1
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Jansen A, Aho N, Groenhof G, Buslaev P, Hess B. phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS. J Chem Inf Model 2024; 64:567-574. [PMID: 38215282 PMCID: PMC10865341 DOI: 10.1021/acs.jcim.3c01313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/14/2024]
Abstract
Constant pH molecular dynamics (MD) is a powerful technique that allows the protonation state of residues to change dynamically, thereby enabling the study of pH dependence in a manner that has not been possible before. Recently, a constant pH implementation was incorporated into the GROMACS MD package. Although this implementation provides good accuracy and performance, manual modification and the preparation of simulation input files are required, which can be complicated, tedious, and prone to errors. To simplify and automate the setup process, we present phbuilder, a tool that automatically prepares constant pH MD simulations for GROMACS by modifying the input structure and topology as well as generating the necessary parameter files. phbuilder can prepare constant pH simulations from both initial structures and existing simulation systems, and it also provides functionality for performing titrations and single-site parametrizations of new titratable group types. The tool is freely available at www.gitlab.com/gromacs-constantph. We anticipate that phbuilder will make constant pH simulations easier to set up, thereby making them more accessible to the GROMACS user community.
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Affiliation(s)
- Anton Jansen
- Department
of Applied Physics and Swedish e-Science Research Center, Science
for Life Laboratory, KTH Royal Institute
of Technology, 100 44 Stockholm, Sweden
| | - Noora Aho
- Nanoscience
Center and Department of Chemistry, University
of Jyväskylä, 40014 Jyväskylä, Finland
| | - Gerrit Groenhof
- Nanoscience
Center and Department of Chemistry, University
of Jyväskylä, 40014 Jyväskylä, Finland
| | - Pavel Buslaev
- Nanoscience
Center and Department of Chemistry, University
of Jyväskylä, 40014 Jyväskylä, Finland
| | - Berk Hess
- Department
of Applied Physics and Swedish e-Science Research Center, Science
for Life Laboratory, KTH Royal Institute
of Technology, 100 44 Stockholm, Sweden
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2
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Lundborg M, Lidmar J, Hess B. On the Path to Optimal Alchemistry. Protein J 2023; 42:477-489. [PMID: 37651042 PMCID: PMC10480267 DOI: 10.1007/s10930-023-10137-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 09/01/2023]
Abstract
Alchemical free energy calculations have become a standard and widely used tool, in particular for calculating and comparing binding affinities of drugs. Although methods to compute such free energies have improved significantly over the last decades, the choice of path between the end states of interest is usually still the same as two decades ago. We will show that there is a fundamentally arbitrary, implicit choice of parametrization of this path. To address this, the notion of the length of a path or a metric is required. A metric recently introduced in the context of the accelerated weight histogram method also proves to be very useful here. We demonstrate that this metric can not only improve the efficiency of sampling along a given path, but that it can also be used to improve the actual choice of path. For a set of relevant use cases, the combination of these improvements can increase the efficiency of alchemical free energy calculations by up to a factor 16.
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Affiliation(s)
| | - Jack Lidmar
- Department of Physics, KTH Royal Institute of Technology, 10691, Stockholm, Sweden
| | - Berk Hess
- Department of Applied Physics, KTH Royal Institute of Technology, 10691, Stockholm, Science for Life Laboratory, Solna, Sweden.
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3
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Lundborg M, Wennberg C, Lidmar J, Hess B, Lindahl E, Norlén L. Skin permeability prediction with MD simulation sampling spatial and alchemical reaction coordinates. Biophys J 2022; 121:3837-3849. [PMID: 36104960 PMCID: PMC9674988 DOI: 10.1016/j.bpj.2022.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/22/2022] [Accepted: 09/08/2022] [Indexed: 11/02/2022] Open
Abstract
A molecular-level understanding of skin permeation may rationalize and streamline product development, and improve quality and control, of transdermal and topical drug delivery systems. It may also facilitate toxicity and safety assessment of cosmetics and skin care products. Here, we present new molecular dynamics simulation approaches that make it possible to efficiently sample the free energy and local diffusion coefficient across the skin's barrier structure to predict skin permeability and the effects of chemical penetration enhancers. In particular, we introduce a new approach to use two-dimensional reaction coordinates in the accelerated weight histogram method, where we combine sampling along spatial coordinates with an alchemical perturbation virtual coordinate. We present predicted properties for 20 permeants, and demonstrate how our approach improves correlation with ex vivo/in vitro skin permeation data. For the compounds included in this study, the obtained log KPexp-calc mean square difference was 0.9 cm2 h-2.
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Affiliation(s)
| | | | - Jack Lidmar
- Department of Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Berk Hess
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Erik Lindahl
- Department of Biophysics and Biochemistry, Science for Life Laboratory, Stockholm University, Solna, Sweden; Department of Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lars Norlén
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden; Dermatology Clinic, Karolinska University Hospital, Stockholm, Sweden.
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4
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Affiliation(s)
- Noora Aho
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland
| | - Pavel Buslaev
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland
| | - Anton Jansen
- Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44Stockholm, Sweden
| | - Paul Bauer
- Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44Stockholm, Sweden
| | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland
| | - Berk Hess
- Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44Stockholm, Sweden
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5
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Abstract
![]()
Various approaches
have been proposed to include the
effect of
pH in molecular dynamics (MD) simulations. Among these, the λ-dynamics approach proposed
by Brooks and
co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414−2423] can be performed
with little computational overhead and hfor each typeence be used
to routinely perform MD simulations at microsecond time scales, as
shown in the accompanying paper [Aho, N. et al. J. Chem. Theory
Comput.2022, DOI: 10.1021/acs.jctc.2c00516]. At
such time scales, however, the accuracy of the molecular mechanics
force field and the parametrization becomes critical. Here, we address
these issues and provide the community with guidelines on how to set
up and perform long time scale constant pH MD simulations. We found
that barriers associated with the torsions of side chains in the CHARMM36m
force field are too high for reaching convergence in constant pH MD
simulations on microsecond time scales. To avoid the high computational
cost of extending the sampling, we propose small modifications to
the force field to selectively reduce the torsional barriers. We demonstrate
that with such modifications we obtain converged distributions of
both protonation and torsional degrees of freedom and hence consistent
pKa estimates, while the sampling of the
overall configurational space accessible to proteins is unaffected
as compared to normal MD simulations. We also show that the results
of constant pH MD depend on the accuracy of the correction potentials.
While these potentials are typically obtained by fitting a low-order
polynomial to calculated free energy profiles, we find that higher
order fits are essential to provide accurate and consistent results.
By resolving problems in accuracy and sampling, the work described
in this and the accompanying paper paves the way to the widespread
application of constant pH MD beyond pKa prediction.
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Affiliation(s)
- Pavel Buslaev
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Noora Aho
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Anton Jansen
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - Paul Bauer
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - Berk Hess
- Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014 Jyväskylä, Finland
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6
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Jansen A, Bauer P, Howard RJ, Lindahl E, Hess B. Constant-Ph molecular dynamics simulations of a proton-gated ion channel. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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7
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Abstract
The accelerated weight histogram method is an enhanced sampling technique used to explore free energy landscapes by applying an adaptive bias. The method is general and easy to extend. Herein, we show how it can be used to efficiently sample alchemical transformations, commonly used for, e.g., solvation and binding free energy calculations. We present calculations and convergence of the hydration free energy of testosterone, representing drug-like molecules. We also include methane and ethanol to validate the results. The protocol is easy to use, does not require a careful choice of parameters, and scales well to accessible resources, and the results converge at least as quickly as when using conventional methods. One benefit of the method is that it can easily be combined with other reaction coordinates, such as intermolecular distances.
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Affiliation(s)
| | - J Lidmar
- Department of Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - B Hess
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
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8
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Zinzani PL, Caimi PF, Carlo‐Stella C, Ai W, Alderuccio JP, Ardeshna KM, Hess B, Kahl BS, Radford J, Solh M, Stathis A, Feingold J, Ungar D, Qin Y, He S, Hamadani M. LOTIS 2 FOLLOW‐UP ANALYSIS: UPDATED RESULTS FROM A PHASE 2 STUDY OF LONCASTUXIMAB TESIRINE IN RELAPSED OR REFRACTORY DIFFUSE LARGE B‐CELL LYMPHOMA. Hematol Oncol 2021. [DOI: 10.1002/hon.89_2880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- P. L. Zinzani
- IRCCS Azienda Ospedaliero‐Universitaria di Bologna Istituto di Ematologia "Seràgnoli" and Diagnostica e Sperimentale Università di Bologna Dipartimento di Medicina Specialistica Bologna Italy
| | - P. F. Caimi
- Case Western Reserve University University Hospitals Cleveland Medical Center Cleveland USA
| | - C. Carlo‐Stella
- Humanitas Clinical and Research Center – IRCCS, and Humanitas University Department of Oncology and Hematology Rozzano Milan Italy
| | - W. Ai
- University of California Division of Hematology and Oncology Department of Medicine San Francisco USA
| | - J. P. Alderuccio
- University of Miami Sylvester Comprehensive Cancer Center Miami USA
| | - K. M. Ardeshna
- University College London Hospitals NHS Foundation Trust Department of Haematology London UK
| | - B. Hess
- Medical University of South Carolina Division of Hematology and Medical Oncology Department of Medicine Charleston USA
| | - B. S. Kahl
- Washington University Department of Medicine Oncology Division St Louis USA
| | - J. Radford
- Christie NHS Foundation Trust and the University of Manchester NIHR Clinical Research Facility Manchester UK
| | - M. Solh
- Northside Hospital Blood and Marrow Transplant Program AtlantaGeorgia USA
| | - A. Stathis
- Oncology Institute of Southern Switzerland Division of Medical Oncology Bellinzona Switzerland
| | - J. Feingold
- ADC Therapeutics America, Inc Clinical Development Murray Hill USA
| | - D. Ungar
- ADC Therapeutics America, Inc Clinical Development Murray Hill USA
| | - Y. Qin
- ADC Therapeutics America, Inc Clinical Development Murray Hill USA
| | - S. He
- ADC Therapeutics America, Inc Clinical Development Murray Hill USA
| | - M. Hamadani
- Medical College of Wisconsin Division of Hematology and Oncology Milwaukee USA
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9
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Waskowski J, Hess B, Cioccari L, Irincheeva I, Pfortmueller CA, Schefold JC. Effects of sodium bicarbonate infusion on mortality in medical-surgical ICU patients with metabolic acidosis-A single-center propensity score matched analysis. Med Intensiva 2021; 46:S0210-5691(21)00106-6. [PMID: 34120787 DOI: 10.1016/j.medin.2021.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/14/2021] [Accepted: 04/23/2021] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Metabolic acidosis is associated with high mortality. Despite theoretical benefits of sodium-bicarbonate (SB), current evidence remains controversial. We investigated SB-related effects on outcomes in ICU patients with metabolic acidosis. DESIGN Retrospective analysis. SETTING Academic medical center. PATIENTS OR PARTICIPANTS 971 ICU patients with metabolic acidosis defined as arterial pH<7.3 and CO2<45mmHg treated between 2012 and 2016. A propensity score (PS) was estimated using logistic regression. Patients were matched in pairs using the PS. INTERVENTIONS 441 patients were treated with SB 8.4% (SB-group) and n=530 patients were not (control group). MAIN VARIABLES OF INTEREST Primary outcome was all-cause mortality at ICU-discharge. Average Treatment Effect (ATE), Average Treatment effect in Treated (ATT), and estimated relative survival effects at 20 days were computed. RESULTS In the full cohort, we observed considerable differences in pH, base excess, additional acidosis-related indices, and ICU mortality (controls 31% vs. SB-group 56%, p<.001) at baseline between the two groups. After PS-matching (n=174 in each group), no significant difference in ICU mortality was observed (controls 32% vs. SB-group 41%; p=.07). Odds ratios (OR) for ATE and ATT showed no association with ICU mortality (OR ATE: 1.08, 95%-CI 0.99-1.17; p=.08; OR ATT 1.09; 95%-CI 0.99-1.2; p=.09). Hazard ratios at 20-days (multivariable HR, matched sample n=348: 1.16, 95%-CI 0.86-1.56, p=.33) showed similar survival in the two study groups. CONCLUSIONS We did not observe effects of SB infusion on all-cause mortality in critically ill patients with metabolic acidosis.
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Affiliation(s)
- J Waskowski
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department of Anaesthesiology and Pain Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
| | - B Hess
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Center of Intensive Care Medicine, Luzerner Kantonsspital, Lucerne, Switzerland
| | - L Cioccari
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - C A Pfortmueller
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - J C Schefold
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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10
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Páll S, Zhmurov A, Bauer P, Abraham M, Lundborg M, Gray A, Hess B, Lindahl E. Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS. J Chem Phys 2020; 153:134110. [PMID: 33032406 DOI: 10.1063/5.0018516] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these benefits, it has been necessary to reformulate some of the most fundamental algorithms, including the Verlet list, pair searching, and cutoffs. Here, we present the heterogeneous parallelization and acceleration design of molecular dynamics implemented in the GROMACS codebase over the last decade. The setup involves a general cluster-based approach to pair lists and non-bonded pair interactions that utilizes both GPU and central processing unit (CPU) single instruction, multiple data acceleration efficiently, including the ability to load-balance tasks between CPUs and GPUs. The algorithm work efficiency is tuned for each type of hardware, and to use accelerators more efficiently, we introduce dual pair lists with rolling pruning updates. Combined with new direct GPU-GPU communication and GPU integration, this enables excellent performance from single GPU simulations through strong scaling across multiple GPUs and efficient multi-node parallelization.
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Affiliation(s)
- Szilárd Páll
- Swedish e-Science Research Center, PDC Center for High Performance Computing, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - Artem Zhmurov
- Swedish e-Science Research Center, PDC Center for High Performance Computing, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - Paul Bauer
- Science for Life Laboratory, Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden
| | - Mark Abraham
- Science for Life Laboratory, Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden
| | | | - Alan Gray
- NVIDIA Corporation, Reading, United Kingdom
| | - Berk Hess
- Science for Life Laboratory, Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden
| | - Erik Lindahl
- Science for Life Laboratory, Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden
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11
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Affiliation(s)
- D. S. Shamshirgar
- Department of Mathematics and Swedish e-Science Research Centre, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - R. Yokota
- Global Scientific Information and Computing Center, Tokyo Institute of Technology, Tokyo, Japan
| | - A.-K. Tornberg
- Department of Mathematics and Swedish e-Science Research Centre, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - B. Hess
- Department of Applied Physics and Swedish e-Science Research Centre, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
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12
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Abstract
Exploring the free-energy landscape along reaction coordinates or system parameters λ is central to many studies of high-dimensional model systems in physics, e.g., large molecules or spin glasses. In simulations this usually requires sampling conformational transitions or phase transitions, but efficient sampling is often difficult to attain due to the roughness of the energy landscape. For Boltzmann distributions, crossing rates decrease exponentially with free-energy barrier heights. Thus, exponential acceleration can be achieved in simulations by applying an artificial bias along λ tuned such that a flat target distribution is obtained. A flat distribution is, however, an ambiguous concept unless a proper metric is used and is generally suboptimal. Here we propose a multidimensional Riemann metric, which takes the local diffusion into account, and redefine uniform sampling such that it is invariant under nonlinear coordinate transformations. We use the metric in combination with the accelerated weight histogram method, a free-energy calculation and sampling method, to adaptively optimize sampling toward the target distribution prescribed by the metric. We demonstrate that for complex problems, such as molecular dynamics simulations of DNA base-pair opening, sampling uniformly according to the metric, which can be calculated without significant computational overhead, improves sampling efficiency by 50%-70%.
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Affiliation(s)
- Viveca Lindahl
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Jack Lidmar
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Berk Hess
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
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13
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Lindahl V, Gourdon P, Andersson M, Hess B. Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function. Sci Rep 2018; 8:2995. [PMID: 29445244 PMCID: PMC5813003 DOI: 10.1038/s41598-018-21357-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/02/2018] [Indexed: 01/16/2023] Open
Abstract
Aquaporin TIP2;1 is a protein channel permeable to both water and ammonia. The structural origin of ammonia selectivity remains obscure, but experiments have revealed that a double mutation renders it impermeable to ammonia without affecting water permeability. Here, we aim to reproduce and explain these observations by performing an extensive mutational study using microsecond long molecular dynamics simulations, applying the two popular force fields CHARMM36 and Amber ff99SB-ILDN. We calculate permeabilities and free energies along the channel axis for ammonia and water. For one force field, the permeability of the double mutant decreases by a factor of 2.5 for water and 4 for ammonia, increasing water selectivity by a factor of 1.6. We attribute this effect to decreased entropy of water in the pore, due to the observed increase in pore-water interactions and narrower pore. Additionally, we observe spontaneous opening and closing of the pore on the cytosolic side, which suggests a gating mechanism for the pore. Our results show that sampling methods and simulation times are sufficient to delineate even subtle effects of mutations on structure and function and to capture important long-timescale events, but also underline the importance of improving models further.
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Affiliation(s)
- Viveca Lindahl
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
| | - Pontus Gourdon
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Magnus Andersson
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Berk Hess
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
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14
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Lindahl V, Villa A, Hess B. Sequence dependency of canonical base pair opening in the DNA double helix. PLoS Comput Biol 2017; 13:e1005463. [PMID: 28369121 PMCID: PMC5393899 DOI: 10.1371/journal.pcbi.1005463] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 04/17/2017] [Accepted: 03/17/2017] [Indexed: 12/15/2022] Open
Abstract
The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair. The DNA double helix, a molecule that stores biological information, has become an iconic image of biomedical research. In order to use or repair the information it carries, the bases that are stacked in the helix need to be chemically exposed. This can happen either by separating the two strands in the helix or by flipping out individual bases. Here, we focus on the latter process. Usually proteins are involved in interactions with bases, but it is still unclear if bases are pulled out actively by proteins or if they act on spontaneously flipped bases. Although experiments can detect base pair opening, it is difficult to detect which base moves in which direction. Here, we present results from molecular dynamics simulations using a recently developed sampling method which improves the statistics in the simulations by enhancing the probability of the base pair opening event. We observe differences in probability, modes and mechanism of opening that depend not only on the types of the bases in the pair, but also strongly on their neighbors. This provides essential information for understanding how DNA functions.
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Affiliation(s)
- Viveca Lindahl
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Stockholm and Uppsala, Stockholm, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Berk Hess
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Stockholm and Uppsala, Stockholm, Sweden
- * E-mail:
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15
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Ullmann RT, Kutzner C, Beckmann A, Kohnke B, Haensel D, Kabadshow I, Dachsel H, Hess B, Grubmüller H. Gromex: Electrostatics with Chemical Variability for Realistic Molecular Simulations on the Exascale. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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16
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Kohnke B, Ullmann RT, Kutzner C, Beckmann A, Haensel D, Kabadshow I, Dachsel H, Hess B, Grubmüller H. A Flexible, GPU - Powered Fast Multipole Method for Realistic Biomolecular Simulations in Gromacs. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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17
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Abstract
By removing the fastest degrees of freedom, constraints allow for an increase of the time step in molecular simulations. In the last decade parallel simulations have become commonplace. However, up till now efficient parallel constraint algorithms have not been used with domain decomposition. In this paper the parallel linear constraint solver (P-LINCS) is presented, which allows the constraining of all bonds in macromolecules. Additionally the energy conservation properties of (P-)LINCS are assessed in view of improvements in the accuracy of uncoupled angle constraints and integration in single precision.
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Affiliation(s)
- Berk Hess
- Max-Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
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18
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de Wijn AS, Hess B, Fine BV. Chaotic properties of spin lattices near second-order phase transitions. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 92:062929. [PMID: 26764796 DOI: 10.1103/physreve.92.062929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Indexed: 06/05/2023]
Abstract
We perform a numerical investigation of the Lyapunov spectra of chaotic dynamics in lattices of classical spins in the vicinity of second-order ferromagnetic and antiferromagnetic phase transitions. On the basis of this investigation, we identify a characteristic of the shape of the Lyapunov spectra, the "G-index," which exhibits a sharp peak as a function of temperature at the phase transition, provided the order parameter is capable of sufficiently strong dynamic fluctuations. As part of this work, we also propose a general numerical algorithm for determining the temperature in many-particle systems, where kinetic energy is not defined.
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Affiliation(s)
- A S de Wijn
- Department of Physics, Stockholm University, 106 91 Stockholm, Sweden
| | - B Hess
- Institute for Theoretical Physics, University of Heidelberg, Philosophenweg 19, 69120 Heidelberg, Germany
| | - B V Fine
- Institute for Theoretical Physics, University of Heidelberg, Philosophenweg 19, 69120 Heidelberg, Germany
- Department of Physics, School of Science and Technology, Nazarbayev University 53 Kabanbai Batyr Avenue, Astana 010000, Kazakhstan
- Skolkovo Institute of Science and Technology, 100 Novaya Str., Skolkovo, Moscow Region 143025, Russia
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19
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Wennberg CL, Murtola T, Páll S, Abraham MJ, Hess B, Lindahl E. Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation. J Chem Theory Comput 2015; 11:5737-46. [PMID: 26587968 DOI: 10.1021/acs.jctc.5b00726] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Long-range lattice summation techniques such as the particle-mesh Ewald (PME) algorithm for electrostatics have been revolutionary to the precision and accuracy of molecular simulations in general. Despite the performance penalty associated with lattice summation electrostatics, few biomolecular simulations today are performed without it. There are increasingly strong arguments for moving in the same direction for Lennard-Jones (LJ) interactions, and by using geometric approximations of the combination rules in reciprocal space, we have been able to make a very high-performance implementation available in GROMACS. Here, we present a new way to correct for these approximations to achieve exact treatment of Lorentz-Berthelot combination rules within the cutoff, and only a very small approximation error remains outside the cutoff (a part that would be completely ignored without LJ-PME). This not only improves accuracy by almost an order of magnitude but also achieves absolute biomolecular simulation performance that is an order of magnitude faster than any other available lattice summation technique for LJ interactions. The implementation includes both CPU and GPU acceleration, and its combination with improved scaling LJ-PME simulations now provides performance close to the truncated potential methods in GROMACS but with much higher accuracy.
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Affiliation(s)
- Christian L Wennberg
- Swedish e-Science Research Center, Department of Theoretical Physics, KTH Royal Institute of Technology , Box 1031, 171 21 Solna, Sweden.,Center for Biomembrane Research, Department of Biophysics & Biochemistry, Stockholm University , 106 91 Stockholm, Sweden
| | - Teemu Murtola
- Swedish e-Science Research Center, Department of Theoretical Physics, KTH Royal Institute of Technology , Box 1031, 171 21 Solna, Sweden.,Center for Biomembrane Research, Department of Biophysics & Biochemistry, Stockholm University , 106 91 Stockholm, Sweden
| | - Szilárd Páll
- Swedish e-Science Research Center, Department of Theoretical Physics, KTH Royal Institute of Technology , Box 1031, 171 21 Solna, Sweden.,Center for Biomembrane Research, Department of Biophysics & Biochemistry, Stockholm University , 106 91 Stockholm, Sweden
| | - Mark J Abraham
- Swedish e-Science Research Center, Department of Theoretical Physics, KTH Royal Institute of Technology , Box 1031, 171 21 Solna, Sweden.,Center for Biomembrane Research, Department of Biophysics & Biochemistry, Stockholm University , 106 91 Stockholm, Sweden
| | - Berk Hess
- Swedish e-Science Research Center, Department of Theoretical Physics, KTH Royal Institute of Technology , Box 1031, 171 21 Solna, Sweden.,Center for Biomembrane Research, Department of Biophysics & Biochemistry, Stockholm University , 106 91 Stockholm, Sweden
| | - Erik Lindahl
- Swedish e-Science Research Center, Department of Theoretical Physics, KTH Royal Institute of Technology , Box 1031, 171 21 Solna, Sweden.,Center for Biomembrane Research, Department of Biophysics & Biochemistry, Stockholm University , 106 91 Stockholm, Sweden
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20
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Abstract
Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies from these simulations remains a major challenge. Fully exploring the free energy landscape of, say, a biological macromolecule typically requires sampling large conformational changes and slow transitions. Often, the only feasible way to study such a system is to simulate it using an enhanced sampling method. The accelerated weight histogram (AWH) method is a new, efficient extended ensemble sampling technique which adaptively biases the simulation to promote exploration of the free energy landscape. The AWH method uses a probability weight histogram which allows for efficient free energy updates and results in an easy discretization procedure. A major advantage of the method is its general formulation, making it a powerful platform for developing further extensions and analyzing its relation to already existing methods. Here, we demonstrate its efficiency and general applicability by calculating the potential of mean force along a reaction coordinate for both a single dimension and multiple dimensions. We make use of a non-uniform, free energy dependent target distribution in reaction coordinate space so that computational efforts are not wasted on physically irrelevant regions. We present numerical results for molecular dynamics simulations of lithium acetate in solution and chignolin, a 10-residue long peptide that folds into a β-hairpin. We further present practical guidelines for setting up and running an AWH simulation.
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Affiliation(s)
- V Lindahl
- Department of Theoretical Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - J Lidmar
- Department of Theoretical Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - B Hess
- Department of Theoretical Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
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21
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Páll S, Abraham MJ, Kutzner C, Hess B, Lindahl E. Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS. Lecture Notes in Computer Science 2015. [DOI: 10.1007/978-3-319-15976-8_1] [Citation(s) in RCA: 339] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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22
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Abstract
At room temperature the chemical reaction between malonic acid (0.2 M) and KBrO3 (0.06 м) in 1 м H2SO4 is catalysed by cerium ions. The oscillation of the yellow Ce4+ ions can be observed directly during the reaction. By silica-gel chromatography the brominated products of the reaction have been identified as dibromoacetic acid and bromomalonic acid.
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Affiliation(s)
- L. Bornmann
- Max-Planck-Institut für Ernährungsphysiologie, Dortmund
| | - H. Busse
- Max-Planck-Institut für Ernährungsphysiologie, Dortmund
| | - B. Hess
- Max-Planck-Institut für Ernährungsphysiologie, Dortmund
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23
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Abstract
In order to elucidate the reaction scheme of the oscillatory malonic acid-KBrO3system in sulphuric acid the products extracted from the reaction system by ether are analysed by gas chromatography and mass spectrometry. After 2 hours reaction time implying approx. 80 to 100 cycles malonic acid, monobromomalonic acid and dibromoacetic acid are identified in a relative ratio of about 1.0, 0.14 and 0.023.
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Affiliation(s)
- L. Bornmann
- Max-Planck-Institut für Ernährungsphysiologie, Dortmund -
| | - H. Busse
- Max-Planck-Institut für Ernährungsphysiologie, Dortmund -
| | - B. Hess
- Max-Planck-Institut für Ernährungsphysiologie, Dortmund
| | - R. Riepe
- Institut für Spektrochemie und angewandte Spektroskopie, Dortmund
| | - C. Hesse
- Institut für Ernährungswissenschaft, Universität Bonn
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24
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Sromicki J, Matter S, Sitzmann K, Hess B. AB0808 Incomplete Distal Renal Tubular Acidosis in Patients with Osteo-Porosis/Osteopenia – Prevalence and Treatment. Ann Rheum Dis 2014. [DOI: 10.1136/annrheumdis-2014-eular.3481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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25
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Visootsak J, Hess B, Bakeman R, Adamson LB. Effect of congenital heart defects on language development in toddlers with Down syndrome. J Intellect Disabil Res 2013; 57:887-92. [PMID: 22998351 PMCID: PMC3565078 DOI: 10.1111/j.1365-2788.2012.01619.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/08/2012] [Indexed: 05/13/2023]
Abstract
BACKGROUND Down syndrome (DS, OMIM #190685) is the most commonly identified genetic form of intellectual disability with congenital heart defect (CHD) occurring in 50% of cases. With advances in surgical techniques and an increasing lifespan, this has necessitated a greater understanding of the neurodevelopmental consequences of CHDs. Herein, we explore the impact of CHD on language development in children with DS. METHODS Twenty-nine children with DS were observed systematically in parent-child interactions using the Communication Play Protocol to evaluate their language use; they also completed the Mullen Scales of Early Learning and MacArthur Communication Development Inventory. Mean ages were 31.2 months for children with DS and CHD (DS + CHD, n = 12) and 32.1 months for children with DS and a structurally normal heart (DS - CHD, n = 17). RESULTS Compared with the DS - CHD controls, the DS + CHD group revealed lower scores in multiple areas, including fine motor skills and expressive and receptive vocabulary. Whereas most differences were not statistically significant, the Communication Development Inventory word count and symbol-infused joint engagement differed significantly (P < 0.01) and marginally (P = 0.09) between groups. CONCLUSIONS Finding that CHDs may account for part of the variation in language delay allows us to consider the specific mechanisms underlying the impact of CHDs on language acquisition in children with DS. Conclusions from this first study on early language outcomes of children with DS + CHD may be useful for clinicians in providing developmental surveillance and early intervention programmes with specific emphasis on language therapy as part of long-term follow-up for children with DS + CHD.
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Affiliation(s)
- J Visootsak
- Human Genetics and Pediatrics, Emory University School of Medicine, Decatur, Georgia 30033, USA.
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26
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Wennberg CL, Murtola T, Hess B, Lindahl E. Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties. J Chem Theory Comput 2013; 9:3527-37. [DOI: 10.1021/ct400140n] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christian L. Wennberg
- Swedish e-Science Research Center and Department of
Theoretical Physics, KTH Royal Institute of Technology, Box 1031, 17121 Solna, Sweden
- Center for Biomembrane
Research, Department of Biophysics
and Biochemistry, Stockholm University,
106 91 Stockholm, Sweden
| | - Teemu Murtola
- Swedish e-Science Research Center and Department of
Theoretical Physics, KTH Royal Institute of Technology, Box 1031, 17121 Solna, Sweden
- Center for Biomembrane
Research, Department of Biophysics
and Biochemistry, Stockholm University,
106 91 Stockholm, Sweden
| | - Berk Hess
- Swedish e-Science Research Center and Department of
Theoretical Physics, KTH Royal Institute of Technology, Box 1031, 17121 Solna, Sweden
- Center for Biomembrane
Research, Department of Biophysics
and Biochemistry, Stockholm University,
106 91 Stockholm, Sweden
| | - Erik Lindahl
- Swedish e-Science Research Center and Department of
Theoretical Physics, KTH Royal Institute of Technology, Box 1031, 17121 Solna, Sweden
- Center for Biomembrane
Research, Department of Biophysics
and Biochemistry, Stockholm University,
106 91 Stockholm, Sweden
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27
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Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D, Hess B, Lindahl E. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 2013; 29:845-54. [PMID: 23407358 PMCID: PMC3605599 DOI: 10.1093/bioinformatics/btt055] [Citation(s) in RCA: 4966] [Impact Index Per Article: 451.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 01/28/2013] [Accepted: 01/29/2013] [Indexed: 01/27/2023] Open
Abstract
MOTIVATION Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. RESULTS Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. AVAILABILITY GROMACS is an open source and free software available from http://www.gromacs.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sander Pronk
- Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden
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28
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Abstract
Microscopic self-organization phenomena inside a living cell should not represent merely a reduced copy of self-organization in macroscopic systems. A cell is populated by active protein machines that communicate via small molecules diffusing through the cytoplasm. Mutual synchronization of machine cycles can spontaneously develop in such networks - an effect which is similar to coherent laser generation. On the other hand, an interplay between reactions, diffusion and phase transitions in biological soft matter may lead to the formation of stationary or traveling nonequilibrium nanoscale structures.
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Affiliation(s)
- A S Mikhailov
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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29
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Kasson PM, Hess B, Lindahl E. Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions. Chem Phys Lipids 2013; 169:106-12. [PMID: 23318532 DOI: 10.1016/j.chemphyslip.2013.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 12/19/2012] [Accepted: 01/02/2013] [Indexed: 11/24/2022]
Abstract
Cellular lipid membranes are spatially inhomogeneous soft materials. Materials properties such as pressure and surface tension thus show important microscopic-scale variation that is critical to many biological functions. We present a means to calculate pressure and surface tension in a 3D-resolved manner within molecular-dynamics simulations and show how such measurements can yield important insight. We also present the first corrections to local virial and pressure fields to account for the constraints typically used in lipid simulations that otherwise cause problems in highly oriented systems such as bilayers. Based on simulations of an asymmetric bacterial ion channel in a POPC bilayer, we demonstrate how 3D-resolved pressure can probe for both short-range and long-range effects from the protein on the membrane environment. We also show how surface tension is a sensitive metric for inter-leaflet equilibrium and can be used to detect even subtle imbalances between bilayer leaflets in a membrane-protein simulation. Since surface tension is known to modulate the function of many proteins, this effect is an important consideration for predictions of ion channel function. We outline a strategy by which our local pressure measurements, which we make available within a version of the GROMACS simulation package, may be used to design optimally equilibrated membrane-protein simulations.
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Affiliation(s)
- Peter M Kasson
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 29908, USA.
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30
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de Wijn AS, Hess B, Fine BV. Largest Lyapunov exponents for lattices of interacting classical spins. Phys Rev Lett 2012; 109:034101. [PMID: 22861854 DOI: 10.1103/physrevlett.109.034101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Indexed: 06/01/2023]
Abstract
We investigate how generic the onset of chaos in interacting many-body classical systems is in the context of lattices of classical spins with nearest-neighbor anisotropic couplings. Seven large lattices in different spatial dimensions were considered. For each lattice, more than 2000 largest Lyapunov exponents for randomly sampled Hamiltonians were numerically computed. Our results strongly suggest the absence of integrable nearest-neighbor Hamiltonians for the infinite lattices except for the trivial Ising case. In the vicinity of the Ising case, the largest Lyapunov exponents exhibit a power-law growth, while further away they become rather weakly sensitive to the Hamiltonian anisotropy. We also provide an analytical derivation of these results.
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Affiliation(s)
- A S de Wijn
- Department of Physics, Stockholm University, 106 91 Stockholm, Sweden.
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31
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Schwaiger CS, Börjesson SI, Hess B, Elinder F, Lindahl E. Phe233 in the Voltage-Sensor is Rate Limiting for Channel Closure but not for the Opening. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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32
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Abstract
This paper presents a finite element (FE) model to identify parameters that affect the performance of an improved cancellous bone screw fixation technique, and hence potentially improve fracture treatment. In cancellous bone of low apparent density, it can be difficult to achieve adequate screw fixation and hence provide stable fracture fixation that enables bone healing. Data from predictive FE models indicate that cements can have a significant potential to improve screw holding power in cancellous bone. These FE models are used to demonstrate the key parameters that determine pull-out strength in a variety of screw, bone and cement set-ups, and to compare the effectiveness of different configurations. The paper concludes that significant advantages, up to an order of magnitude, in screw pull-out strength in cancellous bone might be gained by the appropriate use of a currently approved calcium phosphate cement.
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Affiliation(s)
- C J Brown
- School of Engineering and Design, Brunel University, Uxbridge, UB8 3PH, UK.
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33
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Abstract
SHAKE is a widely used algorithm to impose general holonomic constraints during molecular simulations. By imposing constraints on stiff degrees of freedom that require integration with small time steps (without the constraints) we are able to calculate trajectories with time steps larger by approximately a factor of two. The larger time step makes it possible to run longer simulations. Another approach to extend the scope of Molecular Dynamics is parallelization. Parallelization speeds up the calculation of the forces between the atoms and makes it possible to compute longer trajectories with better statistics for thermodynamic and kinetic averages. A combination of SHAKE and parallelism is therefore highly desired. Unfortunately, the most widely used SHAKE algorithm (of bond relaxation) is inappropriate for parallelization and alternatives are needed. The alternatives must minimize communication, lead to good load balancing, and offer significantly better performance than the bond relaxation approach. The algorithm should also scale with the number of processors. We describe the theory behind different implementations of constrained dynamics on parallel systems, and their implementation on common architectures.
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Affiliation(s)
- Ron Elber
- Institute for Computational Engineering and Sciences, Department of Chemistry and Biochemistry, University of Texas at Austin, TX 78712, USA
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34
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Choi HJ, Lim JS, Park EJ, Jung HJ, Lee YJ, Kwon TH, Cesar KR, Araujo M, de Braganca AC, Magaldi AJ, Freisinger W, Ditting T, Heinlein S, Schatz J, Veelken R, Burki R, Mohebbi N, Wang X, Serra A, Wagner C, Ditting T, Freisinger W, Rodionova K, Heinlein S, Schmieder R, Veelken R, Yano Y, Kudo LH, Magaldi AJ, Choi HJ, Yoon YJ, Lim JS, Hwang GS, Kwon TH, Jo CH, Kim S, Park JS, Lee CH, Kang CM, Kim GH, Kokeny G, Szoleczky P, Fang L, Rosivall L, Mozes MM, Freisinger W, Schatz J, Lampert A, Ditting T, Veelken R, Yano Y, Magaldi AJ, LEE WC, Wang YC, Chen JB, Santos C, Gomes AM, Ventura A, Almeida C, Seabra J, Daher E, Leite de Figueiredo P, Montenegro R, Montenegro R, Martins M, Bezerra da Silva G, Liborio A, Sromicki J, Matter S, Sitzmann K, Hess B, Lee J, Kim S, Lee JW, Oh YK, Na KY, Joo KW, Earm JH, Han JS, Ninchoji T, Kaito H, Nozu K, Hashimura Y, Nakanishi K, Yoshikawa N, Iijima K, Matsuo M, Gorini A, Addesse R, Comegna C, Galderisi C, Cecilia A, Tomaselli M, Di Lullo L, Polito P. Acid-base/Na, K, Cl. Experimental and clinical. Clin Kidney J 2011. [DOI: 10.1093/ndtplus/4.s2.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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35
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Affiliation(s)
- David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Berk Hess
- Center for Biomembrane Research, Stockholm University, Stockholm, Sweden
- Department of Theoretical Physics and Swedish e‐Science Research Center, Royal Institute of Technology, Albanova University Center, Stockholm, Sweden
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36
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Ganguly P, Schravendijk P, Hess B, van der Vegt NFA. Ion Pairing in Aqueous Electrolyte Solutions with Biologically Relevant Anions. J Phys Chem B 2011; 115:3734-9. [DOI: 10.1021/jp201150q] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Schwaiger C, Bjelkmar P, Hess B, Lindahl E. 3₁₀-helix conformation facilitates the transition of a voltage sensor S4 segment toward the down state. Biophys J 2011; 100:1446-54. [PMID: 21402026 PMCID: PMC3059565 DOI: 10.1016/j.bpj.2011.02.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 12/20/2010] [Accepted: 02/02/2011] [Indexed: 10/18/2022] Open
Abstract
The activation of voltage-gated ion channels is controlled by the S4 helix, with arginines every third residue. The x-ray structures are believed to reflect an open-inactivated state, and models propose combinations of translation, rotation, and tilt to reach the resting state. Recently, experiments and simulations have independently observed occurrence of 3(10)-helix in S4. This suggests S4 might make a transition from α- to 3(10)-helix in the gating process. Here, we show 3(10)-helix structure between Q1 and R3 in the S4 segment of a voltage sensor appears to facilitate the early stage of the motion toward a down state. We use multiple microsecond-steered molecular simulations to calculate the work required for translating S4 both as α-helix and transformed to 3(10)-helix. The barrier appears to be caused by salt-bridge reformation simultaneous to R4 passing the F233 hydrophobic lock, and it is almost a factor-two lower with 3(10)-helix. The latter facilitates translation because R2/R3 line up to face E183/E226, which reduces the requirement to rotate S4. This is also reflected in a lower root mean-square deviation distortion of the rest of the voltage sensor. This supports the 3(10) hypothesis, and could explain some of the differences between the open-inactivated- versus activated-states.
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Affiliation(s)
| | | | | | - Erik Lindahl
- Theoretical and Computational Biophysics, Department of Theoretical Physics and Swedish e-Science Research Center, Royal Institute of Technology, Stockholm, Sweden
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38
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Abstract
Renal colic is generated by hyperperistalsis of the obstructed ureter. Peristalsis is modulated by (among others) alpha-receptors (contraction), beta-receptors (relaxation) and prostaglandins (PG F2alpha: contraction, PG E1/E2: relaxation). Non-steroidal anti-inflammatory drugs (NSAID) are highly effective in pain relief and should always be given in the absence of contraindications. The same is true for metamizole, whereas Buscopan® is not superior to placebo. For most severe pain, opioids are indicated. alpha-blockers and calcium channel blockers dilate the distal ureter and increase the likelihood of spontaneous stone passage by up to 65%. Overhydration of patients has no advantage, but carries the risk of pelvic rupture with urine extravasation and infection. Stones of/above diameter 7 mm are unlikely to pass spontaneously and should be interventionally removed.
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Affiliation(s)
- B Hess
- Innere Medizin und Nephrologie/Hypertonie, Klinik im Park, Zürich.
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39
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Affiliation(s)
- Per Larsson
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm Sweden
| | - Berk Hess
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm Sweden
| | - Erik Lindahl
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm Sweden
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40
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Affiliation(s)
- Ozge Engin
- College of Engineering, Koc University, Istanbul, Turkey, Max-Planck Institute for Polymer Research, D-55128, Mainz, Germany, Karolinska Institutet, SE-14157, Huddinge, Sweden, Stockholm Center for Biomembrane Research, Stockholm University, SE-10691 Stockholm, Sweden, and Center of Smart Interfaces, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Alessandra Villa
- College of Engineering, Koc University, Istanbul, Turkey, Max-Planck Institute for Polymer Research, D-55128, Mainz, Germany, Karolinska Institutet, SE-14157, Huddinge, Sweden, Stockholm Center for Biomembrane Research, Stockholm University, SE-10691 Stockholm, Sweden, and Center of Smart Interfaces, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Mehmet Sayar
- College of Engineering, Koc University, Istanbul, Turkey, Max-Planck Institute for Polymer Research, D-55128, Mainz, Germany, Karolinska Institutet, SE-14157, Huddinge, Sweden, Stockholm Center for Biomembrane Research, Stockholm University, SE-10691 Stockholm, Sweden, and Center of Smart Interfaces, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Berk Hess
- College of Engineering, Koc University, Istanbul, Turkey, Max-Planck Institute for Polymer Research, D-55128, Mainz, Germany, Karolinska Institutet, SE-14157, Huddinge, Sweden, Stockholm Center for Biomembrane Research, Stockholm University, SE-10691 Stockholm, Sweden, and Center of Smart Interfaces, Technical University of Darmstadt, D-64287 Darmstadt, Germany
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41
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Abstract
The quantitative structure of the core of the spiral-shaped traveling wave of chemical activity appearing in a thin excitable layer of the Belousov-Zhabotinskii reaction, in which the oxidation and decarboxylation of malonic acid by bromate ions is catalyzed by ferroin, was analyzed experimentally. Light absorption by ferroin as the reduced reaction catalyst and indicator was measured by means of a video-and computer-based two-dimensional spectrophotometer with 10-micrometer spatial, 2-second temporal, and 256-digital units intensity resolution. The spiral core is a singular site (diameter, 30 micrometers or less) at which intensity modulations due to ferroin-ferriin distributions are at least ten times smaller than in the surrounding area of spiral propagation. Archimedian spirals were fitted to isoconcentration lines.
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42
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Abstract
The critical radius for the outward propagation of waves in an excitable solution of the Belousov-Zhabotinskii reaction was experimentally analyzed and found to be approximately 20 mum, being in a range predicted by theory. Thus, the wave initiation depends on the critical radius in an all-or-none fashion. For waves having high positive curvature of wave fronts, a linear relationship between the curvature and their normal velocity was established, allowing computation of a diffusion coefficient of 1.9 x 10(-5) cm(2)/s for the autocatalytic species, which agrees well with results previously obtained for negatively curved wave fronts. The analysis of the dispersion of wave velocity yielded the decrease of wave velocity for small initiation periods as predicted theoretically.
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Affiliation(s)
- P Foerster
- Max-Planck-Institut für Ernährungsphysiologie, Rheinlanddamm 201, D-4600 Dortmund 1, Federal Republic of Germany
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43
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Abstract
A glycolytic model system consisting of the enzymes phosphofructokinase (EC 2.7.1.11) and pyruvate kinase (EC 2.7.1.40) is analyzed when subject to periodic substrate addition. The calculations are performed by using detailed rate laws that have been derived for the enzymes of Escherichia coli. Due to linear relationships between the metabolite concentrations, the numerical solutions can be displayed inside a trapezium, so that the concentrations of four different metabolites are indicated along the trapezium edges. The analysis reveals a rich variety of time patterns, corresponding to different periodic, quasiperiodic, and chaotic attractors. These patterns undergo complex hysteresis loops when bifurcation parameters are slowly changed-for example, by modulating the input amplitude. By using this technique up to four attractors coexisting in phase space are found. The time patterns corresponding to coexisting attractors can be switched into one another by triggering the system with short substrate pulses. Furthermore, conditions exist at which the triggering is autonomous-i.e., self-sustained (intermittent) switchings occur. The time between these switchings can be set externally by the value of the input amplitude. For conditions in which the periods of the oscillations are in the order of minutes, the self-sustained switching-which modulates these oscillations-can be in the order of hours.
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Affiliation(s)
- M Markus
- Max-Planck-Institut für Ernährungsphysiologie, Rheinlanddamm 201, 4600 Dortmund, Federal Republic of Germany
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44
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Abstract
The adsorption of bacteriorhodopsin(bR)-containing purple membranes (PM) to black lipid membranes (BLM) was used to study the charge translocation kinetics of bR upon flash excitation.The discharge of the PM-BLM system after charging upon illumination is found to proceed quite slowly (discharge time up to several minutes) but is considerably accelerated by addition of the protonophore FCCP.Therefore, the dependence of the proton transfer kinetics in bR on electrical potentials generated by preceding flashes of varying repetition rate and intensity was investigated. The kinetics are slowed down with increasing flash intensity as well as repetition rate. This effect is partly abolished by small amounts of FCCP.A new model is introduced which takes into account the instantaneous feedback of the electrical potential on the kinetics of the pump current. It explains the observed deviations from first-order kinetics and renders an approach with "distributed kinetics" unnecessary.
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Affiliation(s)
- C Kleinschmidt
- Max-Planck-Institut für Ernährungsphysiologie, Rheinlanddamm 201, D-4600 Dortmund 1, Federal Republic of Germany
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45
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46
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Abstract
Chain packing in homogeneous blends of carbonate (13)C-labeled bisphenol A polycarbonate with either (i) CF(3)-labeled bisphenol A polycarbonate or (ii) ring-F-labeled bisphenol A polycarbonate has been characterized using (13)C{(19)F} rotational-echo double-resonance (REDOR) nuclear magnetic resonance. In both blends, the (13)C observed spin was at high concentration, and the (19)F dephasing or probe spin was at low concentration. In this situation, an analysis in terms of a distribution of isolated heteronuclear pairs of spins is valid. Nearest-neighbor separation of (13)C and (19)F labels was determined by accurately mapping the initial dipolar evolution using a shifted-pulse version of REDOR. Based on the results of this experiment, the average distance from a ring-fluorine to the nearest (13)C=O is more than 1.2 A greater than the corresponding CF(3)-(13)C=O distance. Next-nearest and more-distant-neighbor separations of labels were measured in a 416-rotor-cycle constant-time version of REDOR for both blends. Statistically significant local order was established for the nearest-neighbor labels in the methyl-labeled blend. These interchain packing results are in qualitative agreement with predictions based on coarse-grained simulations of a specially adapted model for bisphenol A polycarbonate. The model itself has been previously used to determine static and dynamic properties of polycarbonate with results in good agreement with those from rheological and neutron scattering experiments.
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Affiliation(s)
- Dirk Stueber
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
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Bjelkmar P, Larsson P, Cuendet MA, Hess B, Lindahl E. Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models. J Chem Theory Comput 2010; 6:459-66. [PMID: 26617301 DOI: 10.1021/ct900549r] [Citation(s) in RCA: 720] [Impact Index Per Article: 51.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CHARMM27 is a widespread and popular force field for biomolecular simulation, and several recent algorithms such as implicit solvent models have been developed specifically for it. We have here implemented the CHARMM force field and all necessary extended functional forms in the GROMACS molecular simulation package, to make CHARMM-specific features available and to test them in combination with techniques for extended time steps, to make all major force fields available for comparison studies in GROMACS, and to test various solvent model optimizations, in particular the effect of Lennard-Jones interactions on hydrogens. The implementation has full support both for CHARMM-specific features such as multiple potentials over the same dihedral angle and the grid-based energy correction map on the ϕ, ψ protein backbone dihedrals, as well as all GROMACS features such as virtual hydrogen interaction sites that enable 5 fs time steps. The medium-to-long time effects of both the correction maps and virtual sites have been tested by performing a series of 100 ns simulations using different models for water representation, including comparisons between CHARMM and traditional TIP3P. Including the correction maps improves sampling of near native-state conformations in our systems, and to some extent it is even able to refine distorted protein conformations. Finally, we show that this accuracy is largely maintained with a new implicit solvent implementation that works with virtual interaction sites, which enables performance in excess of 250 ns/day for a 900-atom protein on a quad-core desktop computer.
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Affiliation(s)
- Pär Bjelkmar
- Center for Biomembrane Research, Department of Biochemistry & Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, and Molecular Modeling Group, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Per Larsson
- Center for Biomembrane Research, Department of Biochemistry & Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, and Molecular Modeling Group, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Michel A Cuendet
- Center for Biomembrane Research, Department of Biochemistry & Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, and Molecular Modeling Group, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Berk Hess
- Center for Biomembrane Research, Department of Biochemistry & Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, and Molecular Modeling Group, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Erik Lindahl
- Center for Biomembrane Research, Department of Biochemistry & Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, and Molecular Modeling Group, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
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Schwaiger CS, Bjelkmar P, Hess B, Lindahl E. Structural Transition from Alpha- to 3_10-Helix Reduces the Free Energy Required for S4 Translation in Kv1.2/2.1 Voltage Sensors, and F233 Appears to Responsible for the Gating Barrier. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.2827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Finking G, Hess B, Hanke H. The value of phytoestrogens as a possible therapeutic option in postmenopausal women with coronary heart disease. J OBSTET GYNAECOL 2009; 19:455-9. [PMID: 15512363 DOI: 10.1080/01443619964184] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Large epidemiological studies have proved that the risk of coronary heart disease in postmenopausal women can be decreased by oestrogen replacement therapy. The effect is triggered by metabolic processes in the liver (decrease of LDL-cholesterol, increase of HDL-cholesterol) as well as by direct impact on the arterial wall (anti-oxidation, relaxation, anti-proliferation). The therapeutical usage of oestrogens is limited by an increased incidence of breast and endometrial cancer. Cyclic application of progestogens virtually eliminates the risk. Unfortunately, progestogens may antagonise the atheroprotective effect of oestrogens. Structurally modified oestrogens as well as selective oestrogen receptor modulators were investigated in clinical trials. They might provide the desired atheroprotective effects of oestrogen without negative side effects on the mammary gland or the endometrium. In this respect isoflavones also known as phytoestrogens, were analysed. They are widespread and occur naturally in many plants, especially in soy products. Cell culture and animal experiments as well as clinical studies revealed that phytoestrogens such as genistein and daidzein act atheroprotectively in the same way as oestrogen. Effects on the mammary gland or the endometrium could not be detected, but positive side effects on the bone metabolism and the decrease of certain types of cancer could be observed. In total, the therapeutical application of phytoestrogens in postmenopausal women seems to be of real and great benefit. We conclude that in women the risk of death from coronary heart disease increases after the onset of menopause. Recently discovered properties of phyto-oestrogens seem to be of great benefit as they do not seem to have any side effects on the mammary gland and the endometrium which are limiting factors for oestrogen replacement therapy.
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Affiliation(s)
- G Finking
- Division of Cardiology, University of Ulm, Germany.
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