Protocols for Peptide-Related Computational Analysis." Molecules 26, no. 6 (2021): 1664. http://dx.doi.org/10.3390/molecules26061664.

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Peptide research has increased during the last years due to their applications as biomarkers, therapeutic alternatives or as antigenic sub-units in vaccines. The implementation of computational resources have facilitated the identification of novel sequences, the prediction of properties, and the modelling of structures. However, there is still a lack of open source protocols that enable their straightforward analysis. Here, we present PepFun, a compilation of bioinformatics and cheminformatics functionalities that are easy to implement and customize for studying peptides at different levels:

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