Pancreatic trypsin inhibitor molecular dynamics simulation

Niedermeier, C. and K. Schulten. (1992). Molecular-dynamics simulations in Heterogeneous Dielectric and Debye-Huckel Media Application to the Protein Bovine Pancreatic Trypsin-inhibitor. Molecular Simulation. 8 361-387. 

In periodic boimdary conditions, one possible way to avoid truncation of electrostatic interaction is to apply the so-called Particle Mesh Ewald (PME) method, which follows the Ewald summation method of calculating the electrostatic energy for a number of charges [27]. It was first devised by Ewald in 1921 to study the energetics of ionic crystals [28]. PME has been widely used for highly polar or charged systems. York and Darden applied the PME method already in 1994 to simulate a crystal of the bovine pancreatic trypsin inhibitor (BPTI) by molecular dynamics [29]. 

Because of the ease with which molecular mechanics calculations may be obtained, there was early recognition that inclusion of solvation effects, particularly for biological molecules associated with water, was essential to describe experimentally observed structures and phenomena [32]. The solvent, usually an aqueous phase, has a fundamental influence on the structure, thermodynamics, and dynamics of proteins at both a global and local level [3/]. Inclusion of solvent effects in a simulation of bovine pancreatic trypsin inhibitor produced a time-averaged structure much more like that observed in high-resolution X-ray studies with smaller atomic amplitudes of vibration and a fewer number of incorrect hydrogen bonds [33], High-resolution proton NMR studies of protein hydration in aqueous... 

Brunne, R. M., and Van Gunsteren, W. F. (1993) D5mamical properties of bovine pancreatic trypsin inhibitor from a molecular dynamics simulation at 5000 atm, FEBSLetters 323, 215-217... 

To illustrate the solvent effect on the average structure of a protein, we describe results obtained from conventional molecular dynamics simulations with periodic boundary conditions.92,193 This method is well suited for a study of the global features of the structure for which other approaches, such as stochastic boundary simulation methods, would not be appropriate. We consider the bovine pancreatic trypsin inhibitor (BPTI) in solution and in a crystalline environment. A simulation was carried out for a period of 25 ps in the presence of a bath of about 2500 van der Waals particles with a radius and well depth corresponding to that of the oxygen atom in ST2 water.193 The crystal simulation made use of a static crystal environment arising from the surrounding protein molecules in the absence of solvent. These studies, which were the first application of simulation methods to determine the effect of the environment on a protein, used simplified representations of the surround-... 

Recent progress in X-ray diffraction of protein crystals in the diamond anvil cell will also make it possible to obtain quantitative information on the cavities [42, 43]. Optical spectroscopy [44] and neutron scattering [45] should also be valuable tools to probe the role of cavities. High-pressure molecular dynamics simulations should also allow estimating the contributions of the hydration and the cavities. High-pressure simulations on the small protein, bovine pancreatic trypsin inhibitor, indicate an increased insertion of water into the protein interior before unfolding starts to occur [46,47]. 

McCammon et al. have simulated the molecular dynamics of a globular protein molecule, bovine pancreatic trypsin inhibitor, and the water strongly bound to it, to provide, since the rich variety of motions at ordinary temperatures is indicated, an improved picture in comparison to the crystal structure. Fluctuations in some rotation angles tend to correlate with others, thus conserving overall structure, but large scale concerted motions are also demonstrated. The structure of water around lysozyme (EC 3.2.1.17) has been investigated by the Metropolis method, all molecules of the crystal structure being present, ... 

Quasi-harmonic analysis is the computation of the normal modes of a molecule from atomic displacements generated by a molecular dynamics simulation. In this case, the atomic coordinate fluctuations are inversely related to the force constants, which are the second derivatives of the potential function. This formulation allows anharmonic motions, arising either from continuous diffusive motion or from transitions between wells, to be included implicitly within a harmonic representation, Brooks and co-workers " have carried out a comparison of different approaches to calculating the harmonic and quasiharmonic normal modes for the protein bovine pancreatic trypsin inhibitor (BPTI) with different force field and simulation models, Yet another approach, called essential dynamics, differs from quasi-harmonic analysis in that the atomic masses are not considered and motion is not reduced to a harmonic form, ... 

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