Multicanonical algorithms for first order phase transitions

Berg, Bernd A.; Neuhaus, T.

doi:10.1016/0370-2693(91)91256-u

Cited by 1,175 publications

(1,128 citation statements)

References 8 publications

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“…Several methods are available to study chemical reactions, including static quantum approaches or even advanced sampling techniques, e.g., umbrella sampling [21], metadynamics [22][23][24], and parallel tempering [25]. In this work, the reaction mechanism was explored using the static quantum approach [26].…”

Section: Theoretical Calculationsmentioning

confidence: 99%

The mechanism of formate oxidation by metal-dependent formate dehydrogenases

et al. 2011

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Metal-dependent formate dehydrogenases (Fdh) from prokaryotic organisms are members of the dimethyl sulfoxide reductase family of mononuclear molybdenum-containing and tungsten-containing enzymes. Fdhs catalyze the oxidation of the formate anion to carbon dioxide in a redox reaction that involves the transfer of two electrons from the substrate to the active site. The active site in the oxidized state comprises a hexacoordinated molybdenum or tungsten ion in a distorted trigonal prismatic geometry. Using this structural model, we calculated the catalytic mechanism of Fdh through density functional theory tools. The simulated mechanism was correlated with the experimental kinetic properties of three different Fdhs isolated from three different Desulfovibrio species. Our studies indicate that the C-H bond break is an event involved in the rate-limiting step of the catalytic cycle. The role in catalysis of conserved amino acid residues involved in metal coordination and near the metal active site is discussed on the basis of experimental and theoretical results.

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Section: Theoretical Calculationsmentioning

confidence: 99%

The mechanism of formate oxidation by metal-dependent formate dehydrogenases

et al. 2011

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“…A number of methods, such as multicanonical ensemble, 22,23 simulated tempering, 24,25 and the replica exchange method (REM), [26][27][28][29] were designed to address this issue. The REM was proposed 26,30 in the context of Ising spin glasses 31 and introduced to proteinlike systems by Sugita and Okamoto.…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics of Apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations

2006

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A large domain motion in adenylate kinase from E. coli (AKE) is studied with molecular dynamics. AKE undergoes a large-scale rearrangement of its lid and AMP-binding domains when the open form closes over its substrates, AMP, and Mg 2+ -ATP, whereby the AMP-binding and lid domains come closer to the core. The third domain, the core, is relatively stable during this motion. A reaction coordinate that monitors the distance between the AMP-binding and core domains is selected to be able to compare with the results of energy transfer experiments. Sampling along this reaction coordinate is carried out by using a distance replica exchange method (DREM), where systems that differ by a restraint potential enforcing different reaction coordinate values are independently simulated with periodic attempts at exchange of these systems. Several methods are used to study the efficiency and convergence properties of the DREM simulation and compared with an analogous non-DREM simulation. The DREM greatly accelerates the rate and extent of configurational sampling and leads to equilibrium sampling as measured by monitoring collective modes obtained from a principal coordinate analysis. The potential of mean force along the reaction coordinate reveals a rather flat region for distances from the open to a relatively closed AKE conformation. The potential of mean force for smaller distances has a distinct minimum that is quite close to that found in the closed form X-ray structure. In concert with a decrease in the reaction coordinate distance (AMP-binding-to-core distance) the lid-to-core distance of AKE also decreases. Therefore, apo AKE can fluctuate from its open form to conformations that are quite similar to its closed form X-ray structure, even in the absence of its substrates.

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“…[23]. Multicanonical ensemble is based on a probability function in which different energies are equally probable [24]. Multicanonical weights ω(E) ∼ 1/n(E), where n(E) is the density of states, are unknown and calculated at the first stage of the simulation by an iterative procedure.…”

Section: Methodsmentioning

confidence: 99%

Secondary structure prediction of beta-hairpin peptide tryptophan zipper-I

Gökoğlu

Çelik

2008

Physica A: Statistical Mechanics and its Applications

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We have investigated the folding properties of tryptophan zipper-I molecule which folds into a stable β-hairpin motif in aqueous solution as suggested by nuclear magnetic resonance (NMR) experiments. An all-atom presentation, including hydrogen, was used with an implicit solvent. As a simulation technique, simulated tempering algorithm was used to obtain equilibrium conformations of the molecule at ten distinct temperatures. Our minimum energy configuration obtained from simulated tempering algorithm is a β-hairpin motif with 1.30Å backbone root-mean-square deviation from the reference PDB structure (1le0.pdb). Several quantities and exhaustive folding free energy landscapes were determined and discussed in order to clarify the folding behavior.

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Multicanonical algorithms for first order phase transitions

Cited by 1,175 publications

References 8 publications

The mechanism of formate oxidation by metal-dependent formate dehydrogenases

The mechanism of formate oxidation by metal-dependent formate dehydrogenases

Molecular Dynamics of Apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations

Secondary structure prediction of beta-hairpin peptide tryptophan zipper-I

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