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Insights into Enzyme Mechanisms and services from Experimental and Computational Methods is the newest quantity within the renowned Advances in Protein Chemistry and Structural Biology sequence, a vital source for protein chemists. every one quantity brings forth new information regarding protocols and research of proteins, with each one thematically equipped quantity visitor edited by way of top specialists in a large variety of protein-related topics.
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Extra info for Insights into Enzyme Mechanisms and Functions from Experimental and Computational Methods
Eukaryotic mRNAs are capped at their 50 -ends by a m7GTP structure that is involved with regulation of translation, RNA stability, RNA nuclear transport, and splicing. , 2005). Lama et al. (2013) set out to design novel stapled peptide inhibitors of eIF4E that are derived from eIF4G; eIF4G is an another transcription initiation factor that is required by eIF4E to recruit the 40S ribosomal subunit to the cap. Their initial analysis consisted of MD simulations to sample the protein–peptide bound conformations initiated Recent Advances in Computational Models for the Study of Protein–Peptide Interactions 43 from X-ray crystal structures and replica exchange molecular dynamics of the unbound peptides to sample possible conformations.
2013) when developing their HADDOCK protocol, many peptides did not yield good docked poses unless restrained to a bound form usually consisting of an α-helical secondary structure. Therefore one of the first steps in designing small peptide inhibitors is to test the affinity of multiple peptide sequences, of varying length and amino acid content, that mimic the binding residues of the original protein site. Computational studies can assist experimental binding assays by first identifying sequences that retain or form the correct secondary structure needed for binding as well as evaluating amino acid mutations and other structural changes that might result in improved binding.
MedusaDock then uses the MedusaScore algorithm to guide the docking and rank the poses. 2 Global Docking: Peptide Docking to an Unknown Binding Site Global Docking methods are the procedure of choice when the binding site is uncertain. Most often ensembles of peptide conformations are generated first, followed by rigid-body docking of peptide conformers to the surface of the target protein. The computational efficiency and accuracy of these methods are highly dependent on the size of the search area.