Modeling the third loop of short-chain snake venom neurotoxins: roles of the short-range and long-range interactions.
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 beta turn in solution, three of them (KPGI, KPGV, KSGI) turn to type II beta turn and the other five (KKGI, KKGV, KNGI, KQGI, and KRGV) are confined to more rigid type V beta 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.
Liu
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Z
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.
Li
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W
Zhang
H
H
Han
Y
Y
Lai
L
L
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D004546:Elapid Venoms / Q000737:chemistry; D004870:Erabutoxins / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D009498:Neurotoxins / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry; D011487:Protein Conformation; D016415:Sequence Alignment; D012910:Snake Venoms / Q000737:chemistry*; D013816:Thermodynamics
D004546:Elapid Venoms; D009498:Neurotoxins; D010446:Peptide Fragments; D012910:Snake Venoms; D004870:Erabutoxins; C032917:erabutoxin b