Irina Massova

Matrix metalloproteinases: structures, evolution, and diversification

A comprehensive sequence alignment of 64 members of the family of matrix metalloproteinases (MMPs) for the entire sequences, and subsequently the catalytic and the hemopexin‐like domains, have been performed. The 64 MMPs were selected from plants, invertebrates, and vertebrates. The analyses disclosed that as many as 23 distinct subfamilies of these proteins are known to exist. Information from the sequence alignments was correlated with structures, both crystallographic as well as computational, of the catalytic domains for the 23 representative members of the MMP family. A survey of the metal binding sites and two loops containing variable sequences of amino acids, which are important for substrate interactions, are discussed. The collective data support the proposal that the assembly of the domains into multidomain enzymes was likely to be an early evolutionary event. This was followed by diversification, perhaps in parallel among the MMPs, in a subsequent evolutionary time scale. Analysis indicates that a retrograde structure simplification may have accounted for the evolution of MMPs with simple domain constituents, such as matrilysin, from the larger and more elaborate enzymes.—Massova, I., Kotra, L. P., Fridman, R., Mobashery, S. Matrix metalloproteinases: structures, evolution, and diversification. FASEB J. 12, 1075–1095 (1998)

Computational alanine scanning of the 1:1 human growth hormone–receptor complex

The MM‐PBSA (Molecular Mechanics–Poisson–Boltzmann surface area) method was applied to the human Growth Hormone (hGH) complexed with its receptor to assess both the validity and the limitations of the computational alanine scanning approach. A 400‐ps dynamical trajectory of the fully solvated complex was simulated at 300 K in a 101 Å×81 Å×107 Å water box using periodic boundary conditions. Long‐range electrostatic interactions were treated with the particle mesh Ewald (PME) summation method. Equally spaced snapshots along the trajectory were chosen to compute the binding free energy using a continuum solvation model to calculate the electrostatic desolvation free energy and a solvent‐accessible surface area approach to treat the nonpolar solvation free energy. Computational alanine scanning was performed on the same set of snapshots by mutating the residues in the structural epitope of the hormone and the receptor to alanine and recomputing the ΔGbinding. To further investigate a particular structure, a 200‐ps dynamical trajectory of an R43A hormone–receptor complex was simulated. By postprocessing a single trajectory of the wild‐type complex, the average unsigned error of our calculated ΔΔGbinding is ∼1 kcal/mol for the alanine mutations of hydrophobic residues and polar/charged residues without buried salt bridges. When residues involved in buried salt bridges are mutated to alanine, it is demonstrated that a separate trajectory of the alanine mutant complex can lead to reasonable agreement with experimental results. Our approach can be extended to rapid screening of a variety of possible modifications to binding sites.

QM and QM–FE simulations on reactions of relevance to enzyme catalysis: trypsin, catechol O-methyltransferase, β-lactamase and pseudouridine synthase

The application of the quantum mechanics–free energy hybrid technique (QM–FE) to calculate the free energy changes in two enzymatic reaction systems, trypsin and catechol O-methyltransferase (COMT) is reported. The results rationalize the observed rate enhancements by comparing the reactions in enzyme and in aqueous solution. Quantum mechanical studies of the model systems of β-lactamase and pseudouridine synthase systems are also presented. For β-lactamase, the effect of solvation on hydrolysis and methanolysis of β-lactams has been investigated. For pseudouridine synthase, the first steps of two different proposed mechanisms have been modeled.