Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Ornithine delta-aminotransferase (OAT) is an important enzyme in proline biosynthetic pathway and is implicated in salt tolerance in higher plants. OAT transaminates ornithine to pyrroline 5-carboxylate, which is further catalyzed to proline by pyrroline 5-carboxylate reductase. The Vigna aconitifolia OAT cDNA, encoding a polypeptide of 48.1 kDa, was expressed in Escherichia coli and the enzyme was partially characterized following its purification using (NH(4))(2)SO(4) precipitation and gel filtration techniques. Optimal activity of the enzyme was observed at a temperature of 25 degrees C and pH 8.0. The enzyme appeared to be a monomer and exhibited high activity at 4mM ornithine. Proline did not show any apparent effect but isoleucine, valine and serine inhibited the activity when added into the assay mixture along with ornithine. Omission of pyridoxal 5'-phosphate from the reaction mixture reduced the activity of this enzyme by 60%. To further evaluate these biochemical observations, homology modeling of the OAT was performed based on the crystal structure of the ornithine delta-aminotransferase from humans (PDB code 1OAT) by using the software MODELLER6v2. With the aid of the molecular mechanics and dynamics methods, the final model was obtained and assessed subsequently by PROCHECK and VERIFY-3D graph. With this model, a flexible docking study with the substrate and inhibitors was performed and the results indicated that Gly106 and Lys256 in OAT are the important determinant residues in binding as they have strong hydrogen bonding contacts with the substrate and inhibitors. These observations are in conformity with the results obtained from experimental investigations.
J Mol Graph Model 2007 Nov
PMID:Biochemical characterization, homology modeling and docking studies of ornithine delta-aminotransferase--an important enzyme in proline biosynthesis of plants. 1760 99

Disulfide bonds play an important role in protein stability and function. Here, we describe a general procedure for generating disulfide-linked dimers and multimers of proteins of known crystal structures. An algorithm was developed to predict sites in a protein compatible with intermolecular disulfide formation with neighboring molecules in the crystal lattice. A database analysis was carried out on 46 PDB coordinates to verify the general applicability of this algorithm to predict intermolecular disulfide linkages. On the basis of the predictions from this algorithm, mutants were constructed and characterized for a model protein, thioredoxin. Of the five mutants, as predicted, in solution four formed disulfide-linked dimers while one formed polymers. Thermal and chemical denaturation studies on these mutant thioredoxins showed that three of the four dimeric mutants had similar stability to wild-type thioredoxin while one had lower stability. Three of the mutant dimers crystallized readily (in four to seven days) in contrast to the wild-type protein, which is particularly difficult to crystallize and takes more than a month to form diffraction-quality crystals. In two of the three cases, the structure of the dimer was exactly as predicted by the algorithm, while in the third case the relative orientation of the monomers in the dimer was different from the predicted one. This methodology can be used to enhance protein crystallizability, modulate the oligomerization state and to produce linear chains or ordered three-dimensional protein arrays.
J Mol Biol 2007 Oct 05
PMID:Design of disulfide-linked thioredoxin dimers and multimers through analysis of crystal contacts. 1772 80

Cytochrome P450 CYP2D6 is involved in the oxidation of well over 150 drugs and, in general, those which contain a basic nitrogen atom in the molecule. To clarify how the residues of CYP2D6 are utilized for orientating a wide range of its specific substrates and distinguishing them from a variety of other organic compounds, docking studies by AutoDock and molecular dynamics (MD) simulations were conducted. Specific ligands were docked to both the homology model and crystal structures optimally to estimate the site of reaction on the ligand molecule and the binding energy for the complex, which were generally in good agreement with the experimental data. MD simulation for the CYP2D6-propranolol complex was then carried out to reveal the amino acid residues interacting with the substrate at the active site. Phe-120, Glu-216, Asp-301, and Phe-483 are identified as the substrate-binding residues in agreement with previously reported site-directed mutagenesis data and the crystal structure reported recently (PDB code: 2F9Q). As well as these residues, our theoretical prediction suggests that Phe-219 and Glu-222 are also important residues for mediating oxidation of substrates, especially propranolol.
J Mol Graph Model 2008 Feb
PMID:Analysis of CYP2D6 substrate interactions by computational methods. 1776 97

Naturally occurring cyclic tetrapeptides (CTPs) such as tentoxin (Halloin et al., Plant Physiol 1970, 45, 310-314; Saad, Phytopathology 1970, 60, 415-418), ampicidin (Darkin-Rattray, Proc Natl Acad Sci USA 1996, 93, 13143-13147), HC-toxin (Walton, Proc Natl Acad Sci USA 1987, 84, 8444-8447), and trapoxin (Yoshida and Sugita, Jpn J Cancer Res 1992, 83, 324-328; Itazaki et al., J Antibiot (Tokyo) 1990, 43, 1524-1532) have a wide range of biological activity and potential use ranging from herbicides (Walton, Proc Natl Acad Sci USA 1987, 84, 8444-8447; Judson, J Agric Food Chem 1987, 35, 451-456) to therapeutics (Loiseau, Biopolymers 2003, 69, 363-385) for malaria (Darkin-Rattray, Proc Natl Acad Sci USA 1996, 93, 13143-13147) and cancer (Yoshida and Sugita, Jpn J Cancer Res 1992, 83, 324-328). To elucidate scaffolds that have few low-energy conformations and could serve as semirigid reverse-turn mimetics, the flexibility of CTPs was determined computationally. Four analogs of cyclic tetraproline c[Pro-pro-Pro-pro] with alternating L- and D-prolines, namely c[pro-Pro-pro-NMe-Ala], c[pip-Pro-pip-Pro], c[pro-Pip-pro-Pro], and c[Ala-Pro-pip-Pro] were synthesized and characterized by NOESY NMR. Both molecular mechanics and Density Functional Theory quantum calculations found these head-to-tail CTPs to be constrained to one or two relatively stable conformations. NMR structures, while not always yielding the same lowest energy conformation as expected by in silico predictions, confirmed only one or two highly populated solution conformations for all four peptides examined. c[pro-Pro-pro-NMe-Ala] was shown to have a single all trans-amide bond conformation from both in silico predictions and NMR characterization, and to be a reverse-turn mimetic by overlapping four Calpha-Cbeta bonds with those for approximately 6.5% (Tran, J Comput Aided Mol Des 2005, 19, 551-566) of reverse-turns in the Protein Data Bank PDB with a RMSD of 0.57 A.
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PMID:c[D-pro-Pro-D-pro-N-methyl-Ala] adopts a rigid conformation that serves as a scaffold to mimic reverse-turns. 1794 Oct 3

Theoretical studies of RNA and lattice protein models suggest that mutationally robust or the so-called designable phenotypes tend to have special geometric features such as being more compact and more geometrically regular. Such geometrical forms have been also linked to speed of folding and stability properties that may also assist in promoting mutational robustness. Here we test these theoretical predictions on a non-redundant collection of 2,660 experimentally determined structures from the PDB (Protein Data Bank) and CATH (Class Architecture Topology Homologous superfamily) database. We first developed an index summarizing the geometrical regularity of the structures and then used this index to show that the statistical pattern of empirical data is consistent with the theoretical predictions relating geometry to mutational robustness. Mutationally robust proteins tend to be more symmetric and compact. But, the relationship between compactness and robustness cannot be explained simply by the geometrical packing of individual amino acids in proteins; rather, it is the property of the whole system that is related to the statistical characteristics of the folding landscape. Finally, we hypothesize that a triplet relationship between mutational robustness, stability and form is a general properties of objects that optimize real-valued relationships between sequences and discrete structures.
J Exp Zool B Mol Dev Evol 2008 May 15
PMID:Mutational robustness and geometrical form in protein structures. 1797 70

Multiple near-optimal conformations of protein-ligand complexes provide a better chance for accurate representation of biomolecular interactions, compared with a single structure. We present ISE-dock--a docking program which is based on the iterative stochastic elimination (ISE) algorithm. ISE eliminates values that consistently lead to the worst results, thus optimizing the search for docking poses. It constructs large sets of such poses with no additional computational cost compared with single poses. ISE-dock is validated using 81 protein-ligand complexes from the PDB and its performance was compared with those of Glide, GOLD, and AutoDock. ISE-dock has a better chance than the other three to find more than 60% top single poses under RMSD = 2.0 A and more than 80% under RMSD = 3.0 A from experimental. ISE alone produced at least one 3.0 A or better solutions among the top 20 poses in the entire test set. In 98% of the examined molecules, ISE produced solutions that are closer than 2.0 A from experimental. Paired t-tests (PTT) were used throughout to assess the significance of comparisons between the performances of the different programs. ISE-dock provides more than 100-fold docking solutions in a similar time frame as LGA in AutoDock. We demonstrate the usefulness of the large near optimal populations of ligand poses by showing a correlation between the docking results and experiments that support multiple binding modes in p38 MAP kinase (Pargellis et al., Nat Struct Biol 2002;9:268-272] and in Human Transthyretin (Hamilton, Benson, Cell Mol Life Sci 2001;58:1491-1521).
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PMID:High quality binding modes in docking ligands to proteins. 1805 8

The soft-rot fungus Penicillium purpurogenum secretes to the culture medium a variety of enzymes related to xylan biodegradation, among them three acetyl xylan esterases (AXE I, II and III). AXE II has 207 amino acids; it belongs to family 5 of the carbohydrate esterases and its structure has been determined by X-ray crystallography at 0.9 A resolution (PDB 1G66). The enzyme possesses the alpha/beta hydrolase fold and the catalytic triad typical of serine esterases (Ser90, His187 and Asp175). AXE II can hydrolyze esters of a large variety of alcohols, but it is restricted to short chain fatty acids. An analysis of its three-dimensional structure shows that a loop that covers the active site may be responsible for this strict specificity. Cutinase, an enzyme that hydrolyzes esters of long chain fatty acids and shows a structure similar to AXE II, lacks this loop. In order to generate an AXE II with this broader specificity, the preparation of a mutant lacking residues involving this loop (Gly104 to Ala114) was proposed. A set of molecular simulation experiments based on a comparative model of the mutant enzyme predicted a stable structure. Using site-directed mutagenesis, the loop's residues have been eliminated from the AXE II cDNA. The mutant protein has been expressed in Aspergillus nidulans A722 and Pichia pastoris, and it is active towards a range of fatty acid esters of up to at least 14 carbons. The availability of an esterase with broader specificity may have biotechnological applications for the synthesis of sugar esters.
J Comput Aided Mol Des 2008 Jan
PMID:An eleven amino acid residue deletion expands the substrate specificity of acetyl xylan esterase II (AXE II) from Penicillium purpurogenum. 1806 May 6

The visible (alpha) and near-UV (beta) CD bands of rhodopsin have been studied extensively, but their source(s) have never been definitively established. Do they result from the intrinsic chirality of the polyene chromophore of the protonated Schiff base of retinal (retPSB) or from the coupling of the transitions of this chromophore with those of protein groups? We have calculated the contributions of these two mechanisms to the CD of rhodopsin. The intrinsic CD of the retPSB chromophore was calculated using time-dependent density functional theory (TDDFT) and, for comparison, the semiempirical ZINDO method. First-order perturbation theory was used to calculate the effects of coupling of the retPSB transitions with the pi pi* transitions of the aromatic chromophores and the pi pi* and n pi* transitions of the peptide groups in rhodopsin. Calculations were performed for eight structures based upon the two molecules in the asymmetric unit of four crystal structures. The most reliable results were obtained from TDDFT calculations on the structure of Okada et al. (J. Mol. Biol. 2004, 342, 571), PDB 1U19. Averaging over the two molecules in the asymmetric unit, the intrinsic rotational strengths are 0.62 +/- 0.00 DBM (Debye-Bohr magneton) and 0.90 +/- 0.03 DBM for the alpha- and beta-bands, respectively. The contributions from coupling with protein groups are, respectively, -0.32 +/- 0.05 and -0.01 +/- 0.03 DBM. Our results show that the visible/near-UV CD bands of rhodopsin are determined by the intrinsic chirality of the retPSB chromophore and that the contributions of coupling with the protein are significantly smaller for the alpha-band and negligible for the beta-band.
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PMID:Inherent chirality dominates the visible/near-ultraviolet CD spectrum of rhodopsin. 1841 22

Human leukocyte antigen (HLA) molecules involved in immune function by binding to short peptides (8-20 residues) have different sequences in different individuals belonging to distinct ethnic population. Hence, the peptide-binding function of HLA alleles is specific. Class I HLA alleles (alternative forms of a gene) are associated with CD8+ T cells, and their allele-specific sequence information is available at the IMGT/HLA database. The available sequences are one-dimensional (ID), and the peptide-binding functional inference often requires 3-dimensional (3D) structural models of respective alleles. Hence, 3D structures were constructed for 1,000 class I HLA alleles (310 A, 570 B, and 120 C) using MODELLER (a comparative protein modeling program for modeling protein structures). The electrostatic distribution maps were generated for each modeled structure using Deep View (Swiss PDB Viewer Version 3.7). The 1,000 models were then grouped into different categories by visual inspection of their electrostatic distribution maps in the peptide binding grooves. The distribution of the models based on electrostatic distribution was 30% negative (300), 1% positive (12), 8% neutral (84), and 60% (604) mixed (random mixture of negative, positive, and neutral). This grouping provides insight toward the inference for functional overlap among HLA alleles.
Methods Mol Biol 2007
PMID:Grouping of class I HLA alleles using electrostatic distribution maps of the peptide binding grooves. 1845

The ultra-rapid delayed rectifier potassium current (I(Kur)), encoded by Kv1.5 gene, is the critical determinant of Phase I repolarization of action potential duration (APD). The evidences that Kv1.5 gene expresses more extensively in human atrial myocytes than in ventricle and the I(Kur) currents has not been recorded in the human ventricle, suggest Kv1.5 potassium channel as a selective target for the treatment of atrial fibrillation (AF). Recent mutagenesis studies have provided us some evidences that are useful in designing Kv1.5 blockers. In order to further evaluate these molecular biological information, the homology model of Kv1.5 potassium channel was established based on the Kv1.2 crystal structure (PDB entry: 2A79) using MODELLER 9v2 program. After the molecular dynamics refinement, the optimized homology model was assessed as a reliable structure by PROCHECK, ERRAT, WHAT-IF, PROSA2003 and DOPE graph. The results of molecular docking studies on different Kv1.5 inhibitors are in agreement with the published mutagenesis data. Based on the docking conformations, a pharmacophore model was developed by HipHop algorithm in order to probe the common features of blockers. By analyzing the results, active site architecture, certain key residues and pharmacophore common-features that are responsible for substrate specificity were identified on the Kv1.5 potassium channel, which would be very helpful in understanding the blockade mechanism of Kv1.5 potassium channel and providing insights into rational design of novel Kv1.5 blockers.
J Mol Graph Model 2008 Sep
PMID:Modeling the binding modes of Kv1.5 potassium channel and blockers. 1848 68


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