From polymers to proteins -- novel phases of short compact tubes
arXiv:cond-mat/0301220 · doi:10.1103/RevModPhys.75.23
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.
30 pages, 5 figures
Cited by in corpus (32)
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- From toroidal to rod-like condensates of semiflexible polymers
- Functionals linear in curvature and statistics of helical proteins
- Helical Tubes in Crowded Environments
- Lattice tube model of proteins
- Ideally Glassy Hydrogen Bonded Networks
- Physics of thick polymers
- Inferring the effective thickness of polyelectrolytes from stretching measurements at various ionic strengths: applications to DNA and RNA
- Thickness-dependent secondary structure formation of tubelike polymers
- Continuum model for polymers with finite thickness
- Cooperativity and Contact Order in Protein Folding
- Emergence of Secondary Motifs in Tube-Like Polymers in a Solvent
- Geometry of proteins: hydrogen bonding, sterics and marginally compact tubes
- Geometric and physical considerations for realistic protein models
- Proteins and polymers
- Constant spacing in filament bundles
- Folding of Proteins in Go Models with Angular Interactions
- Geometrical model for the native-state folds of proteins
- Mechanical Stretching of Proteins: Calmodulin and Titin
- Geometry of flexible filament cohesion: Better contact through twist?
- A principle for ideal torus knots
- Universal geometrical factor of protein conformations as a consequence of energy minimization
- Ground-state properties of tubelike flexible polymers
- Thermodynamics and Kinetics of a Go Proteinlike Heteropolymer Model with Two-State Folding Characteristics
- Simulating Protein Conformations through Global Optimization
- Remarks on homo- and hetero-polymeric aspects of protein folding
- Correlations in Systems of Complex Directed Macromolecules
- Topological thermal instability and the length of proteins