{beta}-sheet folding of fragment (16-36) of bovine pancreatic trypsin inhibitor as predicted by Monte Carlo simulated annealing |
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Authors: | Nakazawa Takashi; Kawai Hikaru; Okamoto Yuko; Fukugita Masataka |
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Affiliation: | Departments of Chemistry Kyoto 606, Japan
1Department of Physics University of Tokyo Hongo, Tokyo 113
2Physics, Nara Women's University Nara 630
3Yukawa Institute for Theoretical Physics, Kyoto University Kyota 606, Japan |
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Abstract: | A tertiary structure prediction is described using Monte Carlosimulated annealing for the peptide fragment corresponding toresidues 1636 of bovine pancreatic trypsin inhibitor(BPTI). The simulation starts with randomly chosen initial conformationsand is performed without imposing experimental constraints usingenergy functions given for generic interatomic interactions.Out of 20 simulation trials, seven conformations show a sheet-likestructuretwo strands connected by a turnalthoughthis sheet-like structure is not as rigid as that observed innative BPTI. It is also shown that these conformations are mostlylooped and exhibit a native- like right-handed twist. Unlikethe case with the C-peptide of RNase A, no conspicuous -helicalstructure is found in any of the final conformations obtainedin the simulation. However, the lowest-energy conformation doesnot resemble exactly the native structure. This indicates thatthe rigid ß-sheet conformation of native BPTI merelycorresponds to a local minimum of the energy function if thefragment with residues 1636 is isolated from the nativeprotein. A statistical analysis of all 20 final conformationssuggests that the tendency for the peptide segments to formextended ß-strands is strong for those with residues1824, and moderate for those with residues 3035.The segment of residues 2529 does not tend to form anydefinite structure. In native BPTI, the former segments areinvolved in the ß-sheet and the latter in the turn.A folding scenario is also speculated from this analysis. |
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Keywords: | ß -sheet/ BPTI/ conformation/ Monte Carlo/ simulated anncaling |
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