Research Article

Modeling the third loop of short-chain snake venom neurotoxins: Roles of the short-range and long-range interactions

  1. Zhijie Liu,
  2. Weizhong Li,
  3. Hongyu Zhang,
  4. Yuzhen Han,
  5. Luhua Lai*

Article first published online: 2 NOV 2000

DOI: 10.1002/1097-0134(20010101)42:1<6::AID-PROT20>3.0.CO;2-7

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Volume 42, Issue 1, pages 6–16, 1 January 2001

Additional Information

How to Cite

Liu, Z., Li, W., Zhang, H., Han, Y. and Lai, L. (2001), Modeling the third loop of short-chain snake venom neurotoxins: Roles of the short-range and long-range interactions. Proteins: Structure, Function, and Bioinformatics, 42: 6–16. doi: 10.1002/1097-0134(20010101)42:1<6::AID-PROT20>3.0.CO;2-7

Author Information

  1. Institute of Physical Chemistry & College of Chemistry and Molecular Engineering, Peking University, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing, P.R. China

*Institute of Physical Chemistry & College of Chemistry and Molecular Engineering, Peking University, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing 100871, P.R. China

Publication History

  1. Issue published online: 2 NOV 2000
  2. Article first published online: 2 NOV 2000
  3. Manuscript Accepted: 10 AUG 2000
  4. Manuscript Received: 10 MAR 2000

Funded by

  • Department of Science and Technology of China
  • National Natural Science Foundation of China. Grant Numbers: 29525306, 29703001

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Keywords:

  • long-range interactions;
  • loop modeling;
  • protein structure stability;
  • Monte Carlo simulated annealing;
  • snake venom neurotoxin;
  • short-range interactions

Abstract

The influence of long-range interactions on local structures is an important issue in understanding protein folding process and protein structure stability. Using short-chain snake venom neurotoxin as a model system, we have studied the conformational properties of eight different loop III sequences either in the environment of one of the short-chain neurotoxin, erabutoxin b (PDB ID 1nxb), or in free state by Monte Carlo simulated annealing method. The surrounding protein structure was found to be crucial in stabilizing the loop conformation. Although all the eight peptides prefer type V β turn in solution, three of them (KPGI, KPGV, KSGI) turn to type II β turn and the other five (KKGI, KKGV, KNGI, KQGI, and KRGV) are confined to more rigid type V β turn conformation in the protein structure. Using flexible tetra-glycine-peptide to screen the backbone conformational space in the protein environment also validates the results. This study shows that long-range interactions do contribute to the stability and the types of conformation for a surface loop in protein, while short-range interactions may only provide candidate conformations, which then have to be filtered by the long-range interactions further. Proteins 2001;42:6–16. © 2000 Wiley-Liss, Inc.

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