Pomes R

References (2)

Title : Substrate-Based Allosteric Regulation of a Homodimeric Enzyme - Mehrabi_2019_J.Am.Chem.Soc_141_11540
Author(s) : Mehrabi P , Di Pietrantonio C , Kim TH , Sljoka A , Taverner K , Ing C , Kruglyak N , Pomes R , Pai EF , Prosser RS
Ref : Journal of the American Chemical Society , 141 :11540 , 2019
Abstract : Many enzymes operate through half-of-the sites reactivity wherein a single protomer is catalytically engaged at one time. In the case of the homodimeric enzyme, fluoroacetate dehalogenase, substrate binding triggers closing of a regulatory cap domain in the empty protomer, preventing substrate access to the remaining active site. However, the empty protomer serves a critical role by acquiring more disorder upon substrate binding, thereby entropically favoring the forward reaction. Empty protomer dynamics are also allosterically coupled to the bound protomer, driving conformational exchange at the active site and progress along the reaction coordinate. Here, we show that at high concentrations, a second substrate binds along the substrate-access channel of the occupied protomer, thereby dampening interprotomer dynamics and inhibiting catalysis. While a mutation (K152I) abrogates second site binding and removes inhibitory effects, it also precipitously lowers the maximum catalytic rate, implying a role for the allosteric pocket at low substrate concentrations, where only a single substrate engages the enzyme at one time. We show that this outer pocket first desolvates the substrate, whereupon it is deposited in the active site. Substrate binding to the active site then triggers the empty outer pocket to serve as an interprotomer allosteric conduit, enabling enhanced dynamics and sampling of activation states needed for catalysis. These allosteric networks and the ensuing changes resulting from second substrate binding are delineated using rigidity-based allosteric transmission theory and validated by nuclear magnetic resonance and functional studies. The results illustrate the role of dynamics along allosteric networks in facilitating function.
ESTHER : Mehrabi_2019_J.Am.Chem.Soc_141_11540
PubMedSearch : Mehrabi_2019_J.Am.Chem.Soc_141_11540
PubMedID: 31188575
Gene_locus related to this paper: rhopa-q6nam1

Title : The role of dimer asymmetry and protomer dynamics in enzyme catalysis - Kim_2017_Science_355_
Author(s) : Kim TH , Mehrabi P , Ren Z , Sljoka A , Ing C , Bezginov A , Ye L , Pomes R , Prosser RS , Pai EF
Ref : Science , 355 : , 2017
Abstract : Freeze-trapping x-ray crystallography, nuclear magnetic resonance, and computational techniques reveal the distribution of states and their interconversion rates along the reaction pathway of a bacterial homodimeric enzyme, fluoroacetate dehalogenase (FAcD). The crystal structure of apo-FAcD exhibits asymmetry around the dimer interface and cap domain, priming one protomer for substrate binding. This asymmetry is dynamically averaged through conformational exchange on a millisecond time scale. During catalysis, the protomer conformational exchange rate becomes enhanced, the empty protomer exhibits increased local disorder, and water egresses. Computational studies identify allosteric pathways between protomers. Water release and enhanced dynamics associated with catalysis compensate for entropic losses from substrate binding while facilitating sampling of the transition state. The studies provide insights into how substrate-coupled allosteric modulation of structure and dynamics facilitates catalysis in a homodimeric enzyme.
ESTHER : Kim_2017_Science_355_
PubMedSearch : Kim_2017_Science_355_
PubMedID: 28104837
Gene_locus related to this paper: rhopa-q6nam1