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Prep Biochem Biotechnol. 1999 Nov;29(4):339-51.

Influence of medium and long range interactions in protein folding.

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  • 1RIKEN Life Science Center, The Institute of Physical and Chemical Research, Tsukuba, Ibaraki, Japan.

Abstract

Protein structures are stabilized by both local and long range interactions. In this work, we analyze the residue-residue contacts and the role of medium- and long-range interactions in globular proteins belonging to different structural classes. The results show that while medium range interactions predominate in all-alpha class proteins, long-range interactions predominate in all-beta class. Based on this, we analyze the performance of several structure prediction methods in different structural classes of globular proteins and found that all the methods predict the secondary structures of all-alpha proteins more accurately than other classes. Also, we observed that the residues occurring in the range of 21-30 residues apart contributes more towards long-range contacts and about 85% of residues are involved in long-range contacts. Further, the preference of residue pairs to the folding and stability of globular proteins is discussed.

PMID:
10548251
DOI:
10.1080/10826069908544933
[PubMed - indexed for MEDLINE]
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