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https://www.readbyqxmd.com/read/29149762/interaction-of-biologically-relevant-ions-and-organic-molecules-with-titanium-oxide-rutile-surfaces-a-review-on-molecular-dynamics-studies
#1
REVIEW
Azade YazdanYar, Ulrich Aschauer, Paul Bowen
The surface of a biomaterial can play a major role in its biological fate since the surface is the primary pathway for its interaction with the body. As the natural response of the body to a foreign material is to encapsulate it with a fibrous material, the interactions between the body and the biomaterial are mediated by this fibrous layer. Initial interactions occur between the biomaterial surface, water, ionic species and organic molecules, which then mediate further interactions with body tissues. Surface engineering can influence these interactions and hence, improve the biocompatibility of the biomaterial...
November 7, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/29149726/protein-structure-based-drug-design-from-docking-to-molecular-dynamics
#2
REVIEW
Paweł Śledź, Amedeo Caflisch
Recent years have witnessed rapid developments of computer-aided drug design methods, which have reached accuracy that allows their routine practical applications in drug discovery campaigns. Protein structure-based methods are useful for the prediction of binding modes of small molecules and their relative affinity. The high-throughput docking of up to 10(6) small molecules followed by scoring based on implicit-solvent force field can robustly identify micromolar binders using a rigid protein target. Molecular dynamics with explicit solvent is a low-throughput technique for the characterization of flexible binding sites and accurate evaluation of binding pathways, kinetics, and thermodynamics...
November 14, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/29149637/antiviral-potential-of-natural-compounds-against-influenza-virus-hemagglutinin
#3
S Kannan, P Kolandaivel
Influenza virus of different subtypes H1N1, H2N2, H3N2 and H5N1 cause many human pandemic deaths and threatening the people worldwide. The Hemagglutinin (HA) protein mediates viral attachment to host receptors act as an attractive target. The sixteen natural compounds have been chosen to target the HA protein. Molecular docking studies have been performed to find binding affinity of the compounds. Out of the sixteen, three compounds CI, CII and CIII found to posses a higher binding affinity. The molecular dynamics (MD) simulation has been performed to study the structural, dynamical properties for the nine different complexes CI, CII, CIII bound with H1, H2, H3 proteins and the results were compared...
November 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29149592/dynamics-under-the-telomeric-bridge
#4
Sabrina Pisano, Eric Gilson, Marie-Josèphe Giraud-Panis
In this issue of Molecular Cell, Kim et al. (2017) have studied the structure and organization of the shelterin protein complex protecting telomeres in Schizosaccharomyces pombe and humans and discovered an allosteric structural transition that drives the formation of the shelterin complex and participates in telomere length regulation.
November 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29149564/binding-thermodynamics-and-kinetics-calculations-using-chemical-host-and-guest-a-comprehensive-picture-of-molecular-recognition
#5
Zhiye Tang, Chia-En A Chang
Understanding the fine balance between changes of entropy and enthalpy and the competition between a guest and water molecules in molecular binding is crucial in fundamental studies and practical applications. Experiments provide measurements. However, illustrating the binding/unbinding processes gives a complete picture of molecular recognition not directly available from experiments, and computational methods bridge the gaps. Here, we investigated guest association/dissociation with β-cyclodextrin (β-CD) by using microsecond-timescale molecular dynamics (MD) simulations, post-analysis and numerical calculations...
November 17, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29149479/cripsr-cas-expands-dynamic-range-of-gene-expression-from-t7rnap-promoters
#6
Sean R McCutcheon, Kwan Lun Chiu, Daniel D Lewis, Cheemeng Tan
BACKGROUND: Reducing leaky gene expression is critical for improving protein yield of recombinant bacteria and stability of engineered cellular circuits in synthetic biology. Leaky gene expression occurs when a genetic promoter is not fully repressed, leading to unintended protein synthesis in the absence of stimuli. Existing work has devised specific molecular strategies for reducing leaky gene expression of each promoter. Main Method and Results: In contrast, we describe a repurposed, modular CRISPRi system that attenuates leaky gene expression using a series of single-guide RNAs targeting the PT7/LacO1 ...
November 17, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/29149348/mechanistic-insight-into-the-assembly-of-the-hera-nura-helicase-nuclease-dna-end-resection-complex
#7
Zainab Ahdash, Andy M Lau, Robert Thomas Byrne, Katja Lammens, Alexandra Stüetzer, Henning Urlaub, Paula J Booth, Eamonn Reading, Karl-Peter Hopfner, Argyris Politis
The HerA-NurA helicase-nuclease complex cooperates with Mre11 and Rad50 to coordinate the repair of double-stranded DNA breaks. Little is known, however, about the assembly mechanism and activation of the HerA-NurA. By combining hybrid mass spectrometry with cryo-EM, computational and biochemical data, we investigate the oligomeric formation of HerA and detail the mechanism of nucleotide binding to the HerA-NurA complex from thermophilic archaea. We reveal that ATP-free HerA and HerA-DNA complexes predominantly exist in solution as a heptamer and act as a DNA loading intermediate...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29149173/trade-off-and-flexibility-in-the-dynamic-regulation-of-the-cullin-ring-ubiquitin-ligase-repertoire
#8
Ronny Straube, Meera Shah, Dietrich Flockerzi, Dieter A Wolf
Cullin-RING ubiquitin ligases (CRLs) catalyze the ubiquitylation of substrates many of which are degraded by the 26S proteasome. Their modular architecture enables recognition of numerous substrates via exchangeable substrate receptors that competitively bind to a cullin scaffold with high affinity. Due to the plasticity of these interactions there is ongoing uncertainty how cells maintain a flexible CRL repertoire in view of changing substrate loads. Based on a series of in vivo and in vitro studies, different groups proposed that the exchange of substrate receptors is mediated by a protein exchange factor named Cand1...
November 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29148803/hsdhodh-microdomain-membrane-interactions-are-influenced-by-the-lipid-composition
#9
Eduardo Festozo Vicente, Indra Dev Sahu, Edson Crusca, Luis Guilherme Mansor Basso, Claudia Elisabeth Munte, Antonio Jose Costa-Filho, Gary A Lorigan, Eduardo Maffud Maffud Cilli
Human dihydroorotate dehydrogenase (HsDHODH) enzyme has been studied as selective target for inhibitors to block the enzyme activity, intending to prevent proliferative diseases. The N-terminal microdomain seems to play an important role in the enzyme function. However, the molecular mechanism of action and dynamics of this region are not totally understood yet. This study analyzes the interaction and conformation in model membranes of HsDHODH microdomain using peptide analogues containing the paramagnetic amino acid TOAC at strategic positions...
November 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29148735/stereoselective-stabilization-of-polymeric-vitamin-e-conjugate-micelles
#10
Min Gao, Jian Deng, Huiying Chu, Yu Tang, Zheng Wang, Yanjun Zhao, Guohui Li
Vitamin E (α-tocopherol) (TPGS) micelle is a robust nanocarrier in delivering hydrophobic active pharmaceutical ingredients, but is suffering from poor stability that is essential in terms of pharmaceutical and biomedical applications. Taking advantage of the chirality of vitamin E, this work reports the stereoselective stabilization of polymer-vitamin E conjugate micelles. Vitamin E was covalently linked to multivalent methoxy poly(ethylene glycol)-co-poly(glutamic acid), generating amphiphilic conjugates that could self-assemble into micelles...
November 17, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/29148733/fluorescence-and-quenching-assessment-eem-parafac-of-de-facto-potable-reuse-in-the-neuse-river-north-carolina-united-states
#11
Martha J M Wells, Gene A Mullins, Katherine Y Bell, Allegra K Da Silva, Eileen M Navarrete
The Neuse River, North Carolina, U.S., exemplifies a typical de facto potable reuse scenario, where drinking water sources are located downstream of treated wastewater effluent discharges. The study results imply that planned potable water reuse, whether in an indirect or direct potable reuse scenario, might provide better control over water quality than the status quo conditions. Using fluorescence excitation-emission matrix (EEM) measurements, anthropogenic influence of a wastewater treatment plant (WWTP) discharge was observed in samples near the location of drinking water treatment plant (WTP) intakes, eight or more miles downstream of the WWTP, implying that anthropogenic compounds were not fully removed or degraded by natural processes in this reach of the river...
November 17, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/29148557/structural-and-thermodynamical-properties-of-early-human-amylin-oligomers-using-replica-exchange-molecular-dynamics-mutation-effect-of-three-key-residues-f15-h18-and-f23
#12
S Bouzakraoui, N Mousseau
Human islet amyloid polypeptide (hIAPP) is a 37-residue polypeptide, considered to be the main component of the pancreatic islet amyloid associated with type 2 diabetes and is one of the most amyloidogenic polypeptides known. Although the structure of hIAPP fibrils has already been obtained, structures of early oligomers and the mechanism of β-sheet formation remain poorly understood. Herein, we characterize the atomic structure and the thermodynamics of the 14-37 residue fragment of hIAPP wild-type and mutated dimers and trimers...
November 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29148556/co2-adsorption-on-anatase-tio2-101-surfaces-a-combination-of-uhv-ftirs-and-first-principles-studies
#13
Yunjun Cao, Min Yu, Shandong Qi, Tingting Wang, Shiming Huang, Zhengfeng Ren, Shishen Yan, Shujun Hu, Mingchun Xu
The CO2 adsorption and dynamic behaviors on single crystal anatase TiO2(101) surfaces were investigated by UHV-FTIRS and first-principles calculations. The IRRAS results at 90 K show that the ν3(OCO) asymmetric stretching vibration of adsorbed CO2 exhibits band splitting at rather low CO2 coverage in p-polarized IR spectra for the IR beam incident along the [101[combining macron]] direction. Co-adsorbed CO can prevent such band splitting. Ab initio molecular dynamics (AIMD) simulations revealed that the adsorbed CO2 at finite temperature does not keep a stationary adsorption state but keeps a certain swing motion: one end of the linear CO2 molecule binds to surface Ti5c sites and the other end swings within the (010) plane with a tilted angle distribution ranging from 10° to 60° relative to the [101[combining macron]] direction...
November 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29147941/artificial-bio-nanomachines-based-on-protein-needles-derived-from-bacteriophage-t4
#14
REVIEW
Hiroshi Inaba, Takafumi Ueno
Bacteriophage T4 is a natural bio-nanomachine which achieves efficient infection of host cells via cooperative motion of specific three-dimensional protein architectures. The relationships between the protein structures and their dynamic functions have recently been clarified. In this review we summarize the design principles for fabrication of nanomachines using the component proteins of bacteriophage T4 based on these recent advances. We focus on the protein needle known as gp5, which is located at the center of the baseplate at the end of the contractile tail of bacteriophage T4...
November 16, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29147940/interaction-of-proteins-with-ionic-liquid-alcohol-and-dmso-and-in-situ-generation-of-gold-nano-clusters-in-a-cell
#15
REVIEW
Somen Nandi, Sridip Parui, Ritaban Halder, Biman Jana, Kankan Bhattacharyya
In this review, we give a brief overview on how the interaction of proteins with ionic liquids, alcohols and dimethyl sulfoxide (DMSO) influences the stability, conformational dynamics and function of proteins/enzymes. We present experimental results obtained from fluorescence correlation spectroscopy on the effect of ionic liquid or alcohol or DMSO on the size (more precisely, the diffusion constant) and conformational dynamics of lysozyme, cytochrome c and human serum albumin in aqueous solution. The interaction of ionic liquid with biomolecules (e...
November 16, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29147679/dense-fluidized-granular-media-in-microgravity
#16
Philip Born, Johannes Schmitz, Matthias Sperl
Handling and transport of granular media are inevitably governed by the settling of particles. Settling into a dense state is one of the defining characteristics of granular media, among dissipation and absence of thermal agitation. Hence, settling complicates the adaptation of microscopic theories from atomic, molecular, or colloidal media to granular media. It is desirable to provide experiments in which selectively one of the granular characteristics is tuned to test suitable adaptation of a theory. Here we show that gas fluidization of granular media in microgravity is a suitable approach to achieve steady states closer to thermally agitated systems free of settling...
2017: NPJ Microgravity
https://www.readbyqxmd.com/read/29147652/identification-of-potent-chloride-intracellular-channel-protein-1-inhibitors-from-traditional-chinese-medicine-through-structure-based-virtual-screening-and-molecular-dynamics-analysis
#17
Wei Wang, Minghui Wan, Dongjiang Liao, Guilin Peng, Xin Xu, Weiqiang Yin, Guixin Guo, Funeng Jiang, Weide Zhong, Jianxing He
Chloride intracellular channel 1 (CLIC1) is involved in the development of most aggressive human tumors, including gastric, colon, lung, liver, and glioblastoma cancers. It has become an attractive new therapeutic target for several types of cancer. In this work, we aim to identify natural products as potent CLIC1 inhibitors from Traditional Chinese Medicine (TCM) database using structure-based virtual screening and molecular dynamics (MD) simulation. First, structure-based docking was employed to screen the refined TCM database and the top 500 TCM compounds were obtained and reranked by X-Score...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29147518/machine-learning-molecular-dynamics-for-the-simulation-of-infrared-spectra
#18
Michael Gastegger, Jörg Behler, Philipp Marquetand
Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects - typically neglected by conventional quantum chemistry approaches - we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29146971/skin-hydration-interplay-between-molecular-dynamics-structure-and-water-uptake-in-the-stratum-corneum
#19
Enamul Haque Mojumdar, Quoc Dat Pham, Daniel Topgaard, Emma Sparr
Hydration is a key aspect of the skin that influences its physical and mechanical properties. Here, we investigate the interplay between molecular and macroscopic properties of the outer skin layer - the stratum corneum (SC) and how this varies with hydration. It is shown that hydration leads to changes in the molecular arrangement of the peptides in the keratin filaments as well as dynamics of C-H bond reorientation of amino acids in the protruding terminals of keratin protein within the SC. The changes in molecular structure and dynamics occur at a threshold hydration corresponding to ca...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29146354/a-novel-calcium-binding-peptide-from-antarctic-krill-protein-hydrolysates-and-identification-of-binding-sites-of-calcium-peptide-complex
#20
Hu Hou, Shikai Wang, Xiao Zhu, Qiqi Li, Yan Fan, Dong Cheng, Bafang Li
Trypsin was used for preparing peptides with high calcium-binding capacity from Antarctic krill. Hydroxyapatite chromatography (HAC), size-exclusion chromatography (SEC), and reversed phase high performance liquid chromatography (RP-HPLC) were used to capture and purify calcium-binding peptides. The peptide sequence was determined to be VLGYIQIR (N- to C-terminal, MW = 960.58 Da), using LTQ Orbitrap XL. According to the results of FTIR and mass spectrometry, chelating site of calcium ions may possibly involve the carbonal or amino groups of Gln, Ile and Arg residues...
March 15, 2018: Food Chemistry
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