Residue solvent accessibilities in the unfolded polypeptide chain. |
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Authors: | P Zielenkiewicz and W Saenger |
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Institution: | Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa. |
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Abstract: | The difference of solvent accessibilities in the native and unfolded states of the protein is used as a measure of the hydrophobic contribution to the free energy of folding. We present a new approximation of amino acids solvent accessibilities in the unfolded state based on the 1-ns molecular dynamics simulation of Ala-X-Ala tripeptides at a temperature of 368 K. The standard accessibility values averaged from the molecular dynamics study are significantly lower from those previously obtained by considering only selected conformations of Ala-X-Ala tripeptides. |
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