L. Mario Amzel
Dr. L. Mario Amzel is a Professor and director 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+.
Rudzka K, Moreno DM, Eipper B, Mains R, Estrin DA, Amzel LM. (2013) Coordination of peroxide to the Cu(M) center of peptidylglycine α-hydroxylating monooxygenase (PHM): structural and computational study. J Biol Inorg Chem 18(2):223-32. doi: 10.1007/s00775-012-0967-z. Epub 2012 Dec 18. PMID: 23247335 [PubMed – as supplied by publisher] PMCID: 23247335 PubMed Abstract
Armstrong AA, Hildreth JEK, Amzel LM (2013) Structural and thermodynamic insights into the recognition of native proteins by anti-peptide antibodies. J Mol Biology March 6 2013 pii: S0022-2836(13)00146-0. doi: 10.1016/j.jmb.2013.02.031. PMID: 23473830; PMCID: In process
Zhang F, Bhat S, Gabelli SB, Chen X, Miller MS, Nacev BA, Cheng YL, Meyers DJ, Tenney K, Shim JS, Crews P, Amzel LM, Ma D, Liu JO. (2013) Pyridinylquinazolines selectively inhibit human methionine aminopeptidase-1 in cells.J Med Chem. 2013 May 23;56(10):3996-4016. doi: 10.1021/jm400227z. Epub 2013 May 1. PMID: 23634668; PMCID: PMC3714011 PubMed Abstract
Li W, Nicola JP, Amzel LM, Carrasco N. (2013) Asn441 plays a key role in folding and function of the Na+/I-symporter (NIS). FASEB J May 6 PMID: 23650190; PMCID: PMC3714583 [Available on 2014/8/1]
Aripirala S, Szajnman SH, Jakoncic J, Rodriguez JB, Docampo R, Gabelli SB, Amzel LM. (2012) Design, synthesis, calorimetry, and crystallographic analysis of 2-alkylaminoethyl-1,1-biphosphates as inhibitors of Trypanosoma cruzi farnesyl diphosphate synthase. J Med Chem. 012 Jul 26;55(14):6445-54. Epub 2012 Jul 5. PMID: 22715997 [PubMed – indexed for MEDLINE]
Echeverria I, Amzel LM. (2012) Estimation of free energy differences from computed work distributions: an application of Jarzynski’s Equality. J Phys Chem B. 116(36): 10986-95. PubMed PMID: 22849340; PMCID: In process.
Erdemli SB, Gupta R, Bishai WR, Lamichhane G, Amzel LM, Bianchet MA. (2012) Targeting the cell wall of mycobacterium tuberculosis: Structure and mechanism of L,D-transpeptidase 2. Structure 20(12):2103-15. Epub 2012 Oct 23. doi:pii: S0969-2126(12)00350-4. PMID: 23103390; PMCID:PMC357878
Vasta GR, Nita-Lazar M, Giomarelli B, Ahmed H, Du S, Cammarata M, Parrinello N, Bianchet MA, Amzel LM. (2011) Structural and functional diversity of the lectin repertoire in teleost fish: relevance to innate and adaptive immunity. Dec;35(12):1388-99. Review.PMID: 21896283; PMCID: PMC3429948
Mustafa AK, Sikka G, Gazi SK, Steppan J, Jung SM, Bhunia AK, Barodka VM, Gazi FK, Barrow RK, Wang R, Amzel LM, Berkowitz DE, Snyder SH. Hydrogen sulfide as endothelium-derived hyperpolarizing factor sulfhydrates potassium channels. Circ Res. 2011 Nov 11;109(11):1259-68. Epub 2011 Oct 6. PubMed. PMID: 21980127; PMCID: PMC3234531.
Bolduc D, Rahdar M, Tu-Sekine B, Sivakumaren SC, Raben D, Amzel LM, Devreotes P, Gabelli SB, Cole P. Phosphorylation-mediated PTEN conformational closure and deactivation revealed with protein semisynthesis. Elife. 2013 Jul 9;2:e00691. doi: 10.7554/eLife.00691. Print 2013. PMID: 23853711; PMCID: PMC3707082
Duong-Ly KC, Woo HN, Dunn CA, Xu W, Babič A, Bessman MJ, Amzel LM, Gabelli SB.PLoS One. 2013 May 15;8(5):e64241. doi: 10.1371/journal.pone.0064241. Print 2013.PMID: 23691178; PMCID: PMC3655063
Echeverria, I and Amzel, LM. (2011) Disaccharide Binding to Galectin-1: Free Energy Calculations and Molecular Recognition Mechanism, Biophys J 100(9)2283-92.
Vasta GR, Ahmed H, Bianchet MA, Fernandez-Robledo JA, and Amzel LM. (2012) Diversity in recognition of glycans by F-type lectins and galectins: molecular, structural, and biophysical aspects. Ann. N.Y.Acad. Sci.. 1253(1):E14-26. PubMed PMID: 22973821; PMCID: In process.
Boto A, Xu WL, Jakovcic J, Pannuri A, Romeo T, Bessman MJ, Gabelli SB, and Amzel LM. (2011) Structure studies of the Nudix GDP-mannose hydrolase from E. Coli reveals a new motif for mannose recognition. Proteins 79(8):2455-66.
Duong-Ly K, Gabelli, SB, Xu WL, Dunn CA, Bessman MJ, and Amzel LM. (2011) The Nudix hydrolase CDP-Chase, a CDP-choline pyrophosphatase, is an asymmetric dimer with two distinct enzymatic activities. J. Bacteriol. 193(13):3175-85.
Gabelli SB, Mandelker D, Schmidt-Kittler O, Vogelstein B, Amzel LM. (2010) Somatic mutations in PI3Kalpha: Structural basis for enzyme activation and drug design. Biochim Biophys Acta. 1804(3):533-540.
Echeverria I, Amzel LM. (2010) Helix propensities calculations for amino acids in alanine based peptides using Jarzynski’s equality. Proteins. 78(5):1302-10.
Barrila J, Gabelli S, Bacha, U, Amzel L, and Freire E. (2010) Mutation of Asn29 disrupts the dimerization and enzymatic activity of SARS 3CLpro. Biochemistry 49(20):4308-17.
Huang C-H, Gabelli, SB, Oldfield E, and Amzel LM. (2009) Binding of nitrogen-containing bisphosphonates (N-BPs) to the Trypanosoma cruzi farnesyl diphosphate synthase homodimer. Proteins: Structure & Bioinformatics 78(4): 888-99 PubMed Abstract
Chufan, E.E., M. De, B.A. Eipper, R.E. Mains, and L.M. Amzel. (2009) Amidation of bioactive peptides: the structure of the lyase domain of the amidating enzyme. Structure 17:965-973.
Huang CH, Mandelker D, Gabelli SB, Amzel LM. (2008) Insights into the oncogenic effects of /PIK3CA/ mutations from the structure of p110alpha/p85alpha. Cell Cycle Feb 27; 7(9).
Bianchet MA, Erdemli SB, and Amzel LM (2008) Structure, function and mechanism of cytosolic quinone reductases. Vitamins & Hormones vol 78:63-84 (Review).
Huang CH, Mandelker D, Schmidt-Kittler O, Samuels Y, Velculescu VE, Kinzler KW, Vogelstein B, Gabelli SB, Amzel LM. (2007) The structure of a human p110alpha/p85alpha complex elucidates the effects of oncogenic PI3Kalpha mutations. Science 318(5857):1744-8.
Gabelli SB, Bianchet MA, Xu WL, Dunn CA, Niu Z-D, Amzel L, and Bessman MJ. (2007) Structure and function of the E.coli dihydroneopterin triphosphates pyrophosphatase: A Nudix enzyme involved in folate biosynthesis. Structure 15:1014-1022 (C).
Bianchet MA and Amzel LM (2007) Making the right moves. Structure 15(8): 885-6.
Parker JB, Bianchet MA, Krosky DJ, Friedman JI, Amzel LM and Stivers JT. (2007) Enzymatic capture of an extrahelical thymine in the search for uracil in DNA. Nature 449(7161):433-7.
(C) – cover illustration