Ion permeation simulations by Gromacs—an example of high performance molecular dynamics

Krüger, Jens; Fels, Gregor

doi:10.1002/cpe.1666

Cited by 4 publications

(3 citation statements)

References 34 publications

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“…Following equilibration, SMD was applied to a sodium ion previously fixed above the center of the electronegative cavity of ChR2. SMD has previously been used to resolve the conduction pathway in the KcsA potassium channel and ion-binding sites of the sodium symporter LeuT and to identify barriers for glycerol permeation in the closed-state aquaglyceroporin, nicotinic acetylcholine receptor, and aquaporin-1 (35,(42)(43)(44)(45). Additionally, SMD has been used to explore binding pathways in monomeric units of higher-order oligomeric proteins, such as bacteriorhodopsin (46).…”

Section: Conduction Pathwaymentioning

confidence: 99%

Adjacent channelrhodopsin-2 residues within transmembranes 2 and 7 regulate cation selectivity and distribution of the two open states

Richards

Dempski

2017

Journal of Biological Chemistry

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Channelrhodopsin-2 (ChR2) is a light-activated channel that can conduct cations of multiple valencies down the electrochemical gradient. Under continuous light exposure, ChR2 transitions from a high-conducting open state (O1) to a low-conducting open state (O2) with differing ion selectivity. The molecular basis for the O1 → O2 transition and how ChR2 modulates selectivity between states is currently unresolved. To this end, we used steered molecular dynamics, electrophysiology, and kinetic modeling to identify residues that contribute to gating and selectivity in discrete open states. Analysis of steered molecular dynamics experiments identified three transmembrane residues (Val-86, Lys-93, and Asn-258) that form a putative barrier to ion translocation. Kinetic modeling of photocurrents generated from ChR2 proteins with conservative mutations at these positions demonstrated that these residues contribute to cation selectivity (Val-86 and Asn-258), the transition between the two open states (Val-86), open channel stability, and the hydrogen-bonding network (K93I and K93N). These results suggest that this approach can be used to identify residues that contribute to the open-state transitions and the discrete ion selectivity within these states. With the rise of ChR2 use in optogenetics, it will be critical to identify residues that contribute to O1 or O2 selectivity and gating to minimize undesirable effects.

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Section: Conduction Pathwaymentioning

confidence: 99%

Adjacent channelrhodopsin-2 residues within transmembranes 2 and 7 regulate cation selectivity and distribution of the two open states

Richards

Dempski

2017

Journal of Biological Chemistry

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“…Furthermore, a rudimentary understanding of the scientific background, which tools are used and which analysis steps have to be used, is essential to provide the researchers with an intuitive user interface. Jens Krüger and Gregor Fels present in this special issue an example of high-performance molecular dynamics in the case of ion permeation simulations by Gromacs [38]. They compared two methods for the calculation of energy profiles and measured the performance on different HPC clusters and the influence of required CPU hours and real simulation time.…”

Section: Selected Applicationsmentioning

confidence: 99%

Special Issue: Portals for life sciences—Providing intuitive access to bioinformatic tools

Gesing

Hemert

Kacsuk

et al. 2010

Concurrency and Computation

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SUMMARYThe topic 'Portals for life sciences' includes various research fields, on the one hand many different topics out of life sciences, e.g. mass spectrometry, on the other hand portal technologies and different aspects of computer science, such as usability of user interfaces and security of systems. The main aspect about portals is to simplify the user's interaction with computational resources that are concerted to a supported application domain. Copyright ᭧ 2010 John Wiley & Sons, Ltd. IWPLS'09It is our great pleasure to introduce this special issue on the First International Workshop on Portals for Life Sciences held at the e-Science Institute in Edinburgh, U.K., on 14-15 September 2009. The workshop was focused on research contributions for portals and tools in the field of life sciences and brought together scientists from the fields of life science, bioinformatics, and computer science. It formed an international platform to exchange experience, formulate ideas, and catch up on technological advances in molecular and systems biology in the context of portals. The variety of nationalities covered by the delegates reflects the international interest in a platform on scientific portals. Delegates from Austria, Brazil, Germany, Hungary, Italy, The Netherlands, Norway, Spain, The United Kingdom and The United States of America contributed to and attended the workshop. We especially highlight the mix of technology-related and domain-related talks, which mirrors the diverse scientific background of the delegates.Papers and abstracts for the workshop were accepted through a blind peer-reviewing process. Accepted papers resulted in 30-min presentations and were published in an open-access workshop proceedings. Accepted abstracts resulted in a 10-min 'lightning talk'. The speakers gave excellent and thought-provoking presentations. The highlights were presentations from two invited keynote speakers. In addition to the presentations, lively and promising discussions took place after talks, in coffee breaks and even during the social event. The workshop was highly successful and turned out to be the starting point of an international workshop series with the subject extended to science gateways for e-Science: The International Workshop on Science Gateways.We faced the challenge to invite several authors for extended versions of their papers and abstracts for this special issue. Some of the papers in this special edition are combinations of papers * Correspondence to: Sandra Gesing,

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“…In addition, molecular simulations, that is, computations of electron structures or molecular mechanics (MM), are rather costly in their use of computational resources . In most cases, only high performance computing hardware is sufficient for this purpose.…”

Section: Introductionmentioning

confidence: 99%

Standards‐based metadata management for molecular simulations

Grunzke

Breuers

Gesing

et al. 2013

Concurrency and Computation

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SUMMARYState‐of‐the‐art research in a variety of natural sciences depends heavily on methods of computational chemistry, for example, the calculation of the properties of materials, proteins, catalysts, and drugs. Applications providing such methods require a lot of expertise to handle their complexity and the usage of high‐performance computing. The MoSGrid (molecular simulation grid) infrastructure relieves this burden from scientists by providing a science gateway, which eases access to and usage of computational chemistry applications. One of its cornerstones is the molecular simulations markup language (MSML), an extension of the chemical markup language. MSML abstracts all chemical as well as computational aspects of simulations. An application and its results can be described with common semantics. Using such application, independent descriptions users can easily switch between different applications or compare them. This paper introduces MSML, its integration into a science gateway, and its usage for molecular dynamics, quantum chemistry, and protein docking. Copyright © 2013 John Wiley & Sons, Ltd.

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Ion permeation simulations by Gromacs—an example of high performance molecular dynamics

Cited by 4 publications

References 34 publications

Adjacent channelrhodopsin-2 residues within transmembranes 2 and 7 regulate cation selectivity and distribution of the two open states

Adjacent channelrhodopsin-2 residues within transmembranes 2 and 7 regulate cation selectivity and distribution of the two open states

Special Issue: Portals for life sciences—Providing intuitive access to bioinformatic tools

Standards‐based metadata management for molecular simulations

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