Protein nonbonded interactions

Some of the results of our MD simulations of proteins on clay mineral surfaces are summarized in Fig. 8-5. When proteins are placed in the interlayer space of clay minerals, interactions between the surface and the protein compete with intramolecular protein nonbonded interactions. As a result, a protein molecule can gel stretched out along the mineral surface, significantly denatured from its native stale. In the case ol mhredoxiii adsorbed by pyropliyllite. for example, the mole-... 

Guenot, J., Kollman, P.A. Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation. J. Comput. Chem. 14 (1993) 295-311. 

OPES (Optimized Potentials for Liquid Simulations) is based on a force field developed by the research group of Bill Jorgensen now at Yale University and previously at Purdue University. Like AMBER, the OPLS force field is designed for calculations on proteins and nucleic acids. It introduces nonbonded interaction parameters that have been carefully developed from extensive Monte Carlo liquid simulations of small molecules. These nonbonded interactions have been added to the bonding interactions of AMBERto produce anew force field that is expected to be better than AMBER at describing simulations where the solvent is explic-... 

SH Bryant, CE Lawrence. The frequency of lon-pair substructures m proteins is quantitatively related to electrostatic potential A statistical model for nonbonded interactions. Proteins 9 108-119, 1991. 

A. M. Mathiowetz, A. Jain, N. Karasawa, W. A. Goddard III. Protein simulations using techniques suitable for very large systems the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics. CN 8921. Proteins 20 221, 1994. 

Recently, the crystal structure of S-protein complexed with the model peptide has been solved to moderate resolution (3 A) (Taylor et al., 1985). Most of the structural features envisioned in the design of the model peptide were indeed observed in the structure of the complex. The peptide is in a helical conformation, the histidine is held in a reasonable orientation for catalysis, and the complex is stabilized by nonbonded interactions between the hydrophobic cleft of S-protein and the side chains of Phe-8 and Met-13 of the peptide. There were also a number of subtle differences between the structures of the native and the model S-protein S-peptide complexes. Most notably, the N terminus of the peptide has undergone a major reorientation that prevents Glu-2 from forming a hydrogen bond with Arg-10. Further, the 8-nitrogen of the active-site... 

Another difference between protein-protein and protein-small-molecule docking involves the treatment of nonbonded interactions. For the docking of rigid low molecular weight compounds, the receptor s molecular interaction... 

Energetic Effects of Truncating Nonbonded Interactions m an Aqueous Protein Dynamics Simulation. 

The motions of proteins are usually simulated in aqueous solvent. The water molecules can be represented either explicitly or implicitly. To include water molecules explicitly implies more time-consuming calculations, because the interactions of each protein atom with the water atoms and the water molecules with each other are computed at each integration time step. The most expensive part of the energy and force calculations is the nonbonded interactions because these scale as 77 where N is the number of atoms in the system. Therefore, it is common to neglect nonbonded interactions between atoms separated by more than a defined cut-off ( 10 A). This cut-off is questionable for electrostatic interactions because of their 1/r dependence. Therefore, in molecular dynamics simulations, a Particle Mesh Ewald method is usually used to approximate the long-range electrostatic interactions (71, 72). 

Chakrabarti P, Bhattacharyya R. Geometry of nonbonded interactions involving planar groups in proteins. Prog. Biophys. Mol. Biol. 2007 95 83-137. 

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