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MD simulation

Taraknath Mandal, Ronald G Larson
Using fully atomistic and coarse-grained (CG) molecular dynamics (MD) simulations, we report, for the first time, the self-assembly of initially randomly dispersed dodecyl-β-d-maltoside (DDM) surfactants into a striped cylindrical micelle (SCM) with lamellae of surfactant heads and tails alternating along the cylindrical axis, with both heads and tails in contact with the water. By changing the interaction strength of the head group with water relative to itself, we find that such micelles are most likely for head groups with marginal solubility in the water solvent...
March 22, 2018: Soft Matter
Konda Reddy Karnati, Yixuan Wang
Two widely used anticancer drugs, doxorubicin (DOX) and paclitaxel (PTX), possess distinct physical properties and chemotherapy specificity. In order to investigate their interaction mechanism with single-walled carbon nanotubes (SWCNTs), co-loading and releasing from the SWCNTs, all-atom molecular dynamics (MD) simulations were firstly carried out for different SWCNT systems, followed by binding free energy calculation with MM-PBSA. The results indicate that the co-loading of DOX and PTX onto the pristine SWCNT is exothermic and spontaneous...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
Luan Carvalho Martins, Pedro Henrique Monteiro Torres, Renata Barbosa de Oliveira, Pedro Geraldo Pascutti, Elio A Cino, Rafaela Salgado Ferreira
Chagas disease remains a major health problem in South America, and throughout the world. The two drugs clinically available for its treatment have limited efficacy and cause serious adverse effects. Cruzain is an established therapeutic target of Trypanosoma cruzi, the protozoan that causes Chagas disease. Our group recently identified a competitive cruzain inhibitor (compound 1) with an IC50  = 15 µM that is also more synthetically accessible than the previously reported lead, compound 2. Prior studies, however, did not propose a binding mode for compound 1, hindering understanding of the structure-activity relationship and optimization...
March 21, 2018: Journal of Computer-aided Molecular Design
Lei Zhao, Jiangtao Cheng
Besides the Wenzel state, liquid droplets on micro/nanostructured surfaces can stay in the Cassie state and consequently exhibit intriguing characteristics such as a large contact angle, small contact angle hysteresis and exceptional mobility. Here we report molecular dynamics (MD) simulations of the wetting dynamics of Cassie-state water droplets on nanostructured ultrahydrophobic surfaces with an emphasis on the genesis of the contact line friction (CLF). From an ab initio perspective, CLF can be ascribed to the collective effect of solid-liquid retarding and viscous damping...
March 22, 2018: Nanoscale
Nicholas P van der Munnik, Md Symon Jahan Sajib, Melissa A Moss, Tao Wei, Mark J Uline
Amyloid-β (Aβ) protein aggregates through a complex pathway to progress from monomers to soluble oligomers and ultimately insoluble fibrils. Due to the dynamic nature of aggregation, it has proven exceedingly difficult to determine the precise interactions that lead to the formation of transient oligomers. Here, a statistical thermodynamic model has been developed to elucidate these interactions. Aβ1-42 was simulated using fully-atomistic replica exchange molecular dynamics. We use an ensemble of approximately 5×105 configurations taken from simulation as input in a self-consistent field theory that explicitly accounts for the size, shape and charge distribution of both the amino acids comprising Aβ and all molecular species present in solution...
March 21, 2018: Journal of Chemical Theory and Computation
Agnieszka Drozd, Dominika Wojewska, Manuel David Peris-Díaz, Piotr Jakimowicz, Artur Krężel
Metallothioneins (MTs), small cysteine-rich proteins, present in four major isoforms, are key proteins involved in zinc and copper homeostasis in mammals. To date, only one X-ray crystal structure of a MT has been solved. It demonstrates seven bivalent metal ions bound in two structurally independent domains with M4S11 (α) and M3S9 (β) clusters. Recent discoveries indicate that Zn(ii) ions are bound with MT2 with the range from nano- to picomolar affinity, which determines its cellular zinc buffering properties that are demonstrated by the presence of partially Zn(ii)-depleted MT2 species...
March 21, 2018: Metallomics: Integrated Biometal Science
Laura Pérez-Benito, Henrik Keränen, Herman van Vlijmen, Gary Tresadern
A congeneric series of 21 phosphodiesterase 2 (PDE2) inhibitors are reported. Crystal structures show how the molecules can occupy a 'top-pocket' of the active site. Molecules with small substituents do not enter the pocket, a critical leucine (Leu770) is closed and water molecules are present. Large substituents enter the pocket, opening the Leu770 conformation and displacing the waters. We also report an X-ray structure revealing a new conformation of the PDE2 active site domain. The relative binding affinities of these compounds were studied with free energy perturbation (FEP) methods and it represents an attractive real-world test case...
March 20, 2018: Scientific Reports
Fatemeh Janati-Fard, Mohammad Reza Housaindokht, Hassan Monhemi, Abbas Ali Esmaeili, Ali Nakhaei Pour
The search for ionic liquids (ILs) with biochemical and biomedical applications has recently gained great attention. IL containing solvents can change the structure, stability and function of proteins. The study of protein conformation in ILs is important to understand enzymatic activity. In this work, conformational stability and activity of the enzyme in two imidazolium-based ILs (1-butyl 3-methyl-imidozolium and 1-hexyl 3-methyl-imidozoliumbromides) were investigated. We treated glucose oxidase as dimer-active enzyme in different IL concentration and seen that GOx activity was inhibited in the presence of ILs...
March 17, 2018: International Journal of Biological Macromolecules
Hao Li, Ming Li, Zhan Kang
The competition between the out-of-plane rigidity and the van der Waals interaction leads to the scrolled and folded structural configurations of graphene. These configuration changes, as compared with the initially planar geometry, significantly affect the electronic, optical and mechanical properties of graphene, promising exciting applications in graphene-nanoelectronics. We propose a finite-deformation theoretical model, in which no presumed assumptions on the geometries of deformed configurations are required...
March 20, 2018: Nanotechnology
Noam Brown, Jiangtao Lei, Chendi Zhan, Linda J W Shimon, Lihi Adler-Abramovich, Guanghong Wei, Ehud Gazit
Self-assembly is a process of key importance in natural systems and in nanotechnology. Peptides are attractive building blocks due to their relative facile synthesis, biocompatibility and other unique properties. Diphenylalanine (FF) and its derivatives are known to form nanostructures of various architectures and remarkable characteristics. The larger triphenylalanine (FFF) was found to self-assemble as efficiently as FF, forming related but distinct architectures of plate-like and spherical nanostructures...
March 20, 2018: ACS Nano
Gurkamaljit Kaur, Bharati Pandey, Arbind Kumar, Naina Garewal, Abhinav Grover, Jagdeep Kaur
The lipolytic protein LipU was conserved in mycobacterium sp. including M. tuberculosis (MTB LipU) and M. leprae (MLP LipU). The MTB LipU was identified in extracellular fraction and was reported to be essential for the survival of mycobacterium. Therefore to address the problem of drug resistance in pathogen, LipU was selected as a drug target and the viability of finding out some FDA approved drugs as LipU inhibitors in both the cases was explored. Three dimensional (3D) model structures of MTB LipU and MLP LipU were generated and stabilized through molecular dynamics (MD)...
March 20, 2018: Journal of Biomolecular Structure & Dynamics
Gui-Yun Hang, Wen-Li Yu, Tao Wang, Zhen Li
In this work, a CL-20/DNB cocrystal explosive model was established and six different kinds of fluoropolymers, i.e., PVDF, PCTFE, F2311 , F2312 , F2313 and F2314 were added into the (1 0 0), (0 1 0), (0 0 1) crystal orientations to obtain the corresponding polymer bonded explosives (PBXs). The influence of fluoropolymers on PBX properties (energetic property, stability and mechanical properties) was investigated and evaluated using molecular dynamics (MD) methods. The results reveal a decrease in engineering moduli, an increase in Cauchy pressure (i...
March 19, 2018: Journal of Molecular Modeling
Myeongsang Lee, Hyunsung Choi, Gwonchan Yoon, Sungsoo Na
Experimental force spectroscopy has been effectively utilized for measuring structural characterization of biomolecules and mechanical properties of biomaterials. Specifically, atomic force microscopy (AFM) has been widely used to portray biomolecular characterization in single-molecule experiment by observing the unfolding behavior of the proteins. Not only the experimental techniques enable us to characterize globular protein, but computational methods like molecular dynamics (MD) also gives insight into understanding biomolecular structures...
March 12, 2018: Journal of Molecular Graphics & Modelling
Md Abu Manju, Edwin R Van Den Heuvel, Pieta C IJzerman-Boon
The detection proportion of a qualitative microbiological test method is the probability to detect a single micro-organism. A general expression for the moment estimator of the detection proportion is provided. It depends on the distribution of the spikes used in a validation study through its moment-generating function. Several forms of spiking experiments are compared on their estimation performance using simulations and assuming a generalized Poisson distribution (GPD) for the spikes. The optimal design, which minimizes the mean squared error of our proposed moment estimator, depends on the dispersion parameter of the GPD...
March 19, 2018: Journal of Biopharmaceutical Statistics
Shalini Awasthi, Shalini Gupta, Ravi Tripathi, Nisanth N Nair
Enhanced sampling of large number of collective variables (CVs) is inevitable in molecular dynamics (MD) simulations of complex chemical processes such as enzymatic reactions. Due to the computational overhead of hybrid quantum mechanical/molecular mechanical (QM/MM) based (MD) simulations, especially together with density functional theory (DFT), predictions of reaction mechanism and estimation of free energy barriers have to be carried out within few tens of picoseconds. We show here that the recently developed Temperature Accelerated Sliced Sampling (TASS) method allows one to sample large number of CVs, thereby enabling us to obtain rapid convergence in free energy estimates in QM/MM MD simulation of enzymatic reactions...
March 19, 2018: Journal of Physical Chemistry. B
Atsushi Hirano, Kazuki Iwashita, Shun Sakuraba, Kentaro Shiraki, Tsutomu Arakawa, Tomoshi Kameda
Ion-exchange chromatography and multimodal ion-exchange chromatography are widely used for the separation of small molecules, peptides and proteins. Salts generally attenuate the electrostatic interactions between charged moieties of solutes and those of resins through electrostatic screening. However, little is known about how salts affect the interaction between the uncharged moieties of the solutes, such as aromatic moieties, and the charged moieties of the resins. In this study, we used alkyl gallates as model aromatic solutes to investigate the interaction mechanism of aromatic moieties with multimodal and conventional ion-exchange resins...
March 6, 2018: Journal of Chromatography. A
Chengyin Fu, Lihua Xu, Fredy W Aquino, Arthur von Wald Cresce, Mallory Gobet, Steven G Greenbaum, Kang Xu, Bryan M Wong, Juchen Guo
Combining theoretical and experimental approaches, we investigate the solvation properties of Li+ ions in a series of ether solvents (dimethoxyethane, diglyme, triglyme, tetraglyme, and 15-crown-5) and their subsequent effects on the solid-state lithium-sulfur reactions in sub-nano confinement. The ab initio and classical molecular dynamics (MD) simulations predict Li+ ion solvation structures within ether solvent in excellent agreement with experimental evidence from electrospray ionization-mass spectroscopy...
March 17, 2018: Journal of Physical Chemistry Letters
Lulu Ning, Yuguang Mu
Prion diseases are neurodegenerative disorders characterized by the aggregation of an abnormal form of prion protein. The interaction of prion protein and cellular membrane is crucial to elucidate the occurrence and development of prion diseases. Its fragment, residues 106-126, has been proven to maintain the pathological properties of misfolded prion and was used as a model peptide. In this study, explicit solvent molecular dynamics (MD) simulations were carried out to investigate the adsorption, folding and aggregation of PrP106-126 with different sizes (2-peptides, 4-peptides and 6-peptides) on the surface of both pure neutral POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and negatively charged POPC/POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol) (3:1) lipids...
March 14, 2018: Biochimica et Biophysica Acta
Qi Gao, Chao Lu, Xiao-Wen Wang, Jun-Wei Zhang, Youtao Song, You-Lin Xue
Irisin is found closely associated with promoting the browning of beige fat cells in white adipose tissue. The crystal structure reveals that irisin forms a continuous inter-subunit β-sheet dimer. Here, molecular dynamics (MD) simulation and steered molecular dynamics (SMD) simulation were performed to investigate the dissociation process and the intricate interactions between the two irisin monomers. In the process of MD, the interactions between the monomers were roughly analyzed through the average numbers of both hydrophobic contacts and H-bonds...
March 16, 2018: Journal of Molecular Modeling
Masanari Shimada, Hideyuki Mizuno, Atsushi Ikeda
The low-temperature thermal properties of glasses are anomalous with respect to those of crystals. These thermal anomalies indicate that the low-frequency vibrational properties of glasses differ from those of crystals. Recent studies revealed that, in the simplest model of glasses, i.e., the harmonic potential system, phonon modes coexist with soft localized modes in the low-frequency (continuum) limit. However, the nature of low-frequency vibrational modes of more realistic models is still controversial. In the present work, we study the Lennard-Jones (LJ) system using large-scale molecular-dynamics (MD) simulation and establish that the vibrational property of the LJ glass converges to coexistence of the phonon modes and the soft localized modes in the continuum limit as in the case of the harmonic potential system...
February 2018: Physical Review. E
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