Two Algorithms Designed for Realizing Efficient Combination of Fast Multipole Method and Dedicated Hardware for Molecular Dynamics Simulations

Amisaki, Takashi; Toyoda, Shinjiro; Miyagawa, Hiroh; Kïtamura, Kazuo

doi:10.2477/jccj.1.73

Cited by 3 publications

(2 citation statements)

References 11 publications

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“…The van der Waals and electrostatic interactions were calculated using a MD Engine II PC (NEC Corporation, Japan), a computer designed for MD calculation. The electrostatic interactions of all atom pairs were calculated without using the cut‐off method 26. A cut‐off distance of 15 Å was applied to evaluate the van der Waals interactions.…”

Section: Methodsmentioning

confidence: 99%

Roles of conserved basic amino acid residues and activation mechanism of the hyperthermophilic aspartate racemase at high temperature

et al. 2006

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X-ray crystallography has revealed two similar alpha/beta domains of the aspartate racemase from the hyperthermophilic archaeon, Pyrococcus horikoshii OT3. The active site is located in the cleft between the two domains where two cysteine residues face each other. This arrangement allows the substrate to enter the cleft and enables the two cysteine residues to act synergistically. However, the distance between their thiolates was estimated to be 9.6 angstroms, which is beyond the distance for cooperative action of them. We examined the molecular mechanism for the racemization reaction of this hyperthermophilic aspartate racemase by mutational analyses and molecular dynamics simulations. The mutational analyses revealed that Arg48 and Lys164 were essential for catalysis in addition to the putative catalytic cysteine residues. The molecular dynamics simulations revealed that the distance between the two active gamma-sulfur atoms of cysteine residues oscillate to periodically become shorter than the predicted cooperative distance at high temperature. In addition, the conformation of Tyr160, which is located at the entrance of the cleft and inhibits the entry of a substrate, changes periodically to open the entrance at 375 K. The opening of the gate is likely to be induced by the motion of the adjacent amino acid, Lys164. The entrance of an aspartate molecule was observed by molecular dynamics (MD) simulations driven by the force of the electrostatic interaction with Arg48, Lys164, and also Asp47. These results provide insights into the roles of amino acid residues at the catalytic site and also the activation mechanism of a hyperthermophilic aspartate racemase at high temperature.

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Section: Methodsmentioning

confidence: 99%

Roles of conserved basic amino acid residues and activation mechanism of the hyperthermophilic aspartate racemase at high temperature

et al. 2006

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“…The van der Waals and electrostatic interactions were calculated using the MD Server (NEC Corporation, Japan), a computer designed for MD calculation. 23 A cutoff distance of 1000 Å was applied to evaluate the van der Waals and electrostatic interactions. The potential energy minimization of the initial MD system was carried out using the conjugated gradient method.…”

Section: Preliminary Modeling Of the Phpfd Complex With Nonnative Insmentioning

confidence: 99%

Structure and Molecular Dynamics Simulation of Archaeal Prefoldin: The Molecular Mechanism for Binding and Recognition of Nonnative Substrate Proteins

Ohtaki

Kida

Miyata

et al. 2008

Journal of Molecular Biology

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Functionally relevant protein motions: Extracting basin-specific collective coordinates from molecular dynamics trajectories

Pan

Dickson

Gordon

et al. 2005

The Journal of Chemical Physics

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Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fluctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-C(alpha) distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein's known active sites and experimentally determined mobile regions.

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Two Algorithms Designed for Realizing Efficient Combination of Fast Multipole Method and Dedicated Hardware for Molecular Dynamics Simulations

Cited by 3 publications

References 11 publications

Roles of conserved basic amino acid residues and activation mechanism of the hyperthermophilic aspartate racemase at high temperature

Roles of conserved basic amino acid residues and activation mechanism of the hyperthermophilic aspartate racemase at high temperature

Structure and Molecular Dynamics Simulation of Archaeal Prefoldin: The Molecular Mechanism for Binding and Recognition of Nonnative Substrate Proteins

Functionally relevant protein motions: Extracting basin-specific collective coordinates from molecular dynamics trajectories

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