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Article

Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics

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Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA
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Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
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Department of Experimental and Clinical Pharmacology, College Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
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Department of Chemistry, University of Minnesota, Minneapolis, Minneapolis, MN 55455, USA
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Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
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Department of Integrative Biology and Physiology, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
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Authors to whom correspondence should be addressed.
Academic Editor: Joseph P. Albanesi
Int. J. Mol. Sci. 2021, 22(9), 4619; https://doi.org/10.3390/ijms22094619
Received: 6 April 2021 / Revised: 23 April 2021 / Accepted: 26 April 2021 / Published: 28 April 2021
(This article belongs to the Section Macromolecules)
It has long been understood that some proteins undergo conformational transitions en route to the Michaelis Complex to allow chemistry. Examination of crystal structures of glycosyltransferase enzymes in the GT-B structural class reveals that the presence of ligand in the active site triggers an open-to-closed conformation transition, necessary for their catalytic functions. Herein, we describe microsecond molecular dynamics simulations of two distantly related glycosyltransferases that are part of the GT-B structural superfamily, HepI and GtfA. Simulations were performed using the open and closed conformations of these unbound proteins, respectively, and we sought to identify the major dynamical modes and communication networks that interconnect the open and closed structures. We provide the first reported evidence within the scope of our simulation parameters that the interconversion between open and closed conformations is a hierarchical multistep process which can be a conserved feature of enzymes of the same structural superfamily. Each of these motions involves of a collection of smaller molecular reorientations distributed across both domains, highlighting the complexities of protein dynamic involved in the interconversion process. Additionally, dynamic cross-correlation analysis was employed to explore the potential effect of distal residues on the catalytic efficiency of HepI. Multiple distal nonionizable residues of the C-terminal domain exhibit motions anticorrelated to positively charged residues in the active site in the N-terminal domain involved in substrate binding. Mutations of these residues resulted in a reduction in negatively correlated motions and an altered enzymatic efficiency that is dominated by lower Km values with kcat effectively unchanged. The findings suggest that residues with opposing conformational motions involved in the opening and closing of the bidomain HepI protein can allosterically alter the population and conformation of the “closed” state, essential to the formation of the Michaelis complex. The stabilization effects of these mutations likely equally influence the energetics of both the ground state and the transition state of the catalytic reaction, leading to the unaltered kcat. Our study provides new insights into the role of conformational dynamics in glycosyltransferase’s function and new modality to modulate enzymatic efficiency. View Full-Text
Keywords: GT; glycosyltransferase; HepI; heptosyltransferase I; heptose; L-glycero-d-manno-heptose; ADP-heptose or ADPH; ADP-L-glycero-D-manno-heptose; LPS; lipopolysaccharide; ODLA; O-deacylated E. coli Kdo2-lipid A; CD; circular dichroism; MD; molecular dynamics; PDB; Protein Data Bank; PCA; principal component analysis; DCC; dynamic cross-correlation GT; glycosyltransferase; HepI; heptosyltransferase I; heptose; L-glycero-d-manno-heptose; ADP-heptose or ADPH; ADP-L-glycero-D-manno-heptose; LPS; lipopolysaccharide; ODLA; O-deacylated E. coli Kdo2-lipid A; CD; circular dichroism; MD; molecular dynamics; PDB; Protein Data Bank; PCA; principal component analysis; DCC; dynamic cross-correlation
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MDPI and ACS Style

Ramirez-Mondragon, C.A.; Nguyen, M.E.; Milicaj, J.; Hassan, B.A.; Tucci, F.J.; Muthyala, R.; Gao, J.; Taylor, E.A.; Sham, Y.Y. Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics. Int. J. Mol. Sci. 2021, 22, 4619. https://doi.org/10.3390/ijms22094619

AMA Style

Ramirez-Mondragon CA, Nguyen ME, Milicaj J, Hassan BA, Tucci FJ, Muthyala R, Gao J, Taylor EA, Sham YY. Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics. International Journal of Molecular Sciences. 2021; 22(9):4619. https://doi.org/10.3390/ijms22094619

Chicago/Turabian Style

Ramirez-Mondragon, Carlos A., Megin E. Nguyen, Jozafina Milicaj, Bakar A. Hassan, Frank J. Tucci, Ramaiah Muthyala, Jiali Gao, Erika A. Taylor, and Yuk Y. Sham. 2021. "Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics" International Journal of Molecular Sciences 22, no. 9: 4619. https://doi.org/10.3390/ijms22094619

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