New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent-solvent, solvent-solute, and solute-solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volumes, and crystal pressures and structures were used in the optimization. The resulting protein parameters were tested by applying them to noncyclic tripeptide crystals, cyclic peptide crystals, and the proteins crambin, bovine pancreatic trypsin inhibitor, and carbonmonoxy myoglobin in vacuo and in crystals. A detailed analysis of the relationship between the alanine dipeptide potential energy surface and calculated protein φ, χ angles was made and used in optimizing the peptide group torsional parameters. The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals. Extensive comparisons between molecular dynamics simulations and experimental data for polypeptides and proteins were performed for both structural and dynamic properties. Energy minimization and dynamics simulations for crystals demonstrate that the latter are needed to obtain meaningful comparisons with experimental crystal structures. The presented parameters, in combination with the previously published CHARMM all-atom parameters for nucleic acids and lipids, provide a consistent set for condensed-phase simulations of a wide variety of molecules of biological interest.

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. In addition, the CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This paper provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM paper in 1983.

Iron species with terminal oxo ligands are implicated as key intermediates in several synthetic and biochemical catalytic cycles. However, there is a dearth of structural information regarding these types of complexes because their instability has precluded isolation under ambient conditions. The isolation and structural characterization of an iron(III) complex with a terminal oxo ligand, derived directly from dioxygen (O2), is reported. A stable structure resulted from placing the oxoiron unit within a synthetic cavity lined with hydrogen-bonding groups. The cavity creates a microenvironment around the iron center that aids in regulating O2 activation and stabilizing the oxoiron unit. These cavities share properties with the active sites of metalloproteins, where function is correlated strongly with site structure.

Ultrafast absorption spectroscopy is used to study heme-NO recombination at room temperature in aqueous buffer on time scales where the ligand cannot leave its cage environment. While a single barrier is observed for the cage recombination of NO with heme in the absence of globin, recombination in hemoglobin and myoglobin is nonexponential. Examination of hemoglobin with and without inositol hexaphosphate points to proximal constraints as important determinants of the geminate rebinding kinetics. Molecular dynamics simulations of myoglobin and heme-imidazole subsequent to ligand dissociation were used to investigate the transient behavior of the Fe-proximal histidine coordinate and its possible involvement in geminate recombination. The calculations, in the context of the absorption measurements, are used to formulate a distinction between nonexponential rebinding that results from multiple protein conformations (substates) present at equilibrium or from nonequilibrium relaxation of the protein triggered by a perturbation such as ligand dissociation. The importance of these two processes is expected to depend on the time scale of rebinding relative to equilibrium fluctuations and nonequilibrium relaxation. Since NO rebinding occurs on the picosecond time scale of the calculated myoglobin relaxation, a time-dependent barrier is likely to be an important factor in the observed nonexponential kinetics. The general implications of the present results for ligand binding in heme proteins and its time and temperature dependence are discussed. It appears likely that, at low temperatures, inhomogeneous protein populations play an important role and that as the temperature is raised, relaxation effects become significant as well.

A molecular dynamics simulation method is used to determine the contributions of individual amino acid residues and solvent molecules to free energy changes in proteins. Its application to the hemoglobin interface mutant Asp G1(99) beta----Ala shows that some of the contributions to the difference in the free energy of cooperativity are as large as 60 kilocalories (kcal) per mole. Since the overall free energy change is only -5.5 kcal/mole (versus the experimental value of -3.4 kcal/mole), essential elements of the thermodynamics are hidden in the measured results. By exposing the individual contributions, the free energy simulation provides new insights into the origin of thermodynamic changes in mutant proteins and demonstrates the role of effects beyond those usually considered in structural analyses.

In molecular dynamics simulations, the fastest components of the potential field impose severe restrictions on the stability and hence the speed of computational methods. One possibility for treating this problem is to replace the fastest components with algebraic length constraints. In this article the resulting systems of mixed differential and algebraic equations are studied. Commonly used discretization schemes for constrained Hamiltonian systems are discussed. The form of the nonlinear equations is examined in detail and used to give convergence results for the traditional nonlinear solution technique SHAKE iteration and for a modification based on successive overrelaxation (SOR). A simple adaptive algorithm for finding the optimal relaxation parameter is presented. Alternative direct methods using sparse matrix techniques are discussed. Numerical results are given for the new techniques, which have been implemented in the molecular modeling software package CHARMM and show as much as twofold improvement over SHAKE iteration. CONSTRAINED MD ALGORITHMSIntroduction n molecular dynamics, the length of timestep I for numerically integrating the equations of motion is dictated by the contributions to the force vector which maintain pairs of atoms near some equilibrium distance. The imposition of algebraic constraints that fix these lengths removes the associated rapid vibrational modes, enabling the use of longer timesteps without substantially altering important physical characteristics of the motion.' Although we treat only length constraints in the present work, constrained techniques are also of interest for conformational search and conformational free-energy simulations.' In ref. 3 the SHAKE iteration was described for solving the nonlinear equations at each timestep of a constrained version of the Verlet discretization, and a similar scheme was proposed in ref. 4 for use with the RATTLE discretization.We describe in the following section the equations of motion for the molecule with algebraic constraints and discuss these two discretizations. Then we examine the form of the nonlinear equations and discuss the existence of solutions. We describe the SHAKE iteration in a matrix formulation and show its equivalence to the nonlinear Gauss-Seidel-Newton iteration? This leads to a convergence result and theoretical rate of convergence for the SHAKE iteration as well as a more general scheme based on successive overrelaxation (SOR). Experiments with molecules of interest show that SOR improves the performance of SHAKE iteration by a factor of 2 or more for certain choices of relaxation parameter, at no additional cost. We present an algorithm for effective choice of SOR relaxation parameter w. It has often been suggested (e.g., ref. 6) that the SHAKE iteration is an efficient alternative to matrix methods for numerical solution of the nonlinear equations encountered in molecular dynamics, but little discussion of these methods is found in the literature. In this article we present several matrix methods for the ...

In mammals, S-adenosylhomocysteine hydrolase (AdoHcyase) is the only known enzyme to catalyze the breakdown of S-adenosylhomocysteine (AdoHcy) to homocysteine and adenosine. AdoHcy is the product of all adenosylmethionine (AdoMet)-dependent biological transmethylations. These reactions have a wide range of products, and are common in all facets of biometabolism. As a product inhibitor, elevated levels of AdoHcy suppress AdoMet-dependent transmethylations. Thus, AdoHcyase is a regulator of biological transmethylation in general. The three-dimensional structure of AdoHcyase complexed with reduced nicotinamide adenine dinucleotide phosphate (NADH) and the inhibitor (1'R, 2'S, 3'R)-9-(2',3'-dihyroxycyclopenten-1-yl)adenine (DHCeA) was solved by a combination of the crystallographic direct methods program, SnB, to determine the selenium atom substructure and by treating the multiwavelength anomalous diffraction data as a special case of multiple isomorphous replacement. The enzyme architecture resembles that observed for NAD-dependent dehydrogenases, with the catalytic domain and the cofactor-binding domain each containing a modified Rossmann fold. The two domains form a deep active site cleft containing the cofactor and bound inhibitor molecule. A comparison of the inhibitor complex of the human enzyme and the structure of the rat enzyme, solved without inhibitor, suggests that a 17 degrees rigid body movement of the catalytic domain occurs upon inhibitor/substrate binding.

The oxidative modification of methionines within the primary sequence of calmodulin (CaM) results in an inability to activate the PM-Ca-ATPase fully, and may contribute to alterations in calcium homeostasis under conditions of oxidative stress. To identify differences in the sensitivities of CaM isoforms to oxidative modification, we have compared the function and patterns of oxidative modification resulting from the exposure of CaM isolated from bovine testes and wheat germ to H(2)O(2). In comparison to CaM isolated from wheat germ, vertebrate CaM is functionally resistant to oxidant-induced loss of function. The decreased functional sensitivity of vertebrate CaM correlates with a 75 +/- 3% reduction in the rate of oxidative modification of a methionine near the carboxyl terminus (i.e., Met(144) or Met(145)). The extent of oxidative modification to other methionines in these CaM isoforms is similar. These results suggest that the sensitivity of Met(144) or Met(145) to oxidation modulates the ability of CaM to activate the PM-Ca-ATPase. Consistent with this interpretation, a CaM mutant in which glutamines were substituted for Met(144) and Met(145) fully activates the PM-Ca-ATPase irrespective of the oxidative modification of the other seven methionines to their corresponding methionine sulfoxides. The extent of oxidative modification to individual methionines in vertebrate CaM by H(2)O(2) correlates with the time-averaged surface accessibility of individual sulfurs calculated from molecular dynamics simulations. Thus, the sensitivity of individual methionines to oxidative modification is directly related to the solvent accessibility. These results indicate that sequence differences between vertebrate and plant CaM alter the sensitivity of methionines near the carboxyl terminus to oxidative modification because of alterations in their solvent accessibility. We suggest that these sequence differences between CaM isoforms have a regulatory role in modulating the functional sensitivity of CaM to conditions of oxidative stress.