An automatic homology modeling method consisting of database searches and simulated annealing

Ogata, Koji; Umeyama, Hideaki

doi:10.1016/s1093-3263(00)00037-1

Cited by 86 publications

(77 citation statements)

References 33 publications

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“…In the most recent CASP6 held in 2004, the official assessment showed that the predictions using SKE-CHIMERA and FAMS (a fully automated homology modelling system) were successful in the homology modelling category (http://predictioncenter.org/casp6/meeting/presentations/ CASP6_Program.doc). Based on the alignment given by SKE-CHIMERA, FAMS Ligand&Complex (FAMS that constructs proteinligand complex models based on the structure of the reference protein-ligand complex) successfully constructed a three-dimensional model structure (Ogata & Umeyama, 2000;Takeda-Shitaka et al, 2004a, b, 2005, 2006. After the modelling was complete, the quality of the stereochemistry of the SlyA model was verified.…”

Section: Methodsmentioning

confidence: 99%

“…To obtain structural and functional information about the SlyA molecule, we constructed a SlyA homodimer model using SKE-CHIMERA (Takeda-Shitaka et al, 2005) and FAMS Ligand&Complex (Ogata & Umeyama, 2000;TakedaShitaka et al, 2004aTakedaShitaka et al, , b, 2005TakedaShitaka et al, , 2006. The accuracy of comparative models generally depends on sequence identity between the target and the modelled proteins, because errors in alignment or template selection increase for low sequence identities (Baker & Sali, 2001).…”

Section: Construction Of a Structural Model Of The Slya Proteinmentioning

confidence: 99%

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Identification of amino acid residues of Salmonella SlyA that are critical for transcriptional regulation

Okada

Takeda‐Shitaka

et al. 2007

Microbiology

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The type III secretion system encoded by Salmonella pathogenicity island 2 (SPI-2) is essential for the intracellular survival and replication of Salmonella enterica. The expression of SPI-2 genes is dependent on a two-component regulatory system, SsrA (SpiR)/SsrB, encoded in the SPI-2 region. This paper shows that SlyA regulates transcription of the sensor kinase SsrA by binding to the ssrA promoter, indicating that SlyA is directly involved in the regulation of SPI-2 gene expression. A structure model of the SlyA dimer in complex with DNA was constructed. The model of SlyA indicated that its structure is very similar to that of other MarR family proteins. Based on this model, site-directed mutagenesis of residues located in the winged-helix region required for DNA binding and in the a-helices of the N-terminal and C-terminal regions required for dimerization of the SlyA protein was performed to identify the residues that are critical for SlyA function. Nine mutants of SlyA with single substitutions were unable to activate ssrA transcription in vivo. These mutant SlyA proteins revealed that the residues Leu-63, Val-64, Arg-65, Leu-67, Leu-70, Arg-86 and Lys-88 within the winged-helix region are required for DNA binding, and residues Leu-12 and Leu-126 within the a-helices of the N-terminal and C-terminal regions are required for efficient dimer formation. A Salmonella slyA mutant strain carrying a plasmid expressing SlyA derivatives containing mutations at these amino acid positions did not exhibit restored SlyA function in infected HeLa cells, thereby confirming the structural and functional relationships of the SlyA protein. INTRODUCTIONSalmonella enterica, a facultative intracellular pathogen, can replicate within macrophages. The intracellular survival of S. enterica serovar Typhimurium requires a number of virulence-associated proteins encoded in Salmonella pathogenicity island 2 (SPI-2) on the bacterial chromosome (Cirillo et al., 1998;Hensel, 2000;Ochman et al., 1996;Shea et al., 1996). SPI-2 encodes a two-component regulatory system, structural components of a type III secretion system (TTSS), effector proteins and chaperones, which mediate the secretion of the effectors (Cirillo et al., 1998;Hensel et al., 1998;Ochman et al., 1996;Shea et al., 1996). In infected macrophages, Salmonella replicates within a membranebound compartment (Salmonella-containing vacuole, SCV) inside the host cells (Steele-Mortimer et al., 2002). Intracellular activation of SPI-2 function is essential for SCV maturation along the phagolysosomal fusion pathway, which is responsible for the inhibition of bacterial degradation in phagolysosomes. The SPI-2 TTSS functions to export effector proteins across the SCV membrane and into the cytosol of host cells, resulting in the prevention of the recruitment of NADPH oxidase to the SCV (Gallois et al., 2001;Vazquez-Torres et al., 2000), as well as leading to the rearrangement of cellular microfilaments (Meresse et al., 2001;Miao et al., 2002) and microtubule networks (Brumell et al., 20...

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Section: Methodsmentioning

confidence: 99%

Section: Construction Of a Structural Model Of The Slya Proteinmentioning

confidence: 99%

Identification of amino acid residues of Salmonella SlyA that are critical for transcriptional regulation

Okada

Takeda‐Shitaka

et al. 2007

Microbiology

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“…Modeling of nAChRs was carried out using the molecular modeling software package Sybyl, Automatic Modeling System, In-Silico Sciences, Inc., Tokyo, Japan), originally developed by Ogata and Umeyama [22]. The three dimensional structures of the nAChRs were constructed based on the sequence and coordinates of the standard protein, AChR (2BG9 [23]) by the simulated annealing method [24] according to Taly et al, 2006 [25].…”

Section: Computational Protein Modelling and Ivermectin Dockingmentioning

confidence: 99%

Comparative pharmacology and computational modelling yield insights into allosteric modulation of human α7 nicotinic acetylcholine receptors

Sattelle

Akamatsu²,

Matsuda³

et al. 2009

Biochemical Pharmacology

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“…2.0 (Protein Discovery Full Automatic Modeling System; In-Silico Sciences, Inc.; Tokyo, Japan), originally developed by Ogata and Umeyama 24) and Sybyl. Three nucleotide-free structures of mouse P-gp were available as template proteins; a protein without a ligand (PDB code: 3G5U) and complexes with two enantiomeric cyclic peptide P-gp inhibitors (PDB code: 3G60 with QZ59-RRR and 3G61 with QZ59-SSS).…”

Section: Protein Modeling and Dockingmentioning

confidence: 99%

Substrate recognition by P-glycoprotein efflux transporters: Structure-ATPase activity relationship of diverse chemicals and agrochemicals

et al. 2013

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P-glycoprotein (P-gp) is a member of the ATP-binding cassette transporter family. It actively transports a wide variety of compounds out of cells and functions as an energy-dependent efflux pump to protect humans from xenobiotics. P-gp also plays an important role in multidrug resistance in the treatment of cancers. However, the mechanism of P-gp substrate recognition is complicated and still poorly understood. In this study, we screened diverse chemicals, especially agrochemicals by measuring the ATPase activity of human P-gp and found that several classes of chemicals including dibenzoylhydrazine (DBH) insecticides could be substrates of P-gp. ATPase activity was quantitatively analyzed using a 3D quantitative structure-activity relationship, comparative molecular field analysis (CoMFA), and the favorable and unfavorable properties of ligands for ATPase activity were clarified. We also performed a docking simulation of a DBH-type compound with P-gp to predict the binding mode, which was supported by the CoMFA results.

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An automatic homology modeling method consisting of database searches and simulated annealing

Cited by 86 publications

References 33 publications

Identification of amino acid residues of Salmonella SlyA that are critical for transcriptional regulation

Identification of amino acid residues of Salmonella SlyA that are critical for transcriptional regulation

Comparative pharmacology and computational modelling yield insights into allosteric modulation of human α7 nicotinic acetylcholine receptors

Substrate recognition by P-glycoprotein efflux transporters: Structure-ATPase activity relationship of diverse chemicals and agrochemicals

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