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Guang-Hui Ma, Yan Ye, Dan Zhang, Xin Xu, Pei Si, Jian-Long Peng, Yong-Long Xiao, Rui-Yuan Cao, Yu-Ling Yin, Jing Chen, Lin-Xiang Zhao, Yu Zhou, Wu Zhong, Hong Liu, Xiao-Min Luo, Li-Li Chen, Xu Shen
Hand, foot and mouth disease (HFMD) is a serious, highly contagious disease. HFMD caused by Enterovirus 71 (EV71), results in severe complications and even death. The pivotal role of EV71 3C(pro) in the viral life cycle makes it an attractive target for drug discovery and development to treat HFMD. In this study, we identified novel EV71 3C(pro) inhibitors by docking-based virtual screening. Totally 50 compounds were selected to test their inhibitory activity against EV71 3C(pro). The best inhibitor DC07090 exhibited the inhibition potency with an IC50 value of 21...
October 11, 2016: European Journal of Medicinal Chemistry
Christopher T Boughter, Viviana Monje-Galvan, Wonpil Im, Jeffery B Klauda
In this study, the influence of cholesterol on lipid bilayers is investigated by changing phospholipid head group, cholesterol concentration, chain saturation, and temperature. Molecular dynamics (MD) simulations were used to characterize bilayers containing phosphatidylcholine (PC) head groups with either fully saturated dimyristoyl (DM) or monounsaturated dioleoyl (DO) acyl chains and cholesterol concentrations ranging from 5-50%. To further explore the effects of cholesterol on bilayers with different head groups, we also preformed MD simulations of bilayer systems having 15% cholesterol with phosphatidic acid (PA), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylinositol (PI), and phosphatidylserine (PS), each having DM chains and at a temperature above the solid gel phase transition...
October 22, 2016: Journal of Physical Chemistry. B
Davide Sala, Andrea Giachetti, Claudio Luchinat, Antonio Rosato
The binding of paramagnetic metal ions to proteins produces a number of different effects on the NMR spectra of the system. In particular, when the magnetic susceptibility of the metal ion is anisotropic, pseudocontact shifts (PCSs) arise and can be easily measured. They constitute very useful restraints for the solution structure determination of metal-binding proteins. In this context, there has been great interest in the use of lanthanide(III) ions to induce PCSs in diamagnetic proteins, e.g. through the replacement native calcium(II) ions...
October 22, 2016: Journal of Biomolecular NMR
Samir S Roy, Manju Kapoor
Hsp90 contains two distinct Nucleotide Binding Sites (NBS), in its N-terminal domain (NTD) and C-terminal domain (CTD), respectively. The NTD site belongs to the GHKL super-family of ATPases and has been the subject of extensive characterization. However, a structure of the nucleotide-bound form of CTD is still unavailable. In this study molecular modeling was employed to incorporate experimental data using partial constructs of the CTD, from work published by many research groups, onto existing structural models of its apo- form...
October 3, 2016: Journal of Molecular Graphics & Modelling
Bogdan I Costescu, Sebastian Sturm, Frauke Gräter
Protein unfolding often does not obey a simple two-state behavior. Previous single molecule force spectroscopy studies demonstrated stretched exponential kinetics of protein unfolding under a constant pulling force, the molecular origin of which remains subject to debate. We here set out to extensively sample the mechanical unfolding of ubiquitin and NuG2 by Molecular Dynamics (MD) simulations. Both proteins show kinetics best fit by stretched exponentials, with stretching exponents similar to those found in experiments, even though static disorder is absent in our short MD simulations...
October 19, 2016: Journal of Structural Biology
Roberto De Ponti Md Fhrs
No abstract text is available yet for this article.
October 8, 2016: Trends in Cardiovascular Medicine
Richard A Manderville, Stacey D Wetmore
The formation of DNA adducts by the attack of intermediates derived from toxic substances at the C8 position of 2-deoxyguanosine (dG) is a common damaging event. Although the majority of studies on C8-dG adducts have focused on lesions containing a C8-N-C tether between the bulky moiety and the nucleobase, the formation of O-linked lesions with a similar tether topology and C-linked adducts involving direct C8-C connectivity have also been uncovered. Several studies have been done to try to better understand the structural impact and mutagenicity of O-linked and C-linked aryl C8-dG adducts, including lesions arising from unsubstituted and chloro substituted phenols, and the food mutagen ochratoxin A (OTA)...
October 21, 2016: Chemical Research in Toxicology
Lanfang Tian, Siyuan Chen, Haiyan Liu, Mingzhang Guo, Wentao Xu, Xiaoyun He, Yunbo Luo, Xiaozhe Qi, Hongxia Luo, Kunlun Huang
Hepcidin, one kind of antimicrobial peptides, is one of the promising alternatives to antibiotics with broad spectrum of antimicrobial activity. Hepcidins cloned from different kinds of fishes have been produced using exogenous expression systems, and their in vitro antimicrobial effects have been verified. However their in vivo effects on gut microbiota and gut health of hosts remain unclear. Here we performed a safety study of hepcidin so that it can be used to reduce microbial contaminations in the food and feed...
2016: PloS One
Majid Jafari, Faramarz Mehrnejad
Changes in the tertiary structure of proteins and the resultant fibrillary aggregation could result in fatal heredity diseases, such as lysozyme systemic amyloidosis. Human lysozyme is a globular protein with antimicrobial properties with tendencies to fibrillate and hence is known as a fibril-forming protein. Therefore, its behavior under different ambient conditions is of great importance. In this study, we conducted two 500000 ps molecular dynamics (MD) simulations of human lysozyme in sodium dodecyl sulfate (SDS) at two ambient temperatures...
2016: PloS One
Mon-Shu Ho, Chih-Pong Huang, Jyun-Hwei Tsai, Che-Fu Chou, Wen-Jay Lee
This paper reports an array-designed C84-embedded Si substrate fabricated using a controlled self-assembly method in an ultra-high vacuum chamber. The characteristics of the C84-embedded Si surface, such as atomic resolution topography, local electronic density of states, band gap energy, field emission properties, nanomechanical stiffness, and surface magnetism, were examined using a variety of surface analysis techniques under ultra, high vacuum (UHV) conditions as well as in an atmospheric system. Experimental results demonstrate the high uniformity of the C84-embedded Si surface fabricated using a controlled self-assembly nanotechnology mechanism, represents an important development in the application of field emission display (FED), optoelectronic device fabrication, MEMS cutting tools, and in efforts to find a suitable replacement for carbide semiconductors...
September 28, 2016: Journal of Visualized Experiments: JoVE
Blake T Riley, Olga Ilyichova, Mauricio G S Costa, Benjamin T Porebski, Simon J de Veer, Joakim E Swedberg, Itamar Kass, Jonathan M Harris, David E Hoke, Ashley M Buckle
The kallikrein-related peptidase (KLK) family of proteases is involved in many aspects of human health and disease. One member of this family, KLK4, has been implicated in cancer development and metastasis. Understanding mechanisms of inactivation are critical to developing selective KLK4 inhibitors. We have determined the X-ray crystal structures of KLK4 in complex with both sunflower trypsin inhibitor-1 (SFTI-1) and a rationally designed SFTI-1 derivative to atomic (~1 Å) resolution, as well as with bound nickel...
October 21, 2016: Scientific Reports
Shaher Bano Mirza, Ramin Ekhteiari Salmas, M Qaiser Fatmi, Serdar Durdagi
The Klotho is known as lifespan enhancing protein involved in antagonizing the effect of Wnt proteins. Wnt proteins are stem cell regulators, and uninterrupted exposure of Wnt proteins to the cell can cause stem and progenitor cell senescence, which may lead to aging. Keeping in mind the importance of Klotho in Wnt signaling, in silico approaches have been applied to study the important interactions between Klotho and Wnt3 and Wnt3a (wingless-type mouse mammary tumor virus (MMTV) integration site family members 3 and 3a)...
October 21, 2016: Journal of Enzyme Inhibition and Medicinal Chemistry
Erfan Dashtimoghadam, Ghasem Bahlakeh, Hamed Salimi-Kenari, Mohammad Mahdi Hasani-Sadrabadi, Hamid Mirzadeh, Bo Nyström
The temperature-induced gelation of chitosan/glycerophosphate (Chs/GP) systems through physical interactions has shown great potential for various biomedical applications. In the present work, hydroxyethyl cellulose (HEC) was added to the thermosensitive Chs/GP solution to improve the mechanical strength and gel properties of the incipient Chs/HEC/GP gel in comparison with the Chs/GP hydrogel at body temperature. The physical features of the macromolecular complexes formed by the synergistic interaction between chitosan and hydroxyethyl cellulose in the presence of β-glycerophosphate disodium salt solution have been studied essentially from a rheological point of view...
October 21, 2016: Biomacromolecules
Sagar Satpathi, Mandar Kulkarni, Arnab Mukherjee, Partha Hazra
Among different polymorphs of DNA, G-quadruplex (GQ) formation in guanine rich sequences has received special attention due to its direct relevance to cellular aging and abnormal cell growths. To date, smaller ions like Na(+), K(+), Li(+), and NH4(+) are the best possible selective GQ stabilizing materials. Herein, we report that an ionic liquid (IL), i.e. guanidinium tris(pentafluoroethyl)trifluorophosphate, can not only instigate the GQ formation in the absence of conventional GQ forming ions (like Na(+), K(+), NH4(+), etc...
October 21, 2016: Physical Chemistry Chemical Physics: PCCP
Anna V Glyakina, Nikolai K Balabaev, Oxana V Galzitskaya
The amyloidogenic peptide VDSWNVLVAG from Bgl2p-glucantransferase of Saccharomyces cerevisiae cell wall and its modifying analog VESWNVLVAG were taken for the construction of four types of bilayers which differ by orientation of the peptides in the layers and of the layers relative to each other. These bilayers were used as starting models for the molecular dynamics (MD) at three charge states (neutral, pH3, and pH5). The changes of the fraction of secondary structure during 1 ns simulations were received for 96 MD trajectories...
December 2016: Data in Brief
Zhong Ni, Xiting Wang, Tianchen Zhang, Rong Zhong Jin
Anaplastic lymphoma kinase (ALK) has become as an important target for the treatment of various human cancers, especially non-small-cell lung cancer. A mutation, F1174C, suited in the C-terminal helix αC of ALK and distal from the small-molecule inhibitor ceritinib bound to the ATP-binding site, causes the emergence of drug resistance to ceritinib. However, the detailed mechanism for the allosteric effect of F1174C resistance mutation to ceritinib remains unclear. Here, molecular dynamics (MD) simulations and binding free energy calculations [Molecular Mechanics/Generalized Born Surface Area (MM/GBSA)] were carried out to explore the advent of drug resistance mutation in ALK...
October 11, 2016: Computational Biology and Chemistry
Flavia A Mercurio, Daniela Marasco, Concetta Di Natale, Luciano Pirone, Susan Costantini, Emilia M Pedone, Marilisa Leone
The EphA2 receptor controls diverse physiological and pathological conditions and its levels are often upregulated in cancer. Targeting receptor overexpression, through modulation of endocytosis and consequent degradation, appears to be an appealing strategy for attacking tumor malignancy. In this scenario, the Sam domain of EphA2 plays a pivotal role because it is the site where protein regulators of endocytosis and stability are recruited by means of heterotypic Sam-Sam interactions. Because EphA2-Sam heterotypic complexes are largely based on electrostatic contacts, we have investigated the possibility of attacking these interactions with helical peptides enriched in charged residues...
October 20, 2016: Chembiochem: a European Journal of Chemical Biology
Fariba Mortazavi, Mehdi Habibi, Ehsan Nedaaee Oskoee
We study the translocation mechanism of a granular chain in a horizontally vibrated saw-tooth channel using MD simulations and macro-scale experiments and show that the translocation speed is independent of the chain length as long as the chain length is larger than the spatial period of the saw-tooth. With the help of simulation, we explore the effect of geometry of the container and frequency and amplitude of vibration as well as chain flexibility on the chain drift speed. We observe that the most efficient transport is achieved when one of the channel walls is shifted with respect to the other wall by an amount equal to half the spatial period of the saw-tooth...
October 2016: European Physical Journal. E, Soft Matter
Navnit Kumar Mishra, Anil Kumar Sharma, Tapan Kumar Mukherjee
Melanoma is a cancer associated with melanocytes of epidermis. There has been a consistent increase in the number of melanoma patients because of the depletion of the ozone layer which makes it of paramount importance to explore the immunogenic potential of various peptides in melanoma therapy. In the current study, a mutated decapeptide (ELAGIGILTV) epitope ID 12941 was taken from the melanoma antigen recognized by T-cells. This epitope displayed relatively better affinity for histocompatibility leukocyte antigen influencing the proliferation of cytotoxic T-cells...
November 2016: Journal of Molecular Modeling
Tomasz Róg, Adam Orłowski, Alicia Llorente, Tore Skotland, Tuulia Sylvänne, Dimple Kauhanen, Kim Ekroos, Kirsten Sandvig, Ilpo Vattulainen
In this Data in Brief article we provide a data package of GROMACS input files for atomistic molecular dynamics simulations of multicomponent, asymmetric lipid bilayers using the OPLS-AA force field. These data include 14 model bilayers composed of 8 different lipid molecules. The lipids present in these models are: cholesterol (CHOL), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylethanolamine (POPE), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidyl-ethanolamine (SOPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (SOPS), N-palmitoyl-D-erythro-sphingosyl-phosphatidylcholine (SM16), and N-lignoceroyl-D-erythro-sphingosyl-phosphatidylcholine (SM24)...
June 2016: Data in Brief
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