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# molecular dynamics

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#1
REVIEW
Yongming Jia, Na Wang, Xuewei Liu
The amyloid-beta (Aβ) hypothesis that dyshomeostasis between Aβ production and clearance is a very early, key molecular factor in the etiology of Alzheimer's disease (AD) has been proposed and examined in the AD research field. Scientists have focused on seeking natural products or drugs to influence the dynamic equilibrium of Aβ, targeting production and clearance of Aβ. There is emerging evidence that resveratrol (Res), a naturally occurring polyphenol mainly found in grapes and red wine, acts on AD in numerous in vivo and in vitro models...
October 14, 2017: Nutrients
#2
Beibei Ru, Jianlong Sun, Yin Tong, Ching Ngar Wong, Aditi Chandra, Acacia Tsz So Tang, Larry Ka Yue Chow, Wai Lam Wun, Zarina Levitskaya, Jiangwen Zhang
Chromatin regulators (CRs) can dynamically modulate chromatin architecture to epigenetically regulate gene expression in response to intrinsic and extrinsic signalling cues. Somatic alterations or misexpression of CRs might reprogram the epigenomic landscape of chromatin, which in turn lead to a wide range of common diseases, notably cancer. Here, we present CR2Cancer, a comprehensive annotation and visualization database for CRs in human cancer constructed by high throughput data analysis and literature mining...
October 3, 2017: Nucleic Acids Research
#3
Ignacio Faustino, S J Marrink
Summary: We introduce cgHeliParm, a python program that provides the conformational analysis of Martini-based coarse-grained double strand DNA molecules. The software calculates the helical parameters such as base, base pair and base pair step parameters. cgHeliParm can be used for the analysis of coarse grain Martini molecular dynamics trajectories without transformation into atomistic models. Availability and implementation: This package works with Python 2.7 on MacOS and Linux...
July 13, 2017: Bioinformatics
#4
Vikas Bansal
Motivation: The short read lengths of current high-throughput sequencing technologies limit the ability to recover long-range haplotype information. Dilution pool methods for preparing DNA sequencing libraries from high molecular weight DNA fragments enable the recovery of long DNA fragments from short sequence reads. These approaches require computational methods for identifying the DNA fragments using aligned sequence reads and assembling the fragments into long haplotypes. Although a number of computational methods have been developed for haplotype assembly, the problem of identifying DNA fragments from dilution pool sequence data has not received much attention...
July 11, 2017: Bioinformatics
#5
REVIEW
Patrick C A van der Wel
The aggregation of proteins and peptides into a variety of insoluble, and often non-native, aggregated states plays a central role in many devastating diseases. Analogous processes undermine the efficacy of polypeptide-based biological pharmaceuticals, but are also being leveraged in the design of biologically inspired self-assembling materials. This Trends article surveys the essential contributions made by recent solid-state NMR (ssNMR) studies to our understanding of the structural features of polypeptide aggregates, and how such findings are informing our thinking about the molecular mechanisms of misfolding and aggregation...
October 4, 2017: Solid State Nuclear Magnetic Resonance
#6
Jan Zaloga, Artem Feoktystov, Vasil M Garamus, Weronika Karawacka, Alexander Ioffe, Thomas Brückel, Rainer Tietze, Christoph Alexiou, Stefan Lyer
A rational use of superparamagnetic iron oxide nanoparticles (SPIONs) in drug delivery, diagnostics, and other biomedical applications requires deep understanding of the molecular drug adsorption/desorption mechanisms for proper design of new pharmaceutical formulations. The adsorption and desorption of the cytostatic Mitoxantrone (MTO) to lauric acid-albumin hybrid coated particles SPIONs (SEON(LA-HSA)) was studied by Fourier transform infrared spectroscopy (FTIR), dynamic light scattering (DLS), surface titration, release experiments and small-angle neutron and X-ray scattering...
September 28, 2017: Colloids and Surfaces. B, Biointerfaces
#7
Aaron John Wolfe, Wei Si, Zhengqi Zhang, Adam R Blanden, Yi-Ching Hsueh, Jack Fredrick Gugel, Bach Pham, Min Chen, Stewart N Loh, Sharon Rozovsky, Aleksei Aksimentiev, Liviu Movileanu
Although fundamentally significant in structural, chemical, and membrane biology, the interfacial protein-detergent complex (PDC) interactions have been modestly examined because of the complicated behavior of both detergents and membrane proteins in aqueous phase. Membrane proteins are prone to unproductive aggregation resulting from poor detergent solvation, but the participating forces in this phenomenon remain ambiguous. Here, we show that using rational membrane protein design, targeted chemical modification, and steady-state fluorescence polarization spectroscopy, the detergent desolvation of membrane proteins can be quantitatively evaluated...
October 16, 2017: Journal of Physical Chemistry. B
#8
Emily H Pilkington, May Lai, Xinwei Ge, William J Stanley, Bo Wang, Miaoyi Wang, Aleksandr Kakinen, Marc-Antoine Sani, Michael R Whittaker, Esteban N Gurzov, Feng Ding, John F Quinn, Thomas P Davis, Pu Chun Ke
Protein aggregation into amyloid fibrils is a ubiquitous phenomenon across the spectrum of neurodegenerative disorders and type 2 diabetes. A common strategy against amyloidogenesis is to minimize the populations of toxic oligomers and protofibrils by inhibiting protein aggregation with small molecules or nanoparticles. However, melanin synthesis in nature is realized by accelerated protein fibrillation to circumvent accumulation of toxic intermediates. Accordingly, we designed and demonstrated the use of star-shaped poly(2-hydroxyethyl acrylate) (PHEA) nanostructures for promoting the aggregation while ameliorating the toxicity of human islet amyloid polypeptide (IAPP), the peptide involved in glycemic control and the pathology of type 2 diabetes...
October 16, 2017: Biomacromolecules
#9
Pablo G Romano, Marina Giuseppina Guenza
Markov State Models (MSM) are used to model the kinetics of processes sampled by Molecular Dynamics (MD) simulations. MSM reduce the high dimensionality inherent to MD simulations as they partition the free energy landscape into discrete states, generating a kinetic model as a series of uncorrelated jumps between states. Here, we detail a new method, called GRadient Adaptive Decomposition, which optimizes coarse-grained MSM by refining borders with respect to the gradient along the free energy surface. The proposed method requires only a small number of initial microstates because it corrects for errors produced by limited sampling...
October 16, 2017: Journal of Chemical Information and Modeling
#10
Zhihua Sun, Jian Li, Chengmin Ji, Junliang Sun, Maochun Hong, Junhua Luo
The incommensurate (IC) behaviors of ferroelectrics have been widely investigated in inorganic oxides as an exciting branch for aperiodic materials, whereas it still remains a great challenge to achieve such intriguing effects in organic systems. Here, we present that successive ordering of dynamic dipoles in an organic molecular ferroelectric, N-isopropylbenzylaminium trichloroacetate (1), enables unusual incommensurately modulated structures between its paraelectric phase (PEP) and ferroelectric phase (FEP)...
October 16, 2017: Journal of the American Chemical Society
#11
Delin Sun, Jan Forsman, Clifford E Woodward
Membrane-active peptides (MAPs) are able to induce pores in cell membranes via molecular mechanisms, which are still subject to ongoing research. In this work, we present molecular dynamics simulations that suggest that a precursor membrane defect plays an important role in the pore-inducing activity of the prototypical antimicrobial peptide, melittin. The simulations reveal that the hydrophobic N-terminus of melittin is able to recognize and insert into the membrane defect in the lipid bilayer and that this leads to a cascading transfer of adsorbed peptides to the membrane defect, leading to peptide aggregation in the pore...
October 16, 2017: Journal of Physical Chemistry. B
#12
Kasper Damgaard Tidemand, Guenther H H J Peters, Pernille Harris, Eva Stensgaard, Hans E M Christensen
Tryptophan hydroxylase (TPH) catalyses the initial and rate-limiting step in the biosynthesis of serotonin, which is associated with a variety of disorders such as depression and irritable bowel syndrome. TPH exists in two isoforms; TPH1 and TPH2. TPH1 catalyses the initial step in the synthesis of serotonin in the peripheral tissues, while TPH2 catalyses this step in the brain. In this study, the steady-state kinetic mechanism for the catalytic domain of human TPH1 has been determined. Varying substrate tryptophan (Trp) and tetrahydrobiopterin (BH4) results in a hybrid Ping Pong-ordered mechanism in which the reaction can either occur through a Ping Pong or a sequential mechanism depending on the concentration of tryptophan...
October 16, 2017: Biochemistry
#13
Romain Gaillac, Pluton Pullumbi, Kevin A Beyer, Karena W Chapman, David A Keen, Thomas D Bennett, François-Xavier Coudert
Metal-organic frameworks (MOFs) are a family of chemically diverse materials, with applications in a wide range of fields, covering engineering, physics, chemistry, biology and medicine. Until recently, research has focused almost entirely on crystalline structures, yet now a clear trend is emerging, shifting the emphasis onto disordered states, including 'defective by design' crystals, as well as amorphous phases such as glasses and gels. Here we introduce a strongly associated MOF liquid, obtained by melting a zeolitic imidazolate framework...
October 9, 2017: Nature Materials
#14
Cole Mathis, Sanjay N Ramprasad, Sara Imari Walker, Niles Lehman
Cooperation is essential for evolution of biological complexity. Recent work has shown game theoretic arguments, commonly used to model biological cooperation, can also illuminate the dynamics of chemical systems. Here we investigate the types of cooperation possible in a real RNA system based on the Azoarcus ribozyme, by constructing a taxonomy of possible cooperative groups. We construct a computational model of this system to investigate the features of the real system promoting cooperation. We find triplet interactions among genotypes are intrinsically biased towards cooperation due to the particular distribution of catalytic rate constants measured empirically in the real system...
October 16, 2017: Life
#15
Ahmet Gul, Burak Erman
Prediction of peptide binding on specific human leukocyte antigens (HLA) has long been studied with successful results. We herein describe the effects of entropy and dynamics by investigating the binding stabilities of 10 nanopeptides on various HLA Class I alleles using a theoretical model based on molecular dynamics simulations. The fluctuational entropies of the peptides are estimated over a temperature range of 310-460 K. The estimated entropies correlate well with experimental binding affinities of the peptides: Peptides that have higher binding affinities have lower entropies compared to non-binders, which have significantly larger entropies...
October 16, 2017: Physical Biology
#16
Mohamed Shaat
The nanoconfinement of water results in changes in water properties and nontraditional water flow behaviors. The determination of the interfacial interactions between water and hydrophobic surfaces helps in understanding many of the nontraditional behaviors of nanoconfined water. In this study, an approach for the identification of the viscosity of water interfaces with hydrophobic nanopores as a function of the nanopore diameter and water-solid (nanopore) interactions is proposed. In this approach, water in a hydrophobic nanopore is represented as a double phase water with two distinct viscosities: water interface and water core...
October 16, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
#17
Arun Kumar Sagotra, Claudio Cazorla
Finding solid-state electrolytes with high ionic conductivity near room temperature is an important prerequisite for developing all-solid-state electrochemical batteries. Here, we investigate the effects of point defects (vacancies) and biaxial stress on the superionic properties of fast-ion conductors (represented by the archetypal compounds CaF$_{2}$, Li-rich anti-perovskite Li$_{3}$OCl, and AgI) by using classical molecular dynamics and first-principles simulation methods. We find that the critical superionic temperature of all analysed families of fast-ion conductors can be reduced by several hundreds of degrees through the application of relatively small biaxial stresses ($|\sigma| \le 1$~GPa) on slightly defective samples ($c_{v} \sim 1$\%)...
October 16, 2017: ACS Applied Materials & Interfaces
#18
Christian O Plaza-Rivera, Hong T Nguyen, Robert S Hoy
Using molecular dynamics simulations of a tangent-soft-sphere bead-spring polymer model, we examine the degree to which semiflexible polymer melts solidify at isostaticity. Flexible and stiff chains crystallize when they are isostatic as defined by appropriate degree-of-freedom-counting arguments. Semiflexible chains also solidify when isostatic if a generalized isostaticity criterion that accounts for the slow freezing out of configurational freedom as chain stiffness increases is employed. The configurational freedom associated with bond angles (θ) can be associated with the characteristic ratio C∞ = (1 + 〈cos(θ)〉)/(1 - 〈cos(θ)〉)...
October 16, 2017: Soft Matter
#19
REVIEW
Random mutations leading to loss of cell cycle control is not a rare occurrence in an organism but the mutated cells are recognized and eliminated preventing the development of a tumor. These potentially tumorigenic cells release damage-associated molecular patterns (DAMPs), which are recognized by toll-like receptors (TLRs) on macrophages and dendritic cells. The initial TLR-DAMP interactions lead to different responses such as altered antigen presentation and cytokine release that directly affect T cell activation and removal of the tumorigenic cells...
October 9, 2017: Cytokine
#20
Richard Chudoba, Jan Heyda, Joachim Dzubiella
A temperature (T)-dependent coarse-grained (CG) Hamiltonian of polyethylene glycol/oxide (PEG/PEO) in aqueous solution is reported to be used in implicit-solvent material models in a wide temperature (i.e., solvent quality) range. The T-dependent nonbonded CG interactions are derived from a combined "bottom-up" and "top-down" approach. The pair potentials calculated from atomistic replica-exchange molecular dynamics simulations in combination with the iterative Boltzmann inversion are post-refined by benchmarking to experimental data of the radius of gyration...
October 16, 2017: Journal of Chemical Theory and Computation
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