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MD simulation

Ari Hardianto, Fei Liu, Shoba Ranganathan
(-)-Balanol is an ATP mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with little selectivity. While PKA is known as a tumour promoter, PKC isozymes can be tumour promoters or suppressors. In particular, PKCε is frequently involved in tumorigenesis and a potential target for anticancer drugs. We recently reported that stereospecific fluorination of balanol yielded a balanoid with enhanced selectivity for PKCε over other PKC isozymes and PKA, although the global fluorine effect behind the selectivity enhancement is not fully understood...
January 17, 2018: Journal of Chemical Information and Modeling
Faeze Sadat Mohajer, Sepideh Parvizpour, Jafar Razmara, Mohd Shahir Shamsir
Congenital myopathy is a broad category of muscular diseases with symptoms appearing at the time of birth. One type of congenital myopathy is Congenital Fiber Type Disproportion (CFTD), a severely debilitating disease. The G48D and G48C mutations in the D-loop and the actin-myosin interface are the two causes of CFTD. These mutations have been shown to significantly affect the structure and function of muscle fibers. To the author's knowledge, the effects of these mutations have not yet been studied. In this work, the power stroke structure of the head domain of myosin and the wild and mutated types of actin were modeled...
January 17, 2018: Journal of Biomolecular Structure & Dynamics
Mithun Biswas, Benjamin Lickert, Gerhard Stock
Enhanced sampling techniques represent a versatile approach to account for rare conformational transitions in biomolecules. A particularly promising strategy is to combine massive parallel computing of short molecular dynamics (MD) trajectories (to sample the free energy landscape of the system) with Markov state modeling (to rebuild the kinetics from the sampled data). To obtain well-distributed initial structures for the short trajectories, it is proposed to employ Metadynamics MD, which quickly sweeps through the entire free energy landscape of interest...
January 16, 2018: Journal of Physical Chemistry. B
Sergio Decherchi, Giovanni Bottegoni, Andrea Spitaleri, Walter Rocchia, Andrea Cavalli
In this paper, we introduce the BiKi Life Sciences suite. This software makes it easy for computational medicinal chemists to run ad hoc molecular dynamics protocols in a novel and task-oriented environment; as a notebook, BiKi keeps memory of any activity together with dependencies among them. It offers unique accelerated protein-ligand binding/unbinding methods, and other useful tools to gain actionable knowledge from MD simulations and to simplify the drug discovery process.
January 17, 2018: Journal of Chemical Information and Modeling
Eva M Bruening, Jakob Schauss, Torsten Uwe Siebert, Benjamin P Fingerhut, Thomas Elsaesser
The equilibrium structure of the RNA sugar-phosphate backbone and its hydration shell is distinctly different from hydrated DNA. Applying femtosecond two-dimensional infrared (2D-IR) spectroscopy in a range from 950 to 1300 cm-1, we elucidate the character, dynamics, and couplings of backbone modes of a double-stranded RNA A-helix geometry in its aqueous environment. The 2D-IR spectra display a larger number of backbone modes than for DNA, with distinctly different lineshapes of diagonal peaks. Phosphate-ribose interactions and local hydration structures are reflected in the complex coupling pattern of RNA modes...
January 16, 2018: Journal of Physical Chemistry Letters
Jian Tang, Zhou Qu, Jianhui Luo, Lanyan He, Pingmei Wang, Ping Zhang, Xianqiong Tang, Yong Pei, Bin Ding, Baoliang Peng, Yunqing Huang
The detachment process of an oil molecular layer or drop situated above a horizontal substrate was often described by a three-stage process. In this mechanism, the water molecule penetration and diffusion between the oil phase and the solid phase was proposed to be a crucial step to aid in removal of oil drops from solid surfaces. In this work, the detachment process of a two-dimensional alkane molecule layer from a silica surface in aqueous surfactant solutions is studied by means of molecular dynamics (MD) simulations...
January 16, 2018: Journal of Physical Chemistry. B
Batsaikhan Mijiddorj, Shiho Kaneda, Hisako Sato, Yuki Kitahashi, Namsrai Javkhlantugs, Akira Naito, Kazuyoshi Ueda, Izuru Kawamura
Bombinin H4 is an antimicrobial peptide that was isolated from the toad Bombina variegata. Bombinin H family peptides are active against gram-positive, gram-negative bacteria, and fungi as well as the parasite Leishmania. Among them, bombinin H4 (H4), which contains d-allo-isoleucine (d-allo-Ile) as the second residue in its sequence, is the most active, and its l-isomer is bombinin H2 (H2). H4 has a significantly lower LC50 than H2 against Leishmania. However, the atomic-level mechanism of the membrane interaction and higher activity of H4 has not been clarified...
January 11, 2018: Biochimica et Biophysica Acta
Sergio Scudino, Daniel Sopu
Due to the fast dynamics of shear band formation and propagation along with the small size and transient character of the shear transformation zones (STZs), the elementary units of plasticity in metallic glasses, the description of the nanoscale mechanism of shear banding often relies on molecular dynamics (MD) simulations. However, the unrealistic parameters used in the simulations related to time constrains may raise questions about whether quantitative comparison between results from experimental and computational analyses is possible...
January 16, 2018: Nano Letters
Hongwei Zhang, Tienchong Chang
Nanoscale friction is generally found to be a function of the contact area. However, little is known whether and how it is dependent on the contact area shape. In this study, based on molecular dynamics (MD) simulations about a rectangular graphene flake sliding on a diamond-supported graphene substrate, we show that the friction between the flake and the substrate is significantly dependent on the flake edge oriented perpendicular to the sliding direction, but less dependent on the edge along the sliding direction...
January 16, 2018: Nanoscale
Md Tauhidul Islam, Anuj Chaudhry, Ginu Unnikrishnan, J N Reddy, Raffaella Righetti
The mechanical behavior of biological tissues has been studied using a number of mechanical models. Due to the relatively high fluid content and mobility, many biological tissues have been modeled as poroelastic materials. Diseases such as cancers are known to alter the poroelastic response of a tissue. Tissue poroelastic properties such as compressibility, interstitial permeability and fluid pressure also play a key role for the assessment of cancer treatments and for improved therapies. At the present time, however, a limited number of poroelastic models for soft tissues are retrievable in the literature, and the ones available are not directly applicable to tumors as they typically refer to uniform tissues...
January 16, 2018: Physics in Medicine and Biology
Zhiqiang Zhao, Hang Yin, Kun Cai, Wanqi Zhou
The mechanical properties of black phosphorus (BP) are anisotropic. Correspondingly, the properties of the nanotubes formed by bending the same BP ribbon along different directions are different as well. When bending the ribbon along the [110] direction (i.e., stair direction), or along its perpendicular direction (i.e., ps-direction), s- or ps-BPNT can be obtained. The two types of BPNTs are investigated via molecular dynamics (MD) simulations on their thermal and mechanical properties. The results indicate that, for the thermal stability of the s-BPNTs with similar diameters, s-BPNT is weaker than a-BPNTs (armchair type) but stronger than ps-BPNT, and z-BPNT (zigzag type) is the weakest one...
January 15, 2018: Physical Chemistry Chemical Physics: PCCP
M Hassan, M Azhar, Q Abbas, H Reza, A A Moustafa, S Shahzadi, Z Ashraf, S Y Seo
BACKGROUND: Secreted frizzled-related protein 4 (SFRP4) is a glycoprotein that act as a competitor of both canonical and non-canonical Wnt pathways. SFRP4 is mostly expressed in ovary and played a significant role as a target molecule to cure ovarian carcinoma. OBJECTIVE: Multiple chemical agonists are being used to cure ovary melanoma. We are interested to theoretically analyze the compounds through computational approaches for their inhibitory effects against SFRP4...
January 11, 2018: Current Computer-aided Drug Design
Baohe Wang, Yan Nie, Jing Ma
Combing molecular dynamics (MD) and Grand Canonical Monte Carlo (GCMC) simulation, the effect of bioadhesive transition layer on the interfacial compatibility of the pervaporation composite membranes, and the pervaporation performance toward penetrant molecules were investigated. In our previous experimental study, the structural stability and permeability selectivity of the composite membranes were considerably enhanced by the introduction of bioadhesive carbopol (CP). In the present study, the interfacial compatibility and the interfacial energies between the chitosan (CS) separation layer, CP transition layer and the support layer were investigated, respectively...
January 5, 2018: Journal of Molecular Graphics & Modelling
Lu Deng, Jincheng Du
Borosilicate glasses form an important glass forming system in both glass science and technologies. The structure and property changes of borosilicate glasses as a function of thermal history in terms of cooling rate during glass formation and simulation system sizes used in classical molecular dynamics (MD) simulation were investigated with recently developed composition dependent partial charge potentials. Short and medium range structural features such as boron coordination, Si and B Qn distributions, and ring size distributions were analyzed to elucidate the effects of cooling rate and simulation system size on these structure features and selected glass properties such as glass transition temperature, vibration density of states, and mechanical properties...
January 14, 2018: Journal of Chemical Physics
G Lanaro, G N Patey
Molecular dynamics (MD) simulations are employed to investigate crystal nucleation and growth in oversaturated aqueous LiF solutions. Results obtained for a range of temperatures provide evidence that the rate of crystal growth is determined by a substantial energy barrier (∼49 kJ mol-1) related to the loss of water from the ion hydration shells. Employing direct MD simulations, we do not observe spontaneous nucleation of LiF crystals at 300 K, but nucleation is easily observable in NVT simulations at 500 K...
January 14, 2018: Journal of Chemical Physics
Norio Yoshida, Masahiro Higashi, Hideyoshi Motoki, Shun Hirota
The structural stability of a cytochrome c domain-swapped dimer compared with that of the monomer was investigated by molecular dynamics (MD) simulations and by three-dimensional reference interaction site model (3D-RISM) theory. The structural fluctuation and structural energy of cytochrome c were treated by MD simulations, and the solvation thermodynamics was treated by 3D-RISM theory. The domain-swapped dimer state is slightly less stable than the monomer state, which is consistent with experimental observations; the total free energy difference is calculated as 25 kcal mol-1...
January 14, 2018: Journal of Chemical Physics
Chuancai Sun, Lijuan Zhu, Chao Zhang, Ce Song, Cuihong Wang, Meiling Zhang, Yaoming Xie, Henry F Schaefer
The conformational structures and properties of the anticancer drug docetaxel (DTX) are studied theoretically. A total of 3888 trial structures were initially generated by all combinations of internal single-bond rotamers and screened with the B3LYP/3-21G* method. A total of 31 unique conformers were further optimized at the B3LYP/6-311G* method. Their relative energies, dipole moments, rotational constants, and harmonic vibrational frequencies were predicted. Single-point relative energies were then determined at the M06-L/6-311G(2df,p) level...
January 12, 2018: Journal of Computational Chemistry
Ashish Kumar, Harmeet Kaur, Abha Jain, Deepak T Nair, Dinakar M Salunke
Sequence and structural homology suggests that MP-4 protein from Mucuna pruriens belongs to Kunitz-type protease inhibitor family. However, biochemical assays showed that this protein is a poor inhibitor of trypsin. To understand the basis of observed poor inhibition, thermodynamics and molecular dynamics (MD) simulation studies on binding of MP-4 to trypsin were carried out. Molecular dynamics simulations revealed that temperature influences the spectrum of conformations adopted by the loop regions in the MP-4 structure...
January 12, 2018: Scientific Reports
Xue-Song Wang, Qing-Chuan Zheng
The CBP (CREB (cAMP responsive element binding protein) binding protein) bromodomain (BRD) could recognize and bind with acetyl K382 of human tumor suppressor protein p53 which the mutation of encoding gene might cause human cancers. CBP-BRD serves as a promising drug target for several disease pathways and a series of effective drug have been discovered. In this study, molecular dynamics (MD) simulations and molecular mechanics generalized born surface area (MM-GB/SA) approaches were performed to investigate the different binding modes between five inhibitors with CBP-BRD...
December 26, 2017: Bioorganic & Medicinal Chemistry
Shagufta Khan, Faez Iqbal Khan, Taj Mohammad, Parvez Khan, Gulam Mustafa Hasan, Kevin A Lobb, Asimul Islam, Faizan Ahmad, Md Imtaiyaz Hassan
Mammalian cell entry protein (Mce4A) is a member of MCE-family, and is being considered as a potential drug target of Mycobacterium tuberculosis infection because it is required for invasion and latent survival of pathogen by utilizing host's cholesterol. In the present study, we performed molecular docking followed by 100 ns MD simulation studies to understand the mechanism of interaction of Mce4A to the cholesterol derivatives and probucol. The selected ligands, cholesterol, 25-hydroxycholesterol, 5-cholesten-3β-ol-7-one and probucol bind to the predicted active site cavity of Mce4A, and complexes remain stable during entire simulation of 100 ns...
January 9, 2018: International Journal of Biological Macromolecules
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