title: Structure prediction and network analysis of chitinases from the Cape sundew, Drosera capensis.
abstract: Carnivorous plants possess diverse sets of enzymes with novel functionalities applicable to biotechnology, proteomics, and bioanalytical research. Chitinases constitute an important class of such enzymes, with future applications including human-safe antifungal agents and pesticides. Here, we compare chitinases from the genome of the carnivorous plant Drosera capensis to those from related carnivorous plants and model organisms.
  
  
  
  Using comparative modeling, in silico maturation, and molecular dynamics simulation, we produce models of the mature enzymes in aqueous solution. We utilize network analytic techniques to identify similarities and differences in chitinase topology.
  
  
  
  Here, we report molecular models and functional predictions from protein structure networks for eleven new chitinases from D. capensis, including a novel class IV chitinase with two active domains. This architecture has previously been observed in microorganisms but not in plants. We use a combination of comparative and de novo structure prediction followed by molecular dynamics simulation to produce models of the mature forms of these proteins in aqueous solution. Protein structure network analysis of these and other plant chitinases reveal characteristic features of the two major chitinase families.
  
  
  
  This work demonstrates how computational techniques can facilitate quickly moving from raw sequence data to refined structural models and comparative analysis, and to select promising candidates for subsequent biochemical characterization. This capability is increasingly important given the large and growing body of data from high-throughput genome sequencing, which makes experimental characterization of every target impractical.
authors.affiliation: Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
authors.forename: Megha H
authors.initials: MH
authors.lastname: Unhelkar
authors.affiliation: Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA.
authors.forename: Vy T
authors.initials: VT
authors.lastname: Duong
authors.affiliation: Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA.
authors.forename: Kaosoluchi N
authors.initials: KN
authors.lastname: Enendu
authors.affiliation: Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
authors.forename: John E
authors.initials: JE
authors.lastname: Kelly
authors.affiliation: Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
authors.forename: Seemal
authors.initials: S
authors.lastname: Tahir
authors.affiliation: Department of Sociology, University of California, Irvine, Irvine, CA 92697, USA; Department of Electrical Engineering and Computer Science, University of California, Irvine, Irvine, CA 92697, USA; Department of Statistics, University of California, Irvine, CA 92697, USA. Electronic address: buttsc@uci.edu.
authors.forename: Carter T
authors.initials: CT
authors.lastname: Butts
authors.affiliation: Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA. Electronic address: rwmartin@uci.edu.
authors.forename: Rachel W
authors.initials: RW
authors.lastname: Martin
mesh_terms: D002688:Chitinases / Q000235:genetics* / Q000378:metabolism*; D029787:Drosera / Q000235:genetics* / Q000378:metabolism*; D018745:Genome, Plant / Q000235:genetics; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010802:Phylogeny; D000072417:Protein Domains / Q000235:genetics
chemical_list: D002688:Chitinases
keywords: Chitinase; In silico maturation; Molecular dynamics; Protein sequence analysis; Protein structure network; Protein structure prediction