24,558 research outputs found
Exploration of Reaction Pathways and Chemical Transformation Networks
For the investigation of chemical reaction networks, the identification of
all relevant intermediates and elementary reactions is mandatory. Many
algorithmic approaches exist that perform explorations efficiently and
automatedly. These approaches differ in their application range, the level of
completeness of the exploration, as well as the amount of heuristics and human
intervention required. Here, we describe and compare the different approaches
based on these criteria. Future directions leveraging the strengths of chemical
heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
We describe a combination of all-atom simulations with CABS, a
well-established coarse-grained protein modeling tool, into a single multiscale
protocol. The simulation method has been tested on the C-terminal beta hairpin
of protein G, a model system of protein folding. After reconstructing atomistic
details, conformations derived from the CABS simulation were subjected to
replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb
force fields in explicit solvent. Such a combination accelerates system
convergence several times in comparison with all-atom simulations starting from
the extended chain conformation, demonstrated by the analysis of melting
curves, the number of native-like conformations as a function of time and
secondary structure propagation. The results strongly suggest that the proposed
multiscale method could be an efficient and accurate tool for high-resolution
studies of protein folding dynamics in larger systems.Comment: 12 pages, 4 figure
Understanding Hydrogen-Bond Patterns in Proteins using a Novel Statistical Model
Proteins are built from basic structural elements and their systematic characterization is of interest. Searching for recurring patterns in protein contact maps, we found several network motifs, patterns that occur more frequently in experimentally determined protein contact maps than in randomized contact maps with the same properties. Some of these network motifs correspond to sub-structures of alpha helices, including topologies not previously recognized in this context. Other motifs characterize beta-sheets, again some of which appear to be novel. This topological characterization of patterns serves as a tool to characterize proteins, and to reveal a high detailed differences map for comparing protein structures solved by X-ray crystallography, NMR and molecular dynamics (MD) simulations. Both NMR and MD show small but consistent differences from the crystal structures of the same proteins, possibly due to the pair-wise energy functions used. Network motifs analysis can serve as a base for many-body energy statistical energy potential, and suggests a dictionary of basic elements of which protein secondary structure is made
On correlation between protein secondary structure, backbone bond angles, and side-chain orientations
We investigate the fine structure of the sp3 hybridized covalent bond
geometry that governs the tetrahedral architecture around the central
C carbon of a protein backbone, and for this we develop new
visualization techniques to analyze high resolution X-ray structures in Protein
Data Bank. We observe that there is a correlation between the deformations of
the ideal tetrahedral symmetry and the local secondary structure of the
protein. We propose a universal coarse grained energy function to describe the
ensuing side-chain geometry in terms of the C carbon orientations. The
energy function can model the side-chain geometry with a sub-atomic precision.
As an example we construct the C-C structure of HP35 chicken
villin headpiece. We obtain a configuration that deviates less than 0.4 \.A in
root-mean-square distance from the experimental X-ray structure
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