Protein structure networks provide insight into active site flexibility in esterase/lipases from the carnivorous plant Drosera capensis

• Published in: Integrative biology (Cambridge) Vol. 10; no. 12; pp. 768 - 779
• Main Authors: Duong, Vy T, Unhelkar, Megha H, Kelly, John E, Kim, Suhn H, Butts, Carter T, Martin, Rachel W
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 19-12-2018
• Subjects: Algorithms; Catalysis; Catalytic Domain; Chemical synthesis; Cluster Analysis; Computational Biology; Conserved sequence; Drosera; Drosera - enzymology; Drought; Enzymatic activity; Enzyme activity; Enzymes; Esterase; Esterases - chemistry; Flexibility; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Genome, Plant; Genomes; Lipase - chemistry; Models, Molecular; Molecular modelling; Molecular structure; Networks; Organic chemistry; Plant Leaves - enzymology; Plant Proteins - chemistry; Protein Conformation; Protein structure; Proteins; Software; Substrate Specificity; Substrates; Transcriptome; Transesterification
• ISSN: 1757-9694; 1757-9708
• DOI: 10.1039/c8ib00140e

In plants, esterase/lipases perform transesterification reactions, playing an important role in the synthesis of useful molecules, such as those comprising the waxy coatings of leaf surfaces. Plant genomes and transcriptomes have provided a wealth of data about expression patterns and the circumstances under which these enzymes are upregulated, e.g. pathogen defense and response to drought; however, predicting their functional characteristics from genomic or transcriptome data is challenging due to weak sequence conservation among the diverse members of this group. Although functional sequence blocks mediating enzyme activity have been identified, progress to date has been hampered by the paucity of information on the structural relationships among these regions and how they affect substrate specificity. Here we present methodology for predicting overall protein flexibility and active site flexibility based on molecular modeling and analysis of protein structure networks (PSNs). We define two new types of specialized PSNs: sequence region networks (SRNs) and active site networks (ASNs), which provide parsimonious representations of molecular structure in reference to known features of interest. Our approach, intended as an aid to target selection for poorly characterized enzyme classes, is demonstrated for 26 previously uncharacterized esterase/lipases from the genome of the carnivorous plant Drosera capensis and validated using a case/control design. Analysis of the network relationships among functional blocks and among the chemical moieties making up the catalytic triad reveals potentially functionally significant differences that are not apparent from sequence analysis alone.