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https://www.readbyqxmd.com/read/28351017/performance-of-a-docking-molecular-dynamics-protocol-for-virtual-screening-of-nutlin-class-inhibitors-of-mdmx
#1
Nagakumar Bharatham, Kristin E Finch, Jaeki Min, Anand Mayasundari, Michael A Dyer, R Kiplin Guy, Donald Bashford
A virtual screening protocol involving docking and molecular dynamics has been tested against the results of fluorescence polarization assays testing the potency of a series of compounds of the nutlin class for inhibition of the interaction between p53 and Mdmx, an interaction identified as a driver of certain cancers. The protocol uses a standard docking method (AutoDock) with a cutoff based on the AutoDock score (ADscore), followed by molecular dynamics simulation with a cutoff based on root-mean-square-deviation (RMSD) from the docked pose...
February 24, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28350956/improving-the-performance-of-hybrid-functional-based-molecular-dynamics-simulation-through-screening-of-hartree-fock-exchange-forces
#2
Guido Falk von Rudorff, Rasmus Jakobsen, Kevin M Rosso, Jochen Blumberger
Density functional theory-based molecular dynamics calculations of condensed phase systems often benefit from the use of hybrid functionals. However, their use is computationally very demanding and severely limits the system size and time scale that can be simulated. Several methods have been introduced to accelerate hybrid functional molecular dynamics including Schwarz screening and the auxiliary density matrix method (ADMM). Here we present a simple screening scheme that can be applied in addition to these methods...
March 28, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28346838/hiv-1-transmission-networks-across-south-korea
#3
Mi Young Ahn, Joel O Wertheim, Woo Joo Kim, Shin-Woo Kim, Jin Soo Lee, Hea Won Ann, Yongduk Jeon, Jin Young Ahn, Je Eun Song, Dong Hyun Oh, Yong Chan Kim, Eun Jin Kim, In Young Jung, Moo Hyun Kim, Wooyoung Jeong, Su Jin Jeong, Nam Su Ku, June Myung Kim, Davey M Smith, Jun Yong Choi
Molecular epidemiology can help clarify the properties and dynamics of HIV-1 transmission networks in both global and regional scales. We studied 143 HIV-1-infected individuals recruited from four medical centers of three cities in South Korea between April 2013 and May 2014. HIV-1 env V3 sequence data were generated (337-793 bp) and analyzed using a pairwise distance-based clustering approach to infer putative transmission networks. Participants whose viruses were ≤2.0% divergent according to Tamura-Nei 93 genetic distance were defined as clustering...
March 27, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28346821/structure-activity-relationships-on-cynnamoyl-derivatives-as-inhibitors-of-p300-histone-acetyltransferase
#4
Valentina Noemi Madia, Rosaria Benedetti, Maria Letizia Barreca, Liza Ngo, Luca Pescatori, Antonella Messore, Giovanni Pupo, Francesco Saccoliti, Sergio Valente, Antonello Mai, Luigi Scipione, Yujun George Zheng, Cristina Tintori, Maurizio Botta, Violetta Cecchetti, Lucia Altucci, Roberto Di Santo, Roberta Costi
Human p300 is a polyhedric transcriptional coactivator, playing a crucial role by acetylating histones on specific lysine residues. A great deal of evidences shows that p300 is involved in several diseases as leukemia, tumors and viral infection. Its involvement in pleiotropic biological roles and connections to diseases provide the rationale as to how its modulation could represent an amenable drug target. Several p300 inhibitors (HATi) have been described so far, but all suffer from low potency, lack of specificity or low cell-permeability, highlighting the need to find more effective inhibitors...
March 27, 2017: ChemMedChem
https://www.readbyqxmd.com/read/28346778/direct-measurement-of-the-angular-pair-correlations-coefficients-in-molecular-liquids-using-nmr-benchmarking-force-fields-for-atomistic-simulations
#5
Leah Marie Heist, Chi-Duen Poon, Edward Thaddeus Samulski, Demetri J Photinos
High field deuterium NMR spectroscopy is used to characterize a number of molecular liquids and their mixtures in order to probe the directional part of the intermolecular interactions through the orientational ordering induced in the isotropic liquid phase by the spectrometer magnetic field. The systems studied include benzene, chloroform, hexafluorobenzene and thiophene at various concentrations and in mixtures. Dilution with the magnetically isotropic tetramethylsilane provides quantification of ordering at "infinite magnetic dilution", i...
March 27, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28346776/proton-exchange-in-a-paramagnetic-chemical-exchange-saturation-transfer-agent-from-experimental-studies-and-ab-initio-metadynamics-simulation
#6
Rodolphe Pollet, Célia S Bonnet, Pascal Retailleau, Philippe Durand, Éva Tóth
The proton-exchange process between water and a carbamate has been studied experimentally and theoretically in a lanthanide-based paramagnetic chemical exchange saturation transfer agent endowed with potential multimodality detection capabilities (optical imaging, or T1 MRI for the Gd(III) analogue). In addition to an in-depth structural analysis by a combined approach (using X-ray crystallography, NMR, and molecular dynamics), our ab initio simulation in aqueous solution sheds light on the reaction mechanism for this proton exchange, which involves structural Grotthuss diffusion...
March 27, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28346547/a-controllable-water-signal-transistor
#7
Lili Wu, Xiaoyan Zhou, Hangjun Lu, Qing Liang, Jianlong Kou, Fengmin Wu, Jintu Fan
We performed molecular dynamics simulations to study the regulating ability of water chains confined in a Y-shaped nanochannel. It was shown that a signal at the molecular level could be controlled by two other charge-induced signals when the water chains were confined in a Y-shaped nanochannel, demonstrating promising applications as water signal transistors in nanosignal systems. The mechanism of a water signal transistor is similar to a signal logic device. This remarkable ability to control the water signal is attributed to the strong dipole-ordering of the water chains in the nanochannel...
March 27, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28346365/an-amylase-like-protein-amyd-is-the-major-negative-regulator-for-%C3%AE-glucan-synthesis-in-aspergillus-nidulans-during-the-asexual-life-cycle
#8
Xiaoxiao He, Shengnan Li, Susan Kaminskyj
α-Glucan affects fungal cell-cell interactions and is important for the virulence of pathogenic fungi. Interfering with production of α-glucan could help to prevent fungal infection. In our previous study, we reported that an amylase-like protein, AmyD, could repress α-glucan accumulation in Aspergillus nidulans. However, the underlying molecular mechanism was not clear. Here, we examined the localization of AmyD and found it was a membrane-associated protein. We studied AmyD function in α-glucan degradation, as well as with other predicted amylase-like proteins and three annotated α-glucanases...
March 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28346078/molecular-dynamics-simulation-of-three-plastic-additives-diffusion-in-polyethylene-terephthalate
#9
Bo Li, Zhi-Wei Wang, Qin-Bao Lin, Chang-Ying Hu
Accurate diffusion coefficient data of additives in polymer is of paramount importance for estimating the migration of the additives over time. In this article it is shown how this diffusion coefficient can be estimated for three plastic additives [2-(2'-hydroxy-5'-methylphenyl) (UV-P), 2, 6-di-tert-butyl-4-methylphenol (BHT) and di-(2-ethylhexyl) phthalate (DEHP)] in polyethylene terephthalate (PET) using the molecular dynamics (MD) simulation method. MD simulations were performed at temperatures of 293-433 K...
March 27, 2017: Food Additives & Contaminants. Part A, Chemistry, Analysis, Control, Exposure & Risk Assessment
https://www.readbyqxmd.com/read/28345935/targeting-self-binding-peptides-as-a-novel-strategy-to-regulate-protein-activity-and-function-a-case-study-on-the-proto-oncogene-tyrosine-protein-kinase-c-src
#10
Zhengya Bai, Shasha Hou, Shilei Zhang, Zhongyan Li, Peng Zhou
Previously, we have reported a new biomolecular phenomenon spanning between protein folding and binding, termed as self-binding peptides (SBPs), where a short peptide segment in monomeric protein functions as molecular switch by dynamically binding to/unbinding from its cognate domain in the monomer (Yang C, Zhang S, He P, Wang C, Huang J, Zhou P. Self-binding peptides: folding or binding? J. Chem. Inf. MODEL: 2015, 55: 329-342). Here, we attempt to raise the SBP as a new class of druggable targets to regulate the biological activity and function of proteins...
March 27, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28345916/molecular-mechanism-of-nucleotide-dependent-allosteric-regulation-in-amp-activated-protein-kinase
#11
Navjeet Ahalawat, Rajesh Kumar Murarka
The AMP-activated protein kinase (AMPK), a central enzyme in the regulation of energy homeostasis, is an important drug target for type 2 diabetes, obesity and cancer. Binding of adenosine nucleotides to the regulatory γ-subunit tightly regulates the activity of this enzyme. Though recent crystal structures of AMPK have provided important insights into the allosteric activation of AMPK, molecular details of the regulatory mechanism of AMPK activation is still elusive. Here, we have performed extensive all-atom molecular dynamics (MD) simulations and shown that the kinase domain (KD) and γ-subunit comes closer resulting in a more compact heterotrimeric AMPK complex in AMP-bound state compared to the ATP-bound state...
March 27, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28345910/pycgtool-automated-generation-of-coarse-grained-molecular-dynamics-models-from-atomistic-trajectories
#12
James A Graham, Jonathan W Essex, Syma Khalid
Development of coarse-grained (CG) molecular dynamics models is often a laborious process which commonly relies upon approximations to similar models, rather than systematic parametrisation. PyCGTOOL automates much of the construction of CG models via calculation of both equilibrium values and force constants of internal coordinates directly from atomistic molecular dynamics simulation trajectories. The derivation of bespoke parameters from atomistic simulations improves the quality of the CG model compared to the use of generic parameters derived from other molecules, while automation greatly reduces the time required...
March 27, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28345907/simulating-protein-mediated-hydrolysis-of-atp-and-other-nucleoside-triphosphates-by-combining-qm-mm-molecular-dynamics-with-advances-in-metadynamics
#13
Rui Sun, Olaseni Sode, James F Dama, Gregory A Voth
The protein mediated hydrolysis of nucleoside triphosphates such as ATP or GTP is one of the most important and challenging biochemical reactions in nature. The chemical environment (water structure, catalytic metal, and amino acid residues) adjacent to the hydrolysis site contains hundreds of atoms, usually greatly limiting the amount of the free energy sampling that one can achieve from computationally demanding electronic structure calculations such as QM/MM simulations. Therefore, the combination of QM/MM molecular dynamics with the recently developed Transition-tempered Metadynamics (TTMetaD), an enhanced sampling method that can provide a high-quality free energy estimate at an early stage in a simulation, is an ideal approach to address the biomolecular nucleoside triphosphate hydrolysis problem...
March 27, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28345904/ligand-selectivity-mechanism-and-conformational-changes-in-guanine-riboswitch-by-molecular-dynamics-simulations-and-free-energy-calculations
#14
Guodong Hu, Aijing Ma, Ji Hua Wang
Riboswitches regulate gene expression through direct and specific interactions with small metabolite molecules. Binding of a ligand to its RNA target is high selectivity and affinity and induces conformational changes of the RNA's secondary and tertiary structure. The structural difference of two purine riboswitches aptamers is caused by only one single mutation, where cytosine 74 in the guanine riboswitch is corresponding to a uracil 74 in adenine riboswitch. Here we employed molecular dynamics (MD) simulation, molecular mechanics Poisson Boltzmann surface area (MM-PBSA) and thermodynamic integration computational methodologies to evaluate the energetic and conformational changes of ligands binding to purine riboswitches...
March 27, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28345879/vibrational-probes-from-small-molecule-solvatochromism-theory-and-experiments-to-applications-in-complex-systems
#15
Bartosz Błasiak, Casey H Londergan, Lauren J Webb, Minhaeng Cho
The vibrational frequency of a chosen normal mode is one of the most accurately measurable spectroscopic properties of molecules in condensed phases. Accordingly, infrared absorption and Raman scattering spectroscopy have provided valuable information on both distributions and ensemble-average values of molecular vibrational frequencies, and these frequencies are now routinely used to investigate structure, conformation, and even absolute configuration of chemical and biological molecules of interest. Recent advancements in coherent time-domain nonlinear vibrational spectroscopy have allowed the study of heterogeneous distributions of local structures and thermally driven ultrafast fluctuations of vibrational frequencies...
March 27, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28345716/spontaneous-nacl-doped-ice-at-seawater-conditions-focus-on-the-mechanisms-of-ion-inclusion
#16
M M Conde, M Rovere, P Gallo
Molecular dynamics simulations on the microsecond time scale have been performed on an aqueous solution of TIP4P/2005 water and NaCl by using the direct coexistence technique to study the ice growth and the ice/liquid interface water. At ambient pressure, for temperatures above the eutectic point of the salt and at seawater concentrations the brine rejection phenomenon and the spontaneous growth of an ice slab doped by the salt are obtained, as found in natural terrestrial and planetary environments. Experiments indicate that Cl(-) goes via substitution to ice sites...
March 27, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28345697/the-role-of-ion-water-interactions-in-determining-the-soret-coefficient-of-licl-aqueous-solutions
#17
Silvia Di Lecce, Tim Albrecht, Fernando Bresme
The application of a thermal gradient to an aqueous electrolyte solution induces the Soret effect, and the salt migrates towards hot (thermophilic) or cold regions (thermophobic). Experimental studies of LiCl reported changes in the sign of the Soret coefficient as well as a minimum in this coefficient at specific salt concentrations and temperatures. At the minimum the thermodiffusive response of the solution is enhanced significantly. We have performed non-equilibrium molecular dynamics simulations of LiCl solutions to quantify the dependence of the sign change and minimum of the Soret coefficient with salt concentration and temperature...
March 27, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28345346/thermally-activated-delayed-fluorescence-and-aggregation-induced-emission-with-through-space-charge-transfer
#18
Hiroyuki Tsujimoto, Dong-Gwang Ha, Georgios Markopoulos, Hyun Sik Chae, Marc A Baldo, Timothy M Swager
Emissive molecules comprising a donor and an acceptor bridged by 9,9-dimethylxanthene, were studied (XPT, XCT, and XtBuCT). The structures position the donor and acceptor with cofacial alignment at distances of 3.3-3.5 Å wherein efficient spatial charge transfer can occur. The quantum yields were enhanced by excluding molecular oxygen and thermally activated delayed fluorescence with lifetimes on the order of microseconds was observed. Although the molecules displayed low quantum yields in solution, higher quantum yields were observed in the solid state...
March 27, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28345097/tailoring-single-chain-polymer-nanoparticle-thermo-mechanical-behavior-by-cross-link-density
#19
Suwon Bae, Or Galant, Charles E Diesendruck, Meredith N Silberstein
Single chain polymer nanoparticles (SCPNs) are formed from intrachain cross-linking of a single polymer chain, making SCPN distinct from other polymer nanoparticles for which the shape is predefined before polymerization. The degree of cross-linking in large part determines the internal architecture of the SCPNs and therefore their mechanical and thermomechanical properties. Here, we use molecular dynamics (MD) simulations to study thermomechanical behavior of individual SCPNs with different underlying structures by varying the ratio of cross-linking and the degree of polymerization...
March 27, 2017: Soft Matter
https://www.readbyqxmd.com/read/28345074/single-cell-rna-seq-and-computational-analysis-using-temporal-mixture-modelling-resolves-th1-tfh-fate-bifurcation-in-malaria
#20
Tapio Lönnberg, Valentine Svensson, Kylie R James, Daniel Fernandez-Ruiz, Ismail Sebina, Ruddy Montandon, Megan S F Soon, Lily G Fogg, Arya Sheela Nair, Urijah Liligeto, Michael J T Stubbington, Lam-Ha Ly, Frederik Otzen Bagger, Max Zwiessele, Neil D Lawrence, Fernando Souza-Fonseca-Guimaraes, Patrick T Bunn, Christian R Engwerda, William R Heath, Oliver Billker, Oliver Stegle, Ashraful Haque, Sarah A Teichmann
Differentiation of naïve CD4(+) T cells into functionally distinct T helper subsets is crucial for the orchestration of immune responses. Due to extensive heterogeneity and multiple overlapping transcriptional programs in differentiating T cell populations, this process has remained a challenge for systematic dissection in vivo. By using single-cell transcriptomics and computational analysis using a temporal mixtures of Gaussian processes model, termed GPfates, we reconstructed the developmental trajectories of Th1 and Tfh cells during blood-stage Plasmodium infection in mice...
March 3, 2017: Science Immunology
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