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Journal articles on the topic 'Peptide structure analysis'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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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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2

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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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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10

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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11

Mierke, Dale. "NMR analysis of peptide structure and bioactivity." Biopolymers 51, no. 3 (1999): 173. http://dx.doi.org/10.1002/(sici)1097-0282(1999)51:3<173::aid-bip1>3.0.co;2-d.

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Vogel, Hans J., David J. Schibli, Weiguo Jing, Elke M. Lohmeier-Vogel, Raquel F. Epand, and Richard M. Epand. "Towards a structure-function analysis of bovine lactoferricin and related tryptophan- and arginine-containing peptides." Biochemistry and Cell Biology 80, no. 1 (2002): 49–63. http://dx.doi.org/10.1139/o01-213.

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The iron-binding protein lactoferrin is a multifunctional protein that has antibacterial, antifungal, antiviral, antitumour, anti-inflammatory, and immunoregulatory properties. All of these additional properties appear to be related to its highly basic N-terminal region. This part of the protein can be released in the stomach by pepsin cleavage at acid pH. The 25-residue antimicrobial peptide that is released is called lactoferricin. In this work, we review our knowledge about the structure of the peptide and attempt to relate this to its many functions. Microcalorimetry and fluorescence spect

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13

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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Brunel, Florence M., Michael B. Zwick, Rosa M. F. Cardoso, et al. "Structure-Function Analysis of the Epitope for 4E10, a Broadly Neutralizing Human Immunodeficiency Virus Type 1 Antibody." Journal of Virology 80, no. 4 (2006): 1680–87. http://dx.doi.org/10.1128/jvi.80.4.1680-1687.2006.

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ABSTRACT The human immunodeficiency virus type 1 (HIV-1) neutralizing antibody 4E10 binds to a linear, highly conserved epitope within the membrane-proximal external region of the HIV-1 envelope glycoprotein gp41. We have delineated the peptide epitope of the broadly neutralizing 4E10 antibody to gp41 residues 671 to 683, using peptides with different lengths encompassing the previously suggested core epitope (NWFDIT). Peptide binding to the 4E10 antibody was assessed by competition enzyme-linked immunosorbent assay, and the Kd values of selected peptides were determined using surface plasmon

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15

Hallupp, M., F. Buck, and W. H. Strätling. "Structure analysis of purified histone H5 and of H5 in nuclei by limited proteolysis." Biochemical Journal 282, no. 2 (1992): 435–41. http://dx.doi.org/10.1042/bj2820435.

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The structure of purified histone H5 in 1 M-NaClO4 and of H5 in nuclei was analysed by digestion with either one of three endoproteinases, papain, subtilisin or elastase, which preferentially cleave unstructured protein regions (and additionally with trypsin). Digestion with papain and subtilisin produced ‘limiting’ resistant peptides (p1 and s1) that contain the central region between residues 18-20 and residue 114. Digestion of purified H5 with elastase generated resistant peptides e1 and e2, and that of H5 in nuclei, peptide e2. Peptides e1 and e2 contain the region from residues 22 to 114

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Van Obberghen-Schilling, E., U. B. Rasmussen, V. Vouret-Craviari, K. U. Lentes, A. Pavirani та J. Pouysségur. "Structure-activity analysis of synthetic α-thrombin-receptor-activating peptides". Biochemical Journal 292, № 3 (1993): 667–71. http://dx.doi.org/10.1042/bj2920667.

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alpha-Thrombin stimulates G-protein-coupled effectors leading to secretion and aggregation in human platelets, and to a mitogenic response in CCL39 hamster fibroblasts. alpha-Thrombin receptors can be activated by synthetic peptides corresponding to the receptor sequence starting with serine-42, at the proposed cleavage site. We have previously determined that the agonist domain of receptor-activating peptides resides within the five N-terminal residues [Vouret-Craviari, Van Obberghen-Schilling, Rasmussen, Pavirani, Lecocq and Pouysségur (1992) Mol. Biol. Cell. 3, 95-102], although the 7-resid

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Chakraborty, Kausik, P. Shivakumar, S. Raghothama, and Raghavan Varadarajan. "NMR structural analysis of a peptide mimic of the bridging sheet of HIV-1 gp120 in methanol and water." Biochemical Journal 390, no. 2 (2005): 573–81. http://dx.doi.org/10.1042/bj20050442.

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gp120 is a subunit of the Env (viral envelope protein) of HIV-1. The protein consists of inner and outer domains linked by a bridging sheet. Several gp120 residues that bind the neutralizing antibody 17b as well as the cellular co-receptor CCR5 (CC chemokine receptor 5), are located in the bridging sheet. Peptides that mimic the 17b-binding regions of gp120 would be useful potential immunogens for the generation of neutralizing antibodies against HIV-1. Towards this end, a 26-residue, four-stranded β-sheet peptide was designed on the basis of the structure of the bridging sheet, and its struct

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Antunes, Dinler A., Jayvee R. Abella, Sarah Hall-Swan, et al. "HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy." JCO Clinical Cancer Informatics, no. 4 (September 2020): 623–36. http://dx.doi.org/10.1200/cci.19.00123.

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PURPOSE HLA protein receptors play a key role in cellular immunity. They bind intracellular peptides and display them for recognition by T-cell lymphocytes. Because T-cell activation is partially driven by structural features of these peptide-HLA complexes, their structural modeling and analysis are becoming central components of cancer immunotherapy projects. Unfortunately, this kind of analysis is limited by the small number of experimentally determined structures of peptide-HLA complexes. Overcoming this limitation requires developing novel computational methods to model and analyze peptide

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Matsushima, Norio, Hiroki Miyashita, Shinsuke Tamaki, and Robert H. Kretsinger. "Polyproline II Helix as a Recognition Motif of Plant Peptide Hormones and Flagellin Peptide flg22." Protein & Peptide Letters 26, no. 9 (2019): 684–90. http://dx.doi.org/10.2174/0929866526666190408125441.

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Background: Plant peptide hormones play a crucial role in plant growth and development. A group of these peptide hormones are signaling peptides with 5 - 23 amino acids. Flagellin peptide (flg22) also elicits an immune response in plants. The functions are expressed through recognition of the peptide hormones and flg22. This recognition relies on membrane localized receptor kinases with extracellular leucine rich repeats (LRR-RKs). The structures of plant peptide hormones - AtPep1, IDA, IDL1, RGFs 1- 3, TDIF/CLE41 - and of flg22 complexed with LRR domains of corresponding LRRRKs and co-recepto

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Aisawa, Sumio, Aiko Yasutake, Satoshi Takahashi, Hidetoshi Hirahara, and Eiichi Narita. "Intercalation of Collagen and Soybean Peptides into Zn–Al Layered Double Hydroxide." Journal of Nanoscience and Nanotechnology 8, no. 1 (2008): 428–31. http://dx.doi.org/10.1166/jnn.2008.18147.

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In order to develop a new type biocompatible organic/inorganic nanohybrid material, an intercalation of collagen peptides (CP) and soybean peptide (SP) into Zn–Al layered double hydroxide (LDH) by the coprecipitation reaction has been investigated. The peptide/LDH has been characterized by chemical analysis, powder X-ray diffraction (XRD), Raman spectroscopy, thermal gravimetric analysis (TG) and transmission electron microscopy (TEM). According to the XRD patterns and Raman spectra, the solid products were found to contain peptide and to show broad diffraction peaks with LDH structures. The C

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Oppegård, Camilla, Per Rogne, Per Eugen Kristiansen, and Jon Nissen-Meyer. "Structure analysis of the two-peptide bacteriocin lactococcin G by introducing d-amino acid residues." Microbiology 156, no. 6 (2010): 1883–89. http://dx.doi.org/10.1099/mic.0.038430-0.

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The importance of 3D structuring in the N- and C-terminal ends of the two peptides (39-mer LcnG-α and 35-mer LcnG-β) that constitute the two-peptide bacteriocin lactococcin G was analysed by replacing residues in the end regions with the corresponding d-isomeric residues. When assayed for antibacterial activity in combination with the complementary wild-type peptide, LcnG-α with four d-residues in its C-terminal region and LcnG-β with four d-residues in either its N- or its C-terminal region were relatively active (two- to 20-fold reduction in activity). 3D structuring of the C-terminal region

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Apletalina, Ekaterina V., Maria A. Juliano, Luiz Juliano, and Iris Lindberg. "Structure–Function Analysis of the 7B2 CT Peptide." Biochemical and Biophysical Research Communications 267, no. 3 (2000): 940–42. http://dx.doi.org/10.1006/bbrc.1999.2060.

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Moon, Jin Ho, Joon Kyu Park, and Eunice EunKyeong Kim. "Structure analysis of peptide deformylase from Bacillus cereus." Proteins: Structure, Function, and Bioinformatics 61, no. 1 (2005): 217–20. http://dx.doi.org/10.1002/prot.20526.

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Ibrahim, Mohammed A., June C. Serem, Megan J. Bester, Albert W. Neitz та Anabella R. M. Gaspar. "Structure - Function Analysis of Peptide Analogs of SQSPA with Respect to α-glucosidase and α-amylase Inhibition". Protein & Peptide Letters 26, № 6 (2019): 403–13. http://dx.doi.org/10.2174/0929866526666190327121731.

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Background: Peptide-based therapeutics offer a unique avenue for the development of novel agents for the treatment of diabetes mellitus including α-glucosidase inhibitors. The peptide, SQSPA, was reported to possess to α -glucosidase inhibitory activity in addition to resistance to Gastrointestinal Tract (GIT) digestion. Methods: In this study, the in silico and in vitro structure-activity analyses of the peptide was conducted using alanine scanning to identify key amino acid residues. Results: The alanine scanning led to four analogs viz; AQSPA, SASPA, SQAPA and SQSAA which were GIT stable. I

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Trauger, Sunia A., William Webb, and Gary Siuzdak. "Peptide and protein analysis with mass spectrometry." Spectroscopy 16, no. 1 (2002): 15–28. http://dx.doi.org/10.1155/2002/320152.

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Mass spectrometry (MS) is rapidly becoming a fundamental tool for biologists and biochemists in their efforts to characterize cellular function. Recent advancements in MS technology and front-end methodologies, along with the completion of the human genome have greatly popularized its use by researchers for protein identification and characterization. This paper is a general overview of how mass spectrometry is being used for the analysis of peptides and proteins, focusing on its application to molecular weight determination. Sample preparatory and cleanup techniques used in our laboratory for

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Osugi, Tomohiro, Dana Daukss, Kristen Gazda, et al. "Evolutionary Origin of the Structure and Function of Gonadotropin-Inhibitory Hormone: Insights from Lampreys." Endocrinology 153, no. 5 (2012): 2362–74. http://dx.doi.org/10.1210/en.2011-2046.

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Gonadotropin (GTH)-inhibitory hormone (GnIH) is a novel hypothalamic neuropeptide that inhibits GTH secretion in mammals and birds by acting on gonadotropes and GnRH neurons within the hypothalamic-pituitary-gonadal axis. GnIH and its orthologs that have an LPXRFamide (X = L or Q) motif at the C terminus (LPXRFamide peptides) have been identified in representative species of gnathostomes. However, the identity of an LPXRFamide peptide had yet to be identified in agnathans, the most ancient lineage of vertebrates, leaving open the question of the evolutionary origin of GnIH and its ancestral fu

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Grafskaia, Ekaterina, Elizaveta Pavlova, Vladislav V. Babenko, et al. "The Hirudo Medicinalis Microbiome Is a Source of New Antimicrobial Peptides." International Journal of Molecular Sciences 21, no. 19 (2020): 7141. http://dx.doi.org/10.3390/ijms21197141.

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Antimicrobial peptides (AMPs) are considered a promising new class of anti-infectious agents. This study reports new antimicrobial peptides derived from the Hirudo medicinalis microbiome identified by a computational analysis method applied to the H. medicinalis metagenome. The identified AMPs possess a strong antimicrobial activity against Gram-positive and Gram-negative bacteria (MIC range: 5.3 to 22.4 μM), including Staphylococcus haemolyticus, an opportunistic coagulase–negative pathogen. The secondary structure analysis of peptides via CD spectroscopy showed that all the AMPs except pept_

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Sakai, N., A. Morita, Y. Ushijima, M. Yao, N. Watanabe, and I. Tanaka. "Crystal structure analysis of the oligo-peptide binding protein OppA complexed with peptides." Acta Crystallographica Section A Foundations of Crystallography 64, a1 (2008): C279. http://dx.doi.org/10.1107/s0108767308091071.

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29

Buxton, S. E., R. J. Benjamin, C. Clayberger, P. Parham, and A. M. Krensky. "Anchoring pockets in human histocompatibility complex leukocyte antigen (HLA) class I molecules: analysis of the conserved B ("45") pocket of HLA-B27." Journal of Experimental Medicine 175, no. 3 (1992): 809–20. http://dx.doi.org/10.1084/jem.175.3.809.

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Dissection of the peptide binding grooves of seven subtypes of human histocompatibility leukocyte antigen (HLA)-B27 into the six specificity pockets defined by the 2.6-A structure of HLA-A*0201 revealed just one pocket, the B ("45") pocket, that is conserved among all the HLA-B27 subtypes. Functional studies of mutant HLA-B*2705 molecules with point substitutions in residues of the B pocket show that this structure, and the glutamine residue at position 45 in particular, plays a critical role in cell surface expression, peptide binding, and in the presentation of both exogenous and endogenous

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Derache, Chrystelle, Valérie Labas, Vincent Aucagne та ін. "Primary Structure and Antibacterial Activity of Chicken Bone Marrow-Derived β-Defensins". Antimicrobial Agents and Chemotherapy 53, № 11 (2009): 4647–55. http://dx.doi.org/10.1128/aac.00301-09.

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ABSTRACTThree biologically active β-defensins were purified by chromatography from chicken bone marrow extract: avian β-defensin 1 (AvBD1), AvBD2, and the newly isolated β-defensin AvBD7. Mass spectrometry analyses showed that bone marrow-derived AvBD1, -2, and -7 peptides were present as mature peptides and revealed posttranslational modifications for AvBD1 and AvBD7 in comparison to their in silico-predicted amino acid sequences. Tandem mass spectrometry analysis using the nanoelectrospray-quadrupole time of flight method showed N-terminal glutaminyl cyclization of mature AvBD7 and C-termina

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Kuhn-Nentwig, Lucia, Nicolas Langenegger, Manfred Heller, Dominique Koua, and Wolfgang Nentwig. "The Dual Prey-Inactivation Strategy of Spiders—In-Depth Venomic Analysis of Cupiennius salei." Toxins 11, no. 3 (2019): 167. http://dx.doi.org/10.3390/toxins11030167.

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Most knowledge of spider venom concerns neurotoxins acting on ion channels, whereas proteins and their significance for the envenomation process are neglected. The here presented comprehensive analysis of the venom gland transcriptome and proteome of Cupiennius salei focusses on proteins and cysteine-containing peptides and offers new insight into the structure and function of spider venom, here described as the dual prey-inactivation strategy. After venom injection, many enzymes and proteins, dominated by α-amylase, angiotensin-converting enzyme, and cysteine-rich secretory proteins, interact

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Kraft, Jennifer R., Russell E. Vance, Jan Pohl, Amy M. Martin, David H. Raulet, and Peter E. Jensen. "Analysis of Qa-1bPeptide Binding Specificity and the Capacity of Cd94/Nkg2a to Discriminate between Qa-1–Peptide Complexes." Journal of Experimental Medicine 192, no. 5 (2000): 613–24. http://dx.doi.org/10.1084/jem.192.5.613.

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The major histocompatibility complex class Ib protein, Qa-1b, serves as a ligand for murine CD94/NKG2A natural killer (NK) cell inhibitory receptors. The Qa-1b peptide-binding site is predominantly occupied by a single nonameric peptide, Qa-1 determinant modifier (Qdm), derived from the leader sequence of H-2D and L molecules. Five anchor residues were identified in this study by measuring the peptide-binding affinities of substituted Qdm peptides in experiments with purified recombinant Qa-1b. A candidate peptide-binding motif was determined by sequence analysis of peptides eluted from Qa-1 t

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Wentink, Madelon Q., Tilman M. Hackeng, Sebastien P. Tabruyn, et al. "Targeted vaccination against the bevacizumab binding site on VEGF using 3D-structured peptides elicits efficient antitumor activity." Proceedings of the National Academy of Sciences 113, no. 44 (2016): 12532–37. http://dx.doi.org/10.1073/pnas.1610258113.

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Therapeutic targeting of the VEGF signaling axis by the VEGF-neutralizing monoclonal antibody bevacizumab has clearly demonstrated clinical benefit in cancer patients. To improve this strategy using a polyclonal approach, we developed a vaccine targeting VEGF using 3D-structured peptides that mimic the bevacizumab binding site. An in-depth study on peptide optimization showed that the antigen’s 3D structure is essential to achieve neutralizing antibody responses. Peptide 1 adopts a clear secondary, native-like structure, including the typical cysteine-knot fold, as evidenced by CD spectroscopy

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Baxter, Richard. "A Macromolecular approach to peptide-based molecular recognition and catalysis." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1588. http://dx.doi.org/10.1107/s2053273314084113.

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Synthetic peptides incorporating non-natural amino acids provide an opportunity to apply biomimetic principles in the design of both chemical scaffolds and novel pharmaceuticals. Crystallographic analysis can be of significant utility in this area just as elsewhere, but blur the line between small-molecule and macromolecular systems. I will present recent examples combining the tools of macromolecular crystallography techniques with chemical biology to elucidate structures of peptide-based binding and catalytic motifs. First, I will discuss recent structures of a beta-peptide known to spontane

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Zhu, T. M., Y. Peng, H. Lackland, and S. Stein. "Confirmation of Oligonucleotide-Peptide Structure by Amino Acid Analysis." Analytical Biochemistry 214, no. 2 (1993): 585–87. http://dx.doi.org/10.1006/abio.1993.1543.

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36

Ealy, Sam. "TAU Peptide Interactions with Lipid Membranes: Secondary Structure Analysis." Biophysical Journal 114, no. 3 (2018): 222a. http://dx.doi.org/10.1016/j.bpj.2017.11.1235.

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37

Charlton, L. A., J. S. Sanghera, I. Clark-Lewis, and S. L. Pelech. "Structure-function analysis of casein kinase 2 with synthetic peptides and anti-peptide antibodies." Journal of Biological Chemistry 267, no. 13 (1992): 8840–45. http://dx.doi.org/10.1016/s0021-9258(19)50356-8.

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38

Smith, Aaron, Farukh Ali, and Dmitriy Soldatov. "Structure and stability of solid oligoglycines." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C921. http://dx.doi.org/10.1107/s2053273314090780.

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Although peptides have been extensively studied within many disciplines, their solid state chemistry is not sufficiently explored. Crystalline peptide materials could present new opportunities in solid state organic synthesis as well as pharmaceutical, cosmetic and food industries. In order to facilitate these future applications, a better understanding of the relationship between the solid state structure and chemical reactivity in peptide crystals is required. In this work, a series of linear glycine oligomers was studied to see how their crystal structure and thermal reactivity changes with

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Kheeree, Norhameemee, Papassara Sangtanoo, Piroonporn Srimongkol, et al. "ACE inhibitory peptides derived from de-fatted lemon basil seeds: optimization, purification, identification, structure–activity relationship and molecular docking analysis." Food & Function 11, no. 9 (2020): 8161–78. http://dx.doi.org/10.1039/d0fo01240h.

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The study determines optimized process conditions to maximize ACE inhibitory peptide production. The two novel hexa-peptides (LGRNLPPI and GPAGPAGL) from de-fatted lemon basil seeds (DLBS) was achieved.

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Shmulevitz, Maya, Raquel F. Epand, Richard M. Epand, and Roy Duncan. "Structural and Functional Properties of an Unusual Internal Fusion Peptide in a Nonenveloped Virus Membrane Fusion Protein." Journal of Virology 78, no. 6 (2004): 2808–18. http://dx.doi.org/10.1128/jvi.78.6.2808-2818.2004.

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ABSTRACT The avian and Nelson Bay reoviruses are two of only a limited number of nonenveloped viruses capable of inducing cell-cell membrane fusion. These viruses encode the smallest known membrane fusion proteins (p10). We now show that a region of moderate hydrophobicity we call the hydrophobic patch (HP), present in the small N-terminal ectodomain of p10, shares the following characteristics with the fusion peptides of enveloped virus fusion proteins: (i) an abundance of glycine and alanine residues, (ii) a potential amphipathic secondary structure, (iii) membrane-seeking characteristics th

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Soltaninejad, Hossein, Hadi Zare-Zardini, Mahtab Ordooei, et al. "Antimicrobial Peptides from Amphibian Innate Immune System as Potent Antidiabetic Agents: A Literature Review and Bioinformatics Analysis." Journal of Diabetes Research 2021 (June 29, 2021): 1–10. http://dx.doi.org/10.1155/2021/2894722.

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Antimicrobial peptides, as an important member of the innate immune system, have various biological activities in addition to antimicrobial activity. There are some AMPs with antidiabetic activity, especially those isolated from amphibians. These peptides can induce insulin release via different mechanisms based on peptide type. In this review study, we collected all reported AMPs with antidiabetic activity. We also analyze the sequence and structure of these peptides for evaluation of sequence and structure effect on their antidiabetic activity. Based on this review, the biggest peptide famil

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Rogers, Joseph M., Toby Passioura, and Hiroaki Suga. "Nonproteinogenic deep mutational scanning of linear and cyclic peptides." Proceedings of the National Academy of Sciences 115, no. 43 (2018): 10959–64. http://dx.doi.org/10.1073/pnas.1809901115.

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High-resolution structure–activity analysis of polypeptides requires amino acid structures that are not present in the universal genetic code. Examination of peptide and protein interactions with this resolution has been limited by the need to individually synthesize and test peptides containing nonproteinogenic amino acids. We describe a method to scan entire peptide sequences with multiple nonproteinogenic amino acids and, in parallel, determine the thermodynamics of binding to a partner protein. By coupling genetic code reprogramming to deep mutational scanning, any number of amino acids ca

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Osugi, Tomohiro, Katsuhisa Uchida, Masumi Nozaki, and Kazuyoshi Tsutsui. "Characterization of Novel RFamide Peptides in the Central Nervous System of the Brown Hagfish: Isolation, Localization, and Functional Analysis." Endocrinology 152, no. 11 (2011): 4252–64. http://dx.doi.org/10.1210/en.2011-1375.

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RFamide (RFa) peptides play various important roles in the central nervous system in both invertebrates and vertebrates. However, there is no evidence of the existence of any RFamide peptide in the brain of hagfish, one of the oldest lineages of vertebrates. In this study, we sought to identify novel RFamide peptides from the brains of hagfish (Paramyxine atami). We identified four novel RFamide peptides, which had the C-terminal Pro-Gln-Arg-Phe-NH2 structure. cDNA cloning revealed that the identified RFamide peptides are encoded in two types of cDNA. Molecular phylogenetic analysis of the two

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Ziemert, Nadine, Keishi Ishida, Philippe Quillardet, et al. "Microcyclamide Biosynthesis in Two Strains of Microcystis aeruginosa: from Structure to Genes and Vice Versa." Applied and Environmental Microbiology 74, no. 6 (2008): 1791–97. http://dx.doi.org/10.1128/aem.02392-07.

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ABSTRACT Comparative analysis of related biosynthetic gene clusters can provide new insights into the versatility of these pathways and allow the discovery of new natural products. The freshwater cyanobacterium Microcystis aeruginosa NIES298 produces the cytotoxic peptide microcyclamide. Here, we provide evidence that the cyclic hexapeptide is formed by a ribosomal pathway through the activity of a set of processing enzymes closely resembling those recently shown to be involved in patellamide biosynthesis in cyanobacterial symbionts of ascidians. Besides two subtilisin-type proteases and a het

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Suarez, Mougli, Marisa Haenni, Stéphane Canarelli, et al. "Structure-Function Characterization and Optimization of a Plant-Derived Antibacterial Peptide." Antimicrobial Agents and Chemotherapy 49, no. 9 (2005): 3847–57. http://dx.doi.org/10.1128/aac.49.9.3847-3857.2005.

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ABSTRACT Crushed seeds of the Moringa oleifera tree have been used traditionally as natural flocculants to clarify drinking water. We previously showed that one of the seed peptides mediates both the sedimentation of suspended particles such as bacterial cells and a direct bactericidal activity, raising the possibility that the two activities might be related. In this study, the conformational modeling of the peptide was coupled to a functional analysis of synthetic derivatives. This indicated that partly overlapping structural determinants mediate the sedimentation and antibacterial activitie

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Cantisani, Marco, Emiliana Finamore, Eleonora Mignogna, et al. "Structural Insights into and Activity Analysis of the Antimicrobial Peptide Myxinidin." Antimicrobial Agents and Chemotherapy 58, no. 9 (2014): 5280–90. http://dx.doi.org/10.1128/aac.02395-14.

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ABSTRACTThe marine environment has been poorly explored in terms of potential new molecules possessing antibacterial activity. Antimicrobial peptides (AMPs) offer a new potential class of pharmaceuticals; however, further optimization is needed if AMPs are to find broad use as antibiotics. We focused our studies on a peptide derived from the epidermal mucus of hagfish (Myxine glutinosaL.), which was previously characterized and showed high antimicrobial activity against human and fish pathogens. In the present work, the activities of myxinidin peptide analogues were analyzed with the aim of wi

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HENKEL, W. "Cross-link analysis of the C-telopeptide domain from type III collagen." Biochemical Journal 318, no. 2 (1996): 497–503. http://dx.doi.org/10.1042/bj3180497.

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Several peptides were isolated from tryptic digests of insoluble calf aorta matrix by chromatography. Reductive pyridylethylation of a tryptic 15 kDa pool released fragments deriving from the C-terminus of type III collagen. A 50-residue peptide TC(III) was shown by sequence analysis to be the C-terminal peptide from the α1(III)-chain, containing a helical and non-helical region of equal sizes. The peptide was further digested with collagenase to give ColC(III), comprising the complete C-terminal non-helical region of α1(III) including a hydroxylysine in position 16C. The peptide TC(III)×TN(II

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Saxena, Shikhar, Sambhavi Animesh, Melissa J. Fullwood, and Yuguang Mu. "OnionMHC: A deep learning model for peptide — HLA-A*02:01 binding predictions using both structure and sequence feature sets." Journal of Micromechanics and Molecular Physics 05, no. 03 (2020): 2050009. http://dx.doi.org/10.1142/s2424913020500095.

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The peptide binding to Major Histocompatibility Complex (MHC) proteins is an important step in the antigen-presentation pathway. Thus, predicting the binding potential of peptides with MHC is essential for the design of peptide-based therapeutics. Most of the available machine learning-based models predict the peptide-MHC binding based on the sequence of amino acids alone. Given the importance of structural information in determining the stability of the complex, here we have utilized both the complex structure and the peptide sequence features to predict the binding affinity of peptides to hu

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Seeger, Florian H., Markus Schirle, John Gatfield, et al. "The HLA-A*6601 peptide motif: prediction by pocket structure and verification by peptide analysis." Immunogenetics 49, no. 6 (1999): 571–76. http://dx.doi.org/10.1007/s002510050539.

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Ekblad, Bie, Panagiota K. Kyriakou, Camilla Oppegård, Jon Nissen-Meyer, Yiannis N. Kaznessis, and Per Eugen Kristiansen. "Structure–Function Analysis of the Two-Peptide Bacteriocin Plantaricin EF." Biochemistry 55, no. 36 (2016): 5106–16. http://dx.doi.org/10.1021/acs.biochem.6b00588.

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