PyRETIS: A well‐done, medium‐sized python library for rare events

Lervik, Anders; Riccardi, Enrico; Erp, Titus S. van

doi:10.1002/jcc.24900

Cited by 33 publications

(33 citation statements)

References 46 publications

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“…These trajectory fragments constituted the initial points to start the RETIS simulations. The RETIS simulations have been performed via the PyRETIS library [37].…”

Section: Methodsmentioning

confidence: 99%

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Predicting the mechanism and rate of H-NS binding to AT-rich DNA

Riccardi¹,

Mastbergen

Navarre

et al. 2019

PLoS Comput Biol

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Bacteria contain several nucleoid-associated proteins that organize their genomic DNA into the nucleoid by bending, wrapping or bridging DNA. The Histone-like Nucleoid Structuring protein H-NS found in many Gram-negative bacteria is a DNA bridging protein and can structure DNA by binding to two separate DNA duplexes or to adjacent sites on the same duplex, depending on external conditions. Several nucleotide sequences have been identified to which H-NS binds with high affinity, indicating H-NS prefers AT-rich DNA. To date, highly detailed structural information of the H-NS DNA complex remains elusive. Molecular simulation can complement experiments by modelling structures and their time evolution in atomistic detail. In this paper we report an exploration of the different binding modes of H-NS to a high affinity nucleotide sequence and an estimate of the associated rate constant. By means of molecular dynamics simulations, we identified three types of binding for H-NS to AT-rich DNA. To further sample the transitions between these binding modes, we performed Replica Exchange Transition Interface Sampling, providing predictions of the mechanism and rate constant of H-NS binding to DNA. H-NS interacts with the DNA through a conserved QGR motif, aided by a conserved arginine at position 93. The QGR motif interacts first with phosphate groups, followed by the formation of hydrogen bonds between acceptors in the DNA minor groove and the sidechains of either Q112 or R114. After R114 inserts into the minor groove, the rest of the QGR motif follows. Full insertion of the QGR motif in the minor groove is stable over several tens of nanoseconds, and involves hydrogen bonds between the bases and both backbone and sidechains of the QGR motif. The rate constant for the process of H-NS binding to AT-rich DNA resulting in full insertion of the QGR motif is in the order of 106 M−1s−1, which is rate limiting compared to the non-specific association of H-NS to the DNA backbone at a rate of 108 M−1s−1.

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“…These trajectory fragments constituted the initial points to start the RETIS simulations. The RETIS simulations have been performed via the PyRETIS library [37].…”

Section: Methodsmentioning

confidence: 99%

“…For each interface, reactive (from state A to state B) and non-reactive trajectories (from state A back to state A) are collected, from which the probability to reach the next interface can be computed. The product of these probabilities gives the reaction rate [37, 38].…”

Section: Introductionmentioning

confidence: 99%

Predicting the mechanism and rate of H-NS binding to AT-rich DNA

Riccardi¹,

Mastbergen

Navarre

et al. 2019

PLoS Comput Biol

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“…Note that in its original formulation, transition path sampling aimed at the direct generation of continuous pathways joining the end states, starting from an initial guess, exploiting a Markov chain Monte Carlo procedure called shooting [2,186]. The software packages OpenPathSampling [187] and PyRETIS [188] have been specifically developed to perform and analyse path sampling simulations.…”

Section: Theoretical and Computational Approaches To Kineticsmentioning

confidence: 99%

Advanced simulation techniques for the thermodynamic and kinetic characterization of biological systems

Camilloni

Pietrucci

2018

Advances in Physics: X

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This review discusses successful strategies and key open problems in the kinetic and thermodynamic characterization of complex biomolecular systems by computer simulations. The main focus is on established techniques and emerging trends in the fields of enhanced sampling and of kinetic models, as applied to biological problems ranging from protein folding and conformational dynamics to protein-protein and proteinligand interaction. We address especially the following questions: How to choose a computational approach suited to a particular problem? What are the strengths and limitations of alternative approaches? What is the current accuracy of thermodynamic and kinetic predictions? What are today's open challenges and promising development directions? Towards the aim of accurately reproducing and interpreting experimental results, we briefly discuss hybrid approaches that combine together theoretical and experimental information.

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“…Recent open-source software projects such as PyRETIS 43,44 and openpath-sampling 45 are presently under development and will hopefully remove this blockade. Also, the naming is not fully standardized or commonly used in the literature as the method was originally referred to as parallel path swapping 27 and the name RETIS was coined in the follow-up paper.…”

Section: Applications Of Retismentioning

confidence: 99%

Foundations and latest advances in replica exchange transition interface sampling

Cabriolu

Refsnes

Bolhuis

et al. 2017

The Journal of Chemical Physics

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Nearly 20 years ago, transition path sampling (TPS) emerged as an alternative method to free energy based approaches for the study of rare events such as nucleation, protein folding, chemical reactions, and phase transitions. TPS effectively performs Monte Carlo simulations with relatively short molecular dynamics trajectories, with the advantage of not having to alter the actual potential energy surface nor the underlying physical dynamics. Although the TPS approach also introduced a methodology to compute reaction rates, this approach was for a long time considered theoretically attractive, providing the exact same results as extensively long molecular dynamics simulations, but still expensive for most relevant applications. With the increase of computer power and improvements in the algorithmic methodology, quantitative path sampling is finding applications in more and more areas of research. In particular, the transition interface sampling (TIS) and the replica exchange TIS (RETIS) algorithms have, in turn, improved the efficiency of quantitative path sampling significantly, while maintaining the exact nature of the approach. Also, open-source software packages are making these methods, for which implementation is not straightforward, now available for a wider group of users. In addition, a blooming development takes place regarding both applications and algorithmic refinements. Therefore, it is timely to explore the wide panorama of the new developments in this field. This is the aim of this article, which focuses on the most efficient exact path sampling approach, RETIS, as well as its recent applications, extensions, and variations. Published by AIP Publishing.

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PyRETIS: A well‐done, medium‐sized python library for rare events

Cited by 33 publications

References 46 publications

Predicting the mechanism and rate of H-NS binding to AT-rich DNA

Predicting the mechanism and rate of H-NS binding to AT-rich DNA

Advanced simulation techniques for the thermodynamic and kinetic characterization of biological systems

Foundations and latest advances in replica exchange transition interface sampling

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