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At least 1,189 records · Page 66Linked to original sources
PubMed1995

Sequential 1H and 15N nuclear magnetic resonance assignments and secondary structure of the lipoyl domain of the 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii. Evidence for high structural similarity with the lipoyl domain of the pyruvate dehydrogenase complex.

A 79-amino-acid polypeptide, corresponding to the lipoyl domain of the succinyltransferase component of the 2-oxoglutarate dehydrogenase multienzyme complex from Azotobacter vinelandii, has been sub-cloned and produced in Escherichia coli. Complete sequential 1H and 15N resonance assignments for the lipoyl domain have been obtained by using homo- and hetero-nuclear NMR spectroscopy. Two antiparallel beta-sheets of four strands each were identified from characteristic NOE connectivities and 3JHN alpha values. The lipoyl-lysine residue is found in a type-I turn connecting two beta-strands. The secondary structure of the lipoyl domain very much resembles the secondary solution structure of the N-terminal lipoyl domain of the A. vinelandii pyruvate dehydrogenase complex, despite the sequence identity of 25%. A detailed comparison of the NMR-derived parameters of both lipoyl domains, i.e. chemical shifts, NH-exchange rates, NOEs, and 3JHN alpha values suggests a high structural similarity in solution between the two lipoyl domains. Preliminary tertiary-structure calculations confirm that these lipoyl domains have very similar overall folds. The observed specificity of the 2-oxo acid dehydrogenase components of both complexes for these lipoyl domains is discussed in this respect.

Amino Acid Sequence↗
PubMed1995

NMR-based structural studies of the pNR-2/pS2 single domain trefoil peptide. Similarities to porcine spasmolytic peptide and evidence for a monomeric structure.

NMR spectroscopy measurements have been used to obtain structural information about the pNR-2/pS2 single-domain trefoil peptide. NMR data from 2D (two dimensional) double-quantum-filtered correlation spectroscopy (DQF-COSY), total correlation spectroscopy (TOCSY), NOE spectroscopy (NOESY), rotating frame NOE spectroscopy (ROESY) and 2D 13C-1H heteronuclear single-quantum coherence (HSQC) and 13C-1H HSQC-TOCSY spectra have been analysed to provide essentially complete 1H and 13C sequence-specific assignments for the pNR-2/pS2 protein. From a consideration of the NOE intensities, 3J(NH-alpha CH) coupling constants, 1H and 13C chemical shifts of backbone atoms and amide-proton exchange rates, the pNR-2/pS2 was found to contain two short antiparallel beta-strands (32-35 and 43-46), a short helix (25-30) and a type I beta-turn (11-15). These elements of secondary structure are very similar to those found in the two trefoil domains of pSP for which detailed structural information is already available. Similar 1H chemical shifts were noted for several conserved residues in pNR-2/pS2 and pSP and a characteristic Phe residue with a slowly flipping ring was found in the pNR-2/pS2 variant and in both domains of pSP. The tertiary structures of the domains therefore appear to be very similar in the two proteins and it is likely that the pNR-2/pS2 has the same pattern of disulphide bonds (1-5, 2-4, 3-6) as pSP. Correlation time measurements derived from 1H-1H NOE measurements indicate that the Cys58-->Ser form of the pNR-2/pS2 protein used in this study is monomeric in solution at approximately 2 mM.

Amino Acid Sequence↗
PubMed2001

Structure-activity relationships for a collection of structurally diverse inhibitors of purine nucleoside phosphorylase.

Values of inhibition constants, Ki, and concentrations required for 50% inhibition, IC50, for a collection of structurally diverse competitive inhibitors of calf spleen purine nucleoside phosphorylase have been determined employing inosine as substrate. These values have been employed to create predictive quantitative structure-activity relationships (QSAR) which link structure to values of Ki and IC50. These QSAR models have substantial power to predict values and the associated uncertainties for Ki and IC50 for unknown, structurally diverse inhibitors of purine nucleoside phosphorylase.

Enzyme Inhibitors↗
PubMed1989

[X-ray structural studies of nucleic acid molecular structure and nucleic acid-protein interaction mechanism].

Since the discovery of the right-handed double helical structure of deoxyribonucleic acid by Watson and Crick in 1953, many pieces of detailed nucleic acid structural information involving ribonucleic acid have been elucidated and this review describes the results of the X-ray structural studies of nucleic acids and their constituents carried out in my laboratory. In the latter half the nucleic acid-protein interaction mechanism was also discussed on the basis of the molecular model of the stacking interaction between base and aromatic amino acid side chains. The structure-function relationship of ribonuclease T1.guanosine monophosphate complex was used as an example.

Binding Sites↗
PubMedDate not supplied

Comparative modeling of amoebapores and granulysin based on the NK-lysin structure-structural and functional implications.

Amoebapores, the pore-forming polypeptides of the protozoan parasite Entamoeba histolytica, and effector proteins of porcine and human lymphocytes, namely NK-lysin and granulysin, reveal a substantial sequence similarity despite their enormous evolutionary distance. Moreover, all these polypeptides display antibacterial activity and are in higher concentrations cytolytic to eukaryotic cells. The recently solved NMR structure of NK-lysin enabled us to build the three dimensional structures of amoebapores and granulysin by comparative modeling. The generated models revealed the expected similarities, but also fundamental differences with respect to charge distribution, hydrophobicity and core packing. The combination of these structural properties and known biochemical data provides insight in the different membrane-interacting mechanisms of the proteins. For amoebapores, exposed hydrophobic grooves and a locally loosely packed protein core may allow a rearrangement of the protein and therefore may account for its ability to penetrate the target membrane and to form defined ion channels in planar lipid bilayers. In contrast, the structural features of NK-lysin and granulysin appear to be suitable for a membrane-perturbing mode of action rather than for channel formation.

Amino Acid Sequence↗
PubMed1982

Structure investigations of agonists of the natural neurotransmitter acetylcholine, III. X-ray structure analysis of (2-ethoxyethyl)trimethylammonium chloride.

To elucidate the structure-activity correlations we have performed an X-ray structure analysis of the title compound (1), which is a muscarinic agonist of the natural neurotransmitter acetylcholine. 1 crystallizes in the monoclinic space group P2(1)/n with 2 molecules per asymmetric unit. Lattice parameters are: a = 10.375(6), b = 12.468(5), c = 15.274(17) A; beta = 95.32(7) degrees. The structure was solved by direct methods and refined to an R-value of 0.14 for 1828 observed reflections. Both cations in the asymmetric unit are disordered. In the crystal structure at least four conformations of the cation occur, indicating a pronounced conformational flexibility of the neurotransmitter cation. The anions are arranged stereospecifically with respect to the quaternary trimethylammonio methyl group. The geometry of triangles which are defined by a nitrogen of the quaternary ammonium group and an ether oxygen on one hand and an anion occupying a specific type of tetrahedral faces of a (CH3)3N+ CH2 group on the other hand, is characteristic for muscarinic agonists if they contain an ether or ester oxygen in the analogous position to the ester oxygen of acetylcholine.

Acetylcholine↗
PubMedDate not supplied

Structure investigations of agonists of the natural neurotransmitter acetylcholine II [1]. X-ray structure analysis of trimethyl(4-oxopentyl)ammonium-chloride.

The crystal structure of Trimethyl(4-oxopentyl)ammonium-chloride ([(CH3)3N--(CH2)3COCH3]Cl-) (1) was determined by an X-ray structure analysis. 1 crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 10.440 (3), b = 14.600 (9), c = 6.804 (9) A and with four formula units per unit cell. The structure was solved by a Patterson and a successive Fourier synthesis. The least squares refinement yielded an R-value of 0.064 for 1077 observed reflections. The cation of 1 is derived from acetylcholine by replacement of the ester oxygen with a CH2 group. It shows a potent nicotinic activity and a significant difference in conformation as compared with acetylcholine. In the crystal structure the anions are oriented stereospecifically with respect to the tetrahedron of the quaternary ammonium group. The geometry of two triangles formed by the quaternary nitrogen atom, the oxygen atom of the carbonyl group, and by either of the two anions nearest to the quaternary ammonium group is characteristic for the nicotinic activity of 1.

Acetylcholine↗
PubMed2006

Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures.

Many proteins contain flexible structures such as loops and hinged domains. A simple root mean square deviation (RMSD) alignment of two different conformations of the same protein can be skewed by the difference between the mobile regions. To overcome this problem, we have developed a novel method to overlay two protein conformations by their atomic coordinates using a Gaussian-weighted RMSD (wRMSD) fit. The algorithm is based on the Kabsch least-squares method and determines an optimal transformation between two molecules by calculating the minimal weighted deviation between the two coordinate sets. Unlike other techniques that choose subsets of residues to overlay, all atoms are included in the wRMSD overlay. Atoms that barely move between the two conformations will have a greater weighting than those that have a large displacement. Our superposition tool has produced successful alignments when applied to proteins for which two conformations are known. The transformation calculation is heavily weighted by the coordinates of the static region of the two conformations, highlighting the range of flexibility in the overlaid structures. Lastly, we show how wRMSD fits can be used to evaluate predicted protein structures. Comparing a predicted fold to its experimentally determined target structure is another case of comparing two protein conformations of the same sequence, and the degree of alignment directly reflects the quality of the prediction.

Amino Acid Sequence↗
PubMed1988

Thyroid hormone structure-activity relationships: molecular structure of 3,5,3'-triiodothyropropionic acid.

The crystal and molecular structures of 3,5,3'-triiodothyropropionic acid (T3P), determined as an N-diethanolamine salt, were carried out and the results are compared with those of other thyroid hormone structures. These data show that T3P has an unusual conformation with the diphenyl ether bridge outside the range normally observed for other thyroactive acid structures and has the largest deviations from the ideal skewed conformation predicted for 3,5-diiodothyroactive compounds. These conformational properties are not observed in the structures of thyroformic or acetic acid analogues. Biochemical data indicate that thyropropionic acid analogue activity differs from that other acid analogues which could imply that their metabolism and activity can be controlled differently from that of other hormone metabolites.

Crystallography↗
PubMed2002

Structural genomics: bridging functional genomics and structure-based drug design.

Considerable advances in structural genomics have been witnessed in the last year. Several pilot studies have begun to report their initial results, and new centers have been funded to join the endeavor. The legacies of the genome sequencing efforts, namely high-throughput molecular biology and whole-organism genome sequences, have been integrated as front-end modules for structural genomics pipelines. Impressive advances have been made in NMR spectroscopy and X-ray crystallography. New methods in structural bioinformatics and computational chemistry have been published that provide the means to exploit the wealth of new information in drug discovery. Not surprisingly, the biopharmaceutical industry has been quick to recognize the benefits of these new developments and has begun to adopt them. This article reviews recent results from structural genomics initiatives and the potential applications of new information and technologies in the drug discovery process.

Drug Design↗
PubMed1992

Evaluation of the predicted secondary structure of bacteriorhodopsin. Prediction of the bovine rhodopsin secondary structure and its sequence similarity with bacteriorhodopsin.

The secondary structure of bacteriorhodopsin (bacR) is predicted using the Chou and Fasman method in conjunction with the hydropathic index of Kyte and Doolittle. The predicted bacR structure was compared with the structure determined by Henderson et al. (1990) using electron diffraction and was found to correlate extremely well. The secondary structure of bovine rhodopsin (bovR) was then predicted using the same techniques. The proposed transmembrane regions of bovR were then examined and found to have sequence similarity with those transmembrane regions of bacR.

Amino Acid Sequence↗
PubMed2005

Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure.

Despite the advantages provided by the enormous recent increases in the availability of structural information, functional assignment for the large number of proteins represented in the sequence and structural genomics projects remains a pressing problem for genomic era biology. This section describes work relevant to this problem from several perspectives, including new approaches that take advantage of combined structure and sequence-based classification. Leveraging of genomic context and evolutionary information to improve classification and predictive power is a second prominent theme in the papers represented here. Finally, issues in building a database for linking sequence, structural, and functional information are explored.

Genomics↗
PubMed2005

[Quantitative structure-retention relationships of monosubstituted alkanes by dividing its molecular structure into substructure].

In order to investigate the quantitative structure-retention relationship in gas chromatography (GC) , the molecular structure of monosubstituted alkane RX (X = halogen, OH, SH, NH2) is divided into two parts, R and X, to obtain molecular structure parameters, and the retention times in GC for 37 monosubstituted alkanes RX were determined. It was proposed that the retention time in GC is affected by three main factors for RX compounds, alkyl group R, substituted group X, and interaction between R and X. Using four parameters, the eigenvalue of bonding orbital-connection matrix EVM, the polarizability effect index of alkyl group PEI, the mass content for substituted group X, and the partial charge deltaN(H) on hydrogen atom of the group X, a quantitative structure-retention correlation model with correlation coefficient (r) of 0.9948 and standard deviation (S) of 0.0991 was obtained for the 37 RX compounds. The model obtained has good predictive and extrapolation ability. The predicted retention indexes are in good agreement with the experimental ones for alcohols.

Alkanes↗
PubMed1988

Computer-automated structure evaluation of flavonoids and other structurally related compounds as glyoxalase I enzyme inhibitors.

The Computer-Automated Structure Evaluation (CASE) methodology has been applied to a set of flavonoids and other structurally related compounds tested for glyoxalase I enzyme inhibition. CASE identified several structural features believed to be responsible for activity. A total of five fragments were isolated. The most important structural feature is the alpha-hydroxy-alpha,beta-unsaturated carbonyl group attached to a fused ring carbon atom. This fragment tautomerizes into a transition state analog of the substrate of the enzyme. Five tested compounds initially removed from the database were submitted to CASE in the predictive mode. The predictions generally matched the tested values for enzyme inhibition. A set of chromones and phenyl-pyrones, although untested, were also submitted to CASE. CASE predicts that, as a class of compounds, chromones would be more effective inhibitors than phenyl-pyrones.

Computer Simulation↗
PubMed1983

Conformation and structure of acidic dipeptides. Crystal structures of L-alanyl-L-aspartic acid and alpha-L-glutamyl-L-aspartic acid.

The crystal structures of the dipeptides L-alanyl-L-aspartic acid, C7H12N2O5, and alpha-L-glutamyl-L-aspartic acid, C9H14N2O7, have been determined from three-dimensional X-ray diffractometer data. Alanylaspartic acid crystallizes in the orthorhombic space group P2(1)2(1)2(1) with four formula units in a cell of dimensions a = 13.389(5), b = 14.467(3), c = 4.781(1) A. Glutamylaspartic acid also crystallizes in space group P2(1)2(1)2(1) with four formula units in a cell of dimensions a = 13.709(5), b = 16.126(7), c = 4.939(5) A. Both structures were solved by direct methods and refined by full-matrix least squares methods; the final value of the weighted R-factors (on F) were 0.040 based on 790 independent intensities with I greater than or equal to 2 sigma (I) for Ala-Asp and 0.033 based on 1105 intensities with I greater than or equal to 2 sigma (I) for Glu-Asp. Each dipeptide occurs as a zwitterion with the amino terminus protonated and the main chain carboxyl group deprotonated. The conformation of the peptide linkage is trans in both molecules, the omega torsion angle being - 175.9 degrees in Ala-Asp and 174.3 degrees in Glu-Asp. There is considerable intermolecular, but not intramolecular, hydrogen bonding in the crystals. The conformations and structures of Ala-Asp and Glu-Asp are compared to those of other structurally characterized acidic dipeptides.

Dipeptides↗
PubMed1994

Structural basis of the 70-kilodalton heat shock cognate protein ATP hydrolytic activity. II. Structure of the active site with ADP or ATP bound to wild type and mutant ATPase fragment.

The ATPase fragment of the bovine 70-kDa heat shock cognate protein is an attractive construct in which to study its mechanism of ATP hydrolysis. The three-dimensional structure suggests several residues that might participate in the ATPase reaction. Four acidic residues (Asp-10, Glu-175, Asp-199, and Asp-206) have been individually mutated to both the cognate amine (asparagine/glutamine) and to serine, and the effects of the mutations on the kinetics of the ATPase activity (Wilbanks, S. M., DeLuca-Flaherty, C., and McKay, D. B. (1994) J. Biol. Chem. 269, 12893-12898) and the structure of the mutant ATPase fragments have been determined, typically to approximately 2.4 A resolution. Additionally, the structures of the wild type protein complexed with MgADP and Pi, MgAMPPNP (5'-adenylyl-beta, gamma-imidodiphosphate) and CaAMPPNP have been refined to 2.1, 2.4, and 2.4 A, respectively. Combined, these structures provide models for the prehydrolysis, MgATP-bound state and the post-hydrolysis, MgADP-bound state of the ATPase fragment. These models suggest a pathway for the hydrolytic reaction in which 1) the gamma phosphate of bound ATP reorients to form a beta, gamma-bidentate phosphate complex with the Mg2+ ion, allowing 2) in-line nucleophilic attack on the gamma phosphate by a H2O molecule or OH- ion, with 3) subsequent release of inorganic phosphate.

Adenosine Diphosphate↗
PubMed1995

Does prediction of epitopes from the primary structure of a protein represent the epitope in the native structure? A study using cobrotoxin.

In contrast to observations made with S. aureus V8 protease-digest hydrolysates, the antigenic structures of reduced and S-carboxymethylated (RCM)-cobrotixin were notably affected following hydrolysis of RCM-cobrotoxin with chymotrypsin. The peptide separated from the V8 protease-digest hydrolysates with a sequence at positions 22-38 of cobrotoxin exhibited a nearly equal reactivity toward the anti-RCM-cobrotoxin antibodies as RCM-cobrotoxin. Chymotryptic cleavage on this segment caused a precipitous drop in the antigenicity of RCM-cobrotoxin. Alternatively, the N-terminal and C-terminal regions of RCM-cobrotoxin encompassed other antigenic determinants which exhibited low reactivities toward anti-RCM-cobrotoxin antibodies. The epitope structures of RCM-cobrotoxin are in line with those predicted from the hydrophobicity profile of cobrotoxin, but the notably immunoreactive region in the C-terminal region of native toxin molecule (Ref. 1) cannot be predicted from analysis of its primary structure. Moreover, RCM-cobrotoxin had a superior reactivity toward anti-RCM-cobrotoxin antibodies than cobrotoxin did. These results indicate that the epitope structures in RCM-cobrotoxin and cobrotoxin are different.

Antibodies↗
PubMed2003

Assembly of protein tertiary structures from secondary structures using optimized potentials.

We present a simulated annealing-based method for the prediction of the tertiary structures of proteins given knowledge of the secondary structure associated with each amino acid in the sequence. The backbone is represented in a detailed fashion whereas the sidechains and pairwise interactions are modeled in a simplified way, following the LINUS model of Srinivasan and Rose. A perceptron-based technique is used to optimize the interaction potentials for a training set of three proteins. For these proteins, the procedure is able to reproduce the tertiary structures to below 3 A in root mean square deviation (rmsd) from the PDB targets. We present the results of tests on twelve other proteins. For half of these, the lowest energy decoy has a rmsd from the native state below 6 A and, in 9 out of 12 cases, we obtain decoys whose rmsd from the native states are also well below 5 A.

Amino Acids↗