Book contents
- Frontmatter
- Dedication
- Contents
- Preface and outline
- 1 Introduction
- 2 Statistical mechanics: A modern review
- 3 The complexity of minimalistic lattice models for protein folding
- 4 Monte Carlo and chain growth methods for molecular simulations
- 5 First insights to freezing and collapse of flexible polymers
- 6 Crystallization of elastic polymers
- 7 Structural phases of semiflexible polymers
- 8 Generic tertiary folding properties of proteins on mesoscopic scales
- 9 Protein folding channels and kinetics of two-state folding
- 10 Inducing generic secondary structures by constraints
- 11 Statistical analyses of aggregation processes
- 12 Hierarchical nature of phase transitions
- 13 Adsorption of polymers at solid substrates
- 14 Hybrid protein–substrate interfaces
- 15 Concluding remarks and outlook
- References
- Index
10 - Inducing generic secondary structures by constraints
Published online by Cambridge University Press: 05 May 2014
- Frontmatter
- Dedication
- Contents
- Preface and outline
- 1 Introduction
- 2 Statistical mechanics: A modern review
- 3 The complexity of minimalistic lattice models for protein folding
- 4 Monte Carlo and chain growth methods for molecular simulations
- 5 First insights to freezing and collapse of flexible polymers
- 6 Crystallization of elastic polymers
- 7 Structural phases of semiflexible polymers
- 8 Generic tertiary folding properties of proteins on mesoscopic scales
- 9 Protein folding channels and kinetics of two-state folding
- 10 Inducing generic secondary structures by constraints
- 11 Statistical analyses of aggregation processes
- 12 Hierarchical nature of phase transitions
- 13 Adsorption of polymers at solid substrates
- 14 Hybrid protein–substrate interfaces
- 15 Concluding remarks and outlook
- References
- Index
Summary
The intrinsic nature of secondary structures
Resolving structural properties of single molecules is a fundamental issue as molecular functionality strongly depends on the capability of the molecules to form stable conformations. Experimentally, the identification of substructures is typically performed, for example, by means of single-molecule microscopy, X-ray analyses of polymer crystals, or NMR for polymers in solution. With these methods, structural details of specific molecules are identified, but frequently these can not be generalized systematically with respect to characteristic features being equally relevant for different polymers. Therefore, the identification of generic conformational properties of polymer classes is highly desirable. To date the most promising approach to attack this problem is to analyze polymer conformations by means of comparative computer simulations of polymer models on mesoscopic scales, i.e., by introducing relevant cooperative degrees of freedom and additional constraints. In these modeling approaches – we have already made use of it in the previous chapters – the linear polymer is considered as a chain of beads and springs. Monomeric properties are accumulated in an effective, specifically parametrized single interaction point of dimension zero (“united atom approach”). Noncovalent van der Waals interactions between pairs of such interaction points are typically modeled by Lennard-Jones (LJ) potentials. In such models, only the repulsive short-range part of the LJ potentials keeps the monomers pairwisely apart. Although such models have proven to be quite useful in identifying universal aspects of global structure formation processes, these approaches are less useful in this form to describe local symmetric arrangements of segments of the chain.
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- Publisher: Cambridge University PressPrint publication year: 2014