CHARMM distances

Li, Tejero, CONGEN + 2 CHARMM Distance constraints derived... 

This is similar to the simple atom-atom truncation except that dipolar groups will never be split by the cutoff distance. There is still the problem of discontinuities, but these are less extreme than in the case of atom-atom truncations. In cases where water is explicitly included, this approach exhibits the curious phenomena of hot water and cold protein if the entire system is coupled to a heatbath. This is because the more mobile atoms (the water) are subjected to more discontinuities which makes them hotter than the less mobile atoms (the protein) (Levitt, M., Weizmann Institute, personal communication, 1986.). It should be noted that this is one of the most commonly used methods of truncation for simulations where CHARMM is not used. For the group-group truncation, these calculations are in progress and will be reported elsewhere. For this type of truncation, both methods where the list is updated on... 

Leusen et al. studied the crystal packing of ephedrine with several phosphoric acid stereoisomers to verify whether a relationship between enthalpy of formation and separation of enantiomers via diastereomeric salt formation exists.They considered four different force fields and determined that the CHARMM program, as implemented in QUANTA, was the best for their application. Their decision was based mainly on the knowledge that non-bonded cutoff distances are larger in CHARMM. A larger cutoff distance is necessary to account for the interaction between different hydrophobic layers in the crystal (interlayer distances of 14—16 A). These authors were unable to quantitatively determine the validity of their hypothesis, although qualitative explanations were derived for their observations. 

The AMBER (271, 272) and CHARMM (179) nonbonded terms are used as scoring function in several docking programs. As mentioned above (Sections.1.1), protein terms are usually precalculated on a rectangular grid to speed up the energy calculation compared to traditional atom-by-atom evaluations (273). Distance-dependent dielectric constants are... 

Our 2 ns CHARMM simulations of PDT025, lYTB and lAIS (without TFB), and the corresponding free TBPs, serve to reexamine the inferences on the nature and role of TBP dynamics with results from simulations of additional systems that are more completely described (e.g., Miaskiewicz and Omstein did not include the internal water molecules in the TBP structure, while our new calculations do include them [120]). In these new simulations we do not detect evidence for the collapse of the two subdomains of TBP caused by extreme bending. There are indeed oscillations in the distance between the tips of the stirrups of TBP [101] and twisting motions, but these oscillations never acquire such an amplitude as to cause the complete closing of the underside of TBP. This is true for the three free TBP crystal structures simulated as monomers (NP-unpublished results). 

Molecular mechanics minimization and molecular dynamics were chosen to examine the possible conformations for the two acyl enzymes and conclusions were drawn from the time evolution of the two systems. The starting point was a crystal structure of phenylethaneboronic acid bound to alpha-chymotrypsin. QUANTA/CHARMM (Brooks et al, 1983) was employed for the calculations. Ninety-five water molecules from the X-ray structure were included. Distance monitoring and the creation ofH-bonds were the main criteria for differentiating between the two molecules. Both acyl enzymes have their ketone carbonyls H-bonded to Gly-216 NH. Both start with their ester carbonyl in the oxyanion hole (H-bonded to Ser-195 and to Gly-193). The R-acyl enzyme looses both of these hydrogen bonds during the simulation. Attack of water on the R-species should, thus, be less frequently successful. Values for differences in energy were not used because of a small... 

Wang et al. (1994) analyzed by MD the roles of the "double catalytic triad" in papain catalysis, based on the structure of the enzyme, which is not completely known from crystallography (Kamphuis et al., 1984) due to the oxidation state of Cys-25 (present as cysteic acid in the crystal). Stochastic boundary MD (Brooks and Karplus, 1983) was carried out on the whole enzyme + 350 water molecules. Three "layers" were treated according to their distance from the sulfur atom of Cys-25 - atoms within 12A, atoms between 12-16A and the more distant atoms were kept fixed. CHARMM forcefield was employed. The active site geometry was examined as a function of pH, for various mutual states of S-/SH and Im/ImH+. In addition, the mutations of Asp-158 (Menard et al., 1991) were studied. 

Figure 26. A force-field (CHARMm) optimized structure of porphyrin 20 with the peptide gly-gly-phe. Hydrogens are omitted for clarity except those of peptide NH3. The phenyl group of phe is not far from vdW contacts to the pyrrole (dav = 3.95 A) the -NH3 protons have distances from 1.90 to 2.05 A to the crown ether oxygen the carboxylate group comes close to neighboring pyridyl protons with dav = 3.0 A. ...

In force fields such as AMBERS or CHARMM designed for large biological molecules, the Coulombic interaction in Eq. [10] is sometimes modified by use of a distance-dependent dielectric constant. Another modification of Eqs. [10] and [11] is utilized in force fields designed for hydrocarbons and concerns the internuclear distance R, in the van der Waals interaction (the non-Coulom-bicpart of Eq. [10]) when one of the nonbonded atoms is a hydrogen. 

Recendy, Sneddon and Brooks (39), on the basis of their CHARMM simulations of conformational dynamics of Pro peptides in aqueous solution, have postulated involvement in electron transfer across the -(Pro) -bridge of P — a transitions at the i i angle, as the latter occur more rapidly and bring the donor-acceptor distance to a shorter range than the trans cis interconversion... 

MODELLER [49] builds models of three-dimensional structures of proteins by satisfaction of spatial restraints distances and dihedral angles in the target sequence, stereochemical restraints such as bond length and bond angle obtained from the CHARMM forcefield, and statistical preferences of dihedral angles and non-bonded atomic distances obtained from a representative set of all known protein structures. The model is then calculated by an optimization method relying... 

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