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Molecular dynamics simulation free energy

Tarak Karmakar, Sundaram Balasubramanian
Arylmalonate decarboxylase (AMDase) catalyzes the decarboxylation of α-aryl-α-methyl malonates to produce optically pure α-arylpropionates of industrial and medicinal importance. Herein, atomistic molecular dynamics simulations have been carried out to delineate the mechanism of the release of product molecules, phenylacetate (PAC) and carbon dioxide (CO2 ) from the wild-type (WT) and its G74C/C188S mutant enzymes. Both the product molecules follow a crystallographically characterized solvent-accessible channel to come out of the protein interior...
October 24, 2016: Journal of Physical Chemistry. B
Farzaneh Shayeganfar, Rouzbeh Shahsavari
Hydrogen storage capacities have been studied on newly designed three-dimensional pillared boron nitride (PBN) and pillared graphene boron nitride (PGBN). We propose these novel materials based on the covalent connection of BNNTs and graphene sheets, which enhance the surface and free volume for storage within the nanomaterial and increase the gravimetric and volumetric hydrogen uptake capacities. Density functional theory and molecular dynamic simulations show that these lithium- and oxygen-doped pillared structures have improved gravimetric and volumetric hydrogen capacities at room temperature, with values on the order of 9...
October 23, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Rafael Conceição de Souza, Gabriela de Medeiros Muniz, Andrei Santos Siqueira, Adonis de Melo Lima, Alessandra Pereira da Silva, Evonnildo Costa Gonçalves, João Lídio da Silva Gonçalves Vianez Júnior
Human immunodeficiency virus (HIV) infections continue to exert an enormous impact on global human health. This led experts to emphasize the importance of new measures for preventing HIV infections, including the development of vaccines and novel drugs. In this context, a promising approach involves the use of lectins that can bind the surface envelope glycoprotein gp120 of HIV with high affinity, preventing viral entry. The cyanobacterial lectin microvirin (MVN) has been proposed as a candidate for development as a topical microbicide because of its ability to bind to high mannose-type glycans, potently inhibiting HIV-1 entry...
November 2016: Journal of Molecular Modeling
Daniela Rupp, Leonie Flückiger, Marcus Adolph, Tais Gorkhover, Maria Krikunova, Jan Philippe Müller, Maria Müller, Tim Oelze, Yevheniy Ovcharenko, Benjamin Röben, Mario Sauppe, Sebastian Schorb, David Wolter, Rolf Mitzner, Michael Wöstmann, Sebastian Roling, Marion Harmand, Rolf Treusch, Mathias Arbeiter, Thomas Fennel, Christoph Bostedt, Thomas Möller
We studied the nanoplasma formation and explosion dynamics of single large xenon clusters in ultrashort, intense x-ray free-electron laser pulses via ion spectroscopy. The simultaneous measurement of single-shot diffraction images enabled a single-cluster analysis that is free from any averaging over the cluster size and laser intensity distributions. The measured charge state-resolved ion energy spectra show narrow distributions with peak positions that scale linearly with final ion charge state. These two distinct signatures are attributed to highly efficient recombination that eventually leads to the dominant formation of neutral atoms in the cluster...
October 7, 2016: Physical Review Letters
Jesús Ignacio Mendieta-Moreno, Daniel G Trabada, Jesus Mendieta, James P Lewis, Paulino Gómez-Puertas, Jose Ortega
The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics / molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between non-reactive and reactive conformations leading to the photolesion...
October 21, 2016: Journal of Physical Chemistry Letters
Mangesh I Chaudhari, Jijeesh R Nair, Lawrence R Pratt, Fernando A Soto, Perla B Balbuena, Susan Rempe
Lithium ion solvation and diffusion properties in ethylene carbonate (EC) and propylene carbonate (PC) are studied by molecular simulation, experiments, and electronic structure calculations. Studies carried out in water provide a reference for interpretation. Classical molecular dynamics simulation results are compared to ab initio molecular dynamics to as- sess non-polarizable force field parameters for solvation structure of the carbonate solvents. Quasi-chemical theory (QCT) is adapted to take advantage of four-fold occupancy of the near-neighbor solvation structure observed in simulations, and used to calculate solvation free energies...
October 21, 2016: Journal of Chemical Theory and Computation
Zhong Ni, Xiting Wang, Tianchen Zhang, Rong Zhong Jin
Anaplastic lymphoma kinase (ALK) has become as an important target for the treatment of various human cancers, especially non-small-cell lung cancer. A mutation, F1174C, suited in the C-terminal helix αC of ALK and distal from the small-molecule inhibitor ceritinib bound to the ATP-binding site, causes the emergence of drug resistance to ceritinib. However, the detailed mechanism for the allosteric effect of F1174C resistance mutation to ceritinib remains unclear. Here, molecular dynamics (MD) simulations and binding free energy calculations [Molecular Mechanics/Generalized Born Surface Area (MM/GBSA)] were carried out to explore the advent of drug resistance mutation in ALK...
October 11, 2016: Computational Biology and Chemistry
Navnit Kumar Mishra, Anil Kumar Sharma, Tapan Kumar Mukherjee
Melanoma is a cancer associated with melanocytes of epidermis. There has been a consistent increase in the number of melanoma patients because of the depletion of the ozone layer which makes it of paramount importance to explore the immunogenic potential of various peptides in melanoma therapy. In the current study, a mutated decapeptide (ELAGIGILTV) epitope ID 12941 was taken from the melanoma antigen recognized by T-cells. This epitope displayed relatively better affinity for histocompatibility leukocyte antigen influencing the proliferation of cytotoxic T-cells...
November 2016: Journal of Molecular Modeling
Xiaoyu Zhuang, Bing Zhao, Shu Liu, Fengrui Song, Fengchao Cui, Zhiqiang Liu, Yunqi Li
Misfolding and aggregation of Cu, Zn superoxide dismutase (SOD1) is implicated in the etiology amyotrophic lateral sclerosis (ALS). The use of small molecules may stabilize the spatial structure of SOD1 dimer, thus preventing its dissociation and aggregation. In this study, "native" mass spectrometry (MS) was used to study the non-covalent interactions between SOD1 and flavonoid compounds. MS experiments were performed on a quadruple time-of-flight (Q-ToF) mass spectrometer with an electrospray ionization (ESI) source and T-wave ion mobility...
October 19, 2016: Analytical Chemistry
Justin A Lemkul, Alexander D MacKerell
Mg2+ ions are important in biological systems, particularly in stabilizing compact RNA folds. Mg2+ is strongly polarizing, and representing its interactions in heterogeneous environments is a challenge for empirical force field development. To date, the most commonly used force fields in molecular dynamics simulations utilize a pairwise-additive approximation for electrostatic interactions, which cannot account for the significant polarization response in systems containing Mg2+. In the present work, we refine the interactions of Mg2+ with water, Cl- ions, and nucleic acid moieties using a polarizable force field based on the classical Drude oscillator model...
October 19, 2016: Journal of Physical Chemistry. B
András Szilágyi, Dániel Györffy, Péter Závodszky
In an earlier study, we showed that two-domain segment-swapped proteins can evolve by domain swapping and fusion, resulting in a protein with two linkers connecting its domains. We proposed that a potential evolutionary advantage of this topology may be the restriction of interdomain motions, which may facilitate domain closure by a hinge-like movement, crucial for the function of many enzymes. Here, we test this hypothesis computationally on uroporphyrinogen III synthase, a two-domain segment-swapped enzyme essential in porphyrin metabolism...
October 18, 2016: Proteins
Pablo M Piaggi, Omar Valsson, Michele Parrinello
We study by computer simulation the nucleation of a supersaturated Lennard-Jones vapor into the liquid phase. The large free energy barriers to transition make the time scale of this process impossible to study by ordinary molecular dynamics simulations. Therefore we use a recently developed enhanced sampling method [Valsson and Parrinello, Phys. Rev. Lett.113, 090601 (2014)] based on the variational determination of a bias potential. We differ from previous applications of this method in that the bias is constructed on the basis of the physical model provided by the classical theory of nucleation...
October 18, 2016: Faraday Discussions
Malihe Hassanzadeh, Kowsar Bagherzadeh, Massoud Amanlou
Nowadays the ability to prediction of complex behavior rationally based on the computational approaches has been a successful technique in drug discovery. In the present study interactions of a new series of hybrids, which were made by linking colchicine as a tubulin inhibitor and suberoylanilide hydroxamic acid (SAHA) as a HDAC inhibitor, with HDAC8 and HDAC1 were investigated and compared. This research has been facilitated by the availability of experimental information besides employing docking methodology as well as classical molecular dynamics simulations and binding free energy calculation were performed...
October 7, 2016: Journal of Molecular Graphics & Modelling
Xuejuan Liu, Falin Tian, Tongtao Yue, Xianren Zhang, Chongli Zhong
The shape deformation of membrane nanotubes is studied by a combination of theoretical analysis and molecular simulation. First we perform free energy analysis to demonstrate the effects of various factors on two ideal states for the pearling transition, and then we carry out dissipative particle dynamics simulations, through which various types of membrane tube deformation are found, including membrane pearling, buckling, and bulging. Different models for inducing tube deformation, including the osmotic pressure, area difference and spontaneous curvature models, are considered to investigate tubular instabilities...
October 17, 2016: Soft Matter
Prasenjit Das, Sanjay Puri, Moshe Schwartz
We present large-scale molecular dynamics simulations to study the free evolution of granular gases. Initially, the density of particles is homogeneous and the velocity follows a Maxwell-Boltzmann (MB) distribution. The system cools down due to solid friction between the granular particles. The density remains homogeneous, and the velocity distribution remains MB at early times, while the kinetic energy of the system decays with time. However, fluctuations in the density and velocity fields grow, and the system evolves via formation of clusters in the density field and the local ordering of velocity field, consistent with the onset of plug flow...
September 2016: Physical Review. E
Go Hamasaka, Tsubasa Muto, Yoshimichi Andoh, Kazushi Fujimoto, Kenich Kato, Masaki Tanaka, Susumu Okazaki, Yasuhiro Uozumi
Wide-angle X-ray scattering experiments and all-atomistic molecular dynamics calculations were performed to elucidate the detailed structure of bilayer vesicles constructed by self-assembly of an amphiphilic palladium NCN-pincer complex. We found an excellent agreement between the experimental and calculated X-ray spectra and between the membrane thickness determined from a TEM image and that calculated from an electron-density profile, indicating that the calculated structure was highly reliable. The analysis of the simulated bilayer structure showed that the membrane was softer than other phospholipid bilayer membranes in general...
October 13, 2016: Chemistry: a European Journal
Mike O'Connor, Emanuele Paci, Simon McIntosh-Smith, David R Glowacki
The past decade has seen the development of a new class of rare event methods in which molecular configuration space is divided into a set of boundaries/interfaces, and then short trajectories are run between boundaries. For all these methods, an important concern is how to generate boundaries. In this paper, we outline an algorithm for adaptively generating boundaries along a free energy surface in multi-dimensional collective variable (CV) space, building on the boxed molecular dynamics (BXD) rare event algorithm...
October 14, 2016: Faraday Discussions
Qinchang Chen, Xiaoxiang Wang, Wei Shi, Hongxia Yu, Xiaowei Zhang, John P Giesy
Some hydroxylated polybrominated diphenyl ethers (HO-PBDEs), that have been widely detected in the environment and tissues of humans and wildlife, bind to thyroid hormone (TH) receptor (TR) and can disrupt functioning of systems modulated by the TR. However, the mechanism of TH disrupting effect is still equivocal. Here, disruption of functions of TH modulated pathways by HO-PBDEs were evaluated by use of assays of competitive binding, coactivator recruitment and proliferation of GH3 cells. In silico simulations considering effects of co-regulators were carried out to investigate molecular mechanisms and predict potencies for disrupting functions of the TH...
October 14, 2016: Environmental Science & Technology
Vinodhkumar Vijayakumar, Ramadoss Vijayaraj, Günther H Peters
The stability of cyclic peptide assemblies (CPs) forming a macromolecular nanotube structure was investigated in solvents of different polarity using computational methods. The stability and structure of the complexes were studied using traditional molecular dynamics (MD). Energy of dissociation was estimated from steered MD in combination with umbrella sampling simulations. A cyclic peptide nanotube (CPNT) was constructed by stacking of eight cyclo[(D-Trp-L-Gln-D-Trp-L-Glu)2], and hereafter is referred to as (WQWE)8...
November 2016: Journal of Molecular Modeling
Arthitaya Meeprasert, Supot Hannongbua, Nawee Kungwan, Thanyada Rungrotmongkol
Hepatitis C virus (HCV) is a serious cause of liver inflammation, cirrhosis and the development of hepatocellular carcinoma. Its NS3/4A serine protease functions to cleave a specific peptide bond, which is an important step in HCV replication. Thus the NS3/4A protease has become one of the main drug-targets in the design and development of anti-HCV agents. Unfortunately, high mutation rates in HCV have been reported due to the lack of RNA proofreading activity resulting in drug resistance. Herein, all-atom molecular dynamics simulations were employed to understand and illustrate the effects of the NS3/4A D168V mutation on faldaprevir (FDV) and danoprevir (DNV) binding efficiency...
October 12, 2016: Molecular BioSystems
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