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Molecular Dynamics Simulations

Vanessa Petry do Canto, Claudia Elizabeth Thompson, Paulo Augusto Netz
The global production of plastics increases every year, because these materials are widely used in several segments of modern life. Polyurethanes are a very important class of polymers, used in many areas of everyday life, from automotive equipments to mattresses. The waste management usually involves accumulation in landfills, incineration, and reuse processes. However, bioremediation processes are being increasingly tested, due to the efficiency of enzymes in the degradation, besides adding value to the generated waste...
March 6, 2019: Journal of Molecular Graphics & Modelling
Ahmed A El Rashedy, Patrick Appiah-Kubi, Mahmoud E S Soliman
The constitutive BCR-ABL1 active protein fusion has been identified as the main cause of chronic myeloid leukemia. The emergence of T334I and D381N point mutations in BCR-ABL1 confer drug resistance. Recent experimental studies show a synergistic effect in suppressing this resistance when Nilotinib and Asciminib are co-administered to target both the catalytic and allosteric binding site of BCR-ABL1 oncoprotein, respectively. However, the structural mechanism by which this synergistic effect occurs has not been clearly elucidated...
March 15, 2019: Protein Journal
Jorge Estévez, Felipe Rodrigues de Souza, María Romo, Iris Mangas, Tanos Celmar Costa Franca, Eugenio Vilanova
Phenyl valerate (PV) is a substrate for measuring the PVase activity of neuropathy target esterase (NTE), a key molecular event of organophosphorus-induced delayed neuropathy. A protein with PVase activity in chicken (model for delayed neurotoxicity) was identified as butyrylcholinesterase (BChE). Purified human butyrylcholinesterase (hBChE) showed PVase activity with a similar sensitivity to inhibitors as its cholinesterase (ChE) activity. Further kinetic and theoretical molecular simulation studies were performed...
March 15, 2019: Archives of Toxicology
Roser Urreizti, Klaus Mayer, Gilad D Evrony, Edith Said, Laura Castilla-Vallmanya, Neal A L Cody, Guillem Plasencia, Bruce D Gelb, Daniel Grinberg, Ulrich Brinkmann, Bryn D Webb, Susanna Balcells
DPH1variants have been associated with an ultra-rare and severe neurodevelopmental disorder, mainly characterized by variable developmental delay, short stature, dysmorphic features, and sparse hair. We have identified four new patients (from two different families) carrying novel variants in DPH1, enriching the clinical delineation of the DPH1 syndrome. Using a diphtheria toxin ADP-ribosylation assay, we have analyzed the activity of seven identified variants and demonstrated compromised function for five of them [p...
March 15, 2019: European Journal of Human Genetics: EJHG
Magnus Sebastian Bauer, Fabian Baumann, Csaba Daday, Pilar Redondo, Ellis Durner, Markus Andreas Jobst, Lukas Frederik Milles, Davide Mercadante, Diana Angela Pippig, Hermann Eduard Gaub, Frauke Gräter, Daniel Lietha
Focal adhesion kinase (FAK) is a key signaling molecule regulating cell adhesion, migration, and survival. FAK localizes into focal adhesion complexes formed at the cytoplasmic side of cell attachment to the ECM and is activated after force generation via actomyosin fibers attached to this complex. The mechanism of translating mechanical force into a biochemical signal is not understood, and it is not clear whether FAK is activated directly by force or downstream to the force signal. We use experimental and computational single-molecule force spectroscopy to probe the mechanical properties of FAK and examine whether force can trigger activation by inducing conformational changes in FAK...
March 15, 2019: Proceedings of the National Academy of Sciences of the United States of America
Jinqing Li, Zichao Yang, Han Liu, Mengjie Qiu, Tingting Zhang, Wenjuan Li, Zhaofeng Li, Tao Qi, Yurong Qiu, Lin Li, Xuefeng Zhou, Shuwen Liu, Suiyi Tan
Semen-derived amyloid fibrils, composing SEVI (semen-derived enhancer of viral infection) fibrils and SEM1 fibrils, could remarkably enhance HIV-1 sexual transmission and thus, are potential targets for the development of an effective microbicide. Previously, we found that ADS-J1, apart from being an HIV-1 entry inhibitor, could also potently inhibit seminal amyloid fibrillization and block fibril-mediated enhancement of viral infection. However, the remodeling effects of ADS-J1 on mature seminal fibrils were unexplored...
March 15, 2019: Biochemical Journal
Sanaz Asgharzadeh, Behzad Shareghi, Sadegh Farhadian
l-Methionine (l-Met) is one of the necessary amino acids that play unparalleled roles, influencing both the protein structure and metabolism. Understanding the interactions between proteins and small molecules can be realized by various perspectives, and this is significant for the progression of basic sciences and drug development. In this study, the variations in the stability, function, and structure of α-Chymotrypsin (α-Chy) in the presence of l-Met were investigated using spectroscopic and computational approaches...
March 12, 2019: International Journal of Biological Macromolecules
Thomas la Cour Jansen, Shinji Saito, Jonggu Jeon, Minhaeng Cho
Two-dimensional (2D) vibrational spectroscopy has emerged as one of the most important experimental techniques useful to study the molecular structure and dynamics in condensed phases. Theory and computation have also played essential and integral roles in its development through the nonlinear optical response theory and computational methods such as molecular dynamics (MD) simulations and electronic structure calculations. In this article, we present the fundamental theory of coherent 2D vibrational spectroscopy and describe computational approaches to simulate the 2D vibrational spectra...
March 14, 2019: Journal of Chemical Physics
Weijian Li, Xiaoliang Zuo, Xiaoyan Zhou, Hangjun Lu
Using molecular dynamics simulations, we have investigated the hydrophobic interactions and influence of nitrogen molecules on the critical distance of dewetting between the nanoscale hydrophobic plates. We show that dewetting transition is very sensitive to the distribution of nitrogen molecules. The nitrogen molecules prefer to aggregate in the vicinity of the two hydrophobic plates and exclude water molecules. Furthermore, our simulation results indicate that the effective range of hydrophobic attraction between the two nanoscale plates is enhanced by the aggregated nitrogen molecules...
March 14, 2019: Journal of Chemical Physics
James Lincoff, Sukanya Sasmal, Teresa Head-Gordon
Molecular dynamics simulations of intrinsically disordered proteins (IDPs) can provide high resolution structural ensembles if the force field is accurate enough and if the simulation sufficiently samples the conformational space of the IDP with the correct weighting of sub-populations. Here, we investigate the combined force field-sampling problem by testing a standard force field as well as newer fixed charge force fields, the latter specifically motivated for better description of unfolded states and IDPs, and comparing them with a standard temperature replica exchange (TREx) protocol and a non-equilibrium Temperature Cool Walking (TCW) sampling algorithm...
March 14, 2019: Journal of Chemical Physics
Sergio Pérez-Conesa, Francisco Torrico, José M Martínez, Rafael R Pappalardo, Enrique Sánchez Marcos
A set of new ab initio force fields for aqueous [AnO2 ]2+/+ (An = Np(vi,v), Pu(vi), Am(vi)) has been developed using the Hydrated Ion (HI) model methodology previously used for [UO2 ]2+ . Except for the non-electrostatic contribution of the HI-bulk water interaction, the interaction potentials are individually parameterized. Translational diffusion coefficients, hydration enthalpies, and vibrational normal mode frequencies were calculated from the MD simulations. Physico-chemical properties satisfactorily agree with experiments validating the robustness of the force field strategy...
March 14, 2019: Journal of Chemical Physics
Stephen J Cotton, William H Miller
In the previous work of Cotton and Miller [J. Chem. Phys. 145, 144108 (2016)], an improved symmetrical quasi-classical (SQC) windowing model for the molecular dynamics treatment of electronically non-adiabatic processes was developed in order to extend the original SQC approach to the regime of weak-coupling between the electronic states. The improved SQC model-based on triangular-shaped window functions-handled the weak-coupling limit as intended and, as a bonus, was shown to be universally superior to the original square/histogram SQC windowing model over all coupling regimes, but only for treating systems of two electronic states, as no higher-dimensional generalization was evident...
March 14, 2019: Journal of Chemical Physics
Fernando Vargas-Lara, Beatriz A Pazmiño Betancourt, Jack F Douglas
We perform molecular dynamics simulations on a coarse-grained polymer melt to study the dynamics of glass-formation in ring polymer melts of variable knot complexity. After generating melts of non-concatenated polymeric rings having a range of minimum crossing number values, mc , we compute the coherent intermediate scattering function, the segmental α-relaxation time, fragility, and the glass transition temperature as a function of mc . Variation of knot complexity is found to have a pronounced effect on the dynamics of polymer melts since both molecular rigidity and packing are altered, primary physical factors governing glass-formation in polymeric materials...
March 14, 2019: Journal of Chemical Physics
Elvis Awuni, Yuguang Mu
The mechanism of the antibiotic molecule A22 is yet to be clearly understood. In a previous study, we carried out molecular dynamics simulations of a monomer of the bacterial actin-like MreB in complex with different nucleotides and A22, and suggested that A22 impedes the release of Pi from the active site of MreB after the hydrolysis of ATP, resulting in filament instability. On the basis of the suggestion that Pi release occurs on a similar timescale to polymerization and that polymerization can occur in the absence of nucleotides, we sought in this study to investigate a hypothesis that A22 impedes the conformational change in MreB that is required for polymerization through molecular dynamics simulations of the MreB protofilament in the apo, ATP+, and ATP-A22+ states...
March 15, 2019: International Journal of Molecular Sciences
Elena Alvira
Molecular mechanics and dynamics simulations were carried out to study the capacity of isoleucine enantiomers to form inclusion complexes with β⁻cyclodextrin, and to be discriminated by this chiral compound, in vacuo and with different solvents. Solvents were characterized not only by the value of dielectric constant ε in the Coulombic interaction energy, but also by the neutral and zwitterion configurations of isoleucine. Whereas the discrimination between the enantiomers for ε ≤ 2 is due to the electrostatic contribution, these differences are mainly due to the Lennard-Jones potential for ε > 2...
March 14, 2019: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Carlos A Ramos-Guzmán, Kirill Zinovjev, Iñaki Tuñón
The metabolic product of caspase-1, IL-1β, is an important mediator in inflammation and pyroptosis cell death process. Alzheimer's disease, septic shock and rheumatoid arthritis are IL-1β mediated diseases, making the caspase-1 an interesting target of pharmacological value. Many inhibitors have been developed until now, most of them are peptidomimetic with improved potency. In the present study, all-atom molecular dynamics simulations and the MM/GBSA method were employed to reproduce and interpret the results obtained by in vitro experiments for a series of inhibitors...
February 27, 2019: European Journal of Medicinal Chemistry
Joel Ricci-López, Abraham Vidal-Limon, Matías Zunñiga, Verónica A Jimènez, Joel B Alderete, Carlos A Brizuela, Sergio Aguila
High-risk strains of human papillomavirus (HPV) have been identified as the etiologic agent of some anogenital tract, head, and neck cancers. Although prophylactic HPV vaccines have been approved; it is still necessary a drug-based treatment against the infection and its oncogenic effects. The E6 oncoprotein is one of the most studied therapeutic targets of HPV, it has been identified as a key factor in cell immortalization and tumor progression in HPV-positive cells. E6 can promote the degradation of p53, a tumor suppressor protein, through the interaction with the cellular ubiquitin ligase E6AP...
2019: PloS One
Juan F Mora Cardozo, Jan Peter Embs, Antonio Benedetto, Pietro Ballone
Recent experiments on proton conducting ionic liquids point to half-neutralised diamine-triflate salts as promising candidates for applications in power generation and energy conversion electrochemical devices. Structural and dynamical properties of the simplest among these compounds are investigated by a combination of density-functional theory (DFT) and molecular dynamics (MD) simulation based on an empirical force field. Three different cations have been considered, consisting of a pair of amine-ammonium terminations joined by a short aliphatic segment -(CH$_2$)$_n$- with $n=2$, $3$ and $4$...
March 15, 2019: Journal of Physical Chemistry. B
Mayk Caldas Ramos, Vitor A C Horta, Bruno A C Horta
A systematic evaluation of the accuracy of the GROMOS-compatible 2016H66 forcefield in the simulation of dendrimers is performed. More specifically, the poly(amido amine) (PAMAM) and the poly(propylene imine) (PPI) are considered due to the availability of experimental data and simulation results in the literature. A total of 36 molecular systems are simulated and the radius of gyration, asphericity, density profiles and the self-diffusion coefficients are monitored in terms of the generation number and pH (low, medium and high) condition...
March 15, 2019: Journal of Chemical Information and Modeling
Andrés Moreno Carrascosa, Haiwang Yong, Deborah L Crittenden, Peter M Weber, Adam Kirrander
We present a method to calculate total x-ray scattering cross sections directly from ab-initio electronic wavefunctions in atoms and molecules. The approach can be used in conjunction with multiconfigurational wavefunctions and exploits analytical integrals of Gaussian-type functions over the scattering operator, which leads to accurate and efficient calculations. The results are validated by comparison to experimental results and previous theory for the molecules H2 and CO2. Importantly, we find that the inelastic component of the total scattering varies strongly with molecular geometry...
March 15, 2019: Journal of Chemical Theory and Computation
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