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Molecular Dynamics Simulations

Jorge Alfonso Arvayo-Zatarain, Fernando Favela-Rosales, Claudio Contreras-Aburto, Efrain Urrutia-Bañuelos, Amir Maldonado
We report results of a molecular dynamics simulation study of the effect of one general anesthetic, halothane, on some properties of mixed DPPC/DPPE phospholipid membranes. This is a suitable model for the study of simple, two-phospholipid membrane systems. From the simulation runs, we determined several membrane properties for five different molecular proportions of DPPC/DPPE. The effect of halothane on the studied membrane properties (area per lipid molecule, density of membrane, order parameter, etc.) was rather small...
December 15, 2018: Journal of Molecular Modeling
Mahmoud Sharawy, Styliani Consta
Guanine quadruplex (G-quadruplex) structures play a vital role in stabilizing the DNA genome and in protecting healthy cells from transforming into cancer cells. The structural stability of G-quadruplexes is greatly enhanced by the binding of monovalent cations such as Na+ or K+ into the interior axial channel. We computationally study the free energy of binding of Na+ and K+ ions to two intramolecular G-quadruplexes that differ considerably in their degree of rigidity and the presence or absence of terminal nucleotides...
December 14, 2018: Journal of Chemical Physics
Fan Xie, Xiaoqian Ng, Nathan A Seifert, Javix Thomas, Wolfgang Jäger, Yunjie Xu
The conformational landscape of tetrahydro-2-furoic acid (THFA), a chiral carboxylic acid which is often used as a precursor in syntheses of pharmaceuticals, was investigated using rotational spectroscopy and theoretical modeling. Extensive manual searches were carried out to identify possible conformers related to the relative orientations of the carbonyl and hydroxyl groups in the COOH functional group, the COOH rotation, and the ring puckering motions in the system. A large number of initial conformational geometries were generated in parallel using a joint semiempirical-molecular dynamics simulation program...
December 14, 2018: Journal of Chemical Physics
Yoshiyuki Kubota, Tomáš Bučko
The reaction of carbon dioxide (CO2 ) with aqueous 2,2'-iminodiethanol (trivial name is diethanolamine: DEA) has been investigated using both blue moon ensemble and metadynamics approaches combined with ab initio molecular dynamics (AIMD) simulations. A spontaneous direct proton transfer from DEA zwitterion (DEAZW) to DEA but not to H2 O has been observed in straightforward AIMD simulation in the time scale of ps. The ab initio free-energy calculations reproduced the overall free-energy difference, predicting the ionic products DEA carbamate ion (DEAC) and the protonated DEA (DEAH)...
December 14, 2018: Journal of Chemical Physics
Jeffery B Klauda
Modeling lipid bilayers using molecular simulations has progressed from short simulations of single-component lipids to currently having the ability to model complex cellular membranes with nearly 100 different lipid types on a μ s time scale. This perspective article presents a review of how the chemical physics field has provided insight into the structure and dynamics of accurate cellular membrane models. A short review of lipid force fields is presented, and how lower-resolution models can allow for assemblies and time scales not attainable with all-atom models...
December 14, 2018: Journal of Chemical Physics
Junjie Liu, Chang-Yu Hsieh, Dvira Segal, Gabriel Hanna
The modelling of quantum heat transfer processes at the nanoscale is crucial for the development of energy harvesting and molecular electronic devices. Herein, we adopt a mixed quantum-classical description of a device, in which the open subsystem of interest is treated quantum mechanically and the surrounding heat baths are treated in a classical-like fashion. By introducing such a mixed quantum-classical description of the composite system, one is able to study the heat transfer between the subsystem and bath from a closed system point of view, thereby avoiding simplifying assumptions related to the bath time scale and subsystem-bath coupling strength...
December 14, 2018: Journal of Chemical Physics
Xiaoliang Tang, Junsheng Yang, Fucheng Tian, Tingyu Xu, Chun Xie, Wei Chen, Liangbin Li
The nucleation processes of polyethylene under quiescent and shear flow conditions are comparatively studied with all-atom molecular dynamics simulations. Under both conditions, nucleation is demonstrated to be a two-step process, which, however, proceeds via different intermediate orders. Quiescent nucleation is assisted by local order structures, while flow-induced nucleation is promoted by density fluctuation, which is a coupling effect of conformational and orientational orderings. Flow drives the transformation from flexible chains to conformational ordered segments and circumvents the entropic penalty, which is the most peculiar and rate-limited step in polymer crystallization...
December 14, 2018: Journal of Chemical Physics
Derya Meral, Davide Provasi, Marta Filizola
Computational strategies aimed at unveiling the thermodynamic and kinetic properties of G Protein-Coupled Receptor (GPCR) activation require extensive molecular dynamics simulations of the receptor embedded in an explicit lipid-water environment. A possible method for efficiently sampling the conformational space of such a complex system is metadynamics (MetaD) with path collective variables (CVs). Here, we applied well-tempered MetaD with path CVs to one of the few GPCRs for which both inactive and fully active experimental structures are available, the μ-opioid receptor (MOR), and assessed the ability of this enhanced sampling method to estimate the thermodynamic properties of receptor activation in line with those obtained by more computationally expensive adaptive sampling protocols...
December 14, 2018: Journal of Chemical Physics
H T Nguyen, N H Ngo, H Tran
We show in this paper that requantized classical molecular dynamics simulations (rCMDSs) are capable of predicting various refined spectral-shape parameters of absorption lines of CO2 broadened by N2 with high precision. Combining CMDSs and a requantization procedure, we computed the auto-correlation function of the CO2 dipole moment responsible for the absorption transition. Its Fourier-Laplace transform directly yields the spectrum. Calculations were made for two temperatures, 200 and 296 K, at 1 atm and for a large range of Doppler widths, from the near-Doppler to the collision-dominant regimes...
December 14, 2018: Journal of Chemical Physics
X Bidault, N Pineau
The nanostructuration of energetic materials results in interesting properties. In particular, the detonation of carbon-rich explosives leads to the formation of nanodiamonds, the size of which is linked to the initial size of the explosive nanograins. This correlation could come from the role played by the granularity in the shock properties, especially the local temperature, which could be enhanced when the shock front crosses the various interfaces and nanoporosities of the material. More generally, the granularity-dependent reactivity also concerns some aspects of the sensitivity of energetic materials and subsequent inhibition or safety issues...
December 14, 2018: Journal of Chemical Physics
Rasoul Khaledialidusti, Abhishek Kumar Mishra, Afrooz Barnoush
A multi-scale computational methodology based on the density functional theory and molecular dynamics has been used to investigate the rheological properties of super critical CO2 with CuO nano-particle (NP). Density functional theory which treats the electron density as the central variable has been used to explore the adsorption of CO2 molecules on the two most stable CuO surfaces [i.e., (111) and (011)] at absolute zero. The results of this theory would provide valuable information to make CuO NPs with the surface where the CO2 adsorption is maximum in order to have a stronger mono-layer of adsorbed CO2 molecules on the surface of the NP which is the most crucial factor in formation of a stable nanofluid...
December 14, 2018: Journal of Chemical Physics
Marjorie Caroline Liberato Cavalcanti Freire, Yamara Arruda Silva de Menezes, Matheus Vitor Ferreira Ferraz, Carlos Henrique Bezerra da Cruz, Leandro De Santis Ferreira, Matheus de Freitas Fernandes-Pedrosa, Euzébio Guimarães Barbosa
The Tityus stigmurus scorpion is widely distributed in the Northeast of Brazil and is the main causal agent of human envenoming. The venom produced by this scorpion includes neurotoxins, which are peptides belonging to Family 2 toxins and are able to interact with ion channels. The KTx subfamily displays selectivity and affinity for Kv channel subtypes and the result of this interaction is the blockade of potassium channels, impairing vital functions. We report the optimized structural model of a transcript encoding a potassium channel blocker toxin from T...
November 28, 2018: Journal of Molecular Graphics & Modelling
Esmaeil Behmard, Ali Ahmadi, Ali Najafi
The emergence of antibiotic resistance has attracted the attention of scientists and scientific circles over the decades. β-Lactam antibiotics resistance is a worldwide therapeutic challenge in bacterial infections, mediated through several mechanisms of which mutations in Penicillin Binding Proteins (PBPs) are an important issue, making critical therapeutic problems in the human population. Accordingly, investigating the dynamic structures of mutant variants could result in a profound understanding of such a specific resistance...
December 7, 2018: Journal of Molecular Graphics & Modelling
Jasmina Petrova, Gergana Gocheva, Nikoleta Ivanova, Stoyan Iliev, Boyana Atanasova, Galia Madjarova, Anela Ivanova
The study is focused on description of folate and several antifolates at physiological conditions. Knowledge of the molecular structure and dynamics is important for understanding their biological activity and therapeutic application. They are modelled in saline by atomistic molecular dynamics simulations and characterized in detail. In addition, quantum chemical calculations are used for determining the electronic structure of the six compounds. All molecules are highly flexible and have similar interactions with water...
December 4, 2018: Journal of Molecular Graphics & Modelling
Amira Abdelraheem, Ahmed H El-Shazly, Marwa Elkady
With raising awareness of gaseous air pollutants and their harmful impact, adsorption is considered one of the most prominent techniques for gaseous emissions control. The usage of polyaniline as a gas adsorbent is an innovative idea. This work aims to compare the efficacy of synthesized polyaniline nanotubes (PANT) as a novel adsorbent towards inorganic gases (ammonia NH3 ) and volatile organic compounds (toluene vapor). PANT was prepared via a sol-gel preparation technique. The molecular structure of prepared PANT was characterized by Fourier-transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD)...
December 14, 2018: Environmental Science and Pollution Research International
Abbas Tanhaeian, Mahmoud Reza Jaafari, Farajollah Shahriari Ahmadi, Roghayyeh Vakili-Ghartavol, Mohammad Hadi Sekhavati
Nowadays, cancer remains a major cause of death affecting millions of people. Currently, the antimicrobial peptides (AMPs) as potent anticancer therapeutic agents offer specificity and low levels of side effects in cancer therapy. In the present study, a cationic chimeric peptide (cLFchimera), derived from camel lactoferrin, was expressed as a secretory peptide using P170 expression system in L. lactis. Peptide purification was carried out using Ni-NTA agarose column from culture medium with 21 μ/mL concentration...
December 14, 2018: Probiotics and Antimicrobial Proteins
Fei Zheng, Josh V Vermaas, Jie Zheng, Yuan Wang, Tao Tu, Xiaoyu Wang, Xiangming Xie, Bin Yao, Gregg T Beckham, Huiying Luo
Cellulases from glycoside hydrolase (GH) family 5 are key endoglucanase enzymes in the degradation of diverse polysaccharide substrates and are used in industrial enzyme cocktails to break down biomass. The GH5 family shares a canonical (βα)8 -barrel structure, where each (βα) module is essential for the enzyme stability and activity. Despite their shared topology, the thermostability of GH5 endoglucanase enzymes can vary significantly, and highly thermostable variants are often sought for industrial applications...
December 14, 2018: Applied and Environmental Microbiology
Jiong Ning, Rui Li, Jie Ren, Dongting Zhangsun, Xiaopeng Zhu, Yong Wu, Sulan Luo
Recently, the muscle-type nicotinic acetylcholine receptors (nAChRs) have been pursued as a potential target of several diseases, including myogenic disorders, muscle dystrophies and myasthenia gravis, etc. α-conotoxin GI isolated from Conus geographus selectively and potently inhibited the muscle-type nAChRs which can be developed as a tool to study them. Herein, alanine scanning mutagenesis was used to reveal the structure⁻activity relationship (SAR) between GI and mouse α1β1δε nAChRs. The Pro⁵, Gly⁸, Arg⁸, and Tyr11 were proved to be the critical residues for receptor inhibiting as the alanine (Ala) replacement led to a significant potency loss on mouse α1β1δε nAChR...
December 13, 2018: Marine Drugs
Ganjun Yuan, Li Xu, Xuejie Xu, Peibo Li, Qiwang Zhong, Hailin Xia, Yamei Hu, Pingyi Li, Xiaoyuan Song, Junfang Li, Qianru Liu
Azalomycin F5a was a polyhydroxy macrolide produced by streptomycete strains. Our preliminary researches indicated that it could kill methicillin-resistant Staphylococcus aureus (MRSA) likely by increasing the permeability of cell membrane, and that cell-membrane phospholipids were likely important targets. To confirm this, membrane permeability assay was performed and visualized by fluorescence staining, and then the detailed interactions between azalomycin F5a and model membranes prepared with 1,2-dihexadecanoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DPPG) were determined using attenuated total reflectance fourier transform infrared spectroscopy and 31 P nuclear magnetic resonance techniques...
January 2019: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Keigo Gohda
Recent computational simulations on protein-ligand binding/unbinding have precisely been uncovering the ligand-binding process at the atomic level. In the process, the non-specific binding of ligands to the target site is suggested to occur before binding to the target. We in this study analyzed the conformations of ligands under the non-specific binding on a protein surface to figure out the differences in the conformational characteristics in aqueous solution using the 55-ns molecular dynamic simulation. As for the protein surface, we constructed an artificial β-sheet, composed of poly-alanine residues (Ala-sheet)...
December 3, 2018: Journal of Molecular Graphics & Modelling
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