Coarse Grained Simulations of a Small Peptide: Effects of Finite Damping and Hydrodynamic Interactions

Winter, Uwe; Geyer, Tihamér

doi:10.1016/j.bpj.2009.12.3114

Cited by 2 publications

(3 citation statements)

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“…All simulations reported here were performed with the CG simulation code uiowa_BD ( 45 , 48 , 49 ). The conformational dynamics of the polymerase were simulated using the Langevin dynamics algorithm developed by Geyer and Winter ( 50 ), a simple extension of the Ermak-McCammon algorithm of Brownian dynamics ( 51 ). The former algorithm has the important advantage that it allows comparatively long time steps to be employed ( 50 ).…”

Section: Methodsmentioning

confidence: 99%

“…The conformational dynamics of the polymerase were simulated using the Langevin dynamics algorithm developed by Geyer and Winter ( 50 ), a simple extension of the Ermak-McCammon algorithm of Brownian dynamics ( 51 ). The former algorithm has the important advantage that it allows comparatively long time steps to be employed ( 50 ). In all simulations, a time step of 125 fs was used, and a list of pairs of beads engaged in non-bonded interactions was constructed every 100 time steps (every 12.5 ps).…”

Section: Methodsmentioning

confidence: 99%

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The C-terminal region of translesion synthesis DNA polymerase η is partially unstructured and has high conformational flexibility

Powers

Elcock

Washington

2018

Nucleic Acids Research

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Eukaryotic DNA polymerase η catalyzes translesion synthesis of thymine dimers and 8-oxoguanines. It is comprised of a polymerase domain and a C-terminal region, both of which are required for its biological function. The C-terminal region mediates interactions with proliferating cell nuclear antigen (PCNA) and other translesion synthesis proteins such as Rev1. This region contains a ubiquitin-binding/zinc-binding (UBZ) motif and a PCNA-interacting protein (PIP) motif. Currently little structural information is available for this region of polymerase η. Using a combination of approaches—including genetic complementation assays, X-ray crystallography, Langevin dynamics simulations, and small-angle X-ray scattering—we show that the C-terminal region is partially unstructured and has high conformational flexibility. This implies that the C-terminal region acts as a flexible tether linking the polymerase domain to PCNA thereby increasing its local concentration. Such tethering would facilitate the sampling of translesion synthesis polymerases to ensure that the most appropriate one is selected to bypass the lesion.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The C-terminal region of translesion synthesis DNA polymerase η is partially unstructured and has high conformational flexibility

Powers

Elcock

Washington

2018

Nucleic Acids Research

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“…One has a list of the positions and momentums of all of the atoms in the simulation, and the software calculates the forces acting on each of the atoms to determine how they change position and momentum over a very short time step. The key difference between LD and MD simulations, however, is that in LD simulations, the atoms of the protein are randomly nudged during the time step calculations to mimic collisions with solvent atoms [ 40 , 41 ]. As stated above, BD simulations are a simplified, subset of LD simulations in which there is no inertia.…”

Section: Molecular Simulationsmentioning

confidence: 99%

Modeling Conformationally Flexible Proteins With X-ray Scattering and Molecular Simulations

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Gildenberg

Washington

2019

Computational and Structural Biotechnology Journal

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Proteins and protein complexes with high conformational flexibility participate in a wide range of biological processes. These processes include genome maintenance, gene expression, signal transduction, cell cycle regulation, and many others. Gaining a structural understanding of conformationally flexible proteins and protein complexes is arguably the greatest problem facing structural biologists today. Over the last decade, some progress has been made toward understanding the conformational flexibility of such systems using hybrid approaches. One particularly fruitful strategy has been the combination of small-angle X-ray scattering (SAXS) and molecular simulations. In this article, we provide a brief overview of SAXS and molecular simulations and then discuss two general approaches for combining SAXS data and molecular simulations: minimal ensemble approaches and full ensemble approaches. In minimal ensemble approaches, one selects a minimal ensemble of structures from the simulations that best fit the SAXS data. In full ensemble approaches, one validates a full ensemble of structures from the simulations using SAXS data. We argue that full ensemble models are more realistic than minimal ensemble searches models and that full ensemble approaches should be used wherever possible.

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Coarse Grained Simulations of a Small Peptide: Effects of Finite Damping and Hydrodynamic Interactions

Cited by 2 publications

References 1 publication

The C-terminal region of translesion synthesis DNA polymerase η is partially unstructured and has high conformational flexibility

The C-terminal region of translesion synthesis DNA polymerase η is partially unstructured and has high conformational flexibility

Modeling Conformationally Flexible Proteins With X-ray Scattering and Molecular Simulations

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