CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first-or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.

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Bacteria that oxidize methane to methanol are central to mitigating emissions of methane, a potent greenhouse gas. The nature of the copper active site in the primary metabolic enzyme of these bacteria, particulate methane monooxygenase (pMMO), has been controversial owing to seemingly contradictory biochemical, spectroscopic, and crystallographic results. We present biochemical and electron paramagnetic resonance spectroscopic characterization most consistent with two monocopper sites within pMMO: one in the soluble PmoB subunit at the previously assigned active site (CuB) and one ~2 nanometers away in the membrane-bound PmoC subunit (CuC). On the basis of these results, we propose that a monocopper site is able to catalyze methane oxidation in pMMO.

The miscibility behavior of three binary mixtures, solvent with solvent, polymer with solvent, and polymer with polymer, was studied by use of a combination of the Flory-Huggins theory and molecular simulation techniques. Fundamental parameters in the Flory-Huggins theory, including the heat of mixing associated with pairwise interactions (Awn) and the number of possible interaction partners, i.e., coordination number, z, are calculated from molecular simulations. The pair energies (wn, w22, wu) are obtained by averaging a large number of configurations generated by a Monte Carlo approach which includes the constraints associated with excluded volume. The temperature dependence of the interaction parameter x is obtained with the formalism developed in this study. In all cases, the calculated upper critical solution temperatures compare favorably with experimental values. This approach provides an opportunity to test the Flory-Huggins theory for a number of model binary systems and to characterize their miscibility behavior. This combined approach also facilitates study of the thermodynamic behavior of a binary mixture without possessing specific knowledge or experimental data of the system under investigation.

Several rather different models of the Fe-02 bond in

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From ab initio quality calculations on model systems, we conclude that in unliganded Fe-porphyrin the Fe lies in the plane for both the high-spin (q) and intermediate-spin (t) We will discuss the bonding of oxygen to hemoglobin (Hb) or myoglobin (Mb) using the results of theoretical calculations of the electronic structure of model systems representing Feporphyrin, Fe-porphyrin plus an additional nitrogenous axial ligand (deoxy Mb), and 02 bound to the latter five-coordinate complex (MbO2). In all cases the Fe is found to be high-or intermediate-spin (S = 2 or 1) with six electrons in the d orbitals. In no case (not even with the six-coordinate complexes) do we find a low-lying state in which the Fe is in a low-spin state (t2g6, S = 0). We find that the properties of these model complexes are consistent with the observed properties of the active sites of Mb and Hb and that these calculations give additional insight into the protein-modified behavior of the active site of Hb. In this paper we outline the qualitative description that emerges; detailed results will appear elsewhere. Model calculations

Class I major histocompatibility complex (MHC) molecules bind peptides derived from degraded proteins for display to T cells of the immune system. Peptides bind to MHC proteins with varying affinities, depending upon their sequence and length. We demonstrate that the thermal stability of the MHC-peptide complex depends directly on peptide binding affinity. We use this correlation to develop a convenient method to determine peptide dissociation constants by measuring MHC-peptide complex stability using thermal denaturation profiles monitored by circular dichroism.