L. Mario Amzel
Dr. L. Mario Amzel is a Professor of the Department of Biophysics and Biophysical Chemistry of the Department at the Johns Hopkins University School of Medicine.
Structural enzymology of redox and phosphoryl-transfer enzymes: MICAL, PI3K, FPPS, PAM, and Nudix hydrolases. Selected areas of structural thermodynamics, and regulation and mechanism of channels and transferases.
Structural Mechanistic Biochemistry. Enzymes play a key role in all metabolic and cell-signaling processes. Characterization of an enzyme’s biological function must include the description of its mechanisms at an atomic level. Our laboratory is deciphering the catalytic mechanism of several enzyme families, using a combination of molecular biology, biochemistry, and structural Biology. Systems under study fall into two classes: 1) Enzymes that recognize or process phosphates (pyrophosphate hydrolases (Nudix enzymes), farnesyl pyrophosphate synthases, phosphinositide-3-kinases (PI3K), and redox enzymes (flavoenzymes, and copper hydroxylases, and non-heme iron diooxygenases). All experiments necessary to address mechanistic questions are carried out in the laboratory. Cloning and expression, ultrapurification, kinetic characterization, mutational analysis, mass spectrometry, crystallization, and structure determination by x-ray diffraction are some of the techniques we bring to bear to characterize the mechanisms of these enzymes. In addition to being intrinsically interesting some of these systems are being developed as targets for drug design.
Structural Thermodynamics. Most biological processes rely upon recognition and binding among macromolecules. We have developed several systems, such as anti-peptide antibodies and lectins, that we are using to study protein-ligand interactions. As part of this research, we are developing computational methods to calculate the changes in the thermodynamic variables (ΔG, ΔH, ΔS) that take place when a protein recognized another macromolecule or a small ligand. Techniques used in this work involve monoclonal antibody development, x-ray diffraction and calorimetry, followed by empirical parameterization, and molecular mechanics/dynamics and statistical mechanics calculations. Results of these studies have a major impact on our understanding of binding energetics, including the estimation of binding affinities for structure-based drug design.
Mechanism and regulation of channels and transporters. We are studying the regulation of the cardiac voltage regulated Na+ channel Nav 1.5 by calmodulin using structural and thermodynamic techniques.
A major project involves studying the structure and the mechanisms of the I– transport by the Na+ / I– symporter. We are using experimental and computational methods to identify the different molecular species that participate in the transport cycle.
Transporters and channels. Ion movements across biological membranes are highly specific processes at the core of numerous moving physiological conditions and disease states. We are studying the mechanism of the Na+ / I–symporter, NIS, and the control of the activity of voltage- activated Na+ channels by two key effectors – calmodulin and Ca2+.
Ravera S, Quick M, Nicola JP, Carrasco N, Amzel, L.M. (2015) Beyond non-integer Hill coefficients: A novel approach to analyzing binding data, applied to Na+-driven transporters. J Gen Physiol. 145(6):555-63. doi: 10.1085/jgp.201511365. PMID: 26009546
Gabelli SB, Yoder JB, Tomaselli GF, Amzel, L.M. (2016) Calmodulin and Ca(2+) control of voltage gated Na(+) channels. Channels (Austin). 10(1):45-54. doi:10.1080/19336950.2015.1075677. Review. PubMed PMID: 26218606; PubMed Central PMCID: PMC4802738.
Ravera S, Reyna-Neyra A, Ferrandino G, Amzel, L.M., Carrasco N. (2017) The sodium/iodide symporter (NIS): Molecular physiology and preclinical and clinical applications. Annu Rev Physiol. 79:261-289. doi: 10.1146/annurev-physiol-022516-034125. PMID: 28192058
Maheshwari S, Miller MS, O’Meally R, Cole RN, Amzel, L.M., and Gabelli SB. (2017) Kinetic and structural analyses reveal residues in phosphoinositide 3-kinase alpha that are critical for catalysis and substrate recognition. J Biol Chem. pii: jbc.M116.772426. doi: 10.1074/jbc.M116.772426. [Epub ahead of print] PMID: 28676499 [PubMed – as supplied by publisher]
Maheshwari S, Shimokawa C, Rudzka K, Kline CD, Eipper BA, Mains RE, Gabelli SB, Blackburn N and Amzel, L.M.. (2018) Effects of copper occupancy on the conformational landscape of peptidylglycine α-hydoxylating monooxygenase. Communications Biology 1:74. doi: 10.1038/s42003-018-0082-y. eCollection 2018. PMID: 30271955 [PubMed]
Yoder JB, Ben-Johny M, Farinelli F, Srinivasan L, Shoemaker SR, Tomaselli GF, Gabelli SB, Amzel, L.M..(2019) Ca(2+)-dependent regulation of sodium channels Na(V)1.4 andNa(V)1.5 is controlled by the post-IQ motif. Nat Commun. Apr 3;10(1):1514. doi: 10.1038/s41467-019-09570-7. PubMed PMID: 30944319; PubMed Central PMCID: PMC6447637.
Schott, ET, Di Lella S, Bachvaroff, TR, Amzel, L.M., Vasta, GR. (2019) Lacking catalase, a protistan parasite draws on its photsynthetic ancestry to complete an antioxidant repertoire with ascorbate peroxidase. BMC Evol Biol 19(1): 146. Doi: 10.1186/s12862-019-1465-5.
Chakrabarti M, Gabelli SB, Amzel, L.M. (2020) Allosteric Activation of PI3Kα Results in Dynamic Access to Catalytically Competent Conformations. pii: S0969-2126(20)30010-1. doi: 10.1016/j.str.2020.01.010. [Epub ahead of print] PMID: 32049032 [PubMed – as supplied by publisher]
Maheshwari S, Kim YS, Aripirala S, Murphy M, Amzel, L.M., Gabelli SB. (2020) Identifying structural determinants of product specificity in Leishmania major farnesyl diphosphate synthase. Biochemistry. doi: 10.1021/acs.biochem.0c00432. [Epub ahead of print] PMID: 32584028
Llorente-Esteban A, Manville RW, Reyna-Neyra A, Abbott GW,Amzel, L.M., Carrasco N. (2020) Allosteric regulation of mammalian Na+/I– symporter activity by perchlorate. Nat Struct Mol Biol. 27(6):533-539. doi: 10.1038/s41594-020-0417-5. Epub PMID:
Nathan S, Gabelli SB, Yoder JB, Srinivasan L, Aldrich RW, Tomaselli GF, Ben-Johny M, Amzel, L.M.. (2021) Structural basis of cytoplasmic NaV1.5 and NaV1.4 regulation. J Gen Physiol. 153(1):e202012722. doi: 10.1085/jgp.202012722. PMID: 33306788