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D Bordo

Publications and source records attributed to D Bordo.

35 records · Page 2Linked to original sources
PubMed1998

The three-dimensional structure of the nitrogen regulatory protein IIANtr from Escherichia coli.

The bacterial rpoN operon codes for sigma 54, which is the key sigma factor that, under nitrogen starvation conditions, activates the transcription of genes needed to assimilate ammonia and glutamate. The rpoN operon contains several other open reading frames that are cotranscribed with sigma 54. The product of one of these, the 17.9 kDa protein IIANtr, is homologous to IIA proteins of the phosphoenolpyruvate:sugar phosphotransferase (PTS) system. IIANtr influences the transcription of sigma 54-dependent genes through an unknown mechanism and may thereby provide a regulatory link between carbon and nitrogen metabolism. Here we describe the 2.35 A X-ray structure of Escherichia coli IIANtr. It is the first structure of a IIA enzyme from the fructose-mannitol family of the PTS. The enzyme displays a novel fold characterized by a central mixed parallel/anti-parallel beta-sheet surrounded by six alpha-helices. The active site His73 is situated in a shallow depression on the protein surface.

Amino Acid Sequence↗
PubMed1996

Patterns in ionizable side chain interactions in protein structures.

In a selected set of 44 high-resolution, non-homologous protein structures, the intramolecular hydrogen bonds or salt bridges formed by ionizable amino acid side chains were identified and analyzed. The analysis was based on the investigation of several properties of the involved residues such as their solvent exposure, their belonging to a certain secondary structural element, and their position relative to the N- and C-termini of their respective structural element. It was observed that two-thirds of the interactions made by basic or acidic side chains are hydrogen bonds to polar uncharged groups. In particular, the majority (78%) of the hydrogen bonds between ionizable side chains and main chain polar groups (sch:mch bonds) involved at least one buried atom, and in 42% of the cases both interacting atoms were buried. In alpha-helices, the sch:mch bonds observed in the proximity of the C- and N-termini show a clear preference for acidic and basic side chains, respectively. This appears to be due to the partial charges of peptide group atoms at the termini of alpha-helices, which establish energetically favorable electrostatic interactions with side chain carrying opposite charge, at distances even greater than 4.5 angstrom. The sch:mch interactions involving ionizable side chains that belong either to beta-strands or to the central part of alpha-helices are based almost exclusively on basic residues. This results from the presence of main chain carbonyl oxygen atoms in the protein core which have unsatisfied hydrogen bonding capabilities.

Hydrogen Bonding↗
PubMed1995

Comparison of side chain interactions performed by structurally equivalent residues in homologous protein structures.

The present work describes the computer program Hom-Bond, which allows to identify and compare intra-molecular interactions performed by side chain polar atoms as observed in a family of homologous protein structures with known and conserved 3-D conformation. For this purpose, the side chain to side chain and the side chain to main chain hydrogen bonds, the disulfide and the salt bridges are identified in each considered protein structure. Subsequently, the side chain interactions are displayed according to the multiple sequence alignment. The presented approach allows to easily identify bonds which are conserved in homologous proteins and to analyse rearrangements of the network of side chain interactions that characterize each protein structure.

Amino Acid Sequence↗
PubMed1994

The role of side-chain hydrogen bonds in the formation and stabilization of secondary structure in soluble proteins.

Intra-molecular side-chain:main-chain (sch:mch) and side-chain (sch:sch) hydrogen bonds observed in 44 well refined crystallographic protein structures with non-homologous sequences have been identified, classified and analysed to detect recurring structural patterns. Each observed bond was characterized by the position of its acceptor and donor groups relative to the N and C termini of the particular secondary structure in which they occur and according to their appearance within the same of sequentially separated secondary structures. The role of short-range hydrogen bonds in the formation and stabilization of a secondary structure and the importance of long-range hydrogen bonds as a cohesive force for different structural segments were also examined. It was found that the N terminus of alpha-helices is characterized by recurring sch:mch and sch:sch bonds with elements of the preceding coil segment, while at the C terminus a frequent intra-helix sch:mch hydrogen bond was frequently observed. The residues at or near the beta-strand termini often cross-linked, through hydrogen-bonding, non-sequential coil segments. Coil structures were characterized by recurring, internal sch:mch hydrogen bonding involving small polar side-chain groups situated at or near their N termini (coil N-capping). The significance of hydrogen bonds as formers and stabilizers of a protein fold and the association of its secondary structural units was also considered through an examination of bond density and distribution throughout the protein tertiary structure.

Amino Acids↗
PubMed1994

Conserved patterns in the Cu,Zn superoxide dismutase family.

Conserved structural and functional features of Cu,Zn superoxide dismutase enzymes have been studied by comparison of known three-dimensional structures and analysis of the currently available amino acid sequences. For this purpose, the three-dimensional structures of the bovine, spinach and yeast enzymes have been superimposed and the structure-based sequence alignment of 38 different superoxide dismutases has been produced. The evolutionary tree obtained from the alignment indicates that cytosolic and extracellular enzymes followed independent evolutionary paths, and that horizontal gene transfer, if any, occurred at an early stage in eukaryota evolution. Based on the sequence alignment and on the analysis of clusters of spatially neighboring residues, the conservation/variation of functionally relevant intramolecular interactions has been investigated. Seven alternative residue arrangements have been identified in the upper rim of the active site, which form an important determinant of the electrostatic field at the catalytic center. The total nominal charge of this region is constantly -1 through the phyla. The seven residues which coordinate the two metal ions at the active site are conserved, with only one known exception. Among the residues involved in maintenance of the active site structure, Gly59, Gly80, Gly136 and Gly139 are fully conserved; mutations of Gly42 and Pro64 have been observed, concerted with replacements in their structural surroundings. Coordinated mutations affecting residue pairs which maintain the packing geometry of the Greek-key beta-barrel have been identified. Furthermore, the unique disulfide bridge involving Cys55-Cys144 in eukaryota, shows the alternative Cys50A-Cys144 arrangement in prokaryotic enzymes.

Amino Acid Sequence↗
PubMed1993

ENVIRON: a software package to compare protein three-dimensional structures with homologous sequences using local structural motifs.

This work presents a method to compare local clusters of interacting residues as observed in a known three-dimensional protein structure with corresponding clusters inferred from homologous protein sequences, assuming conserved protein folding. For this purpose the local environment of a selected residue in a known protein structure is defined as the ensemble of amino acids in contact with it in the folded state. Using a multiple sequence alignment to identify corresponding residues in homologous proteins, a detailed comparison can be performed between the local environment of a selected amino acid in the template protein structure and the expected local environments at the sets of equivalent residues, derived from the aligned protein sequences. The comparison makes it possible to detect conserved local features such as hydrogen bonding or complementarity in residue substitution. A global measure of environmental similarity is also defined, to search for conserved amino acid clusters subject to functional or structural constraints. The proposed approach is useful for investigating protein function as well as for site-directed mutagenesis experiments, where appropriate amino acid substitutions can be suggested by observing naturally occurring protein variants.

Algorithms↗
PubMed1992

Structural study and preliminary crystallographic data for the hemoglobin from reindeer (Rangifer tarandus tarandus)

The ferric form of reindeer hemoglobin (Rangifer tarandus tarandus) has been crystallized in an orthorhombic crystalline form from polyethylene glycol solutions, at pH 8.2. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit cell edges a = 84.2 A, b = 59.9 A, c = 119.5 A; one hemoglobin tetramer is contained in the asymmetric unit. The crystals diffract X-rays to a limit spacing of 3.0 A. Inspection of amino acid sequences in the N-terminal region of beta-chains, and analysis of hemoglobin three-dimensional models, allows one to rationalize, on a molecular basis, the reduced O2 affinity and the decreased effect of organic phosphates observed in ruminant hemoglobins. By analogy, the analysis is extended to birds and reptiles, whose hemoglobin beta-chains display, as in ruminants, the deletion of the N-terminal residue and a methionine at the NA2 position.

2,3-Diphosphoglycerate↗
PubMed1991

Suggestions for "safe" residue substitutions in site-directed mutagenesis.

The conserved topological structure observed in various molecular families such as globins or cytochromes c allows structural equivalencing of residues in every homologous structure and defines in a coherent way a global alignment in each sequence family. A search was performed for equivalent residue pairs in various topological families that were buried in protein cores or exposed at the protein surface and that had mutated but maintained similar unmutated environments. Amino acid residues with atoms in contact with the mutated residue pairs defined the environment. Matrices of preferred amino acid exchanges were then constructed and preferred or avoided amino acid substitutions deduced. Given the conserved atomic neighborhoods, such natural in vivo substitutions are subject to similar constrains as point mutations performed in site-directed mutagenesis experiments. The exchange matrices should provide guidelines for "safe" amino acid substitutions least likely to disturb the protein structure, either locally or in its overall folding pathway, and most likely to allow probing the structural and functional significance of the substituted site.

Amino Acid Sequence↗
PubMed1990

Evolution of protein cores. Constraints in point mutations as observed in globin tertiary structures.

The amino acid sequences of ten globin chain tertiary structures were aligned and structurally equivalenced by spatial superposition of main-chain C alpha atoms. A search was then performed for structurally equivalent residue pairs that were buried in the protein core and that had mutated but maintained similar unmutated environments. Residues with atoms in contact with such central residue pairs define their environments. Such examples of point mutations would represent in vivo site-directed mutagenesis as would be observed in evolution. A search for mutated but exposed equivalent central residues was also performed. The constraints placed on the characteristics of the mutated residues (e.g., side-chain volume, polarity, radius of gyration) allow suggestions for the evolutionary modes of protein core and surface development as well as residue substitution guidelines to maintain structural stability in protein engineering and design.

Amino Acid Sequence↗