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molecular dynamics

Toby Lawrence
The functional and phenotypic diversity of macrophages has long been appreciated, and it is now clear that it reflects a complex interplay between hard-wired differentiation pathways and instructive signals in specific tissues (Lawrence T, Natoli G. 2011, Nat Rev Immunol11:750-761). Recent studies have begun to unravel the molecular basis for the integration of these intrinsic developmental pathways with extracellular signals from the tissue microenvironment that confer the distinct phenotypes of tissue-resident macrophages (Lavin Y et al...
October 2016: Microbiology Spectrum
Elena Meirzadeh, Liel Sapir, Hagai Cohen, Sidney R Cohen, David Ehre, Daniel Harries, Meir Lahav, Igor Lubomirsky
The riddle of anomalous polar behavior of the centrosymmetric crystal of α-glycine is resolved by the discovery of a polar, several hundred nanometer thick hydrated layer, created at the {010} faces during crystal growth. This layer was detected by two independent pyroelectric analytical methods: (i) periodic temperature change technique (Chynoweth) at ambient conditions and (ii) contactless X-ray photoelectron spectroscopy under ultrahigh vacuum. The total polarization of the surface layer is extremely large, yielding ≈1 μC·cm(-2), and is preserved in ultrahigh vacuum, but disappears upon heating to 100 °C...
October 25, 2016: Journal of the American Chemical Society
Hao Liu, Wei Ye, Hai-Feng Chen
Acetylcholinesterase is a potent enzyme that regulates neurotransmission by rapidly hydrolyzing the neurotransmitter acetylcholine in synapses of the nervous system. As drug target of anti-AD, it has catalytic and peripheral anionic sites. However, the regulation relation between these two sites is unclear. Therefore, we constructed dynamics fluctuation network based on all-atom molecular dynamics simulations to reveal the regulation mechanism. The results suggest that the correlation network in double site system (hAChE/TZ5) is distinctly different from that in the free state and single site systems (hAChE/huprine and hAChE/1YL)...
October 25, 2016: Chemical Biology & Drug Design
Malachi W Gillick-Healy, Elizabeth V Jennings, Helge Muller-Bunz, Yannick Ortin, Kirill Nikitin, Declan G Gilheany
The energy barriers in our recently discovered Walden inversion of chlorophosphonium salts are similar to those in Cope rearrangements of caged cyclic hydrocarbons. We have therefore designed a molecular system integrating the two processes, thereby producing the first embodiment in a chemical species of two entirely different and independent stereomutation mechanisms at the same nominal asymmetric centre. Thus, the energy barrier to the rearrangement of 9-phenyl-9-phosphabarbaralane oxide, easily prepared by a new high-yielding synthesis, was found to be ca...
October 25, 2016: Chemistry: a European Journal
Xi Chen, Qi Li, Xiao-Xi Kan, Ya-Jie Wang, Yu-Jie Li, Qing Yang, Hong-Bin Xiao, Ying Chen, Xiao-Gang Weng, Wei-Yan Cai, Xiao-Xin Zhu
Metastasis of breast cancer is the vital step for malignant progression. During such a process, hematogenous metastasis is an indispensable approach for the dissemination of cancer cells. A platelet, contributes to hypercoagulable state, and is also identified the crucial factor in the coagulation system for supporting metastasis. Therefore, the relationship of a platelet and a tumor cell plays a critical role in tumor cell metastasis. Consequently, inhibiting tumor cell‑induced platelet aggregation (TCIPA) is recongnized as a crucial target on suppression of tumor metastasis such as aspirin (ASA)...
October 19, 2016: Oncology Reports
Sudip Das, Tarak Karmakar, Sundaram Balasubramanian
Thermomyces lanuginosus lipase (TLL) is an industrially significant catalyst for the production of biodiesel due to its operability over a wide range of pH and temperature. Molecular dynamics simulations of TLL in aqueous solutions of a biocompatible ionic liquid (IL), cholinium glycinate (ChGly) have been carried out to investigate the microscopic reasons for the experimentally observed enhancement in the activity of TLL, upon addition of room temperature IL, especially at an optimal concentration. Eight different TLL systems in both its open and closed forms at various concentrations of the room temperature IL in water have been studied...
October 25, 2016: Journal of Physical Chemistry. B
Mostafa Fakhraee, Mohammad Reza Gholami
The effects of ester addition on structural and dynamic properties of biodegradable ILs composed of the 1-(alkoxycarbonyl)-3-alkylimidazolium cation ([C1COOCnC1im](+), n = 1, 2, 4) coupled with [Br](-), [NO3](-), [BF4](-), [PF6](-), [TfO](-), and [Tf2N](-) are explored using the molecular dynamics (MD) simulations and quantum theory of atoms in molecules (QTAIM) at 400 K. Formation of the intramolecular H bonds between O atoms of the ester group and H atoms of the imidazolium ring as well as the nearest H atom of the alkyl chain to the ester group are disclosed from reduced density gradient (RDG) results...
October 25, 2016: Journal of Physical Chemistry. B
Anurag Mishra, Yuanyuan Jiang, Sheryl Roberts, Vasilis Ntziachristos, Gil Gregor Westmeyer
Photoacoustic imaging (PAI) is an attractive imaging modality that can volumetrically map the distribution of photoabsorbing molecules with deeper tissue penetration than multiphoton microscopy. To enable dynamic sensing of divalent cations via PAI, we have engineered a new reversible near infrared probe that is more sensitive to calcium as compared to other biologically relevant cations. The metallochromic compound showed a strong reduction of its peak absorbance at 765 nm upon addition of calcium ions that was translated into robust signal changes in photoacoustic images...
October 25, 2016: Analytical Chemistry
Zhi Zhu, Nan Sheng, Haiping Fang, Rongzheng Wan
Thermal noise is of fundamental importance to many processes. Traditionally, thermal noise has been treated as white noise on the macroscopic scale. Using molecular dynamics simulations and power spectrum analysis, we show that the thermal noise of solute molecules in water is non-white on the molecular scale, which is in contrast to the conventional theory. In the frequency domain from 2 × 10(11) Hz to 10(13) Hz, the power spectrum of thermal noise for polar solute molecules resembles the spectrum of 1/f noise...
October 25, 2016: Physical Chemistry Chemical Physics: PCCP
Z W Wu, F X Li, C W Huo, M Z Li, W H Wang, K X Liu
The temperature evolution of icosahedral medium-range order formed by interpenetrating icosahedra in CuZr metallic glassforming liquids was investigated via molecular dynamics simulations. Scaling analysis based on percolation theory was employed, and it is found that the size distribution of clusters formed by the central atoms of icosahedra at various temperatures follows a very good scaling law with the cluster number density scaled by S(-τ) and the cluster size S scaled by |1 - Tc/T|(-1/σ), respectively...
October 25, 2016: Scientific Reports
Ji Hoon Park, Minsup Kim, Masaharu Shiratani, Art E Cho, Eun Ha Choi, Pankaj Attri
Over the last few years, the variation in liquid chemistry due to the development of radicals generated by cold atmospheric plasma (CAP) has played an important role in plasma medicine. CAP direct treatment or CAP activated media treatment in cancer cells shows promising anticancer activity for both in vivo and in vitro studies. However, the anticancer activity or antimicrobial activity varies between plasma devices due to the different abilities among plasma devices to generate the reactive oxygen and nitrogen species (RONS) at different ratios and in different concentrations...
October 25, 2016: Scientific Reports
Anna Starzyk, Michał Wojciechowski, Marek Cieplak
We perform molecular dynamics simulations for a simple coarse-grained model of a protein placed inside of a softly repulsive sphere of radius R. The protein is surrounded either by a number of same molecules or a number of spherical crowding particles that immitate other biomolecules such as the osmolytes. The two descriptions are shown to lead to distinct results when testing thermal stability as assessed by studying the unfolding times as a function of temperature. We consider three examples of proteins and show that crowding increases the thermal stability provided the inter-protein or protein-crowder interactions are repulsive...
October 25, 2016: Physical Biology
Sebastian Schneider, Davide Provasi, Marta Filizola
Substantial attention has recently been devoted to G protein-biased agonism of the µ-opioid receptor (MOR) as an ideal new mechanism for the design of analgesics devoid of serious side effects. However, designing opioids with appropriate efficacy and bias is challenging because it requires an understanding of the ligand binding process and of the allosteric modulation of the receptor. Here, we investigated these phenomena for TRV-130, a G protein-biased MOR small-molecule agonist that has been shown to exert analgesia with less respiratory depression and constipation than morphine, and that it is currently being evaluated in human clinical trials for acute pain management...
October 25, 2016: Biochemistry
Joanna Krysiak, Stephan A Sieber
Understanding the molecular mechanisms of bacterial pathogenesis and virulence is of great importance from both an academic and clinical perspective, especially in view of an alarming increase in bacterial resistance to existing antibiotics and antibacterial agents. Use of small molecules to dissect the basis of these dynamic processes is a very attractive approach due to their ability for rapid spatiotemporal control of specific biochemical functions. Activity-based protein profiling (ABPP), employing small molecule probes to interrogate enzyme activities in complex proteomes, has emerged as a powerful tool to study bacterial pathogenesis...
2017: Methods in Molecular Biology
Garold Murdachaew, Gilbert M Nathanson, R Benny Gerber, Lauri Halonen
Deprotonation of organic acids at aqueous surfaces has important implications in atmospheric chemistry and other disciplines, yet it is not well-characterized or understood. This article explores the interactions of formic acid (FA), including ionization, in collisions at the air-water interface. Ab initio molecular dynamics simulations with dispersion-corrected density functional theory were used. The 8-50 picosecond duration trajectories all resulted in the adsorption of FA within the interfacial region, with no scattering, absorption into the bulk or desorption into the vapor...
October 25, 2016: Physical Chemistry Chemical Physics: PCCP
Prabir Khatua, Jaya C Jose, Neelanjana Sengupta, Sanjoy Bandyopadhyay
Accumulation of the amyloid beta (Aβ) peptide in the brain is responsible for debilitating neurodegenerative diseases, such as Alzheimer's disease (AD). We have carried out atomistic molecular dynamics simulations of the full-length Aβ42 peptide monomer with a wide range of conformations at room temperature. Efforts have been made to probe the conformational features of different segments of the peptide, namely the two terminal segments (N-term and C-term), the central hydrophobic regions (hp1 and hp2) and the central turn region joining hp1 and hp2, and their nonuniform influence on the spatial arrangements and binding energies of the surrounding water molecules...
October 25, 2016: Physical Chemistry Chemical Physics: PCCP
Anna C Lawson McLean, Steffen K Rosahl
OBJECT: Neurofibromatosis type 2 is an autosomal-dominant disorder caused by a defective gene locus 22q12. Patients with NF2 are prone to develop multiple intracranial neoplasms, such as vestibular schwannomas, meningiomas and schwannomas of other cranial nerves. To date, little is known about the growth dynamics of these tumors. The aim of our study was to investigate a) the median growth rate per year, b) the growth-free intervals, and c) the growth patterns of these tumors. METHODS: Patient records from the regional neurofibromatosis center were evaluated for their suitability in this analysis...
October 21, 2016: World Neurosurgery
Castrese Morrone, Riccardo Miggiano, Mario Serpe, Alberto Massarotti, Anna Valenti, Giovanni Del Monaco, Mosè Rossi, Franca Rossi, Menico Rizzi, Giuseppe Perugino, Maria Ciaramella
BACKGROUND: Alkylated DNA-protein alkyltransferases (AGTs) are conserved proteins that repair alkylation damage in DNA by using a single-step mechanism leading to irreversible alkylation of the catalytic cysteine in the active site. Trans-alkylation induces inactivation and destabilization of the protein, both in vitro and in vivo, likely triggering conformational changes. A complete picture of structural rearrangements occurring during the reaction cycle is missing, despite considerable interest raised by the peculiarity of AGT reaction, and the contribution of a functional AGT in limiting the efficacy of chemotherapy with alkylating drugs...
October 21, 2016: Biochimica et Biophysica Acta
Rainer Bomblies, Manuel P Luitz, Martin Zacharias
Protein phosphorylation can affect the interaction with partner proteins but can also induce conformational transitions. In case of the eukaryotic translation initiation factor 4E-binding protein 2 (4E-BP2) threonine (Thr) phosphorylation at two turn motifs results in transition from a disordered to a folded structure. In order to elucidate the stabilizing mechanism we employed comparative Molecular Dynamics (MD) free energy simulations on the turn motifs indicating that Thr-phosphorylation favors a folded whereas de-phosphorylation or substitution by Glu residues destabilizes the turn structure...
October 25, 2016: Journal of Physical Chemistry. B
Satyabrata Pany, Youngki You, Joydip Das
Curcumin is a polyphenolic nutraceutical that acts on multiple biological targets, including protein kinase C (PKC). PKC is a family of serine-threonine kinases central to intracellular signal transduction. We have recently shown that curcumin selectively inhibits PKCα, but not PKCε in CHO-K1 cells (Pany, S. (2016) Biochemistry 55, 2135-43). To understand which domain(s) of PKCα is/are responsible for curcumin binding and inhibitory activity, we made several domain-swapped mutants in which the C1 (combination of C1A and C1B) and C2 domains are swapped between PKCα and PKCε...
October 24, 2016: Biochemistry
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