The H and C Nuclear Magnetic Resonance (NMR) spectra of the retinyl chromophore in rhodopsin are investigated by using Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid methods at the Density Functional Theory (DFT) B3LYP/631G*:Amber level, in conjunction with the Gauge Independent Atomic Orbital (GIAO) method for the ab initio Self-Consistent-Field (SCF) calculation of NMR chemical shifts. ...

Gyrase is a molecular motor that harnesses the free energy of ATP hydrolysis to perform mechanical work on DNA. The enzyme specifically introduces negative supercoiling in a process that must coordinate fuel consumption with DNA cleavage and religation and with numerous conformational changes in both the protein and DNA components of a large nucleoprotein complex. Here we present a current unde...

Continuum solvent models predict a quadratic charge dependence (linear response) of the free energy of a system of charged solutes. The relation between this prediction and the structure of the solvation shell around the solutes is discussed. Studies of the derivative of the free energy with respect to the charges for different reference states are shown to be a convenient way of testing the li...

Titin is a giant filamentous protein traversing the half sarcomere of striated muscle with putative functions as diverse as providing structural template, generating elastic response, and sensing and relaying mechanical information. The Z-disk region of titin, which corresponds to the N-terminal end of the molecule, has been thought to be a hot spot for mechanosensing while also serving as anch...

Hybrid quantum/molecular mechanics models (QM/MM methods) are widely used in material and molecular simulations when MM do not provide sufficient accuracy but pure QM computationa...

Novel techniques are revealing the movements and forces associated with single interactions of motor proteins, such as myosin and kinesin, and also of processive enzymes, such as RNA polymerase.

The quantum mechanics/molecular mechanics (QM/MM) method (e.g., density functional theory (DFT)/MM) is important in elucidating enzymatic mechanisms. It is indispensable to study "multiple" conformations of enzymes to get unbiased energetic and structural results. One challenging problem, however, is to determine the minimum number of conformations for DFT/MM calculations. Here, we propose two ...

Research activities in the fine chemicals industry involve the generation and analysis of huge amounts of chemical and biological data, and this has led to the development of highly sophisticated, computer-based, chemical information systems to support the research [ 11. Most chemical databases contain two-dimensional structural data, i.e. planar chemical structure diagrams, but there is also i...