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Synphilin-1 is a novel α-synuclein interacting protein presenting in the Lewy bodies, the N-terminal 12 residues peptide of α-synuclein (α-syn12) can binding to the coiled-coil domain of Synphilin-1. However, the complex structure in water has not been determined by experimental methods, so that the possible structure of this complex and interaction sites have been studied by docking algorithms and...
Differences in the terahertz spectral features and the assignment of terahertz absorptions and hydrogen bond networking of tyrosines were examined. The inter- and intra-molecular absorptions in a terahertz region were calculated by the structural optimization simulation “Gaussian 03” at B3LYP/6-31G (d) level using the mid-IR absorptions.
The use of the far IR spectral range presents a novel approach for analysis of proteins. Here it is presented for the analysis of Fe-S vibrations (500-200 cm-1) and of the intra-and intermolecular H-bonding signature (300-50 cm-1) in Rieske proteins and lipids in function of T, redox state and pH.
The THz absorption of the intermolecular vibrational modes of the hydrogen bond network of water has recently been found to define a dynamical solvation shell around solutes that extends beyond the first hydration layer. Here, we study the vibrations and dynamical processes in the hydrogen bond network of water using molecular dynamics (MD) simulations to understand its properties.
Abstract-The crystal morphology of orthorhombic lysozyme is predicted using the Bravais-Friedel-Donnay-Harker (BFDH) and the attachment energy (AE) models of molecular simulation software Cerius2 in vacuo. The morphology predicted by two models is approximately consistent. The morphology predicted by AE model is in good agreement with the morphology of crystals grown from solution at pH 6.5. The main...
Hyaluronidases are enzymes degrading hyaluronic acid, which is an important component in all tissues and body fluids. Flexible docking simulation between hyaluronidase and chlorogenic acid as a potent hyaluronidase inhibitor with IC50 value 2.25mmol/L was performed using ArgusLab docking method and the binding free energy of the docked complex is -10.33 kcal/mol. The binding mode of interaction at...
Protein tyrosine phosphatase 1B (PTP1B) is a negative regulator of insulin and leptin signaling, and is therefore a major molecular target for the treatment of type II diabetes and obesity. WPD loop is a key element in the mechanism of PTP1B catalysis. In the apo form, WPD loop is usually in an “open” conformation, whereas it closes over the active site upon substrate binding. Here, targeted molecular...
The present paper compares a protein hydrogen bonding network (HBN) to a microelectronic circuit. The HBN properties that are applicable to the microelectronic circuit are simulated in Matlab. The hydrogen bonds are coded in Matlab as tree- and four- terminal microelectronic block elements which build up the respective electrical circuit. The simulations demonstrate that the circuit can operate in...
Prediction of protein-ligand binding affinities is an important issue in molecular recognition and virtual screening. We have developed a scoring function, namely GemAffinity, to predict binding affinities by analyzing 88 descriptors derived from 891 protein-ligand structures selected from the protein data bank (PDB). Based on these 88 descriptors, we derived GemAffinity using a stepwise regression...
HER2 over-expression associates with many cancer symptoms, and the HER2 protein kinase was regarded as the target for cancer treatment. To develop the novel potent leads, homology modeling and structure-based design were employed to this research. Three clinical trail drugs and traditional Chinese medicine (TCM) database were employed to perform the docking. The top 7 compounds from database with...
Terahertz time-domain spectroscopy of a protein in a reverse micelle has been done as a function of the micelle size. The amplitude of its absorption is enhanced at a certain size of the micelle. This is explained in terms of the hydration effect of the protein which changes a hydrogen-bonded network not only between the protein and the surrounding water but also within the protein.
The binding free energies of several benzamidine-like inhibitors to trypsin were examined using a polarizable molecular mechanics potential. All the computed binding free energies are in good agreement with the experimental data. From free energy decomposition, electrostatic interaction was indicated to be the driving force for the binding. MD simulations show that the ligands form hydrogen bonds...
Enfuvirtide is a fusion inhibitor that was obtained from the C-terminal region of the ectodomain of gp41 in HIV-1. Nevertheless, the viral resistance to enfuvirtide limits the long-term efficacy of treatment patients of HIV infection. In order to study molecular mechanism of resistance, we build the ectodomain of gp41 trimer using the homology modeling and molecular dynamics (MD) simulations. A few...
We present an ATRIPPI model for analyzing protein-protein interactions. This model is a 167-atom-type and residue-specific interaction preferences with distance bins derived from 641 co-crystallized protein-protein interfaces. The ATRIPPI model is able to yield physical meanings of hydrogen bonding, disulfide bonding, electrostatic interactions, van der Waals and aromatic-aromatic interactions. We...
Identifying calcium-binding sites in proteins help acknowledge protein functions. We thus developed a graph theory and geometry approach to improve the accuracy for predicting calcium-binding sites, we enhance our previous approach at a high level to find biggest local oxygen clusters with a graph algorithm to find maximal cliques and propose a new geometric criterion embedding the bidentate property...
Heat shock protein 90 (HSP90) regulates the correct folding of nascent protein in tumor cells. Through the ATPase domain of HSP90, inhibition of its activity is a manipulation for anticancer treatment. Two series of anticancer compounds, flavonoids and YC-1 derivatives, were employed in this study. The reference ligand in the docking simulation showed the significant RMSD of 0.87 with respect to the...
The prediction of the binding affinity of protein- ligand complexes is important for the molecular docking and rational drug discovery. In this study, we have analyzed the descriptors, which affect the binding affinities of protein-ligand complexes, from five dimensions, including protein-ligand interactions, protein properties, structural and physicochemical descriptors of ligands, metal-ligand bonding,...
Molecular simulations show that hydrogen bond energies are stable between oxidized and unoxidized variants of the same protein, and that, consequentially, the secondary-structure elements are stable. Whilst there is no change in the energy of hydrogen bonds, it is shown that oxidation increases the number of hydrogen bonds between the oxidized histone octamer and its solvation layer. This analysis...
We have developed a density functional (DF) program, ProteinDF, for all-electron calculation on proteins. In order to overcome difficulties of a convergence problem in large-scale molecules, we have already proposed new localized orbital (LO), which named quasi-canonical LO (QCLO). In this study, improved convergence process which focused on the secondary structure such as hydrogen bonds and salt-bridge...
An improved self-avoiding lattice model was put forward to study coil-helix transition via dynamic Monte Carlo simulation. Each residue occupies eight simple lattices. By introducing a virtual-imino group and a virtual-carbonyl group, the helical period is not necessarily to be an integer. The Go-like restriction of hydrogen bonding interaction has also been partially released. The coil-helix transition...
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