Colloquium: Geometrical approach to protein folding: a tube picture

DOI10.1103/REVMODPHYS.75.23MaRDI QIDQ3077097zbMATH OpenOpenAlexFDO

Authors Jayanth R. Banavar, Amos Maritan

Publication date 21 February 2011

Published in Reviews of Modern Physics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/cond-mat/0301220

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Biophysics (92C05)

Abstract: A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed characteristics of protein structures. The authors show here that proteins may be regarded as tubes of nonzero thickness. This approach allows one to bridge the conventional compact polymer phase with a novel phase employed by Nature to house biomolecular structures. The continuum description of a tube (or a sheet) of arbitrary thickness entails using appropriately chosen many-body interactions rather than two-body interactions. The authors suggest that the structures of folded proteins are selected based on geometrical considerations and are poised at the edge of compaction, thus accounting for their versatility and flexibility. This approach also offers an explanation for why helices and sheets are the building blocks of protein structures.

Cites work

• Geometry and physics of knots
• Global curvature, thickness, and the ideal shapes of knots
• Self-interactions of strands and sheets

Cited in

(7)

• Langevin dynamics simulations reveal biologically relevant folds arising from the incorporation of a torsional potential
• Functionals linear in curvature and statistics of helical proteins
• A comment on the protein folds as platonic forms
• Helices for mathematical modelling of proteins, nucleic acids and polymers
• On the number of tubes touching a sphere or a tube
• Dynamical models of molecular chains and efficient integration algorithms
• Folding of proteins in Go models with angular interactions

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