Protein folding and fold recognition for square lattice models. 1997

G M Crippen
College of Pharmacy, University of Michigan, Ann Arbor 48109-1065, USA. gcrippen@umich.edu

Protein folding and inverse protein folding problems are examined for the extremely simplified model of short self-avoiding square lattice walks involving only two or three residue types. Simple interresidue contact free energy functions are given and are used to determine which sequences fold uniquely to which conformations. Contrary to general theories of protein folding, this model system shows little correlation between free energy and conformational distance from the native, nor is there any marked energy gap between the native and the best non-native structures. Furthermore, even the given free energy function sometimes fails to identify which sequences fold to a particular target structure. If current ideas about protein folding and structure/sequence compatibility fail in this model system, it is unclear why they should be valid for real proteins.

UI MeSH Term Description Entries
D008956 Models, Chemical Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment. Chemical Models,Chemical Model,Model, Chemical
D017510 Protein Folding Processes involved in the formation of TERTIARY PROTEIN STRUCTURE. Protein Folding, Globular,Folding, Globular Protein,Folding, Protein,Foldings, Globular Protein,Foldings, Protein,Globular Protein Folding,Globular Protein Foldings,Protein Foldings,Protein Foldings, Globular

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