An optimal structure-discriminative amino acid index for protein fold recognition.

Identifying the fold class of a protein sequence of unknown structure is a fundamental problem in modern biology. We apply a supervised learning algorithm to the classification of protein sequences with low sequence identity from a library of 174 structural classes created with the Combinatorial Extension structural alignment methodology. A class of rules is considered that assigns test sequences to structural classes based on the closest match of an amino acid index profile of the test sequence to a profile centroid for each class. A mathematical optimization procedure is applied to determine an amino acid index of maximal structural discriminatory power by maximizing the ratio of between-class to within-class profile variation. The optimal index is computed as the solution to a generalized eigenvalue problem, and its performance for fold classification is compared to that of other published indices. The optimal index has significantly more structural discriminatory power than all currently known indices, including average surrounding hydrophobicity, which it most closely resembles. It demonstrates >70% classification accuracy over all folds and nearly 100% accuracy on several folds with distinctive conserved structural features. Finally, there is a compelling universality to the optimal index in that it does not appear to depend strongly on the specific structural classes used in its computation.

Crystallization and rhenium MAD phasing of the acyl-homoserinelactone synthase EsaI.

Acyl-homoserine-L-lactones (AHLs) are diffusible chemical signals that are required for virulence of many Gram-negative bacteria. AHLs are produced by AHL synthases from two substrates, S-adenosyl-L-methionine and acyl-acyl carrier protein. The AHL synthase EsaI, which is homologous to the AHL synthases from other pathogenic bacterial species, has been crystallized in the primitive tetragonal space group P4(3), with unit-cell parameters a = b = 66.40, c = 47.33 A. The structure was solved by multiple-wavelength anomalous diffraction with a novel use of the rhenium anomalous signal. The rhenium-containing structure has been refined to a resolution of 2.5 A and the perrhenate ion binding sites and liganding residues have been identified.

Domain architecture of a Caenorhabditis elegans AKAP suggests a novel AKAP function.

A-kinase anchoring proteins (AKAPs) are adapter proteins that are involved in directing cAMP-dependent protein kinase and some other signaling enzymes to certain intracellular locations. In this study, we investigate the domain architecture of an AKAP from Caenorhabditis elegans (AKAP(CE)). We show that AKAP(CE) shares two domains with the Smad anchor for receptor activation, a FYVE-finger and a transforming growth factor beta (TGFbeta) receptor binding domain, suggesting that AKAP(CE) may interact with a receptor belonging to the TGFbeta receptor family. This predicted novel AKAP function supports the recent view of AKAPs as adapter proteins that can be involved in various signaling pathways.

Continuum electrostatic methods applied to pH-dependent properties of antibody-antigen association.

Protein association events are a critical component of the functioning of biological systems. Antibody/antigen association, which involves extraordinarily specific interactions, has been a paradigm for the study of structural factors and intermolecular forces controlling protein-protein association. As new experimental approaches to the study of antibody/antigen affinity have become routine, and as more structures of complexes of antibodies and their antigens have become available, it has become possible to use computational approaches to study these interactions. Electrostatic interactions are known to play an important role in protein complex formation. In this review, we focus on the use of continuum electrostatic methods to compute pH-dependent properties of proteins and discuss the use of these methods in the study of antibody/antigen complexes.

Histone acetyltransferase activity of yeast Gcn5p is required for the activation of target genes in vivo.

Gcn5p is a transcriptional coactivator required for correct expression of various genes in yeast. Several transcriptional regulators, including Gcn5p, possess intrinsic histone acetyltransferase (HAT) activity in vitro. However, whether the HAT activity of any of these proteins is required for gene activation remains unclear. Here, we demonstrate that the HAT activity of Gcn5p is critical for transcriptional activation of target genes in vivo. Core histones are hyperacetylated in cells overproducing functional Gcn5p, and promoters of Gcn5p-regulated genes are associated with hyperacetylated histones upon activation by low-copy Gcn5p. Point mutations within the Gcn5p catalytic domain abolish both promoter-directed histone acetylation and Gcn5p-mediated transcriptional activation. These data provide the first in vivo evidence that promoter-specific histone acetylation, catalyzed by functional Gcn5p, plays a critical role in gene activation.