Kenji Mizuguchi

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. ncbi request reprint The common phospholipid-binding activity of the N-terminal domains of PEX1 and VCP/p97
    Kumiko Shiozawa
    International Graduate School of Arts and Sciences, Yokohama City University, 1 7 29 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    FEBS J 273:4959-71. 2006
  2. ncbi request reprint JOY: protein sequence-structure representation and analysis
    K Mizuguchi
    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
    Bioinformatics 14:617-23. 1998
  3. ncbi request reprint Analysis of conservation and substitutions of secondary structure elements within protein superfamilies
    K Mizuguchi
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Old Addenbrookes Site, Cambridge CB2 1GA, UK
    Bioinformatics 16:1111-9. 2000
  4. pmc Environment specific substitution tables for thermophilic proteins
    K Mizuguchi
    Department of Biochemistry, University of Cambridge, UK
    BMC Bioinformatics 8:S15. 2007
  5. ncbi request reprint [An informatic perspective on structural proteomics]
    Kenji Mizuguchi
    Department of Biochemistry, University of Cambridge
    Tanpakushitsu Kakusan Koso 47:1058-63. 2002
  6. ncbi request reprint The guanidino-group modifying enzymes: structural basis for their diversity and commonality
    Hiroki Shirai
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 64:1010-23. 2006
  7. pmc HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database
    Lucy A Stebbings
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    Nucleic Acids Res 32:D203-7. 2004
  8. ncbi request reprint Exploring ligand recognition and ion flow in comparative models of the human GABA type A receptor
    Younes Mokrab
    Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
    J Mol Graph Model 26:760-74. 2007
  9. ncbi request reprint Functional restraints on the patterns of amino acid substitutions: application to sequence-structure homology recognition
    Vijayalakshmi Chelliah
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 61:722-31. 2005
  10. doi request reprint A structural dissection of amino acid substitutions in helical transmembrane proteins
    Younes Mokrab
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 78:2895-907. 2010

Collaborators

Detail Information

Publications24

  1. ncbi request reprint The common phospholipid-binding activity of the N-terminal domains of PEX1 and VCP/p97
    Kumiko Shiozawa
    International Graduate School of Arts and Sciences, Yokohama City University, 1 7 29 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    FEBS J 273:4959-71. 2006
    ..By mutational analysis, we demonstrate that a conserved arginine surrounded by hydrophobic residues is essential for lipid binding, despite very low sequence similarity between PEX1 and valosine-containing protein...
  2. ncbi request reprint JOY: protein sequence-structure representation and analysis
    K Mizuguchi
    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
    Bioinformatics 14:617-23. 1998
    ..It was developed to display 3D structural information in a sequence alignment and to help understand the conservation of amino acids in their specific local environments...
  3. ncbi request reprint Analysis of conservation and substitutions of secondary structure elements within protein superfamilies
    K Mizuguchi
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Old Addenbrookes Site, Cambridge CB2 1GA, UK
    Bioinformatics 16:1111-9. 2000
    ....
  4. pmc Environment specific substitution tables for thermophilic proteins
    K Mizuguchi
    Department of Biochemistry, University of Cambridge, UK
    BMC Bioinformatics 8:S15. 2007
    ....
  5. ncbi request reprint [An informatic perspective on structural proteomics]
    Kenji Mizuguchi
    Department of Biochemistry, University of Cambridge
    Tanpakushitsu Kakusan Koso 47:1058-63. 2002
  6. ncbi request reprint The guanidino-group modifying enzymes: structural basis for their diversity and commonality
    Hiroki Shirai
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 64:1010-23. 2006
    ..These findings will be useful for predicting the precise mechanism of action for potential novel targets and designing therapeutic compounds against them...
  7. pmc HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database
    Lucy A Stebbings
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    Nucleic Acids Res 32:D203-7. 2004
    ..Altogether, this makes HOMSTRAD and its new BETA version, an excellent resource both for comparative modelling and for identifying distant sequence/structure similarities between proteins...
  8. ncbi request reprint Exploring ligand recognition and ion flow in comparative models of the human GABA type A receptor
    Younes Mokrab
    Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
    J Mol Graph Model 26:760-74. 2007
    ....
  9. ncbi request reprint Functional restraints on the patterns of amino acid substitutions: application to sequence-structure homology recognition
    Vijayalakshmi Chelliah
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 61:722-31. 2005
    ..02, according to the Wilcoxon signed rank test for alignment accuracy). The alignments near the active site are greatly improved with pronounced improvements at lower percentage identities (less than 30%)...
  10. doi request reprint A structural dissection of amino acid substitutions in helical transmembrane proteins
    Younes Mokrab
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 78:2895-907. 2010
    ....
  11. ncbi request reprint A novel mechanism of allosteric regulation of archaeal phosphoenolpyruvate carboxylase: a combined approach to structure-based alignment and model assessment
    Hiroyoshi Matsumura
    Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
    Protein Eng Des Sel 19:409-19. 2006
    ..Our novel observations will help design more efficient molecules for ecological and industrial use...
  12. ncbi request reprint A model of a transmembrane drug-efflux pump from Gram-negative bacteria
    Juan Fernandez-Recio
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    FEBS Lett 578:5-9. 2004
    ..coli, and for the AcrA homologue MexA from Pseudomonas aeruginosa. Based on homology modelling and molecular docking, we show how AcrA, AcrB and TolC might assemble to form a tripartite pump, and how allostery may occur during transport...
  13. doi request reprint Docking of cytochrome c6 and plastocyanin to the aa3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum
    Sarah E Hart
    Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW
    Protein Eng Des Sel 21:689-98. 2008
    ..laminosum (e.g. plastocyanin or cytochrome c(6) with cytochrome f and photosystem I)...
  14. doi request reprint Lipophobicity and the residue environments of the transmembrane alpha-helical bundle
    Younes Mokrab
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 74:32-49. 2009
    ..These results provided a coherent description of lipophobicity in the distinct layers of the membrane and gave clarity to the widely discussed notion of whether membrane proteins can be regarded as "inside out" of globular proteins...
  15. pmc Distinct protein interfaces in transmembrane domains suggest an in vivo folding model
    Timothy J Stevens
    Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    Protein Sci 13:3028-37. 2004
    ..The model takes into account the different interfaces of membrane helices defined herein, and the available data regarding folding in the translocation channel...
  16. ncbi request reprint Prediction of the structure and function of AstA and AstB, the first two enzymes of the arginine succinyltransferase pathway of arginine catabolism
    Hiroki Shirai
    Department of Biochemistry, University of Cambridge, Old Addenbrooks Site, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
    FEBS Lett 555:505-10. 2003
    ..These findings shed light on the structures, catalytic mechanisms and evolution of diverse enzymes involved in arginine catabolism...
  17. ncbi request reprint The SWIB and the MDM2 domains are homologous and share a common fold
    Riccardo Bennett-Lovsey
    Department of Biochemistry, University of Cambridge, Old Addenbrookes Site, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    Bioinformatics 18:626-30. 2002
    ..The homology suggests that the SWIB domain would adopt a structure similar to that of the MDM2 domain and that these two families of proteins may share a similar functional mechanism...
  18. pmc Identification and classification of bacterial Type III toxin-antitoxin systems encoded in chromosomal and plasmid genomes
    Tim R Blower
    Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
    Nucleic Acids Res 40:6158-73. 2012
    ..This study shows that active Type III toxin-antitoxin systems are far more diverse than previously known, and suggests that more remain to be identified...
  19. pmc FlyMine: an integrated database for Drosophila and Anopheles genomics
    Rachel Lyne
    Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
    Genome Biol 8:R129. 2007
    ..It provides web access to integrated data at a number of different levels, from simple browsing to construction of complex queries, which can be executed on either single items or lists...
  20. ncbi request reprint Organic anion transporting polypeptides of the OATP/SLCO superfamily: identification of new members in nonmammalian species, comparative modeling and a potential transport mode
    Fabienne Meier-Abt
    Department of Biochemistry, University of Cambridge, Old Addenbrookes Site, 80 Tennis Court Road, Cambridge, CB1 1GA, United Kingdom
    J Membr Biol 208:213-27. 2005
    ..Several amino acid residues were identified that may play crucial roles in the proposed transport mechanism...
  21. pmc Structure of the periplasmic domain of Pseudomonas aeruginosa TolA: evidence for an evolutionary relationship with the TonB transporter protein
    Michael Witty
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    EMBO J 21:4207-18. 2002
    ..aeruginosa TolA is presented that may explain the inferred allosteric properties of members of the TolA family. The mechanisms of TolA-mediated entry of bateriophages in P.aeruginosa and E.coli are likely to be similar...
  22. pmc A phylogenomic profile of hemerythrins, the nonheme diiron binding respiratory proteins
    Xavier Bailly
    Station Biologique de Roscoff, 29680, Roscoff, France
    BMC Evol Biol 8:244. 2008
    ..Hemerythrins, are the non-heme, diiron binding respiratory proteins of brachiopods, priapulids and sipunculans; they are also found in annelids and bacteria, where their functions have not been fully elucidated...
  23. ncbi request reprint A model of globin evolution
    Serge N Vinogradov
    Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Gene 398:132-42. 2007
    ..The last stage encompassed the lateral gene transfers of some members of the three globin lineages to specific groups of Archaea and Eukaryotes...
  24. ncbi request reprint The export of coat protein from enteroaggregative Escherichia coli by a specific ATP-binding cassette transporter system
    Junichiro Nishi
    Center for Vaccine Development, Departments of Pediatrics, Medicine, and Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    J Biol Chem 278:45680-9. 2003
    ..We propose that the aat cluster encodes a specialized ABC transporter, which plays a role in the pathogenesis of EAEC by transporting dispersin out of the bacterial cell...