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https://www.readbyqxmd.com/read/28644624/extensive-assessment-of-various-computational-methods-for-aspartate-s-pka-shift
#1
Zhaoxi Sun, Xiaohui Wang, Jianing Song
A series of computational methods for pKa shift prediction are extensively tested on a set of benchmark protein systems, aiming at identifying pitfalls and evaluating their performance on high variants. Including 19 ASP residues in 10 protein systems, the benchmark set consists of both residues with highly shifted pKa values as well as those varying little from the reference value, with an experimental RMS free energy differences of 2.49 kcal/mol with respect to blocked amino acid, namely the RMS pKa shift being 1...
June 23, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28644500/in-situ-nanomechanical-characterization-of-multi-layer-mos2-membranes-from-intraplanar-to-interplanar-fracture
#2
Peifeng Li, Chenchen Jiang, Shang Xu, Yu Zhuang, Libo Gao, Alice Hu, Hongtao Wang, Yang Lu
Layered molybdenum disulfide (MoS2) exhibits rich electronic and optical properties and possesses vastly differing characteristic dimensions. A multi-layer MoS2 membrane represents the critical hierarchical structure which bridges the length-scale of monolayer and bulk material architectures. In this study, the in-plane mechanical properties of MoS2 membranes were investigated by in situ SEM tensile testing. Under the uniaxial tensile loading, brittle fracture caused failure in a highly localized region of the MoS2 membranes and their mechanical properties showed a thickness effect: the strengths of the relatively thicker MoS2 membranes (thickness around hundreds of nanometers) distribute from ∼100 to ∼250 MPa, while the corresponding values of the MoS2 nanosheets (thickness around tens of nanometers) increase significantly to more than 1 GPa...
June 23, 2017: Nanoscale
https://www.readbyqxmd.com/read/28641432/local-structure-of-dilute-aqueous-dmso-solutions-as-seen-from-molecular-dynamics-simulations
#3
Abdenacer Idrissi, Bogdan A Marekha, Mohammed Barj, François Alexandre Miannay, Toshiyuki Takamuku, Vasilios Raptis, Jannis Samios, Pál Jedlovszky
The information about the structure of dimethyl sulfoxide (DMSO)-water mixtures at relatively low DMSO mole fractions is an important step in order to understand their cryoprotective properties as well as the solvation process of proteins and amino acids. Classical MD simulations, using the potential model combination that best reproduces the free energy of mixing of these compounds, are used to analyze the local structure of DMSO-water mixtures at DMSO mole fractions below 0.2. Significant changes in the local structure of DMSO are observed around the DMSO mole fraction of 0...
June 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28641267/a-cpu-mic-collaborated-parallel-framework-for-gromacs-on-tianhe-2-supercomputer
#4
Shaoliang Peng, Shunyun Yang, Wenhe Su, Xiaoyu Zhang, Tenglilang Zhang, Weiguo Liu, Xingming Zhao
Molecular Dynamics (MD) is the simulation of the dynamic behavior of atoms and molecules. As the most popular software for molecular dynamics, GROMACS cannot work on large-scale data because of limit computing resources. In this paper, we propose a CPU and Intel® Xeon Phi Many Integrated Core (MIC) collaborated parallel framework to accelerate GROMACS using the offload mode on a MIC coprocessor, with which the performance of GROMACS is improved significantly, especially with the utility of Tianhe-2 supercomputer...
June 16, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28641189/qualitative-and-quantitative-simulation-of-androgen-receptor-antagonists-a-case-study-of-polybrominated-diphenyl-ethers
#5
Yang Wu, Wei Shi, Pu Xia, Xiaowei Zhang, Hongxia Yu
Recently, great attention has been paid to the identification and prediction of the androgen disrupting potencies of polybrominated diphenyl ethers (PBDEs). However, few existing models can discriminate active and inactive compounds, which make the quantitative prediction process including the quantitative structure-activity relationship (QSAR) technique unreliable. In this study, different grouping methods were investigated and compared for qualitative identification, including molecular docking and molecular dynamics simulations (MD)...
June 19, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28640620/using-complementary-nmr-data-sets-to-detect-inconsistencies-and-model-flaws-in-the-structure-determination-of-human-interleukin-4
#6
Lorna J Smith, Wilfred F van Gunsteren, Niels Hansen
The derivation of protein structure from values of observable quantities measured in NMR experiments is a rather non-trivial task due to (i) the limited number of data compared to degrees of freedom of a protein, (ii) the uncertainty inherent to the function connecting an observable quantity to molecular structure, (iii) the finite quality of biomolecular models and force fields used in structure refinement, and (iv) the conformational freedom of a protein in aqueous solution, which requires extensive conformational sampling and appropriate conformational averaging when calculating or restraining to sets of NMR data...
June 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28640581/molecular-insight-of-water-desalination-across-multilayer-graphene-oxide-membranes
#7
Bo Chen, Haifeng Jiang, Xiang Liu, Xuejiao Hu
Transport of ionic solutions through graphene oxide (GO) membranes is a complicated issue because the complex and tortuous structure inside make it very hard to clarify. Using molecular dynamics (MD) simulations, we investigated the mechanism of water transport and ions movement across the multilayer graphene oxide. The significant flow rate is considerably influenced by the structural parameters of GO membranes. Due to the size effect on shrunken real flow area, there is disagreement between classical continuum model and nano-scaled flow...
June 22, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28640309/computational-analysis-of-histidine-mutations-on-the-structural-stability-of-human-tyrosinases-leading-to-albinism-insurgence
#8
Mubashir Hassan, Qamar Abbas, Hussain Raza, Ahmed A Moustafa, Sung-Yum Seo
Misfolding and structural alteration in proteins lead to serious malfunctions and cause various diseases in humans. Mutations at the active binding site in tyrosinase impair structural stability and cause lethal albinism by abolishing copper binding. To evaluate the histidine mutational effect, all mutated structures were built using homology modelling. The protein sequence was retrieved from the UniProt database, and 3D models of original and mutated human tyrosinase sequences were predicted by changing the residual positions within the target sequence separately...
June 22, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28639260/improving-thermostability-of-r-selective-amine-transaminase-from-aspergillus-terreus-through-introduction-of-disulfide-bonds
#9
Dong-Fang Xie, Hui Fang, Jia-Qi Mei, Jin-Yan Gong, Hong-Peng Wang, Xiu-Ying Shen, Jun Huang, Le-He Mei
To improve the thermostability of (R)-selective amine transaminase from Aspergillus terreus (AT-ATA), we used computer software Disulfide by Design (DbD) and Modelling of Disulfide Bonds in Proteins (MODIP) to identify mutation sites where the disulfide bonds were most likely to form. We obtained three stabilised mutants (N25C-A28C, R131C-D134C, M150C-M280C) from seven candidates by site-directed mutagenesis. Compared to the wild-type, the best two mutants N25C-A28C and M150C-M280C showed improved thermal stability with a 3...
June 21, 2017: Biotechnology and Applied Biochemistry
https://www.readbyqxmd.com/read/28637405/molecular-dynamics-simulations-challenges-and-opportunities-a-biologist-s-prospective
#10
Indu Kumari, Padmani Sandhu, Mushtaq Ahmed, Yusuf Akhter
Molecular dynamics (MD) is a computational technique which is used to study biomolecules in virtual environment. Each of the constituent atoms represents a particle and hence the biomolecule embodies a multi-particle mechanical system analyzed within a simulation box during MD analysis. The potential energies of the atoms are explained by a mathematical expression consisting of different forces and space parameters. There are various software and force fields that have been developed for MD studies of the biomolecules...
June 21, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28636916/structural-behavior-of-the-peptaibol-harzianin-hk-vi-in-a-dmpc-bilayer-insights-from-md-simulations
#11
Marina Putzu, Sezgin Kara, Sergii Afonin, Stephan L Grage, Andrea Bordessa, Grégory Chaume, Thierry Brigaud, Anne S Ulrich, Tomáš Kubař
Microsecond molecular dynamics simulations of harzianin HK VI (HZ) interacting with a dimyristoylphosphatidylcholine bilayer were performed at the condition of low peptide-to-lipid ratio. Two orientations of HZ molecule in the bilayer were found and characterized. In the orientation perpendicular to the bilayer surface, HZ induces a local thinning of the bilayer. When inserted into the bilayer parallel to its surface, HZ is located nearly completely within the hydrophobic region of the bilayer. A combination of solid-state NMR and circular dichroism experiments found the latter orientation to be dominant...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636914/peptide-protein-binding-investigated-by-far-ir-spectroscopy-and-molecular-dynamics-simulations
#12
Yoann Cote, Yves Nominé, Juan Ramirez, Petra Hellwig, Roland H Stote
Molecular dynamics (MD) simulations and far-infrared (far-IR) spectroscopy were combined to study peptide binding by the second PDZ domain (PDZ1) of MAGI1, which has been identified as an important target for the Human Papilloma Virus. PDZ1 recognizes and binds to the C-terminal end of the E6 protein from high-risk Human Papilloma Virus. The far-IR spectra of two forms of the protein, an unbound APO form and a HOLO form (where the PDZ1 is bound to an 11-residue peptide derived from the C terminus of HPV16 E6), were obtained...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636909/electric-field-induced-protein-translocation-via-a-conformational-transition-in-secdf-an-md-study
#13
Emel Ficici, Daun Jeong, Ioan Andricioaei
SecDF is an important component of the Sec protein translocation machinery embedded in the bacterial membrane, which is associated with many functions, such as stabilizing other Sec translocon components within the membrane, maintaining the transmembrane (TM) potential, and facilitating the ATP-independent stage of the translocation mechanism. Related studies suggest that SecDF undergoes functionally important conformational changes that involve mainly its P1-head domain and that these changes are coupled with the proton motive force (Δp)...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636905/a-kepler-workflow-tool-for-reproducible-amber-gpu-molecular-dynamics
#14
Shweta Purawat, Pek U Ieong, Robert D Malmstrom, Garrett J Chan, Alan K Yeung, Ross C Walker, Ilkay Altintas, Rommie E Amaro
With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28634293/intrinsic-map-dynamics-exploration-for-uncharted-effective-free-energy-landscapes
#15
Eliodoro Chiavazzo, Roberto Covino, Ronald R Coifman, C William Gear, Anastasia S Georgiou, Gerhard Hummer, Ioannis G Kevrekidis
We describe and implement a computer-assisted approach for accelerating the exploration of uncharted effective free-energy surfaces (FESs). More generally, the aim is the extraction of coarse-grained, macroscopic information from stochastic or atomistic simulations, such as molecular dynamics (MD). The approach functionally links the MD simulator with nonlinear manifold learning techniques. The added value comes from biasing the simulator toward unexplored phase-space regions by exploiting the smoothness of the gradually revealed intrinsic low-dimensional geometry of the FES...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28633355/how-proteins-bind-to-dna-target-discrimination-and-dynamic-sequence-search-by-the-telomeric-protein-trf1
#16
Milosz Wieczór, Jacek Czub
Target search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments of chromosomal DNA. In this study, we use extensive (>0.5 ms in total) MD simulations to study the dynamical aspects of sequence-specific binding of TRF1 at both telomeric and non-cognate DNA...
June 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28632973/molecular-modeling-study-on-the-tubulin-binding-modes-of-epothilone-derivatives-insight-into-the-structural-basis-for-epothilones-activity
#17
Verónica A Jiménez, Joel B Alderete, Karen R Navarrete
Molecular dynamics (MD) simulations were employed to study the tubulin-binding modes of 20 epothilone derivatives spanning a wide range of antitumor activity. Trajectory analysis revealed that active ligands shared a common region of association and similar binding poses compared to the high-resolution crystal structure of the tubulin complex with epothilone A, the stathmin-like protein RB3, and tubulin tyrosine ligase (PDB code 4I50). Conformational analysis of epothilones in aqueous solution and tubulin-bound states indicated that the bound conformations of active species can be found to a significant extent within the ensemble of conformers available in aqueous solution...
June 20, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28632421/novel-urushiol-derivatives-as-hdac8-inhibitors-rational-design-virtual-screening-molecular-docking-and-molecular-dynamics-studies
#18
Hao Zhou, Chengzhang Wang, Tao Deng, Ran Tao, Wenjun Li
Three series of novel urushiol derivatives were designed by introducing a hydroxamic acid moiety into the tail of an alkyl side chain and substituents with differing electronic properties or steric bulk onto the benzene ring and alkyl side chain. The compounds' binding affinity towards HDAC8 was screened by Glide docking. The highest-scoring compounds were processed further with molecular docking, MD simulations and binding free energy studies to analyze the binding modes and mechanisms. Ten compounds had Glide scores of -8...
June 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28632385/fatigue-resistant-bioinspired-composite-from-synergistic-two-dimensional-nanocomponents
#19
Sijie Wan, Qi Zhang, Xiaohang Zhou, Dechang Li, Baohua Ji, Lei Jiang, Qunfeng Cheng
Portable and wearable electronics require much more flexible graphene-based electrode with high fatigue life, which could repeatedly bend, fold, or stretch without sacrificing its mechanical properties and electrical conductivity. Herein, a kind of ultrahigh fatigue resistant graphene-based nanocomposite via tungsten disulfide (WS2) nanosheets is synthesized by introducing a synergistic effect with covalently cross-linking inspired by the orderly layered structure and abundant interfacial interactions of nacre...
June 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/28629581/impact-of-a-teamstepps-trauma-nurse-academy-at-a-level-1-trauma-center
#20
V Kristen Peters, Ellen M Harvey, Andi Wright, Jennifer Bath, Dan Freeman, Bryan Collier
PROBLEM: Nurses are crucial members of the team caring for the acutely injured trauma patient. Until recently, nurses and physicians gained an understanding of leadership and supportive roles separately. With the advent of a multidisciplinary team approach to trauma care, formal team training and simulation has transpired. METHODS: Since 2007, our Level I trauma system has integrated TeamSTEPPS (Team Strategies & Tools to Enhance Performance & Patient Safety; Agency for Healthcare Research and Quality, Rockville, MD) into our clinical care, joint training of nurses and physicians, using simulations with participation of all health care providers...
June 16, 2017: Journal of Emergency Nursing: JEN: Official Publication of the Emergency Department Nurses Association
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