Journal ArticleDOI
The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics
Oren M. Becker,Martin Karplus +1 more
TLDR
In this article, the authors explored the topological characteristics of multidimensional potential energy surfaces and mapped the full conformation space on the set of local minima, which is used to express the temporal behavior of the system in terms of basin-to-basin kinetics.Abstract:
Topological characteristics of multidimensional potential energy surfaces are explored and the full conformation space is mapped on the set of local minima. This map partitions conformation space into energy-dependent or temperature-dependent “attraction basins’’ and generates a “disconnectivity’’ graph that reflects the basin connectivity and characterizes the shape of the multidimensional surface. The partitioning of the conformation space is used to express the temporal behavior of the system in terms of basin-to-basin kinetics instead of the usual state-to-state transitions. For this purpose the transition matrix of the system is expressed in terms of basin-to-basin transitions and the corresponding master equation is solved. As an example, the approach is applied to the tetrapeptide, isobutyryl-(ala)3-NH-methyl (IAN), which is the shortest peptide that can form a full helical turn. A nearly complete list of minima and barriers is available for this system from the work of Czerminiski and Elber. The multidimensional potential energy surface of the peptide is shown to exhibit an overall “funnel’’ shape. The relation between connectivity and spatial proximity in dihedral angle space is examined. It is found that, although the two are similar, closeness in one does not always imply closeness in the other. The basin to basin kinetics is examined using a master equation and the results are interpreted in terms of kinetic connectivity. The conformation space of the peptide is divided up in terms of the surface topography to model its “folding’’ behavior. Even in this very simple system, the kinetics exhibit a “trapping’’ state which appears as a “kinetic intermediate,’’ as in the folding of proteins. The approach described here can be used more generally to classify multidimensional potential energy surfaces and the time development of complex systems.read more
Citations
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Supercooled liquids and the glass transition
TL;DR: Current theoretical knowledge of the manner in which intermolecular forces give rise to complex behaviour in supercooled liquids and glasses is discussed.
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Structural properties of nanoclusters: Energetic, thermodynamic, and kinetic effects
TL;DR: In this paper, a review of the experimental methods for the production of free nanoclusters is presented, along with theoretical and simulation issues, always discussed in close connection with the experimental results.
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Perspective: Coarse-grained models for biomolecular systems.
TL;DR: This review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network- based, native-centric, knowledge-based, and bottom-up modeling strategies.
Journal ArticleDOI
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.
TL;DR: In this article, the authors present an automatic algorithm for the discovery of kinetically metastable states that is general applicable to solvated macromolecules, given molecular dynamics trajectories initiated from a well-defined starting distribution.
Journal ArticleDOI
Folding funnels, binding funnels, and protein function
TL;DR: The shape of the funnels is described in light of protein synthesis and folding; flexibility, conformational diversity, and binding mechanisms; and the associated binding funnels, illustrating the multiple routes and the range of complexed conformers.
References
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Bernard R. Brooks,Robert E. Bruccoleri,Barry D. Olafson,David J. States,S. Swaminathan,Martin Karplus +5 more
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