title: Challenges within the linear response approximation when studying enzyme catalysis and effects of mutations.
abstract: Various aspects of the linear response approximation (LRA) approach were examined when calculating reaction barriers within an enzyme and its different mutants. Scaling the electrostatic interactions is shown to slightly affect the absolute values of the barriers but not the overall trend when comparing wild-type and mutants. Convergence of the overall energetics was shown to depend on the sampling. Finally, the contribution of particular residues was shown to be significant, despite its small value.
authors.affiliation: Institute for Drug Design, School of Pharmacy, The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem , Jerusalem 91120, Israel.
authors.forename: Avital
authors.initials: A
authors.lastname: Sharir-Ivry
authors.affiliation: Institute for Drug Design, School of Pharmacy, The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem , Jerusalem 91120, Israel.
authors.forename: Rajapandian
authors.initials: R
authors.lastname: Varatharaj
authors.affiliation: Institute for Drug Design, School of Pharmacy, The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem , Jerusalem 91120, Israel.
authors.forename: Avital
authors.initials: A
authors.lastname: Shurki
mesh_terms: D000438:Alcohols / Q000737:chemistry / Q000378:metabolism; D055162:Biocatalysis; D006846:Hydrocarbons, Halogenated / Q000737:chemistry / Q000378:metabolism; D006867:Hydrolases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D050505:Mutant Proteins / Q000378:metabolism*; D009154:Mutation; D011789:Quantum Theory; D055672:Static Electricity
chemical_list: D000438:Alcohols; D006846:Hydrocarbons, Halogenated; D050505:Mutant Proteins; D006867:Hydrolases; C046137:haloalkane dehalogenase