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Replica exchange molecular dynamics (REMD) and subsequent principal component analysis (PCA) of the dynamical modes of α-conotoxins, GI and its two mutants, in water and an aqueous biocompatible ionic liquid, 1-ethyl-3-methyl-imidazolium acetate (50% v/v) provide perceptions into how the mutations affect the global correlated motions in the peptide backbone, eventually ending up influencing the combination of disulfide links in such multiple cysteine containing venom toxins. Region-wise breakup of the contribution of the three peptides to the first two principal components (PCs) reveals disparate dynamical patterns in water and water/IL mixture. Additionally, K-means clustering within the conformation space spanned by PC1 and PC2 compares and contrasts the different peptide-solvent systems, sorting further, the disulfide bond isoforms into specific clusters. In each cluster, and also in a particular disulfide bond isoform, an estimation of the amino acid block loadings towards PC1 and PC2 helps relate the mutations in GI sequence to targeted synthesis of a given isoform in a given solvent system.
This article was published in the following journal.
Name: The journal of physical chemistry. B
Phα1β peptide isolated from the venom of the Phoneutria nigriventer spider has shown higher analgesic action in pre-clinical studies than ω-conotoxin MVIIA peptide used to treat severe chronic pain...
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Cross-linking mass spectrometry is an emerging structural biology technique. Almost exclusively, the analyzer of choice for such an experiment has been the Orbitrap. For the first time we present an o...
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Crosslinking mass spectrometry draws structural information from covalently-linked peptide pairs. When these links do not match to previous structural models, they may indicate changes in protein conf...
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A neurotoxic peptide, which is a cleavage product (VIa) of the omega-Conotoxin precursor protein contained in venom from the marine snail, CONUS geographus. It is an antagonist of CALCIUM CHANNELS, N-TYPE.
A process that includes the determination of an amino acid sequence of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.
Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.
One of three principal openings in the SUBARACHNOID SPACE. They are also known as cerebellomedullary cistern, and collectively as cisterns.
Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.