Structural requirements for catalysis and dimerization of human methionine adenosyltransferase I/III

We have used site-directed mutagenesis to probe the structural requirements for catalysis and dimerization of human hepatic methionine adenosyltransferase (hMAT). We built a homology model of the dimeric hMAT III inferred by the crystal structure of the highly homologous Escherichia coli MAT dimer. The active sites of both enzymes comprise the same amino acids and are located in the inter-subunit interface. All of the amino acids predicted to be in the hMAT III active site were mutated, as well as residues in a conserved ATP binding region. All of the mutations except one severely affected catalytic activity. On the other hand, dimerization was affected only by single mutations of three different residues, all on one monomer. The homology model suggested that the side chains of these residues stabilized the monomer and participated in a bridge between subunits consisting of a network of metal and phosphate ions. In agreement with this observation, we demonstrated that dimerization cannot occur in the absence of phosphate.

Antibody immunodiversity: a study on the marked specificity difference between two anti-yeast iso-1 cytochrome c monoclonal antibodies whose epitopes are closely related

Anti-yeast iso-1 cytochrome c (cyt. c) monoclonal antibodies 2-96-12 and 4-74-6 have closely related epitopes (antigenic determinants). However, while the specificity of 4-74-6 is stringent, 2-96-12 cross-reacts with many evolutionarily related cytochromes c. Such a marked difference in specificity of antibodies with overlapping epitopes may represent unique antibody immunodiversity. Thus, we constructed Fv fragment models consisting of the variable domains of the heavy and light chains of 2-96-12 and 4-74-6 and that of another anti-iso-1 cyt. c as a control to gain insight into the origin of this difference in specificity. Our models show that 4-74-6 and 2-96-12 contain five and two aromatic side chains, respectively, in or near the central area of the antigen-combining site. The side chains of Arg95H (heavy chain) in 2-96-12 and Arg91L (light chain) in 4-74-6 project toward the central area of the combining site in our model. Antigen docking to our Fv models, combined with previous immunological studies, suggests that iso-1 cyt. c Asp60 may interact with Arg95H in 2-96-12 and Arg91L in 4-74-6 and that both epitopes of 2-96-12 and 4-74-7 may include iso-1 cyt. c Leu58, Asp60, Asn62, and Asn63. The effect of the Arg95H to Lys mutation on the antigen binding is also in accord with our model. The difference in specificity may be partly explained by a greater degree of conformational flexibility in and around the central area of the combining site in 2-96-12 compared to 4-74-6 due to differences in aromatic side chain packing.

Comparative molecular field analysis of selective A3 adenosine receptor agonists

A series of 48 N6-benzyladenosine 5'-uronamide derivatives has been described recently as moderately selective A3 adenosine receptor agonists of nanomolar potency (Gallo-Rodriguez, C. et al. J. Med. Chem. 1994, 37, 636). Quantitative structure activity relationships in this series, including some novel derivatives, have been investigated using a Comparative Molecular Field Analysis (CoMFA), with emphasis on the N6-substituent. The resulting three dimensional pharmacophore model defines the steric and electronic factors which modulate in vitro affinities in binding to rat brain A3 adenosine receptors. The model indicates a positive correlation of affinity with the steric characteristics of the compounds (major factor), particularly toward the 3-position of the benzyl ring of N6-benzyl NECA, and a weak correlation with the electrostatic effects of the N6-substituent. A comparison of active and inactive compounds using volume maps showed that bulk at the 3-position of the benzyl ring of the molecule is conducive to high affinity at A3 receptors, while steric bulk at other positions of the benzyl ring leads to poor binding. t-Boc-amino acid conjugates of a 3-aminobenzyl derivative were synthesized to probe the steric and hydrophobic limitations at that position. We have discovered a subregion of the N6-benzyl binding pocket occupied by a 3-(L-prolylamino) group that is sterically disallowed at A3 receptors and allowed in A1 and A2a receptors. 6-N-Phenylhydrazino and 6-O-phenylhydroxylamino derivatives, incorporating major changes in electrostatic character of the ligand proximal to the purine, were predicted by the CoMFA model to have high A3 affinity. Such analogs were synthesized and found to be well tolerated at the A3 receptor binding site.

A quantitative structure-activity relationship analysis of some 4-aminodiphenyl sulfone antibacterial agents using linear free energy and molecular modeling methods

A set of 36 congeneric 4-aminodiphenyl sulfones with measured inhibition potencies of dihydropteroate synthase were studied by using both linear free energy and molecular modeling methods. The goals of the investigation were to identify the "active" conformation for these compounds as inhibitors and, correspondingly, to contruct a quantitative structure-activity relationship (QSAR). These molecules are quite flexible and possess multiple conformational energy minima. Application of molecular shape analysis (MSA), using all intramolecular energy minima as part of the analysis, was not successful in generating a QSAR. However, the calculated intramolecular conformational entropy of these compounds was found to correlate with inhibition potency leading to a highly significant QSAR. Inhibition potency increases as entropy decreases. A decrease in entropy enhances the population of specific, symmetry-related minimum-energy conformations. In this indirect way, it was possible to postulate an "active" conformation. This investigation illustrates that specific knowledge of the "active" shape of a molecule may not provide the information needed to quantitatively explain the observed structure-activity relationship.

Computer graphics presentation modes for biologic data. Types and examples

New advances in automated cytology, computer microscopy, densitometry and other instrumentation for feature/scene acquisition or analysis have resulted in higher information densities than heretofore encountered. Two-, three- and four-space computer graphics provide favorable bandwidth conditions for transforming complex, large-scale data sets into visual displays that allow a human observer, utilizing the brain's efficient processing of visual information, to rapidly grasp relationships and synthesize concepts. Examples of multidimensional displays are presented, all developed by neuroscientists who are not computer specialists. Because modern graphics and image-synthesis techniques can now be implemented on any one of several commercially available very-high-speed integrated-circuit-based display systems, at moderate cost, exploitation of specifically visual presentation should be carefully considered in any system generating information in high density.

A multimodal system for reconstruction and quantification of neurologic structures

The utility of computers and computer graphics as aids in the study of nervous system architecture is growing. However, modern histologic, immunocytologic and biochemical methods for revealing the underlying microarchitecture and macroarchitecture of the nervous system yield data formats requiring disparate computer acquisition, analysis and display approaches, capable of spanning many orders of magnitude of scale. This paper describes the Image Graphics Laboratory data acquisition, processing and display system, whose various components and programs may be used singly or in concert to enable definition of various tissue properties at different levels of resolution and integration. Examples are given of the system's use in light microscopic two-dimensional and three-dimensional reconstructions, autoradiographic reconstructions, reconstructions from projected images, reconstructions of impregnated cells (e.g., whole neurons) and peripheral nerve image analysis.

Toward an open architecture for morphometric computing

Prototype biomedical computing and graphics systems developed since the early 1970s for computer microscopy, architectonic or morphometric analysis and visual display have been marked by the highly local character of their designs. Such approaches, while often heroic and unusually creative in character, have limited the exportability of hardware or software products to the larger biomedical community. A general systems orientation, based on a shared, "open" architecture of hardware and software, with known and published standards, is proposed. The incremental nature and funding character of such a system is also discussed.

Sex differences in the shape of the sexually dimorphic nucleus of the preoptic area and suprachiasmatic nucleus of the rat: 3-D computer reconstructions and morphometrics

Three-dimensional images of nuclei facilitate morphological comparisons between differing animal groups. As revealed by computer-assisted techniques, the greater volume in male rats of the sexually dimorphic nucleus of the preoptic area was not proportional in all directions. The nucleus was more elongated in males than females, indicating a sex-dependent shape. This study also indicated that the volume of the suprachiasmatic nucleus was larger in males.

Physical association modeling of DNA alkylation. Some DNA conformational aspects

The widespread occurrence of physical binding between biological macromolecules and small molecules has prompted us to hypothesize that physical binding contributes to DNA alkylation specificity. The preferred physical binding sites for a CH+3-like test probe were predicted for several sequences of DNA using molecular mechanics free space calculation methods. Sequences containing A = T basepairs direct physical binding to the minor groove, whereas sequences containing G identical to C basepairs direct physical binding to the major groove. Physical binding calculations were also performed for model 'unwound' DNA conformations. The results of the test probe studies were subsequently employed as starting points to predict the preferred physical binding sites for the more complicated case of an actual alkylating agent, the dimethylaziridinium ion. These studies demonstrate that physical binding specificity is highly dependent upon DNA sequence and conformation, and correlates well with the DNA alkylation site specificity observed for alkylating agents in th dimethylaziridine class.