Modeling the Structures of Proteins and Protein Complexes

Kajava, Andrey V.

Abstract

Conformational features of polyglycine were evaluated. Polyglycine serves as a model of polypeptide backbones and several important biological structures (collagen, silk fibroin). A new structure of a polyglycine crystal has been determined based on molecular modeling and X-ray diffraction calculations. A paper was published. Performed amino acid sequence analysis of bacterial proteins having arrays of tandem repeats. Based on this analysis and molecular modeling, a beta-helix model was suggested for the filamentous hemagglutinin adhesin of Bordetella pertussis and related bacterial secretory proteins. A manuscript will be submitted for publication soon. Performed amino acid sequence analysis of signal peptides and regions adjacent to them in order to understand the mechanism of protein translocation across the cytoplasmic membrane. Established that the net charge of the first 18 residues of the mature sequence is essential for protein translocation of gram-negative bacteria. A manuscript will be submitted for publication soon. A short coiled-coil peptide with the potential to self-assemble into long fibrils has been designed, synthesized and analyzed. A manuscript is in preparation. - molecular modeling, protein structure, sequence analysis, tandem repeats

Funding Agency

• Agency: National Institute of Health (NIH)
• Institute: Center for Information Technology (CIT)
• Type: Intramural Research (Z01)
• Project #: 1Z01CT000259-04
• Application #: 6289569
• Study Section: Special Emphasis Panel (CMM)
• Support Year: 4
• Fiscal Year: 1999

Institution

• Name: Center for Information Technology
• Country: United States

Publications

Henry, L Keith; Field, Julie R; Adkins, Erika M et al. (2006) Tyr-95 and Ile-172 in transmembrane segments 1 and 3 of human serotonin transporters interact to establish high affinity recognition of antidepressants. J Biol Chem 281:2012-23

Kajava, Andrey V; Kobe, Bostjan (2002) Assessment of the ability to model proteins with leucine-rich repeats in light of the latest structural information. Protein Sci 11:1082-90

Kalinin, Andrey E; Kajava, Andrey V; Steinert, Peter M (2002) Epithelial barrier function: assembly and structural features of the cornified cell envelope. Bioessays 24:789-800

Terskikh, Alexey V; Fradkov, Arkady F; Zaraisky, Andrey G et al. (2002) Analysis of DsRed Mutants. Space around the fluorophore accelerates fluorescence development. J Biol Chem 277:7633-6

Kajava, A V; Cheng, N; Cleaver, R et al. (2001) Beta-helix model for the filamentous haemagglutinin adhesin of Bordetella pertussis and related bacterial secretory proteins. Mol Microbiol 42:279-92

Kobe, B; Kajava, A V (2001) The leucine-rich repeat as a protein recognition motif. Curr Opin Struct Biol 11:725-32

Kajava, A V (2001) Review: proteins with repeated sequence--structural prediction and modeling. J Struct Biol 134:132-44

Potekhin, S A; Melnik, T N; Popov, V et al. (2001) De novo design of fibrils made of short alpha-helical coiled coil peptides. Chem Biol 8:1025-32

Kajava, A V; Zolov, S N; Kalinin, A E et al. (2000) The net charge of the first 18 residues of the mature sequence affects protein translocation across the cytoplasmic membrane of gram-negative bacteria. J Bacteriol 182:2163-9

Simon-Nobbe, B; Probst, G; Kajava, A V et al. (2000) IgE-binding epitopes of enolases, a class of highly conserved fungal allergens. J Allergy Clin Immunol 106:887-95