title: Insights into cellulase-lignin non-specific binding revealed by computational redesign of the surface of green fluorescent protein.
abstract: Biological-mediated conversion of pretreated lignocellulosic biomass to biofuels and biochemicals is a promising avenue toward energy sustainability. However, a critical impediment to the commercialization of cellulosic biofuel production is the high cost of cellulase enzymes needed to deconstruct biomass into fermentable sugars. One major factor driving cost is cellulase adsorption and inactivation in the presence of lignin, yet we currently have a poor understanding of the protein structure-function relationships driving this adsorption. In this work, we have systematically investigated the role of protein surface potential on lignin adsorption using a model monomeric fluorescent protein. We have designed and experimentally characterized 16 model protein variants spanning the physiological range of net charge (-24 to +16 total charges) and total charge density (0.28-0.40 charges per sequence length) typical for natural proteins. Protein designs were expressed, purified, and subjected to in silico and in vitro biophysical measurements to evaluate the relationship between protein surface potential and lignin adsorption properties. The designs were comparable to model fluorescent protein in terms of thermostability and heterologous expression yield, although the majority of the designs unexpectedly formed homodimers. Protein adsorption to lignin was studied at two different temperatures using Quartz Crystal Microbalance with Dissipation Monitoring and a subtractive mass balance assay. We found a weak correlation between protein net charge and protein-binding capacity to lignin. No other single characteristic, including apparent melting temperature and 2nd virial coefficient, showed correlation with lignin binding. Analysis of an unrelated cellulase dataset with mutations localized to a family I carbohydrate-binding module showed a similar correlation between net charge and lignin binding capacity. Overall, our study provides strategies to identify highly active, low lignin-binding cellulases by either rational design or by computational screening genomic databases. Biotechnol. Bioeng. 2017;114: 740-750. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, 48824.
authors.forename: Carolyn N
authors.initials: CN
authors.lastname: Haarmeyer
authors.affiliation: Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, 48824.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Smith
authors.affiliation: Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, Michigan.|Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey.
authors.forename: Shishir P S
authors.initials: SP
authors.lastname: Chundawat
authors.affiliation: Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado.
authors.forename: Deanne
authors.initials: D
authors.lastname: Sammond
authors.affiliation: Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, 48824.|Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, Michigan, 48824.
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Whitehead
mesh_terms: D018533:Biomass; D002480:Cellulase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D049452:Green Fluorescent Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008031:Lignin / Q000737:chemistry / Q000378:metabolism*; D009154:Mutation; D011485:Protein Binding; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D013499:Surface Properties
chemical_list: D049452:Green Fluorescent Proteins; D008031:Lignin; D002480:Cellulase
keywords: biomass deconstruction; cellulase; computational protein design; lignin; protein engineering