“Lomonosov”: Supercomputing at Moscow State University

Sadovnichy, Victor; Tikhonravov, Alexander V.; Voevodin, Vladimir V.; Opanasenko, V. V.

doi:10.1201/9781351104005-11

Cited by 207 publications

(132 citation statements)

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“…Molecular dynamics (MD) simulations were performed with the NAMD 2.11 program (Phillips et al, 2005) at the Lomonosov Moscow State University supercomputer (Sadovnichy et al, 2013b). During MD simulations, systems were maintained at a constant temperature of 298 K and under pressure of 1 atm (NPT ensemble) by using Langevin dynamics and Nose-Hoover barostat.…”

Section: Methodsmentioning

confidence: 99%

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Characterization of butyrylcholinesterase in bovine serum

Dafferner

Lushchekina

Masson

et al. 2017

Chemico-Biological Interactions

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Human butyrylcholinesterase (HuBChE) protects from nerve agent toxicity. Our goal was to determine whether bovine serum could be used as a source of BChE. Bovine BChE (BoBChE) was immunopurified from 100 mL fetal bovine serum (FBS) or 380 mL adult bovine serum by binding to immobilized monoclonal mAb2. Bound proteins were digested with trypsin and analyzed by liquid chromatography-tandem mass spectrometry. The results proved that FBS and adult bovine serum contain BoBChE. The concentration of BoBChE was estimated to be 0.04 μg/mL in FBS, and 0.03 μg/mL in adult bovine serum, values lower than the 4 μg/mL BChE in human serum. Nondenaturing gel electrophoresis showed that monoclonal mAb2 bound BoBChE but not bovine acetylcholinesterase (BoAChE) and confirmed that FBS contains BoBChE and BoAChE. Recombinant bovine BChE (rBoBChE) expressed in serum-free culture medium spontaneously reactivated from inhibition by chlorpyrifos oxon at a rate of 0.0023 min−1 (t1/2=301 min−1) and aged at a rate of 0.0138 min−1 (t1/2=50 min−1). Both BoBChE and HuBChE have 574 amino acids per subunit and 90% sequence identity. However, the apparent size of serum BoBChE and rBoBChE tetramers was much greater than the 340,000 Da of HuBChE tetramers. Whereas HuBChE tetramers include short polyproline rich peptides derived from lamellipodin, no polyproline peptides have been identified in BoBChE. We hypothesize that BoBChE tetramers use a large polyproline-rich protein to organize subunits into a tetramer and that the low concentration of BoBChE in serum is explained by limited quantities of an unidentified polyproline-rich protein.

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Section: Methodsmentioning

confidence: 99%

“…We thank the Supercomputing Center of Lomonosov Moscow State University for supercomputing time (Sadovnichy et al, 2013a). Mass spectra were obtained with the support of the Mass Spectrometry and Proteomics Core Facility at the University of Nebraska Medical Center.…”

mentioning

confidence: 99%

Characterization of butyrylcholinesterase in bovine serum

Dafferner

Lushchekina

Masson

et al. 2017

Chemico-Biological Interactions

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“…It is shown that the program is able to perform docking of a flexible ligand into the active site of the target protein taking mobility of assigned protein atoms into account: up to 157 degrees of freedom in the conformation space using about 9 h at 512 core of the Lomonosov supercomputer [73]. As far as we know this is the first time when the docking program is able to perform successfully the global energy minimum search in the conformational space with such a large dimensionality.…”

Section: Discussionmentioning

confidence: 99%

“…FLM performs exhaustive search of low energy local minima of protein-ligand complexes in the rigid protein and flexible ligand approximation performing massive parallel energy minima search and employing large computing resources (about 20,000 CPU ∗ h per one complex) available at supercomputer Lomonosov of Moscow State University [73].…”

Section: Methodsmentioning

confidence: 99%

Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms

Сулимов

Zheltkov

Oferkin³

et al. 2017

Computational and Structural Biotechnology Journal

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We present the novel docking algorithm based on the Tensor Train decomposition and the TT-Cross global optimization. The algorithm is applied to the docking problem with flexible ligand and moveable protein atoms. The energy of the protein-ligand complex is calculated in the frame of the MMFF94 force field in vacuum. The grid of precalculated energy potentials of probe ligand atoms in the field of the target protein atoms is not used. The energy of the protein-ligand complex for any given configuration is computed directly with the MMFF94 force field without any fitting parameters. The conformation space of the system coordinates is formed by translations and rotations of the ligand as a whole, by the ligand torsions and also by Cartesian coordinates of the selected target protein atoms. Mobility of protein and ligand atoms is taken into account in the docking process simultaneously and equally. The algorithm is realized in the novel parallel docking SOL-P program and results of its performance for a set of 30 protein-ligand complexes are presented. Dependence of the docking positioning accuracy is investigated as a function of parameters of the docking algorithm and the number of protein moveable atoms. It is shown that mobility of the protein atoms improves docking positioning accuracy. The SOL-P program is able to perform docking of a flexible ligand into the active site of the target protein with several dozens of protein moveable atoms: the native crystallized ligand pose is correctly found as the global energy minimum in the search space with 157 dimensions using 4700 CPU ∗ h at the Lomonosov supercomputer.

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“…43 We used the simulation resources of the Supercomputing Center of Lomonosov Moscow State University. 44 In MD simulation, the excluded volume between any two beads is interpreted in terms of a repulsion potential of the Lennard-Jones type,…”

Section: The Model and Simulation Techniquementioning

confidence: 99%

New strategy to create ultra-thin surface layer of grafted amphiphilic macromolecules

Lazutin

Govorun

Vasilevskaya

et al. 2015

The Journal of Chemical Physics

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It was found first that macromolecules made of amphiphilic monomer units could form spontaneously an ultra-thin layer on the surface which the macromolecules are grafted to. The width of such layer is about double size of monomer unit consisting of hydrophilic A (repulsive) and hydrophobic (attractive) B beads. The hydrophilic A beads are connected in a polymer chain while hydrophobic B beads are attached to A beads of the backbone as side groups. Three characteristic regimes are distinguished. At low grafting density, the macromolecules form ultra-thin micelles of the shape changing with decrease of distance d between grafting points as following: circular micelles-prolonged micelles-inverse micelles-homogeneous bilayer. Those micelles have approximately constant height and specific top-down A-BB-A structure. At higher grafting density, the micelles start to appear above the single bilayer of amphiphilic macromolecules. The thickness of grafted layer in these cases is different in different regions of grafting surface. Only at rather high density of grafting, the height of macromolecular layer becomes uniform over the whole grafting surface. The study was performed by computer modeling experiments and confirmed in framework of analytical theory.

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“Lomonosov”: Supercomputing at Moscow State University

Cited by 207 publications

References 0 publications

Characterization of butyrylcholinesterase in bovine serum

Characterization of butyrylcholinesterase in bovine serum

Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms

New strategy to create ultra-thin surface layer of grafted amphiphilic macromolecules

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