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Structural comparison of the Arabidopsis thaliana family of β‐amylases
Author(s) -
Chandrasekharan Nithesh,
Monroe Jonathan,
Berndsen Christopher
Publication year - 2018
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.2018.32.1_supplement.792.12
Subject(s) - arabidopsis , arabidopsis thaliana , chemistry , biochemistry , molecular dynamics , homology modeling , enzyme , amino acid , hydrolysis , biophysics , biology , gene , computational chemistry , mutant
The β‐amylase (BAM) family in Arabidopsis thaliana has nine members, some of which are known to hydrolyze starch to maltose. The members of this family show unique functional, regulatory, and catalytic behaviors due to changes in sequence or domain composition. However, the molecular basis for functional specificity and regulation is not always clear. Some of the inactive members of the lack the catalytic amino acids required for hydrolysis. However, this is not the case for all the enzymes such as BAM2, which appears to be allosterically regulated and requires KCl for activity. Given the lack of structural information on any member of this protein family, we homology modeled all 9 BAM proteins from Arabidopsis and performed molecular dynamics simulations to propose how these proteins may differ at a functional level. All simulations were equilibrated for at least 50 ns in explicit solvent, the equilibrated models were aligned structurally, and then analyzed to compare the structure, dynamics, and chemical properties. All 9 proteins modeled well as TIM barrel proteins with most of the structural deviations occurring in predicted loops. Comparison of the simulated dynamics shows that overall the BAM proteins show similar areas of high and low motion. Interestingly, BAM4 and BAM9 showed fluctuation profiles that were distinct from the other BAM proteins, which matches their predicted lack of catalytic activity and distinct active site sequences. BAM7 and BAM8 which also have distinct active sites however these enzymes show dynamics similar to those of the catalytically active BAM1 and BAM3 suggesting that BAM7 and BAM8 may also have activity, however the proper conditions are not known. We further modeled BAM2 as a tetramer based on recent biochemical information to identify how allostery and solution conditions may influence the activity of this protein. We identified predicted changes in the dynamics upon binding to a ligand in the starch‐binding site as well as changes in hydrogen bonding within the protein in potassium. Both findings provide testable proposals for the regulation of BAM2 activity. Support or Funding Information This work was supported by a National Science Foundation Research at Undergraduate Institutions Grant MCB‐1616467 and National Science Foundation Research Experience for Undergraduates Grant CHE‐1461175 This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .