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The G proteins transduce hormonal and other signals into regulation of enzymes such as adenylyl cyclase and retinal cGMP phosphodiesterase. Each G protein contains an alpha subunit that binds and hydrolyzes guanine nucleotides and interacts with beta gamma subunits and specific receptor and effector proteins. Amphipathic and secondary structure analysis of the primary sequences of five different alpha chains (bovine alpha s, alpha t1 and alpha t2, mouse alpha i, and rat alpha o) predicted the secondary structure of a composite alpha chain (alpha avg). The alpha chains contain four short regions of sequence homologous to regions in the GDP binding domain of bacterial elongation factor Tu (EF-Tu). Similarities between the predicted secondary structures of these regions in alpha avg and the known secondary structure of EF-Tu allowed us to construct a three-dimensional model of the GDP binding domain of alpha avg. Identification of the GDP binding domain of alpha avg defined three additional domains in the composite polypeptide. The first includes the amino terminal 41 residues of alpha avg, with a predicted amphipathic alpha helical structure; this domain may control binding of the alpha chains to the beta gamma complex. The second domain, containing predicted beta strands and alpha helices, several of which are strongly amphipathic, probably contains sequences responsible for interaction of alpha chains with effector enzymes. The predicted structure of the third domain, containing the carboxy terminal 100 amino acids, is predominantly beta sheet with an amphipathic alpha helix at the carboxy terminus. We propose that this domain is responsible for receptor binding.(ABSTRACT TRUNCATED AT 250 WORDS)

We apply Shanno's conjugate gradient algorithm to the problem of minimizing the potential energy function associated with molecular mechanical calculations. Shanno's algorithm is stable with respect to roundoff errors and inexact line searches and converges rapidly to a minimum. Equally important, this algorithm can improve the rate of convergence to a minimum by a factor of 5 relative to Fletcher-Reeves or Polak-RibiBre minimizers when used within the molecular mechanics package AMBER. Comparable improvements are found for a limited number of simulations when the Polak-RibiBre direction vector is incorporated into the Shanno algorithm.

GenoGraphics is a generic utility for constructing and querying one.dimensional linear plots. The outgrowth of a request from Dr. Cassandra Smith for a tool to facilitate her genome mapping research. OenoGraphics development has benefitted fw a continued ct_llaborationwith. bcr. Written in StmMicrosystems's OpenWindmvs'_ environment and tl'_eBTOL" toolkit developed at Argonne National Labt_ato_,, OenoOraphics prtwides an interactive, intuitive, graphical interface. Its features include • viewing multiple maps simultaneously, • zooming, and • querying by mouse clicking, By expediting plot generation, Gent_raphics gives the scientist more time to analyze data and a novel means for deducing conclusions.

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