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5 results for “Pentapeptide”
Dataset for: Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins
<p>This dataset provides input/output files and scripts for the publication: Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins.</p>
EGSCyP_REMD_20_cyclic_pentapeptides
<p>IMPMC, Sorbonne University, Paris, France<br> LAAS-CNRS, University of Toulouse, France</p> <p>16 july 2020</p> <p>This zenodo-repository contains the data presented in the article:</p> <p>Maud Jusot, Jaysen Sawmynaden, Juan Cortes, Jacques Chomilier, Dirk Stratmann<br> "How chemical modifications affect the conformation landscape of small cyclic peptides"<br> July 2020, bioRxiv.org</p> <p>There are two tar archives in the repository:<br> EGSCyP.tar<br> REMD.tar</p> <p>EGSCyP.tar contains the data generated with the EGSCyP method that has been published previously:<br> https://doi.org/10.1021/acs.jcim.8b00375</p> <p>REMD.tar contains the data generated with replica-exchange molecular dynamics simulations (REMD)<br> in implicit solvent using 8 replicas from 300K to 450K generated with GROMACS 5.1.4</p> <p>Both archives contain the data of 20 cyclic penta-peptides, as presented in the article cited above.<br> One sub-directory per peptide.</p> <p>For the EGSCyP data:<br> Generated 3D structures where assembled in a single xtc file, which is not a standard trajectory here,<br> just one frame per generated structure.<br> To be able to read the xtc file, an arbitrary structure is given in a PDB file.</p> <p>For the REMD data:<br> Each number correspond to a replica: 0 for 300K to 7 for 450K.<br> Trajectories are either available as trr or xtc files. Coordinates are available in a gro file.</p> <p><br> Contact:</p> <p>dirk.stratmann@upmc.fr<br> jacques.chomilier@upmc.fr<br> juan.cortes@laas.fr</p>
Molecular dynamics simulations data of Caspase-3 enzyme with pentapeptide ligand DEVDG and its chiral mutant DEVdG having D-Asp at fourth position
<p>Amino acids in proteins are maintained in one specific L chiral form in the body. D-amino acids are not normally incorporated into proteins and their accumulation has been associated with several conditions including schizophrenia, amyotrophic lateral sclerosis, and other age-related disorders. However, the mechanisms by which the accumulation of D-amino-acids in proteins may lead to pathophysiological consequences remain poorly understood. In this work, we studied a model protease system, caspase-3 that specifically hydrolyses the 4’–5’ peptide bond of the pentapeptide substrate DEVDG. Through extensive molecular dynamics simulations, free energy calculations and distance maps, we reveal that caspase-3 naturally rejects the pentapeptide containing D-Asp substrate, DEVdG and prevents catalytic activity by caspase. The importance of this chiral discriminating capacity is evident from chiral-selective in vivo experimental assays to detect caspase-bound D-Asp in Drosophila where altering the chiral balance created impaired caspase activity and impaired apoptosis, increased tumour formation, and premature death. The modelling data reveals the molecular level charge balancing that enforces the chiral recognition necessary to maintain homeostasis across the cell, tissue, and organ level.</p>
The Effect of VTC-G15 (a Pentapeptide Cleavage Product og GLP-1) on Whole Body Glucose Metabolism in Man
ClinicalTrials.gov study NCT02518932. IPD Sharing: Not stated. Countries: 1. Publications: 0.
GENE EXPRESSION OF AN ANTI-INFLAMMATORY PENTAPEPTIDE ON CIA MURINE DEVELOPMENT
GEO Series GSE14721. Mus musculus. 8 samples. Type: Expression profiling by array.
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