Abstract
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.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
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.
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.
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.
Thomas P D, Dill K A. Local and Nonlocal Interactions in Globular Proteins and Mechanisms of Alcohol Denaturation.Protein Science, 1993,2: 2050–2065.
Stillinger F H, Gordon T H, Hirshfeld C L. Toy Model for Protein Folding.Physical Review E, 1993,48(2): 1469–1477.
Foerster H, Wascher G. Simulated Annealing for Order Spread Minimization in Sequencing Cutting Patterns.European Journal of Operational Research, 1998,110: 272–281.
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.
Thorton J, Taylor W R. Structure Prediction. In: Findlay J B C, Geisow M J Eds.Protein Aequencing. Oxford: IRL Press, 1989. 147–190.
Dill K A, Fiebig K M, Chan H S. Cooperativity in Protein Folding Kinetics.Proc Natl Acad Sci USA, 1993,90: 748–752.
Author information
Authors and Affiliations
Corresponding author
Additional information
Foundation item: Supported by the National Natural Science Foundation of China((60301009)
Biography: WANG Long-hui (1976-), female, Ph. D candidate, research direction: machine learning, bioinformatics.
Rights and permissions
About this article
Cite this article
Long-hui, W., Min, H., Huai-bei, Z. et al. Respective roles of short-and long-range interactions in protein folding. Wuhan Univ. J. Nat. Sci. 9, 962–966 (2004). https://doi.org/10.1007/BF02850809
Received:
Issue Date:
DOI: https://doi.org/10.1007/BF02850809