A new method was presented to discuss the respective roles of short- and long-range interactions in protein folding. It's based on an off-lattice model, which is also being called as toy model. Simulated annealing algorithm was used to search its native conformation. When it is applied to analysis proteins 1agt and 1aho, we find that helical segment cannot fold into native conformation without the influence of long-range interactions. That's to say that long-range interactions are the main determinants in protein folding.
toy model protein folding simulated annealing algorithm short and long range interactions
O 242.28 Q71
This is a preview of subscription content, log in to check access.
Gromiha M M, Selvaraj S. Comparison Between Long-Range Interactions and Contact Order in Determining the Folding Rate of Two-State Proteins: Application of Long-Range Order to Folding Rate Prediction.J Mol Biol, 2001,310: 27–32.CrossRefGoogle Scholar
Sanzo M, Jernigan R L. Long- and Short-Range Interactions in Native Protein Structures are Consistent/Minimally Frustrated in Sequence Space.Proteins: Structure, Function, and Genetics, 2003,50:35–43.CrossRefGoogle Scholar
Gromiha M M, Selvaraj S. Importance of Long-Range Interactions for Determining the Folding Rate and Transition State Structures of Two-State Proteins.Genome Informatics, 2002,13: 348–349.Google Scholar
Thomas P D, Dill K A. Local and Nonlocal Interactions in Globular Proteins and Mechanisms of Alcohol Denaturation.Protein Science, 1993,2: 2050–2065.CrossRefGoogle Scholar
Stillinger F H, Gordon T H, Hirshfeld C L. Toy Model for Protein Folding.Physical Review E, 1993,48(2): 1469–1477.CrossRefGoogle Scholar
Foerster H, Wascher G. Simulated Annealing for Order Spread Minimization in Sequencing Cutting Patterns.European Journal of Operational Research, 1998,110: 272–281.MATHCrossRefGoogle Scholar
Alkhamis T M, Hasan M, Ahmed M A. Simulated Annealing for the Unconstrained Quadratic Pseudo-Boolean Function.European Journal of Operational Research, 1998,108: 641–652.MATHCrossRefGoogle Scholar
Thorton J, Taylor W R. Structure Prediction. In: Findlay J B C, Geisow M J Eds.Protein Aequencing. Oxford: IRL Press, 1989. 147–190.Google Scholar
Dill K A, Fiebig K M, Chan H S. Cooperativity in Protein Folding Kinetics.Proc Natl Acad Sci USA, 1993,90: 748–752.CrossRefGoogle Scholar