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Molecular Dynamics Simulations

Maria Bykhovskaia
Molecular dynamics (MD) simulations enable in silico investigations of the dynamic behavior of proteins and protein complexes. Here, we describe MD simulations of the SNARE complex and its interactions with the neuronal protein complexin. Complexin is an effector of neuronal secretion that inhibits spontaneous fusion and is thought to clamp the fusion process via the interactions with the SNARE complex. We describe MD simulations of the SNARE complex alone and bound to complexin. The MD simulations under external forces imitating the repulsion between lipid bilayers enabled us to investigate unraveling and assembly of the SNARE complex...
2019: Methods in Molecular Biology
Peng Tang, Yongchun Liu, Yiming Liu, Hongru Meng, Zeying Liu, Ke Li, Daocheng Wu
To improve the inherent defects of chemotherapy and photothermal therapy (PTT), we design a novel thermochromism-induced temperature self-regulation and alternating photothermal system based on iodine (I2 )-loaded acetylated amylose nanohelix clusters (ILAA NHCs) under the guidance of molecular dynamic simulation in which I2 is loaded into the helical cavity of acetylated amylose (AA) by hydrophobic interaction. ILAA NHCs perform versatile photothermal conversion through their unique reversible thermochromism...
October 8, 2018: Biomaterials
Sooram Banesh, Vibin Ramakrishnan, Vishal Trivedi
CD36-PS interaction is an important affair to identify and remove dead/aged cells to control inflammation. CD36 ectodomain was cloned, over-expressed in bacterial expression system and purified to homogeneity. The dot-blot analysis shows that the CD36_ecto selectively binds PS vesicles blotted on the nitrocellulose membrane. PS binds strongly to CD36_ecto with a dissociation constant KD of 53.7 ± 0.48 μM. The stoichiometry of interaction between CD36 and PS is 1:2. The hCD36_ecto-PS thermogram revealed that the hydrophobic and salt bridge interactions play crucial role in their interactions...
October 11, 2018: Archives of Biochemistry and Biophysics
Nicholas J Hestand, J L Skinner
The origin of liquid water's anomalous behavior continues to be a subject of interest and debate. One possible explanation is the liquid-liquid critical point hypothesis, which proposes that supercooled water separates into two distinct liquids at low temperatures and high pressures. According to this hypothesis, liquid water's anomalies can be traced back to the critical point associated with this phase separation. If such a critical point actually exists, it is located in a region of the phase diagram known as No Man's Land (NML), where it is difficult to characterize the liquid using conventional experimental techniques due to rapid crystallization...
October 14, 2018: Journal of Chemical Physics
Alexis Torres-Carbajal, Victor M Trejos, Luz Adriana Nicasio-Collazo
We present a systematic study of the self-diffusion coefficient for a fluid of particles interacting via the square-well pair potential by means of molecular dynamics simulations in the canonical ( N , V , T ) ensemble. The discrete nature of the interaction potential is modeled by the constant force approximation, and the self-diffusion coefficient is determined for several fluid densities at supercritical thermodynamic states. The dependence of the self-diffusion coefficient on the potential range λ is analyzed in the range of 1...
October 14, 2018: Journal of Chemical Physics
Hao Jiang, Pablo G Debenedetti, Athanassios Z Panagiotopoulos
In this work, we use molecular dynamics simulations with a polarizable force field, namely, the modified AH/BK3 model [J. Kolafa, J. Chem. Phys. 145 , 204509 (2016)], in combination with the forward flux sampling technique, to calculate the rates of homogeneous nucleation of NaCl from supersaturated aqueous solutions at 298 K and 1 bar. A non-polarizable model that reproduces the experimental equilibrium solubility {AH/TIP4P-2005 of Benavides et al. [J. Chem. Phys. 147 , 104501 (2017)]} is also used for comparison...
October 14, 2018: Journal of Chemical Physics
Jorge I Amaro-Estrada, Jorge Hernández-Cobos, Humberto Saint-Martin, Laurent Maron, Alejandro Ramírez-Solís
We address the aqueous microsolvation of the CH3 HgCl and CH3 HgOH molecules using a stepwise hydration scheme including up to 33 water molecules and compare our results with the previously studied HgCl2 , HgClOH, and Hg(OH)2 complexes. Optimized geometries and Gibbs free energies were obtained at the B3PW91/aug-RECP(Hg)-6-31G(d,p) level. At least 33 water molecules were required to build the first solvation shell around both methylmercury compounds. Optimized geometries were found having favorable interactions of water molecules with Hg, Cl, and the OH moiety...
October 14, 2018: Journal of Chemical Physics
Ryo Urano, George A Pantelopulos, Shanshan Song, John E Straub
Reverse micelles (RMs) are recognized as a paradigm of molecular self-assembly and used in a variety of applications, such as chemical synthesis and molecular structure refinement. Nevertheless, many fundamental properties including their equilibrium size distribution, internal structure, and mechanism of self-assembly remain poorly understood. To provide an enhanced microscopic understanding of the assembly process and resulting structural distribution, we perform multiple nonequilibrium molecular dynamics simulations of dioctyl sulfosuccinate sodium salt (AOT) RM assembly, quantifying RM size, water core structure, and dynamics...
October 14, 2018: Journal of Chemical Physics
Tamoghna Das, Jack F Douglas
We investigate local structural fluctuations in a model equilibrium fluid with the aim of better understanding the structural basis of locally heterogeneous dynamics identified in recent simulations and experimental studies of glass-forming liquids and other strongly interacting particle systems, such as lipid membranes, dusty plasmas, interfacial dynamics of crystals, the internal dynamics of proteins, etc. In particular, we utilize molecular dynamics simulation methods to study a single component Lennard-Jones condensed material at constant temperature in two dimensions over a range of densities covering both liquid and crystalline phase regimes...
October 14, 2018: Journal of Chemical Physics
Nikhil Agrawal, Md Summon Hossain, Adam A Skelton, Kambadur Muralidhar, Sandeep Kaushik
l-Gulonate dehydrogenase (GuDH) is a crucial enzyme in the non-phosphorylated sugar metabolism or glucuronate-xylulose (GX) pathway. Some naturally occurring compounds inhibit GuDH. Ascorbic acid is one of such inhibitors for GuDH. However, the exact mechanism by which ascorbic acid inhibits GuDH is still unknown. In this study, we try to investigate GuDH inhibition using computational approaches by generating a model for buffalo GuDH. We used this model to perform blind dockings of ascorbic acid to GuDH. Some docked conformations of ascorbic acid bind near Asp39 and have steric clashes with crystal structure conformation of NADH...
September 27, 2018: Computational Biology and Chemistry
Vijay Kumar, Wahiduzzaman, Amresh Prakash, Anil Kumar Tomar, Ankit Srivastava, Bishwajit Kundu, Andrew M Lynn, Md Imtaiyaz Hassan
TDP-43 (transactive- response DNA binding protein) amazes structural biologist as its aberrant ubiquitinated cytosolic inclusions is largely involved in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). An important question in TDP-43 research is to identify the structural region mediating the formation of cytoplasmic pathological aggregates. In this study, we attempted to delineate the aggregation-prone sequences of the structural domain of TDP-43. Here, we investigated the self-assembly of peptides of TDP-43 using aggregation prediction algorithms, Zipper DB and AMYLPRED2...
October 10, 2018: Biochimica et biophysica acta. Proteins and proteomics
Shreyasi Asthana, Zaved Hazarika, Parth Sarathi Nayak, Jyoti Roy, Anupam Nath Jha, Bibekanand Mallick, Suman Jha
BACKGROUND: Injection localized amyloidosis is one of the most prevalent disorders in type II diabetes mellitus (TIIDM) patients relying of insulin injections. Previous studies have reported that nanoparticles can play a role in the amyloidogenic process of proteins. Hence, the present study deals with the effect of zinc oxide nanoparticles (ZnONP) on the amyloidogenicity and cytotoxicity of insulin. METHODS: ZnONP is synthesized and characterized using XRD, Zeta Sizer, UV-Visible spectroscope and TEM...
October 10, 2018: Biochimica et biophysica acta. General subjects
Casper Wilkens, Manish K Tiwari, Helen Webb, Murielle Jam, Mirjam Czjzek, Birte Svensson
In the marine environment agar degradation is assured by bacteria that contain large agarolytic systems with enzymes acting in various endo- and exo-modes. Agarase A (AgaA) is an endo-glycoside hydrolase of family 16 considered to initiate degradation of agarose. Agaro-oligosaccharide binding at a unique surface binding site (SBS) in AgaA from Zobellia galactanivorans was investigated by computational methods in conjunction with a structure/sequence guided approach of site-directed mutagenesis probed by surface plasmon resonance binding analysis of agaro-oligosaccharides of DP 4-10...
October 13, 2018: Proteins
Byungkwan Jeong, Jaemin Kim, Taegu Lee, Seong-Woong Kim, Seunghwa Ryu
We propose a theoretical framework to predict the deformation mechanism of the γ-TiAl single crystal without lattice defects by combining the generalized stacking fault energy and the Schmid factor. Our theory is validated against an excellent testbed, the single crystal nanowire, by correctly predicting four major deformation mechanisms, namely, ordinary slip, super slip, twinning, and mixed slip/fracture observed during the tensile and compressive tests along 10 different orientations using molecular dynamics simulations...
October 12, 2018: Scientific Reports
Yan Xu, Shixin Li, Zengshuai Yan, Zhen Luo, Hao Ren, Baosheng Ge, Fang Huang, Tongtao Yue
A growing number of proteins have been identified as knotted in their native structures, with such entangled topological features being expected to play stabilizing roles maintaining both the global fold and the nature of proteins. However, the molecular mechanism underlying the stabilizing effect is ambiguous. Here, we combine unbiased and mechanical atomistic molecular dynamics simulations to investigate how a protein is stabilized by an inherent knot by directly comparing chemical, thermal, and mechanical denaturing properties of two proteins having the same sequence and secondary structures but differing in the presence or absence of an inherent knot...
September 22, 2018: Biophysical Journal
Christina Susan Abraham, S Muthu, Johanan Christian Prasana, Sanja J Armaković, Stevan Armaković, Fathima Rizwana B, Ben Geoffrey A S
Spectroscopic profiling in terms of FT-IR, FT-Raman, UV-vis and NMR in addition to reactivity study by density functional theory (DFT) and molecular dynamics (MD) simulations of 3-(4-chlorophenyl)-N,N-dimethyl-3-pyridin-2-ylpropan-1-amine (C16 H19 ClN2 ) have been discussed. In order to assign principal vibrational numbers, the Potential energy distribution (PED) analysis has been executed. Frontier molecular orbitals (FMOs) analysis in addition to the stabilization energy and natural hybrid orbital analysis has been done...
September 3, 2018: Computational Biology and Chemistry
Yong-Bao Chu, Min Li, Jin-Wei Liu, Wei Xu, Shi-Han Cheng, Hua-Zhang Zhao
Types and structures of phosphorus compounds influence the removal of phosphorus by coagulation. Until now, the molecular-level interaction between coagulants and phosphorus (especially organophosphates) and the relationship between removal efficiency and phosphorus structure have not been clear. This work investigated the removal of phosphorus with different structures using conventional coagulants (poly aluminum chloride (PACl) and polymerized ferric sulfate (PFS)) and a novel covalently-bound inorganic-organic hybrid coagulant (CBHyC)...
October 5, 2018: Water Research
Calvin A Omolo, Rahul S Kalhapure, Nikhil Agrawal, Mahantesh Jadhav, Sanjeev Rambharose, Chunderika Mocktar, Thirumala Govender
The development of novel materials is essential for the efficient delivery of drugs. Therefore, the aim of the study was to synthesize a linear polymer dendrimer hybrid star polymer (3-mPEA) comprising of a generation one poly (ester-amine) dendrimer (G1-PEA) and a diblock copolymer of methoxy poly (ethylene glycol)-b-poly(ε-caprolactone) (mPEG-b-PCL) for formulation of nanovesicles for efficient drug delivery. The synthesized star polymer was characterized by FTIR, 1 H and 13 C NMR, HRMS, GPC and its biosafety was confirmed by MTT assays...
October 9, 2018: Journal of Controlled Release: Official Journal of the Controlled Release Society
M E Caplan, A S Schneider, C J Horowitz
The elastic properties of neutron star crusts are relevant for a variety of currently observable or near-future electromagnetic and gravitational wave phenomena. These phenomena may depend on the elastic properties of nuclear pasta found in the inner crust. We present large-scale classical molecular dynamics simulations where we deform nuclear pasta. We simulate idealized samples of nuclear pasta and describe their breaking mechanism. We also deform nuclear pasta that is arranged into many domains, similar to what is known for the ions in neutron star crusts...
September 28, 2018: Physical Review Letters
Huaping Li, Alkan Kabakçıoğlu
We study hairpin folding dynamics by means of extensive molecular dynamics simulations, with particular attention paid to the influence of helicity on the folding time. We find that the dynamical exponent α in the anomalous scaling n(t)∼t^{1/α} of the hairpin length n with time changes from 1.6 (≃1+ν, where ν is the Flory exponent) to 1.2 (≃2ν) in three dimensions, when duplex helicity is removed. The relation α=2ν in rotationless hairpin folding is further verified in two dimensions (ν=0.75) and for a ghost chain (ν=0...
September 28, 2018: Physical Review Letters
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