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• W2029391344 abstract "We investigate the relationship between the motions of the same peptide loop segment incorporated within a protein structure and motions of free or end-constrained peptides. As a reference point we also compare against alanine chains having the same length as the loop. Both the analysis of atomic molecular dynamics trajectories and structure-based elastic network models, reveal no general dependence on loop length or on the number of solvent exposed residues. Rather, the whole structure affects the motions in complex ways that depend strongly and specifically on the tertiary structure of the whole protein. Both the Elastic Network Models and Molecular Dynamics confirm the differences in loop dynamics between the free and structured contexts; there is strong agreement between the behaviors observed from molecular dynamics and the elastic network models. There is no apparent simple relationship between loop mobility and its size, exposure, or position within a loop. Free peptides do not behave the same as the loops in the proteins. Surface loops do not behave as if they were random coils, and the tertiary structure has a critical influence upon the apparent motions. This strongly implies that entropy evaluation of protein loops requires knowledge of the motions of the entire protein structure." @default.
• W2029391344 created "2016-06-24" @default.
• W2029391344 creator A5023494109 @default.
• W2029391344 creator A5054127002 @default.
• W2029391344 date "2012-04-10" @default.
• W2029391344 modified "2023-10-18" @default.
• W2029391344 title "Protein Loop Dynamics Are Complex and Depend on the Motions of the Whole Protein" @default.
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• W2029391344 doi "https://doi.org/10.3390/e14040687" @default.
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