Directory

Patrick A. Frantom

Patrick A. Frantom

Associate Professor

Education

  • Postdoctoral Fellow, Albert Einstein College of Medicine, 2005-2009
  • PhD, Texas A&M University, 2005
  • BS, Louisiana State University, 1999

Labs

  • Frantom Lab

Bio

Work in the Frantom group is focused on identifying structure/function relationships that govern the catalytic and regulatory properties of enzymes. In broad terms, we 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 techniques including enzyme kinetics, hydrogen/deuterium exchange mass spectrometry (HDX-MS), and bioinformatics sequence similarity networks. Current projects include the following:

1. Conformational Dynamics and Allosteric Regulation in the Suf Fe-S Cluster Biogenesis Pathway (funded by NIH R01-GM112919)

Fe-S clusters are essential enzyme cofactors in living organisms. Several conserved pathways have been identified that catalyze the formation of these clusters from cysteine-derived sulfur and iron atoms. Our work in this field focuses on the Suf Fe-S cluster biogenesis pathway. This pathway consists of six proteins (SufABCDSE) and is prevalent in bacteria, including many pathogenic species, making proteins in this pathway excellent targets for the development of new antibiotics. In Escherichia coli, the Suf systems acts as a stress-responsive system that is utilized in times of oxidative stress; in Mycobacterium tuberculosis the Suf system is the only pathway for making Fe-S clusters. As the building blocks of Fe-S clusters are reactive species, the Suf pathway is highly regulated by protein-protein interactions. The Frantom lab works to identify functional roles for protein-protein interactions using backbone amide HDX-MS. These experiments are run using our recently acquired Waters Xevo QToF mass spectrometer with dedicated HDX Manager UPLC system. HDX-MS data is complemented by kinetic characterization, structural characterization (in collaboration with Dr. Jack Dunkle at UA), and genetic/biophysical studies (in collaboration with Dr. Wayne Outten at Univ. of South Carolina). These studies will provide insight into this fundamental biological pathway and potential targets for novel antibiotics based on disruption of protein-protein interactions.

2. 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. 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.

3. Role of Protein Conformational Dynamics in Glycosyltransferase Enzymes

Modification of biomolecules by sugars is a fundamental aspect of life. In comparison to other biomolecular building blocks, sugars provide unparalleled chemical diversity combined with multiple reactive centers. Because of this, the “sugar code” is one of life’s most complicated information storage and recognition systems. The code is assembled from sugar building blocks by enzymes called glycosyltransferase (GTs). GTs catalyze the transfer of activated mono- and oligosaccharides to every major type of biomolecule and are ubiquitous across all domains of life. Despite the wide variety of biomolecular targets and pathways, glycosyltransferases are remarkably conservative in tertiary structure and can be categorized into one of two main folds: GT-A and GT-B. The GT-B fold is especially interesting as it requires a large conformational change upon substrate binding and product release may play a role in the rate-limiting step. These results suggest that control of protein dynamics is critical to function in the GT-B fold. To investigate these dynamics, the Frantom lab utilizes backbone amide HDX-MS to map changes in protein dynamics in GT-B enzymes. Biochemical studies are then used to link changes in dynamics with changes in function. This work provides a fundamental understanding of this important class of enzymes and improves our ability to design potent and selective inhibitors.

Selected Publications

Recent Publications:

Function and Regulation of the Suf Fe-S Cluster Biogenesis Pathway

“Changes in Protein Dynamics in Escherichia coli SufS Reveal a Possible Conserved Regulatory Mechanism in Type II Cysteine Desulfurase Systems” Kim, D.: Singh, H.; Dai, Y.; Dong, G.; Busenlehner, L.S.; Outten, F.W.; and Frantom, P.A. Biochemistry, 2018, 57, 5210-5217.

“SufE D74R Substitution Alters Active Site Loop Dynamics to Further Enhance SufE Interaction with the SufS Cysteine Desulfurase” Dai, Y.; Kim, D.; Dong, G.; Busenlehner, L. S.; Frantom, P. A.; and Outten, F. W. Biochemistry, 2015, 54, 4824-4833.

Functional and Regulatory Diversity in an Enzyme Superfamily

“Improving Functional Annotation in the DRE-TIM Metallolyase Superfamily Through Identification of Active Site Fingerprints. Kumar, G; Johnson, J.L.; and Frantom, P.A. Biochemistry, 2016, 55, 1863-1872.

“Evolutionarily Distinct Versions of the Multi-domain Enzyme a-Isopropylmalate Synthase Share Discrete Mechanisms of V-type Allosteric Regulation” Kumar, G; and Frantom, P. A. Biochemistry, 2014, 53, 4847-4856.

“Mechanistic and Bioinformatic Investigation of a Conserved Active Site Helix in is a-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.

Functional Dynamics in Glycosyltransferase Enzymes

“Biochemical Characterization of the Retaining Glycosyltransferase Glucosyl-3-Phosphoglycerate Synthase from Mycobacterium tuberculosis” Kumar, G.; Guan, S.; and Frantom, P. A. Arch. Biochem. Biophys., 2014, 564, 120-127.