Biomedical subjects

Mayuko Takeda-Shitaka

Publications and source records attributed to Mayuko Takeda-Shitaka.

12 recordsLinked to original sources

PubMed2006

FAMS complex: a fully automated homology modeling system for protein complex structures.

The formation of a protein-protein complex is responsible for many biological functions; therefore, three-dimensional structures of protein complexes are essential for deeper understandings of protein functions and the mechanisms of diseases at the atomic level. However, compared with individual proteins, complex structures are difficult to solve experimentally because of technical limitations. Thus a method that can predict protein complex structures would be invaluable. In this study, we developed new software, FAMS Complex; a fully automated homology modeling system for protein complex structures consisting of two or more molecules. FAMS Complex requires only sequences and alignments of the target protein as input and constructs all molecules simultaneously and automatically. FAMS Complex is likely to become an essential tool for structure-based drug design, such as in silico screening to accelerate drug discovery before an experimental structure is solved. Moreover, in this post-genomic era when huge amounts of protein sequence information are available, a major goal is the determination of protein-protein interaction networks on a genomic scale. FAMS Complex will contribute to this goal, because its procedure is fully automated and so is suited for large-scale genome wide modeling.

Automation↗

PubMed2005

Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues.

In CAPRI Rounds 1 and 2, we assumed that because there are many ionic charges that weaken electrostatic interaction forces in living cells, the hydrophobic interaction force might be important entropically. As a result of Rounds 1 and 2, the predictions for binding sites and geometric centers were acceptable, but those of the binding axes were poor, because only the largest benzene cluster was used for generating the initial docking structures. These were generated by fitting of benzene clusters formed on the surface of receptor and ligand. In CAPRI Rounds 3-5, the grid-scoring sum on the protein-protein interaction surface and the pairwise potential of the amino acid residues, which were indicated as coming easily into the protein-protein interaction regions, were used as the calculation methods, along with the smaller benzene clusters that participated in benzene cluster fitting. Good predicted models were obtained for Targets 11 and 12. When the modeled receptor proteins were superimposed on the experimental structures, the smallest ligand root-mean-square deviation (RMSD) values corresponding to the RMSD between the model and experimental structures were 6.2 A and 7.3 A, respectively.

Algorithms↗

PubMed2005

Protein structure prediction in CASP6 using CHIMERA and FAMS.

In CASP6, the CHIMERA-group predicted full-atom models of all targets using SKE-CHIMERA, a Web-user interface system for protein structure prediction that allows human intervention at necessary stages; we used a lot of information from our own data and from publicly available data. Using SKE-CHIMERA, we iterated manual step (template selection and alignment by the in-house program CHIMERA) and automatic step (three-dimensional model building by the in-house program FAMS). The official CASP6 assessment showed that CHIMERA-group was one of the most successful predictors in homology modeling, especially for FR/H (Fold Recognition/Homologous). In this article, we introduce the method of CHIMERA-group and discuss its successes and failures in CASP6.

Algorithms↗

PubMed2004

Remarkably different structures and reaction mechanisms of ketoreductases for the opposite stereochemical control in the biosynthesis of BIQ antibiotics.

Two ketoreductases, RED1 and RED2, are involved in the biosynthesis of actinorhodin in Streptomyces coelicolor A3(2) and dihydrogranaticin in S. violaceoruber Tu22, respectively. They are responsible for the stereospecific reductions of the bicyclic intermediate to give (S)- or (R)-DNPA, although there is no similarity between their amino acid sequences. Biotransformation using synthetic analogous substrates revealed that the substrate specificities are quite different. Homology modelling studies and site directed mutagenesis showed remarkable differences in three-dimensional structures and catalytic mechanisms between RED1 and RED2.

Alcohol Oxidoreductases↗

PubMed2004

Evaluation of homology modeling of the severe acute respiratory syndrome (SARS) coronavirus main protease for structure based drug design.

To accelerate the development of drugs against severe acute respiratory syndrome (SARS), we constructed a homology model of the SARS coronavirus main protease using our modeling software, FAMS Ligand&Complex, and released it before the X-ray structure was solved. The X-ray structure showed our model as accurately predicted and useful for structure based drug design.

Antiviral Agents↗

PubMed2004

Protein structure prediction in structure based drug design.

The human genome and other genome sequencing projects have generated huge amounts of protein sequence information. Recently, a structural genomics project that aims to determine at least one representative three-dimensional structure from every protein family experimentally has been started. Homology modeling will play an essential role in structure based drug design such as in silico screening; because based on these representative structures the three-dimensional structures of the remaining proteins encoded in the various genomes can be predicted by homology modeling. The results of the last Critical Assessment of Techniques for Protein Structure Prediction (CASP5) demonstrated that the quality of homology modeling prediction has improved; reaching a level of reliability that biologists can now confidently use homology modeling. With improvements in modeling software and the growing number of known protein structures, homology modeling is becoming a more and more powerful and reliable tool. The present paper discusses the features and roles of homology modeling in structure based drug design, and describes the CHIMERA and FAMS modeling systems as examples. For a sample application, homology modeling of non-structural proteins of the severe acute respiratory syndrome (SARS) coronavirus is discussed. Many biological functions involve formation of protein-protein complexes; in which the protein molecules behave dynamically in the course of binding. Therefore, an understanding of protein-protein interaction will be very important for structure based drug design. To this end, normal mode analysis is useful. The present paper discusses the prediction of protein-protein interaction using normal mode analysis and examples of applications are given.

Amino Acid Sequence↗

PubMed2003

Molecular characterization of ADAMTS13 gene mutations in Japanese patients with Upshaw-Schulman syndrome.

We report here 7 new mutations in the ADAMTS13 gene responsible for Upshaw-Schulman syndrome (USS), a catastrophic phenotype of congenital thrombotic thrombocytopenic purpura, by analyzing 5 Japanese families. There were 3 mutations that occurred at exon-intron boundaries: 414+1G>A at intron 4, 686+1G>A at intron 6, and 1244+2T>G at intron 10 (numbered from the A of the initiation Met codon), and we confirmed that 2 of these mutations produced aberrantly spliced messenger RNAs (mRNAs). The remaining 4 mutations were missense mutations: R193W, I673F, C908Y, and R1123C. In expression experiments using HeLa cells, all mutants showed no or a marginal secretion of ADAMTS13. Taken together with the findings in our recent report we determined the responsible mutations in a total of 7 Japanese patients with USS with a uniform clinical picture of severe neonatal hyperbilirubinemia, and in their family members, based on ADAMTS13 gene analysis. Of these patients, 2 were homozygotes and 5 were compound heterozygotes. The parents of one homozygote were related (cousins), while those of the other were not. Molecular models of the metalloprotease, fifth domain of thrombospondin 1 (Tsp1-5), and Tsp1-8 domains of ADAMTS13 suggest that the missense mutations could cause structural defects in the mutants.

ADAM Proteins↗

PubMed2003

Evaluation of the third solvent clusters fitting procedure for the prediction of protein-protein interactions based on the results at the CAPRI blind docking study.

To predict protein-protein interactions, rough or coarse handling for the induced fit problem is proposed. Our method involves the overlap of two hydrophobic interactions as "third solvent clusters fitting." Predictions for binding sites and geometric centers were acceptable, but those of the binding axes were poor. In this study, only the largest benzene cluster was used for the third solvent clusters fitting. For the next CAPRI targets, we must perform protein-protein interaction analyses, which include other smaller benzene clusters.

Benzene↗

PubMed2003

Interaction between the antigen and antibody is controlled by the constant domains: normal mode dynamics of the HEL-HyHEL-10 complex.

The antigen binding fragment (Fab) of a monoclonal antibody (HyHEL-10) consists of variable domains (Fv) and constant domains (CL-CH1). Normal modes have been calculated from the three-dimensional structures of hen egg lysozyme (HEL) with Fab, those of HEL with Fv, and so on. Only a small structural change was found between HEL-Fab and HEL-Fv complexes. However, HEL-Fv had a one order of magnitude lower dissociation constant than HEL-Fab. The Calpha fluctuations of HEL-Fab differed from those of HEL-Fv with normal mode calculation, and the dynamics can be thought to be related to the protein-protein interactions. CL-CH1 may have influence not only around local interfaces between CL-CH1 and Fv, but also around the interacting regions between HEL and Fv, which are longitudinally distant. Eighteen water molecules were found in HEL-Fv around the interface between HEL and Fv compared with one water molecule in HEL-Fab. These solvent molecules may occupy the holes and channels, which may occur due to imperfect complementarity of the complex. Therefore, the suppression of atomic vibration around the interface between Fv and HEL can be thought to be related to favorable and compact interface formation by complete desolvation. It is suggested that the ability to control the antigen-antibody affinity is obtained from modifying the CL-CH1. The second upper loop in the constant domain of the light chain (UL2-CL), which is a conserved gene in several light chains, showed the most remarkable fluctuation changes. UL2-CL could play an important role and could be attractive for modification in protein engineering.

Animals↗

PubMed2003

Dynamic character of human growth hormone and its receptor: normal mode analysis.

Human growth hormone (hGH) induces dimerization of its binding protein (hGHbp). hGH binds to the first hGHbp (bp1) on site 1, and then the hGH-bp1 heterodimer complex binds to the second hGHbp (bp2) on site 2. Although the interactions of hGH and hGHbps have been studied from different viewpoints, few studies from a dynamic viewpoint have been reported. Especially, since in the SCOP domain database hGHbp is classified as two clear immunoglobulin-like domains, it is of interest to understand how hGH interacts with the hGHbp domains. Therefore, we carried out normal mode analysis (NMA) of free hGH, free bp1, free bp2, and the hGH-bp1 heterodimer complex, as well as the hGH-bp1-bp2 ternary complex to investigate how the dynamics of the proteins change before and after forming the complexes. NMA showed that the domain motion between the N-terminal and the C-terminal domains of free bp1 markedly decreased after binding to hGH, and that the domain motion of bp2 decreased similarly after binding to the hGH-bp1 heterodimer complex. The present study demonstrates that hGH regulates the inter-domain motions of both hGHbps.

Human Growth Hormone↗

PubMed2003

Dynamic flexibility of a peptide-binding groove of human HLA-DR1 class II MHC molecules: normal mode analysis of the antigen peptide-class II MHC complex.

Class II major histocompatibility complex (MHC) has tolerance for binding longer antigen peptides than those bound by class I MHC. In this paper, a normal mode analysis on HLA-DR1 class II MHC involving an antigen peptide indicated that the peptide-binding groove had some different dynamic characteristics from that of HLA-A2 class I MHC. The dynamic changes in the class I groove with removal of the bound peptide were limited primarily to the central region and the C-terminal side (corresponding to the C-terminal side of the bound peptide) of the groove, while the dynamic changes in the class II groove with removal of the bound peptide extended to the whole of the groove, and were especially remarkable around a strand located in the N-terminal side (corresponding to the N-terminal side of the bound peptide) of the groove. These results suggest that the N-terminal side of the class II groove is more flexible than the same side of the class I groove, and this flexibility may allow some N-terminal residues of the bound peptide to extend outside the class II groove. Definite anti-correlative motions with removal of the bound peptide appeared between two alpha-helical regions of class II MHC as in the case of class I MHC. These motions of the class II groove may play an important role in obtaining "a flexible dynamic fit" against diverse longer peptides both of whose terminals extend outside the groove.

Binding Sites↗

PubMed2002

Dynamic characteristics of a peptide-binding groove of human HLA-A2 class I MHC molecules: normal mode analysis of the antigen peptide-class I MHC complex.

Class I major histocompatibility complex (MHC) binds antigen peptides with various sequences. We performed a normal mode analysis of HLA-A2 MHC that binds three peptides with different affinity. HLA-A2 MHC has a peptide-binding groove composed of two alpha-helices (residue 49-84, residue 140-179). Some residues in the center of the groove showed an increase in fluctuations and some residue pairs between two helix groups showed a negative change in correlations by removing the antigen peptide. The extent of the fluctuation and correlation changes correlated well with the experimental ranking of the three peptides in binding affinity. Some definite anti-correlative motions were found between two helix groups in low frequency modes (<50 cm(-1)) by removing the antigen peptide. We propose that the above anti-correlative motions play an important role to bind the antigen peptide, especially in obtaining a "dynamic fit."

Crystallography, X-Ray↗