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Article ; Online: Chemical potentials of alkaline earth metal halide aqueous electrolytes and solubility of their hydrates by molecular simulation: Application to CaCl

Moučka, Filip / Kolafa, Jiří / Lísal, Martin / Smith, William R

2018 Volume 148, Issue 22, Page(s) 222832

Abstract: We present a molecular-level simulation study of ... ...

Abstract	We present a molecular-level simulation study of CaCl
Language	English
Publishing date	2018-06-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/1.5024212
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Article ; Online: Review. Proton-coupled gating in chloride channels.

Lísal, Jirí / Maduke, Merritt

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2009 Volume 364, Issue 1514, Page(s) 181–187

Abstract: The physiologically indispensable chloride channel (CLC) family is split into two classes of membrane proteins: chloride channels and chloride/proton antiporters. In this article we focus on the relationship between these two groups and specifically ... ...

Abstract	The physiologically indispensable chloride channel (CLC) family is split into two classes of membrane proteins: chloride channels and chloride/proton antiporters. In this article we focus on the relationship between these two groups and specifically review the role of protons in chloride-channel gating. Moreover, we discuss the evidence for proton transport through the chloride channels and explore the possible pathways that the protons could take through the chloride channels. We present results of a mutagenesis study, suggesting the feasibility of one of the pathways, which is closely related to the proton pathway proposed previously for the chloride/proton antiporters. We conclude that the two groups of CLC proteins, although in principle very different, employ similar mechanisms and pathways for ion transport.
MeSH term(s)	Chloride Channels/metabolism ; Chlorides/metabolism ; Ion Channel Gating/physiology ; Protons
Chemical Substances	Chloride Channels ; Chlorides ; Protons
Language	English
Publishing date	2009-01-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2008.0123
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Article ; Online: The ClC-0 chloride channel is a 'broken' Cl-/H+ antiporter.

Lísal, Jirí / Maduke, Merritt

Nature structural & molecular biology

2008 Volume 15, Issue 8, Page(s) 805–810

Abstract: Ion channels have historically been viewed as distinct from secondary active transporters. However, the recent discovery that the CLC 'chloride channel' family is made up of both channels and active transporters has led to the hypothesis that the ion- ... ...

Abstract	Ion channels have historically been viewed as distinct from secondary active transporters. However, the recent discovery that the CLC 'chloride channel' family is made up of both channels and active transporters has led to the hypothesis that the ion-transport mechanisms of these two types of membrane proteins may be similar. Here we use single-channel analysis to demonstrate that ClC-0 channel gating (opening and closing) involves the transmembrane movement of protons. This result indicates that ClC-0 is a 'broken' Cl(-)/H(+) antiporter in which one of the conformational states has become leaky for chloride ions. This finding clarifies the evolutionary relationship between the channels and transporters and conveys that similar mechanisms and analogous protein movements are used by both.
MeSH term(s)	Animals ; Biological Transport ; Cell Membrane/metabolism ; Chloride Channels/chemistry ; Chloride Channels/metabolism ; Chlorides/chemistry ; Electric Conductivity ; Electrochemistry ; Ions ; Membrane Proteins/chemistry ; Molecular Conformation ; Oocytes/metabolism ; Protons ; Thermodynamics ; Torpedo ; Xenopus laevis
Chemical Substances	Chloride Channels ; Chlorides ; Ions ; Membrane Proteins ; Protons
Language	English
Publishing date	2008-07-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/nsmb.1466
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Article: Time-Reversible Velocity Predictors for Verlet Integration with Velocity-Dependent Right-Hand Side.

Kolafa, Jiří / Lísal, Martin

Journal of chemical theory and computation

2011 Volume 7, Issue 11, Page(s) 3596–3607

Abstract: Time-reversible velocity predictors (TRVPs) with increasing orders of the time-reversibility error are developed to be used with the Verlet integrator for equations of motion with the right-hand side depending on velocities. The method performs outside a ...

Abstract	Time-reversible velocity predictors (TRVPs) with increasing orders of the time-reversibility error are developed to be used with the Verlet integrator for equations of motion with the right-hand side depending on velocities. The method performs outside a possible SHAKE algorithm to constrain bond lengths and does not require repeated SHAKE iterations nor RATTLE. We have tested the TRVPs with the Nosé-Hoover thermostat on four model systems (coupled harmonic and anharmonic oscillators, liquid argon, SPC/E water, and a small peptide), comparing them to the Gear integrator with the Lagrangian formulation of constraint dynamics, the Martyna, Tuckerman, Tobias, and Klein (MTTK) method, and the velocity iteration method. The TRVP method performs similarly to the iteration method. In addition, we discuss three methodology improvements: (i) We tested several formulas for the kinetic energy compatible with the Verlet/SHAKE algorithm and found that the leapfrog velocities are usually the best; (ii) we proposed two modifications of the MTTK method; and (iii) we suggest that thermostats directly controlling the translational kinetic temperature may give more accurate values of some thermodynamic quantities.
Language	English
Publishing date	2011-11-08
Publishing country	United States
Document type	Journal Article
ISSN	1549-9618
ISSN	1549-9618
DOI	10.1021/ct200108g
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Article: Cooperative mechanism of RNA packaging motor.

Lísal, Jirí / Tuma, Roman

The Journal of biological chemistry

2005 Volume 280, Issue 24, Page(s) 23157–23164

Abstract: P4 is a hexameric ATPase that serves as the RNA packaging motor in double-stranded RNA bacteriophages from the Cystoviridae family. P4 shares sequence and structural similarities with hexameric helicases. A structure-based mechanism for mechano-chemical ... ...

Abstract	P4 is a hexameric ATPase that serves as the RNA packaging motor in double-stranded RNA bacteriophages from the Cystoviridae family. P4 shares sequence and structural similarities with hexameric helicases. A structure-based mechanism for mechano-chemical coupling has recently been proposed for P4 from bacteriophage phi12. However, coordination of ATP hydrolysis among the subunits and coupling with RNA translocation remains elusive. Here we present detailed kinetic study of nucleotide binding, hydrolysis, and product release by phi12 P4 in the presence of different RNA and DNA substrates. Whereas binding affinities for ATP and ADP are not affected by RNA binding, the hydrolysis step is accelerated and the apparent cooperativity is increased. No nucleotide binding cooperativity is observed. We propose a stochastic-sequential cooperativity model to describe the coordination of ATP hydrolysis within the hexamer. In this model the apparent cooperativity is a result of hydrolysis stimulation by ATP and RNA binding to neighboring subunits rather than cooperative nucleotide binding. The translocation step appears coupled to hydrolysis, which is coordinated among three neighboring subunits. Simultaneous interaction of neighboring subunits with RNA makes the otherwise random hydrolysis sequential and processive.
MeSH term(s)	Adenosine Diphosphate/chemistry ; Adenosine Triphosphatases/chemistry ; Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/chemistry ; Bacteriophages/chemistry ; Binding, Competitive ; Biological Transport ; Dose-Response Relationship, Drug ; Escherichia coli/metabolism ; Hydrolysis ; Kinetics ; Macromolecular Substances/chemistry ; Models, Biological ; Nucleotides/chemistry ; Phosphates/chemistry ; Protein Binding ; RNA/chemistry ; RNA Phages/chemistry ; RNA, Double-Stranded/metabolism ; RNA, Viral/genetics ; Stochastic Processes
Chemical Substances	Macromolecular Substances ; Nucleotides ; Phosphates ; RNA, Double-Stranded ; RNA, Viral ; Adenosine Diphosphate (61D2G4IYVH) ; RNA (63231-63-0) ; Adenosine Triphosphate (8L70Q75FXE) ; Adenosine Triphosphatases (EC 3.6.1.-)
Language	English
Publishing date	2005-04-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M502658200
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Article ; Online: Adsorption and Diffusion of C

Rezlerová, Eliška / Zukal, Arnošt / Čejka, Jiří / Siperstein, Flor R / Brennan, John K / Lísal, Martin

Langmuir : the ACS journal of surfaces and colloids

2017 Volume 33, Issue 42, Page(s) 11126–11137

Abstract: We employ grand canonical Monte Carlo and molecular dynamics simulations to systematically study the adsorption and diffusion of ... ...

Abstract	We employ grand canonical Monte Carlo and molecular dynamics simulations to systematically study the adsorption and diffusion of C
Language	English
Publishing date	2017--24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2005937-1
ISSN	1520-5827 ; 0743-7463
ISSN (online)	1520-5827
ISSN	0743-7463
DOI	10.1021/acs.langmuir.7b01772
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Article: Molecular simulations of aqueous electrolyte solubility: 1. The expanded-ensemble osmotic molecular dynamics method for the solution phase.

Lísal, Martin / Smith, William R / Kolafa, Jirí

The journal of physical chemistry. B

2005 Volume 109, Issue 26, Page(s) 12956–12965

Abstract: We have developed a molecular-level simulation technique called the expanded-ensemble osmotic molecular dynamics (EEOMD) method, for studying electrolyte solution systems. The EEOMD method performs simulations at a fixed number of solvent molecules, ... ...

Abstract	We have developed a molecular-level simulation technique called the expanded-ensemble osmotic molecular dynamics (EEOMD) method, for studying electrolyte solution systems. The EEOMD method performs simulations at a fixed number of solvent molecules, pressure, temperature, and overall electrolyte chemical potential. The method combines elements of constant pressure-constant temperature molecular dynamics and expanded-ensemble grand canonical Monte Carlo. The simulated electrolyte solution systems contain, in addition to solvent molecules, full and fractional ions and undissociated electrolyte molecular units. The fractional particles are coupled to the system via a coupling parameter that varies between 0 (no interaction between the fractional particle and the other particles in the system) and 1 (full interaction between the fractional particle and the other particles in the system). The time evolution of the system is governed by the constant pressure-constant temperature equations of motion and accompanied by random changes in the coupling parameter. The coupling-parameter changes are accepted with a probability derived from the expanded-ensemble osmotic partition function corresponding to the prescribed electrolyte chemical potential. The coupling-parameter changes mimic insertion/deletion of particles as in a crude grand canonical Monte Carlo simulation; if the coupling parameter becomes 0, the fractional particles disappear from the system, and as the coupling parameter reaches unity, the fractional particles become full particles. The method is demonstrated for a model of NaCl in water at ambient conditions. To test our approach, we first determine the chemical potential of NaCl in water by the thermodynamic integration technique and by the expanded-ensemble method. Then, we carry out EEOMD simulations for different specified values of the overall NaCl chemical potential and measure the concentration of ions resulting from the simulations. Both computations give consistent results, validating the EEOMD methodology.
Language	English
Publishing date	2005-07-07
Publishing country	United States
Document type	Journal Article
ISSN	1520-6106
ISSN	1520-6106
DOI	10.1021/jp0507492
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Article ; Online: Packaging motor from double-stranded RNA bacteriophage phi12 acts as an obligatory passive conduit during transcription.

Kainov, Denis E / Lísal, Jirí / Bamford, Dennis H / Tuma, Roman

Nucleic acids research

2004 Volume 32, Issue 12, Page(s) 3515–3521

Abstract: Double-stranded RNA viruses sequester their genomes within a protein shell, called the polymerase complex. Translocation of ssRNA into (packaging) and out (transcription) of the polymerase complex are essential steps in the life cycle of the dsRNA ... ...

Abstract	Double-stranded RNA viruses sequester their genomes within a protein shell, called the polymerase complex. Translocation of ssRNA into (packaging) and out (transcription) of the polymerase complex are essential steps in the life cycle of the dsRNA bacteriophages of the Cystoviridae family (phi6-phi14). Both processes require a viral molecular motor P4, an NTPase, which bears structural and functional similarities to hexameric helicases. In effect, switching between the packaging and the transcription mode requires the translocation direction of the P4 motor to reverse. However, the mechanism of the reversal remains elusive. Here we characterize the P4 protein from bacteriophage phi12 and exploit its purine nucleotide specificity to delineate P4 role in transcription. The results indicate that while P4 actively translocates RNA during packaging it acts as a passive conduit for RNA export. The directionality switching is accomplished via the regulation of P4 NTPase activity within the polymerase core.
MeSH term(s)	Bacteriophage phi 6/genetics ; Biological Transport ; Cystoviridae/enzymology ; Cystoviridae/genetics ; Cystoviridae/growth & development ; DNA-Directed RNA Polymerases/metabolism ; Molecular Motor Proteins/metabolism ; Nucleoside-Triphosphatase/metabolism ; RNA/metabolism ; RNA Helicases/metabolism ; RNA, Double-Stranded/genetics ; RNA, Double-Stranded/metabolism ; Transcription, Genetic ; Viral Proteins/metabolism ; Virus Assembly
Chemical Substances	Molecular Motor Proteins ; RNA, Double-Stranded ; Viral Proteins ; RNA (63231-63-0) ; DNA-Directed RNA Polymerases (EC 2.7.7.6) ; Nucleoside-Triphosphatase (EC 3.6.1.15) ; RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2004
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205588-5
ISSN	1362-4962 ; 1746-8272 ; 0305-1048 ; 0261-3166
ISSN (online)	1362-4962 ; 1746-8272
ISSN	0305-1048 ; 0261-3166
DOI	10.1093/nar/gkh680
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Article ; Online: Molecular simulation of aqueous electrolyte solubility. 2. Osmotic ensemble Monte Carlo methodology for free energy and solubility calculations and application to NaCl.

Moučka, Filip / Lísal, Martin / Škvor, Jiří / Jirsák, Jan / Nezbeda, Ivo / Smith, William R

The journal of physical chemistry. B

2011 Volume 115, Issue 24, Page(s) 7849–7861

Abstract: We present a new and computationally efficient methodology using osmotic ensemble Monte Carlo (OEMC) simulation to calculate chemical potential-concentration curves and the solubility of aqueous electrolytes. The method avoids calculations for the solid ... ...

Abstract	We present a new and computationally efficient methodology using osmotic ensemble Monte Carlo (OEMC) simulation to calculate chemical potential-concentration curves and the solubility of aqueous electrolytes. The method avoids calculations for the solid phase, incorporating readily available data from thermochemical tables that are based on well-defined reference states. It performs simulations of the aqueous solution at a fixed number of water molecules, pressure, temperature, and specified overall electrolyte chemical potential. Insertion/deletion of ions to/from the system is implemented using fractional ions, which are coupled to the system via a coupling parameter λ that varies between 0 (no interaction between the fractional ions and the other particles in the system) and 1 (full interaction between the fractional ions and the other particles of the system). Transitions between λ-states are accepted with a probability following from the osmotic ensemble partition function. Biasing weights associated with the λ-states are used in order to efficiently realize transitions between them; these are determined by means of the Wang-Landau method. We also propose a novel scaling procedure for λ, which can be used for both nonpolarizable and polarizable models of aqueous electrolyte systems. The approach is readily extended to involve other solvents, multiple electrolytes, and species complexation reactions. The method is illustrated for NaCl, using SPC/E water and several force field models for NaCl from the literature, and the results are compared with experiment at ambient conditions. Good agreement is obtained for the chemical potential-concentration curve and the solubility prediction is reasonable. Future improvements to the predictions will require improved force field models.
MeSH term(s)	Electrolytes/chemistry ; Models, Molecular ; Monte Carlo Method ; Osmolar Concentration ; Pressure ; Sodium Chloride/chemistry ; Solubility ; Temperature ; Water/chemistry
Chemical Substances	Electrolytes ; Water (059QF0KO0R) ; Sodium Chloride (451W47IQ8X)
Language	English
Publishing date	2011-06-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/jp202054d
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Article: Functional visualization of viral molecular motor by hydrogen-deuterium exchange reveals transient states.

Lísal, Jirí / Lam, Tukiet T / Kainov, Denis E / Emmett, Mark R / Marshall, Alan G / Tuma, Roman

Nature structural & molecular biology

2005 Volume 12, Issue 5, Page(s) 460–466

Abstract: Molecular motors undergo cyclical conformational changes and convert chemical energy into mechanical work. The conformational dynamics of a viral packaging motor, the hexameric helicase P4 of dsRNA bacteriophage phi8, was visualized by hydrogen-deuterium ...

Abstract	Molecular motors undergo cyclical conformational changes and convert chemical energy into mechanical work. The conformational dynamics of a viral packaging motor, the hexameric helicase P4 of dsRNA bacteriophage phi8, was visualized by hydrogen-deuterium exchange and high-resolution mass spectrometry. Concerted changes of exchange kinetics revealed a cooperative unit that dynamically links ATP-binding sites and the central RNA-binding channel. The cooperative unit is compatible with a structure-based model in which translocation is mediated by a swiveling helix. Deuterium labeling also revealed the transition state associated with RNA loading, which proceeds via opening of the hexameric ring. The loading mechanism is similar to that of other hexameric helicases. Hydrogen-deuterium exchange provides an important link between time-resolved spectroscopic observations and high-resolution structural snapshots of molecular machines.
MeSH term(s)	Adenosine Triphosphate/metabolism ; Adenosine Triphosphate/pharmacology ; Binding Sites ; Deuterium Exchange Measurement ; Kinetics ; Models, Molecular ; Molecular Motor Proteins/chemistry ; Molecular Motor Proteins/genetics ; Molecular Motor Proteins/metabolism ; Mutation/genetics ; Nuclear Magnetic Resonance, Biomolecular ; Protein Structure, Quaternary/drug effects ; RNA/chemistry ; RNA/metabolism ; Viral Proteins/chemistry ; Viral Proteins/genetics ; Viral Proteins/metabolism
Chemical Substances	Molecular Motor Proteins ; Viral Proteins ; RNA (63231-63-0) ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2005-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/nsmb927
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