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MD simulation

Sridhar Kumar Kannam, Daniel P Oehme, Monika S Doblin, Michael J Gidley, Antony Bacic, Matthew T Downton
There is increasing experimental and computational evidence that cellulose microfibrils can exist in a stable twisted form. In this study, atomistic molecular dynamics (MD) simulations are performed to investigate the importance of intrachain hydrogen bonds on the twist in cellulose microfibrils. We systematically enforce or block the formation of these intrachain hydrogen bonds by either constraining dihedral angles or manipulating charges. For the majority of simulations a consistent right handed twist is observed...
November 1, 2017: Carbohydrate Polymers
Sergey Shityakov, Norbert Roewer, Carola Förster, Jens-Albert Broscheit
All-atom molecular dynamics (MD) simulations are presented on general anesthetic propofol bound to human serum albumin (HSA) due to the drug pharmacokinetics and pharmacodynamics in the circulatory system. We implemented the explicit and implicit solvation models to compare the binding affinity of propofol at the different binding sites (PR1 and PR2) in the HSA protein. Only the implicit solvation models provided the evidence in accordance with the experimental data indicating that the HSA-ligand interactions are dominanted by hydrophobic forces due to the higher drug affinity at the PR1 position with a ΔGMM-PB/SA value of -23...
July 4, 2017: Computational Biology and Chemistry
Tao Jiang, Kuai Yu, H Criss Hartzell, Emad Tajkhorshid
From bacteria to mammals, different phospholipid species are segregated between the inner and outer leaflets of the plasma membrane by ATP-dependent lipid transporters. Disruption of this asymmetry by ATP-independent phospholipid scrambling is important in cellular signaling, but its mechanism remains incompletely understood. Using MD simulations coupled with experimental assays, we show that the surface hydrophilic transmembrane cavity exposed to the lipid bilayer on the fungal scramblase nhTMEM16 serves as the pathway for both lipid translocation and ion conduction across the membrane...
September 16, 2017: ELife
Md Symon Jahan Sajib, Mohammadreza Samieegohar, Tao Wei, Katherine Shing
Ethylene production plays a key role in the petrochemical industry. The severe operation conditions of ethylene thermal cracking, such as high-temperature and coke-formation, pose challenges for the development of new corrosion-resistant and coking-resistant materials for ethylene reactor radiant coils tubes (RCTs). We investigated the performance of ceramic materials such as silicon carbide (SiC) in severe pyrolysis conditions by using reactive forcefield molecular dynamics (ReaxFF MD) simulation method. Our results indicate that β-SiC surface remains fully stable at 1500 K, whereas increased temperature results in melted interface...
September 15, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Lucas Sawle, Jonathan Huihui, Kingshuk Ghosh
Thermophilic proteins denature at much higher temperature compared to their mesophilic homologues, in spite of high structural and sequential similarity. Computational approaches to understand this puzzle faces three major challenges: i) unfolded ensembles are usually neglected, ii) simulation studies of the folded states are often too short and iii) majority of investigations focus on a few protein pairs, obscuring the prevalence of different strategies across multiple protein systems. We address these concerns by carrying out all-atom simulations to characterize physicochemical properties of both the folded and disordered ensemble in multiple (12) thermophilic-mesophilic homologous protein pairs...
September 15, 2017: Journal of Chemical Theory and Computation
Matthias Ernst, Steffen Wolf, Gerhard Stock
While adequately chosen reaction coordinates are expected to reveal the mechanism of a dynamical process, it proves to be notoriously difficult to model the complex structural rearrangement of a macromolecule by a low-dimensional collective coordinate. Adopting the hinge-bending motion of T4 lysozyme (T4L) as a prominent example and performing a 50 microsecond long unbiased molecular dynamics (MD) simulation of T4L, a general strategy to identify reaction coordinates of protein functional dynamics is developed...
September 15, 2017: Journal of Chemical Theory and Computation
Marianne T Luetmer, Beth A Cloud, James W Youdas, Wojciech Pawlina, Nirusha Lachman
Quality of healthcare delivery is dependent on collaboration between professional disciplines. Integrating opportunities for interprofessional learning in health science education programs prepares future clinicians to function as effective members of a multi-disciplinary care team. This study aimed to create a modified team-based learning (TBL) environment utilizing ultrasound technology during an interprofessional learning activity to enhance musculoskeletal anatomy knowledge of first year medical (MD) and physical therapy (PT) students...
September 15, 2017: Anatomical Sciences Education
Tsvetan G Gantchev, Peicho St Petkov, Darel J Hunting
The major structural aberrations of DNA induced by a cis-diammineplatinum (II) 1,2-d(GG) intrastrand cross-link (CPT) have been known for decades. To gain deeper insights into the structural dynamics of the sequence-dependent DNA distortions adjacent to the CPT adduct, we employed molecular modeling and molecular dynamics (MD) simulations. The structural dynamics of native (N-DNA) and cisPt 1,2-d(GG) crosslinked (CPT-DNA) in the form of symmetric 36 nt d(G2T15G*G*T15G2)●C2A15CCA15C2) oligonucleotide duplexes is compared...
September 14, 2017: Journal of Molecular Modeling
Nandakumar Rajasekaran, Ashok Sekhar, Athi N Naganathan
Understanding the extent to which information is transmitted through the intra-molecular interaction network of proteins upon a perturbation, i.e. an allosteric effect, has long remained an unsolved problem. Through an analysis of high-resolution NMR data from the literature on 28 different proteins and 49 structural perturbations, we show that the extent of induced structural changes through mutations, and molecular events including protein-protein, protein-peptide, protein-ligand binding and post-translational modifications exhibit a near-universal exponential functional form...
September 14, 2017: Journal of Physical Chemistry Letters
Oliviero Andreussi, Ingrid Guarnetti Prandi, Marco Campetella, Giacomo Prampolini, Benedetta Mennucci
Classical molecular dynamics is more and more often coupled to quantum mechanical based techniques as statistical tool to sample configurations of molecular systems embedded in complex environments. Nonetheless, the classical potentials describing the molecular systems are seldom parameterized to reproduce electronic processes, such as electronic excitations, which are instead very sensitive to the underlining description of the molecular structure. Here we analyze the challenging case of the peridinin molecule, a natural apocarotenoid responsible for the light-harvesting process in the PCP antenna protein of dinoflagellates...
September 14, 2017: Journal of Chemical Theory and Computation
Debabrata Pramanik, Prabal K K Maiti
Separation and sorting of pristine carbon nanotubes (CNTs) from bundle geometry is a very challenging task due to non-soluble and non-dispersive nature of CNTs in aqueous medium. Recently many studies have been performed to address this problem using various organic and inorganic solutions, surfactant molecules and biomolecules as dispersing agents. Recent experimental studies have reported the DNA to be highly efficient in dispersion of CNTs from bundle geometry. But there is no microscopic study and also quantitative estimation of the dispersion efficiency of the DNA...
September 14, 2017: ACS Applied Materials & Interfaces
Matthew McDougall, Olga Francisco, Candice Viddal, Roy Roshko, Markus Meier, Jörg Stetefeld
Elemental sulfur exists primarily as an S80 ring and serves as terminal electron acceptor for a variety of Sulfur-fermenting bacteria. Hyperthermophilic archaea from black smoker vents are an exciting research tool to advance our knowledge of sulfur respiration under extreme conditions. Here we use a hybrid method approach to demonstrate that the proteinaceous cavities of the S-layer nanotube of the hyperthermophilic archaeon Staphylothermus marinus act as a storage reservoir for cyclo-octasulfur S(8) . Fully atomistic molecular dynamics simulations were performed and the method of Multi-Configurational Thermodynamic Integration was employed to compute the absolute free energy for transferring a ring of elemental sulfur S8 from an aqueous bath into the largest hydrophobic cavity of a fragment of archaeal tetrabrachion...
September 14, 2017: Proteins
Mohamed M Aboelnga, John J Hayward, James W Gauld
Glutaminyl-tRNA synthetase (GlnRS) catalyzes the aminoacylation of glutamine to the corresponding tRNA(Gln). However, most bacteria and all archaea lack GlnRS and thus an indirect noncanonical aminoacylation is required. With the assistance of a non-discriminating version of Glutamyl-tRNA synthetases (ND-GluRS) the tRNA(Gln) is misaminoacylated by glutamate. In this study, we have computationally investigated the aminoacylation mechanism in GlnRS and ND-GluRS employing Molecular Dynamics (MD) simulations, Quantum Mechanics (QM) cluster and Quantum Mechanics/Molecular Mechanics (QM/MM) calculations...
September 14, 2017: Physical Chemistry Chemical Physics: PCCP
Xiaorong Liu, Zhiguang Jia, Jianhan Chen
Anti-apoptotic Bcl-xL plays central roles in regulating programed cell death. Partial unfolding of Bcl-xL has been observed at the interface upon specific binding to the pro-apoptotic BH3-only protein PUMA, which in turn disrupts the interaction of Bcl-xL with tumor suppressor p53 and promotes apoptosis. Previous analysis of existing Bcl-xL structures and atomistic molecular dynamics (MD) simulations have suggested that substantial intrinsic structure heterogeneity exists at the BH3-only protein binding interface of Bcl-xL to facilitate its conformational transitions upon binding...
September 13, 2017: Journal of Physical Chemistry. B
S Sahmani, M M Aghdam, M Bahrami
Understanding the size-dependent behavior of structures at nanoscale is essential in order to have an effective design of nanosystems. In the current investigation, the surface elasticity theory is extended to study the nonlinear buckling and postbuckling response of axially loaded silicon cylindrical naoshells. Thereby, an efficient size-dependent shear deformable shell model is developed including the size effect of surface free energy. A boundary layer theory of shell buckling in conjunction with a perturbation-based solution methodology is employed to predict the size dependency in the buckling loads and postbuckling behavior of silicon nanoshells having various thicknesses...
August 24, 2017: Journal of Molecular Graphics & Modelling
Kai Liu, Hironori Kokubo
Docking has become an indispensable approach in drug discovery research to predict the binding mode of a ligand. One great challenge in docking is to efficiently refine the correct pose from various putative docking poses through score functions. We recently examined the stability of self-docking poses under molecular dynamics (MD) simulations and showed that equilibrium MD simulations have some capability to discriminate between correct and decoy poses. Here, we have extended our previous work to cross-docking studies for practical applications...
September 13, 2017: Journal of Chemical Information and Modeling
Tahsin F Kellici, Maria V Chatziathanasiadou, Min-Sung Lee, Nisar Sayyad, Elena G Geromichalou, Eirinaios I Vrettos, Antonis D Tsiailanis, Seung-Wook Chi, George D Geromichalos, Thomas Mavromoustakos, Andreas G Tzakos
Anti-apoptotic proteins, like the Bcl-2 family proteins, present an important therapeutic cancer drug target. Their activity is orchestrated through neutralization upon interaction of pro-apoptotic protein counterparts that leads to immortality of cancer cells. Therefore, generating compounds targeting these proteins is of immense therapeutic importance. Herein, Induced Fit Docking (IFD) and Molecular Dynamics (MD) simulations were performed to rationally design quercetin analogues that bind in the BH3 site of the Bcl-xL protein...
September 13, 2017: Organic & Biomolecular Chemistry
Sanjay Basu, Bruce E Landon, John W Williams, Asaf Bitton, Zirui Song, Russell S Phillips
BACKGROUND: New payments from Medicare encourage behavioral health services to be integrated into primary care practice activities. OBJECTIVE: To evaluate the financial impact for primary care practices of integrating behavioral health services. DESIGN: Microsimulation model. PARTICIPANTS: We simulated patients and providers at federally qualified health centers (FQHCs), non-FQHCs in urban and rural high-poverty areas, and practices outside of high-poverty areas surveyed by the National Association of Community Health Centers, National Ambulatory Medical Care Survey, National Health and Nutrition Examination Survey, and National Health Interview Survey...
September 12, 2017: Journal of General Internal Medicine
Volker Knecht, Günter Reiter, Renate Reiter
The emergence of polymer-free water surface in a Langmuir polymer films at conditions where a homogeneous coverage has been expected previously is explained on the basis of the surface tensions of polymer and water, γ_(pv) and γ_(wv), respectively, as well as the interfacial tension between the two materials, γ_(pw). The polymer molecules considered are 22-residue poly(γ-benzyl-L-glutamate)(PBLG) peptides in α-helical conformation. Values for γ_(pv) and γ_(pw) derived from MD simulations are consistent with values inferred from experiments considering the emergence of polymer-free surface area for ultra thin films studied using the surface forces apparatus in earlier work...
September 12, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Nathalie Clement, Nicolas Renault, Jean-Luc Guillaume, Erika Cecon, Anne-Sophie Journé, Xavier Laurent, Kenjiro Tadagaki, Francis Cogé, Arnaud Gohier, Philippe Delagrange, Philippe Chavatte, Ralf Jockers
BACKGROUND AND PURPOSE: Recent crystal structures of G protein-coupled receptors (GPCRs) highlight the previously unappreciated role of the 2(nd) extracellular (E2) loop in ligand binding and gating and receptor activation. Here we studied the role of the E2 loop in the activation of the melatonin MT1 receptor (MT1 ) and in the inactivation of the closely related orphan GPR50 receptor. EXPERIMENTAL APPROACH: Chimeric MT1 -GPR50 receptors were generated and analyzed for 2-[(125) I]iodomelatonin binding, Gi /cAMP signaling and β-arrestin 2 recruitment assisted by computational molecular dynamics (MD) simulations...
September 12, 2017: British Journal of Pharmacology
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