Conformational change of proteins arising from normal mode calculations

Clicks: 18
ID: 301481
2001
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Abstract
A normal mode analysis of 20 proteins in 'open' or 'closed' forms was performed using simple potential and protein models. The quality of the results was found to depend upon the form of the protein studied, normal modes obtained with the open form of a given protein comparing better with the conformational change than those obtained with the closed form. Moreover, when the motion of the protein is a highly collective one, then, in all cases considered, there is a single low-frequency normal mode whose direction compares well with the conformational change. When it is not, in most cases there is still a single low-frequency normal mode giving a good description of the pattern of the atomic displacements, as they are observed experimentally during the conformational change. Hence a lot of information on the nature of the conformational change of a protein is often found in a single low-frequency normal mode of its open form. Since this information can be obtained through the normal mode analysis of a model as simple as that used in the present study, it is likely that the property captured by such an analysis is for the most part a property of the shape of the protein itself. One of the points that has to be clarified now is whether or not amino acid sequences have been selected in order to allow proteins to follow a single normal mode direction, as least at the very beginning of their conformational change.
Reference Key
openalex_W2140889378 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Florence Tama, Yves‐Henri Sanejouand
Journal Protein Engineering Design and Selection
Year 2001
DOI
10.1093/protein/14.1.1
URL
https://doi.org/10.1093/protein/14.1.1
Keywords Keywords not found

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