Coarse grained simulations of a small peptide: Effects of finite damping and hydrodynamic interactions

Winter, Uwe; Geyer, Tihamér

doi:10.1063/1.3216573

Cited by 21 publications

(27 citation statements)

References 30 publications

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“…All simulations were performed using software written in-house and using the Langevin dynamics algorithm developed as an extension of the Ermak-McCammon algorithm by the Geyer group69. Simulations were performed at 310K, with the solvent dielectric constant and viscosity set to the corresponding experimental values for water.…”

Section: Methodsmentioning

confidence: 99%

Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins

Natan¹,

Endoh

Haim-Vilmovsky

et al. 2018

Nat Struct Mol Biol

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Cotranslational protein folding can facilitate rapid formation of functional structures. However, it might also cause premature assembly of protein complexes, if two interacting nascent chains are in close proximity. By analyzing known protein structures, we show that homomeric protein contacts are enriched towards the C-termini of polypeptide chains across diverse proteomes. We hypothesize that this is the result of evolutionary constraints for folding to occur prior to assembly. Using high-throughput imaging of protein homomers in vivo in E. coli and engineered protein constructs with N- and C-terminal oligomerization domains, we show that, indeed, proteins with C-terminal homomeric interface residues consistently assemble more efficiently than those with N-terminal interface residues. Using in vivo, in vitro and in silico experiments, we identify features that govern successful assembly of homomers, which have implications for protein design and expression optimization.

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Section: Methodsmentioning

confidence: 99%

Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins

Natan¹,

Endoh

Haim-Vilmovsky

et al. 2018

Nat Struct Mol Biol

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“…If so, a recent advance made by Geyer & Winter is likely to be extremely important: in highly original work [74• •], this group has shown that an approximate factorization of the diffusion tensor (which is norm ally achieved by a computationally nightmarish Cholesky decomposition) can capture ~95% of the HI effect at a fraction of the computational cost. This advance, together with a subsequent extension of the thinking to a Langevin dynamics setting [75], may provide something of a revolution in the scale over which hydrodynamic effects are modeled in concentrated protein system s.…”

Section: The Status Of the Fieldmentioning

confidence: 99%

Models of macromolecular crowding effects and the need for quantitative comparisons with experiment

Elcock¹

2010

Current Opinion in Structural Biology

268

228

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SummaryIn recent years significant effort has been devoted to exploring the potential effects of macromolecular crowding on protein folding and association phenomena. Theoretical calculations and molecular simulations have, in particular, been exploited to describe aspects of protein behavior in crowded and confined conditions and many aspects of the simulated behavior have reflected, at least at a qualitative level, the behavior observed in experiments. One major and immediate challenge for the theorists is to now produce models capable of making quantitatively accurate predictions of in vitro behavior. A second challenge is to derive models that explain results obtained from experiments performed in vivo, the results of which appear to call into question the assumed dominance of excluded volume effects in vivo.

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“…Second, intermolecular interactions can be modeled as the interaction of fixed interaction sites on one solute with a precomputed interaction potential grid on another solute, reducing the formal scaling of the calculation of intermolecular forces to O ( N ), with N the number of solute atoms, compared to the

O (N^{2})

O (N ln N)

algorithms in MD. This treatment of forces between solutes is used in simulation of diffusional association (SDA) and is also employed in other BD simulation software packages, namely, UHBD, Browndye, BrownMove, and Macrodox …”

Section: Introductionmentioning

confidence: 99%

SDA 7: A modular and parallel implementation of the simulation of diffusional association software

et al. 2015

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The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein–protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to simulate the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration‐dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the parallelization of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object‐oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the parallel performance. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

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Coarse grained simulations of a small peptide: Effects of finite damping and hydrodynamic interactions

Cited by 21 publications

References 30 publications

Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins

Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins

Models of macromolecular crowding effects and the need for quantitative comparisons with experiment

SDA 7: A modular and parallel implementation of the simulation of diffusional association software

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