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Calculation of protein conformation by global optimization of a potential energy function

✍ Scribed by Jooyoung Lee; Adam Liwo; Daniel R. Ripoll; Jaroslaw Pillardy; Harold A. Scheraga

Publisher
John Wiley and Sons
Year
1999
Tongue
English
Weight
235 KB
Volume
37
Category
Article
ISSN
0887-3585

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✦ Synopsis

A novel hierarchical approach to protein folding has been applied to compute the unknown structures of seven target proteins provided by CASP3. The approach is based exclusively on the global optimization of a potential energy function for a united-residue model by conformational space annealing, followed by energy refinement using an all-atom potential. Comparison of the submitted models for five globular proteins with the experimental structures shows that the conformations of large fragments (Ο³60 aa) were predicted with rmsds of 4.2-6.8 Γ… for the C ␣ atoms. Our lowest-energy models for targets T0056 and T0061 were particularly successful, producing the correct fold of approximately 52% and 80% of the structures, respectively. These results support the thermodynamic hypothesis that protein structure can be computed solely by global optimization of a potential energy function for a given amino acid sequence.

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