frantom
  • 3097E Shelby Hall
  • (205) 348-8349
  • (205) 348-9104
Patrick A. Frantom
Assistant Professor
Education: Undergraduate Degree

BS, 1999, Louisiana State University

Education: Doctoral Degree

Ph.D., 2005, Texas A&M University

Education: Other

Postdoctoral Fellow 2005-2009, Albert Einstein College of Medicine

Research Interests

Work in the Frantom group is focused on the field of mechanistic enzymology. In broad terms, mechanistic enzymologists seek a chemical understanding of how enzymes are able to dramatically increase reaction rates, perform unique and stereospecific chemistry, and provide mechanisms for regulation using a limited toolbox consisting of 20 amino acids and various cofactors. In order to answer these types of questions, we utilize a wide array of genetic, biochemical, bioinformatics, biophysical, kinetic, and spectroscopic techniques. Current projects include the following:

1. Investigating Mechanisms of Regulatory and Functional Diversity in an Enzyme Superfamily (funded by NSF CAREER Award MCB-1254077)

As a long-term research goal, the Frantom laboratory looks to understand how allosteric and catalytic mechanisms evolve and work together in multi-domain enzymes. Advances in understanding the dynamic nature of enzymes have identified networks of amino acids involved in inter-domain communication in allosteric systems failing to exhibit large structural changes upon effector binding. However, the underlying mechanisms are not well understood at the molecular level. This lack of understanding creates a major stumbling block for the manipulation of allosterically regulated enzymes, such as engineered biosensors, through modular design methods. Our approach to this problem utilizes “genomic enzymology” where mechanistic enzymology, used to identify mechanisms of catalysis and regulation, is integrated with cutting-edge bioinformatics techniques to identify patterns of evolution within an enzyme superfamily. The DRE-TIM metallolyase superfamily serves as a model system for this project due to its diversity of functions involving the making and breaking of C-C bonds and the allosterically regulated subgroup of Claisen-condensation-like enzymes including α-isopropylmalate synthase (IPMS) and citramalate synthase (CMS). Recent work has focused on comparing mechanisms of allostery and substrate selectivity in evolutionarily distinct IPMS and CMS enzymes. Future projects include functional annotation of enzymes of unknown function in the DRE-TIM metallolyase superfamily, identifying mechanisms of functional evolution between subgroups of the superfamily, and using directed evolution approaches to engineer enzymes with novel C-C bond making and breaking abilities.

2. Investigating Mechanisms of Functional and Catalytic Diversity in Glycosyltransferases

The target of this project is a large class of enzymes called glycosyltransferases (GT). This class of enzymes catalyzes the transferof a sugar molecule (such as glucose) from a nucleotide donor (NDP) to either oxygen or nitrogen atoms in various acceptor molecules including proteins, nucleic acids, lipids, and small molecules. This reaction is involved in many cellular processes such as bacterial cell wall biosynthesis and the cell’s ability to sense its environment. Despite the variety of acceptor molecules, the 3D structures of all GT enzymes to date (nearly 800 individual structures) fall into one of two structures, termed GT-A and GT-B. The GT-A motif is characterized by two independent globular domains in compact association. In contrast, the GT-B motif is more extended and composed of two domains connected by a small linker region. The chemical reaction takes place at the interface of the two domains in both structures. As the two structures are strongly conserved despite the diversity of substrates, we hypothesize that there are regions of the structure critical to function in this class of enzymes. This project integrates biochemical, structural, and bioinformatics approaches to identify structure/function relationships in this enzyme class. Recently, in conjunction with the Busenlehner laboratory, we utilized backbone amide hydrogen/deuterium exchange to identify regions of both GT-A and GT-B enzymes that undergo changes in flexibility upon substrate binding. In the future we will apply bioinformatics and biochemical approaches to investigate if areas with differences in flexibility are evolutionarily conserved and determine their contribution to catalysis. Results from these studies may support the development of novel inhibitors against this important class of enzymes.

Representative Publications

“Evolutionarily Distinct Versions of the Multi-domain Enzyme α-Isopropylmalate Synthase Share Distinct Mechanisms of V-type Allosteric Regulation” Kumar, G. and Frantom, P.A. Biochemistry, in press.

“Mechanistic and Bioinformatic Investigation of a Conserved Active Site Helix in is α-Isopropylmalate Synthase from Mycobacterium tuberculosis, a Member of the DRE-TIM Metallolyase Superfamily” Casey, A.K.; Hicks, M.A.; Johnson, J.L.; Babbitt, P.C.; and Frantom, P.A. Biochemistry 2014, 53, 2915-2925.

“V-type Allosteric Inhibition is Described by a Shift in the Rate-Determining Step for α-Isopropylmalate Synthase from Mycobacterium tuberculosis” Casey, A.K.; Schwalm, E. L.; Hays, B.N.; Frantom, P.A. Biochemistry 2013, 52, 6737-6739.

“The Slow-Onset Nature of Allosteric Inhibition in α-Isopropylmalate Synthase from Mycobacterium tuberculosis is Mediated by a Flexible Loop.” Casey, A. K.; Baugh, J.; and Frantom, P. A. Biochemistry 2012, 51, 4773-4775.

“Structural and Functional Characterization of α-Isopropylmalate Synthase and Citramalate Synthase, members of the LeuA dimer superfamily.” Frantom, P. A.Arch. Bioch. Biophys. 2012, 519, 202-209.

“UDP-(5F)-GlcNAc acts as a slow-binding inhibitor of MshA, a retaining glycosyltransferase.” Frantom, P. A.; Coward, J. K.; and Blanchard, J. S., Journal of the American Chemical Society, 2010, 132, 6626–6627.