title: Molecular simulations provide new insights into the role of the accessory immunoglobulin-like domain of Cel9A.
abstract: Cel9A from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius belongs to the subfamily E1 of family 9 glycoside hydrolases, many members of which have an N-terminal Ig-like domain followed by the catalytic domain. The Ig-like domain is not directly involved in either carbohydrate binding or biocatalysis; however, deletion of the Ig-domain promotes loss of enzymatic activity. We have investigated the functional role of the Ig-like domain using molecular dynamics simulations. Our simulations indicate that residues within the Ig-like domain are dynamically correlated with residues in the carbohydrate-binding pocket and with key catalytic residues of Cel9A. Free energy perturbation simulations indicate that the Ig-like domain stabilizes the catalytic domain and may be responsible for the enhanced thermostability of Cel9A.
authors.affiliation: Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.
authors.forename: Hanbin
authors.initials: H
authors.lastname: Liu
authors.forename: Jose Henrique
authors.initials: JH
authors.lastname: Pereira
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
authors.forename: Rajat
authors.initials: R
authors.lastname: Sapra
authors.forename: Blake A
authors.initials: BA
authors.lastname: Simmons
authors.forename: Kenneth L
authors.initials: KL
authors.lastname: Sale
mesh_terms: D056450:Alicyclobacillus / Q000378:metabolism*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D055162:Biocatalysis; D018360:Crystallography, X-Ray; D006868:Hydrolysis; D007136:Immunoglobulins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D007136:Immunoglobulins; D050505:Mutant Proteins