title: Sequence comparison, molecular modeling, and network analysis predict structural diversity in cysteine proteases from the Cape sundew, Drosera capensis.
abstract: Carnivorous plants represent a so far underexploited reservoir of novel proteases with potentially useful activities. Here we investigate 44 cysteine proteases from the Cape sundew, Drosera capensis, predicted from genomic DNA sequences. D. capensis has a large number of cysteine protease genes; analysis of their sequences reveals homologs of known plant proteases, some of which are predicted to have novel properties. Many functionally significant sequence and structural features are observed, including targeting signals and occluding loops. Several of the proteases contain a new type of granulin domain. Although active site residues are conserved, the sequence identity of these proteases to known proteins is moderate to low; therefore, comparative modeling with all-atom refinement and subsequent atomistic MD-simulation is used to predict their 3D structures. The structure prediction data, as well as analysis of protein structure networks, suggest multifarious variations on the papain-like cysteine protease structural theme. This in silico methodology provides a general framework for investigating a large pool of sequences that are potentially useful for biotechnology applications, enabling informed choices about which proteins to investigate in the laboratory.
authors.affiliation: Department of Sociology, UC Irvine, USA; Department of Sociology, UC Irvine, USA; Department of Electrical Engineering and Computer Science, UC Irvine, USA.
authors.forename: Carter T
authors.initials: CT
authors.lastname: Butts
authors.affiliation: Department of Sociology, UC Irvine, USA.
authors.forename: Xuhong
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Chemistry, UC Irvine, USA.
authors.forename: John E
authors.initials: JE
authors.lastname: Kelly
authors.affiliation: Department of Chemistry, UC Irvine, USA.
authors.forename: Kyle W
authors.initials: KW
authors.lastname: Roskamp
authors.affiliation: Department of Chemistry, UC Irvine, USA.
authors.forename: Megha H
authors.initials: MH
authors.lastname: Unhelkar
authors.affiliation: Department of Chemistry, UC Irvine, USA.
authors.forename: J Alfredo
authors.initials: JA
authors.lastname: Freites
authors.affiliation: Department of Chemistry, UC Irvine, USA.
authors.forename: Seemal
authors.initials: S
authors.lastname: Tahir
authors.affiliation: Department of Chemistry, UC Irvine, USA; Department of Molecular Biology & Biochemistry, UC Irvine, Irvine, CA, 92697 USA.
authors.forename: Rachel W
authors.initials: RW
authors.lastname: Martin
keywords: Carnivorous plant; Cysteine protease; Digestive enzyme; In silico maturation; Molecular dynamics; Protein sequence analysis; Protein structure network; Protein structure prediction; Rosetta