Research Output 1969 2018

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2018

Bilobal architecture is a requirement for calmodulin signaling to CaV1.3 channels

Banerjee, R., Yoder, J. B., Yue, D. T., Amzel, L. M., Tomaselli, G. F., Gabelli, S. B. & Ben-Johny, M. Mar 27 2018 In : Proceedings of the National Academy of Sciences of the United States of America. 115, 13, p. E3026-E3035

Research output: Contribution to journalArticle

Calmodulin
Calcium Channels
Proteins
2017

A Tunable Brake for HECT Ubiquitin Ligases

Chen, Z., Jiang, H., Xu, W., Li, X., Dempsey, D. R., Zhang, X., Devreotes, P., Wolberger, C., Amzel, L. M., Gabelli, S. B. & Cole, P. A. May 4 2017 In : Molecular Cell. 66, 3, p. 345-357.e6

Research output: Contribution to journalArticle

Ligases
Ubiquitin
Ubiquitin-Protein Ligases
Immune System Diseases
Post Translational Protein Processing

Identification of allosteric binding sites for PI3Kα oncogenic mutant specific inhibitor design

Miller, M. S., Maheshwari, S., McRobb, F. M., Kinzler, K. W., Amzel, L. M., Vogelstein, B. & Gabelli, S. B. Feb 15 2017 In : Bioorganic and Medicinal Chemistry. 25, 4, p. 1481-1486 6 p.

Research output: Contribution to journalArticle

Phosphatidylinositol 3-Kinase
Allosteric Site
Binding Sites
X ray crystallography
X Ray Crystallography

Kinetic and structural analyses reveal residues in phosphoinositide 3-kinase α that are critical for catalysis and substrate recognition

Maheshwari, S., Miller, M. S., O’Meally, R., Cole, R. N., Amzel, L. M. & Gabelli, S. B. 2017 In : Journal of Biological Chemistry. 292, 33, p. 13541-13550 10 p.

Research output: Contribution to journalArticle

1-Phosphatidylinositol 4-Kinase
Phosphatidylinositols
Catalysis
Phosphotransferases
Kinetics
2016

Calmodulin and Ca2+ control of voltage gated Na+ channels

Gabelli, S. B., Yoder, J. B., Tomaselli, G. F. & Amzel, L. M. Jan 1 2016 In : Channels. 10, 1, p. 45-54 10 p.

Research output: Contribution to journalArticle

Sodium Channels
Calmodulin
Calcium
Mutation
Electric potential

Kinetic and mutational studies of the adenosine diphosphate ribose hydrolase from Mycobacterium tuberculosis

O’Handley, S. F., Thirawatananond, P., Kang, L. W., Cunningham, J. E., Leyva, J. A., Amzel, L. M. & Gabelli, S. B. Sep 28 2016 (Accepted/In press) In : Journal of Bioenergetics and Biomembranes. p. 1-11 11 p.

Research output: Contribution to journalArticle

Adenosine Diphosphate Ribose
Hydrolases
Mycobacterium tuberculosis
Catalysis
Cats

Modulation of MICAL Monooxygenase Activity by its Calponin Homology Domain: Structural and Mechanistic Insights

Alqassim, S. S., Urquiza, M., Borgnia, E., Nagib, M., Amzel, L. M. & Bianchet, M. A. Mar 3 2016 In : Scientific Reports. 6, 22176

Research output: Contribution to journalArticle

Mixed Function Oxygenases
Actins
Actin Depolymerizing Factors
Small Angle Scattering
X Ray Crystallography

Na+ coordination at the Na2 site of the Na+ /I- symporter

Ferrandino, G., Nicola, J. P., Sánchez, Y. E., Echeverria, I., Liu, Y., Amzel, L. M. & Carrasco, N. Sep 13 2016 In : Proceedings of the National Academy of Sciences of the United States of America. 113, 37, p. E5379-E5388

Research output: Contribution to journalArticle

Symporters
Binding Sites
Active Biological Transport
Thyroid Hormones
Thyroid Gland
2015

A Redox Regulatory System Critical for Mycobacterial Survival in Macrophages and Biofilm Development

Wolff, K. A., de la Peña, A. H., Nguyen, H. T., Pham, T. H., Amzel, L. M., Gabelli, S. B. & Nguyen, L. Apr 1 2015 In : PLoS Pathogens. 11, 4, e1004839

Research output: Contribution to journalArticle

Biofilms
NAD
Oxidation-Reduction
Macrophages
Flavin-Adenine Dinucleotide

Beyond non-integer Hill coefficients: A novel approach to analyzing binding data, applied to Na+-driven transporters

Ravera, S., Quick, M., Nicola, J. P., Carrasco, N. & Mario Amzel, L. 2015 In : Journal of General Physiology. 145, 6, p. 555-563 9 p.

Research output: Contribution to journalArticle

Ions
Symporters
Active Biological Transport
Thyroid Hormones
Iodine

Oncogenic mutations weaken the interactions that stabilize the p110α-p85α heterodimer in phosphatidylinositol 3-kinase α

Echeverria, I., Liu, Y., Gabelli, S. B. & Amzel, L. M. Sep 1 2015 In : FEBS Journal. 282, 18, p. 3528-3542 15 p.

Research output: Contribution to journalArticle

Phosphatidylinositol 3-Kinase
Cell signaling
Macromolecular Substances
Cell growth
Computational methods

Role of the outer pore domain in transient receptor potential vanilloid 1 dynamic permeability to large cations

Munns, C. H., Chung, M. K., Sanchez, Y. E., Amzel, L. M. & Caterina, M. J. Feb 27 2015 In : Journal of Biological Chemistry. 290, 9, p. 5707-5724 18 p.

Research output: Contribution to journalArticle

Cations
Permeability
Capsaicin
Phenotype
Substitution reactions

Sodium/iodide symporter mutant V270E causes stunted growth but no cognitive deficiency

Nicola, J. P., Reyna-Neyra, A., Saenger, P., Rodriguez-Buritica, D. F., Godoy, J. D. G., Muzumdar, R., Amzel, L. M. & Carrasco, N. Oct 1 2015 In : Journal of Clinical Endocrinology and Metabolism. 100, 10, p. E1353-E1361

Research output: Contribution to journalArticle

Growth Disorders
Cell membranes
Genes
Thyroid Hormones
Symporters

Structural and enzymatic characterization of a nucleoside diphosphate sugar hydrolase from Bdellovibrio bacteriovorus

De La Peña, A. H., Suarez, A., Duong-Ly, K. C., Schoeffield, A. J., Pizarro-Dupuy, M. A., Zarr, M., Pineiro, S. A., Amzel, L. M. & Gabelli, S. B. Nov 2 2015 In : PLoS One. 10, 11, e141716

Research output: Contribution to journalArticle

Nucleoside Diphosphate Sugars
Bdellovibrio bacteriovorus
nucleosides
Hydrolases
hydrolases
2014

Activation of PI3Kα by physiological effectors and by oncogenic mutations: Structural and dynamic effects

Gabelli, S. B., Echeverria, I., Alexander, M., Duong-Ly, K. C., Chaves-Moreira, D., Brower, E. T., Vogelstein, B. & Amzel, L. M. Mar 2014 In : Biophysical Reviews. 6, 1, p. 89-95 7 p.

Research output: Contribution to journalArticle

Mutation
Phosphotransferases
Phosphatidylinositols
Enzymes
Lipids

Physiological sodium concentrations enhance the iodide affinity of the Na+ /I- symporter

Nicola, J. P., Carrasco, N. & Mario Amzel, L. Jun 3 2014 In : Nature Communications. 5, 3948

Research output: Contribution to journalArticle

Symporters
Statistical mechanics
Oncology
Iodides
Stoichiometry

Regulation of the NaV 1.5 cytoplasmic domain by calmodulin

Gabelli, S. B., Boto, A., Kuhns, V. H., Bianchet, M. A., Farinelli, F., Aripirala, S., Yoder, J., Jakoncic, J., Tomaselli, G. F. & Amzel, L. M. 2014 In : Nature Communications. 5, 5126

Research output: Contribution to journalArticle

calmodulin
Calmodulin
Chemical activation
activation
Voltage-Gated Sodium Channels

Structural and thermodynamic basis of the inhibition of Leishmania major farnesyl diphosphate synthase by nitrogen-containing bisphosphonates

Aripirala, S., Gonzalez-Pacanowska, D., Oldfield, E., Kaiser, M., Amzel, L. M. & Gabelli, S. B. Mar 2014 In : Acta Crystallographica Section D: Biological Crystallography. 70, 3, p. 802-810 9 p.

Research output: Contribution to journalArticle

Geranyltranstransferase
Leishmania major
Diphosphonates
Thermodynamics
Nitrogen

Structural basis of nSH2 regulation and lipid binding in PI3Kα

Miller, M. S., Schmidt-Kittler, O., Bolduc, D. M., Brower, E. T., Chaves-Moreira, D., Allaire, M., Kinzler, K. W., Jennings, I. G., Thompson, P. E., Cole, P. A., Amzel, L. M., Vogelstein, B. & Gabelli, S. B. 2014 In : Oncotarget. 5, 14, p. 5198-5208 11 p.

Research output: Contribution to journalArticle

src Homology Domains
Lipids
Phosphotransferases
Binding Sites
Phosphatidylinositol 3-Kinase
2013

Asn441 plays a key role in folding and function of the Na +/I- symporter (NIS)

Li, W., Nicola, J. P., Amzel, L. M. & Carrasco, N. Aug 2013 In : FASEB Journal. 27, 8, p. 3229-3238 10 p.

Research output: Contribution to journalArticle

Symporters
Cell membranes
Cell Membrane
Defects
Active Biological Transport

A UDP-X Diphosphatase from Streptococcus pneumoniae Hydrolyzes Precursors of Peptidoglycan Biosynthesis

Duong-Ly, K. C., Woo, H. N., Dunn, C. A., Xu, W. L., Babič, A., Bessman, M. J., Amzel, L. M. & Gabelli, S. B. May 15 2013 In : PLoS One. 8, 5, e64241

Research output: Contribution to journalArticle

Streptococcus pneumoniae
Peptidoglycan
peptidoglycans
Biosynthesis
biosynthesis

Coordination of peroxide to the CuM center of peptidylglycine α-hydroxylating monooxygenase (PHM): Structural and computational study

Rudzka, K., Moreno, D. M., Eipper, B., Mains, R., Estrin, D. A. & Amzel, L. M. Feb 2013 In : Journal of Biological Inorganic Chemistry. 18, 2, p. 223-232 10 p.

Research output: Contribution to journalArticle

Peroxides
Copper
Hydroxylation
Hydrogen Peroxide
Ligands

Phosphorylation-mediated PTEN conformational closure and deactivation revealed with protein semisynthesis

Bolduc, D., Rahdar, M., Tu-Sekine, B., Sivakumaren, S. C., Raben, D., Amzel, L. M., Devreotes, P., Gabelli, S. B. & Cole, P. Jul 9 2013 In : eLife. 2013, 2, e00691

Research output: Contribution to journalArticle

Phosphorylation
PTEN Phosphohydrolase
Membranes
Proteins
Cell membranes

Pyridinylpyrimidines selectively inhibit human methionine aminopeptidase-1

Zhang, P., Yang, X., Zhang, F., Gabelli, S. B., Wang, R., Zhang, Y., Bhat, S., Chen, X., Furlani, M., Amzel, L. M., Liu, J. O. & Ma, D. May 1 2013 In : Bioorganic and Medicinal Chemistry. 21, 9, p. 2600-2617 18 p.

Research output: Contribution to journalArticle

Aminopeptidases
Methionine
Structure-Activity Relationship
Mammals
Pharmaceutical Chemistry

Pyridinylquinazolines selectively inhibit human methionine aminopeptidase-1 in cells

Zhang, F., Bhat, S., Gabelli, S. B., Chen, X., Miller, M. S., Nacev, B. A., Cheng, Y. L., Meyers, D. J., Tenney, K., Shim, J. S., Crews, P., Amzel, L. M., Ma, D. & Liu, J. O. May 23 2013 In : Journal of Medicinal Chemistry. 56, 10, p. 3996-4016 21 p.

Research output: Contribution to journalArticle

Aminopeptidases
Methionine
Quinazolines
Mammals
Metals

Structural and thermodynamic insights into the recognition of native proteins by anti-peptide antibodies

Armstrong, A., Hildreth, J. E. K. & Amzel, L. M. Jun 12 2013 In : Journal of Molecular Biology. 425, 11, p. 2027-2038 12 p.

Research output: Contribution to journalArticle

Thermodynamics
Anti-Idiotypic Antibodies
Peptides
Proteins
Micrococcal Nuclease
2012

Design, synthesis, calorimetry, and crystallographic analysis of 2-alkylaminoethyl-1,1-bisphosphonates as inhibitors of trypanosoma cruzi farnesyl diphosphate synthase

Aripirala, S., Szajnman, S. H., Jakoncic, J., Rodriguez, J. B., Docampo, R., Gabelli, S. B. & Amzel, L. M. Jul 26 2012 In : Journal of Medicinal Chemistry. 55, 14, p. 6445-6454 10 p.

Research output: Contribution to journalArticle

Geranyltranstransferase
Calorimetry
Trypanosoma cruzi
Diphosphonates
Chagas Disease

Diversity in recognition of glycans by F-type lectins and galectins: molecular, structural, and biophysical aspects.

Vasta, G. R., Ahmed, H., Bianchet, M. A., Fernández-Robledo, J. A. & Amzel, L. M. Apr 2012 In : Annals of the New York Academy of Sciences. 1253

Research output: Contribution to journalArticle

Galectins
Lectins
Polysaccharides
Carbohydrates
Ligands

Estimation of free-energy differences from computed work distributions: An application of Jarzynski's equality

Echeverria, I. & Amzel, L. M. Sep 13 2012 In : Journal of Physical Chemistry B. 116, 36, p. 10986-10995 10 p.

Research output: Contribution to journalArticle

Free energy
free energy
Trajectories
trajectories
estimates

Targeting the cell wall of mycobacterium tuberculosis: Structure and mechanism of L,D-transpeptidase 2

Erdemli, S. B., Gupta, R., Bishai, W. R., Lamichhane, G., Amzel, L. M. & Bianchet, M. A. Dec 5 2012 In : Structure. 20, 12, p. 2103-2115 13 p.

Research output: Contribution to journalArticle

Peptidyl Transferases
Mycobacterium tuberculosis
Cell Wall
Peptidoglycan
Mycobacterium

Unfolding ubiquitin by force: Water mediated H-bond destabilization

Pabón, G. & Amzel, L. M. 2012 In : Universitas Scientiarum. 17, 3, p. 273-281 9 p.

Research output: Contribution to journalArticle

destabilization
water
molecules
simulation
pulling
2011

A compact β model of huntingtin toxicity

Zhang, Q. C., Yeh, T. L., Leyva, A., Frank, L. G., Miller, J., Kim, Y. E., Langen, R., Finkbeiner, S., Amzel, M. L., Ross, C. A. & Poirier, M. A. Mar 11 2011 In : Journal of Biological Chemistry. 286, 10, p. 8188-8196 9 p.

Research output: Contribution to journalArticle

Toxicity
Aptitude
Poisons
Huntington Disease
Pathology

Capitalizing on tumor genotyping: Towards the design of mutation specific inhibitors of phosphoinsitide-3-kinase

Gabelli, S. B., Duong-Ly, K. C., Brower, E. T. & Amzel, L. M. 2011 In : Advances in Enzyme Regulation. 51, 1, p. 273-279 7 p.

Research output: Contribution to journalArticle

Protein Conformation
Molecular Models
Protein Subunits
Protein Kinase Inhibitors
Phosphatidylinositol 3-Kinases

Direct activation of Epac by sulfonylurea is isoform selective

Herbst, K. J., Coltharp, C., Amzel, L. M. & Zhang, J. Feb 25 2011 In : Chemistry and Biology. 18, 2, p. 243-251 9 p.

Research output: Contribution to journalArticle

Protein Isoforms
Chemical activation
Proteins
Sulfonylurea Receptors
Enzyme Activators

Disaccharide binding to galectin-1: Free energy calculations and molecular recognition mechanism

Echeverria, I. & Mario Amzel, L. May 4 2011 In : Biophysical Journal. 100, 9, p. 2283-2292 10 p.

Research output: Contribution to journalArticle

Galectin 1
Disaccharides
Binding Sites
Galectins
Ligands

Hydrogen sulfide as endothelium-derived hyperpolarizing factor sulfhydrates potassium channels

Mustafa, A. K., Sikka, G., Gazi, S. K., Steppan, J., Jung, S. M., Bhunia, A. K., Barodka, V. M., Gazi, F. K., Barrow, R. K., Wang, R., Amzel, L. M., Berkowitz, D. E. & Snyder, S. H. Nov 11 2011 In : Circulation Research. 109, 11, p. 1259-1268 10 p.

Research output: Contribution to journalArticle

Hydrogen Sulfide
Potassium Channels
Endothelium
Endothelium-Dependent Relaxing Factors
Vasodilation

Mechanism of anion selectivity and stoichiometry of the Na +/I - symporter (NIS)

Paroder-Belenitsky, M., Maestas, M. J., Dohán, O., Nicola, J. P., Reyna-Neyra, A., Follenzi, A., Dadachova, E., Eskandari, S., Amzele, L. M. & Carrasco, N. Nov 1 2011 In : Proceedings of the National Academy of Sciences of the United States of America. 108, 44, p. 17933-17938 6 p.

Research output: Contribution to journalArticle

Symporters
Anions
Bacterial Structures
Environmental Pollutants
Ion Transport

Structural and functional diversity of the lectin repertoire in teleost fish: Relevance to innate and adaptive immunity

Vasta, G. R., Nita-Lazar, M., Giomarelli, B., Ahmed, H., Du, S., Cammarata, M., Parrinello, N., Bianchet, M. A. & Amzel, L. M. Dec 2011 In : Developmental and Comparative Immunology. 35, 12, p. 1388-1399 12 p.

Research output: Contribution to journalArticle

Adaptive Immunity
Lectins
Innate Immunity
Fishes
Ligands

Structural studies of the Nudix GDP-mannose hydrolase from E. coli reveals a new motif for mannose recognition

Boto, A. N., Xu, W., Jakoncic, J., Pannuri, A., Romeo, T., Bessman, M. J., Gabelli, S. B. & Amzel, L. M. Aug 2011 In : Proteins. 79, 8, p. 2455-2466 12 p.

Research output: Contribution to journalArticle

Guanosine Diphosphate Mannose
Adenosine Diphosphate Ribose
Pyrophosphatases
Hydrolases
Mannose

The hypoxic regulator of sterol synthesis Nro1 is a nuclear import adaptor

Yeh, T. L., Lee, C. Y. S., Amzel, L. M., Espenshade, P. J. & Bianchet, M. A. Apr 13 2011 In : Structure. 19, 4, p. 503-514 12 p.

Research output: Contribution to journalArticle

Cell Nucleus Active Transport
Sterols
Oxygen
Transcription Factors
Schizosaccharomyces pombe Proteins

The Nudix hydrolase CDP-chase, a CDP-choline pyrophosphatase, is an asymmetric dimer with two distinct enzymatic activities

Duong-Ly, K. C., Gabelli, S. B., Xu, W., Dunn, C. A., Schoeffield, A. J., Bessman, M. J. & Amzel, L. M. Jul 2011 In : Journal of Bacteriology. 193, 13, p. 3175-3185 11 p.

Research output: Contribution to journalArticle

Cytidine Diphosphate Choline
Cytidine Diphosphate
Pyrophosphatases
Enzymes
Exonucleases
2010
Diphosphates
Trypanosoma cruzi
Nitrogen
Geranyltranstransferase
Chagas Disease

Differential reactivity between two copper sites in Peptidylglycine α-hydroxylating monooxygenase

Chufán, E. E., Prigge, S. T., Siebert, X., Eipper, B. A., Mains, R. E. & Amzel, L. M. Nov 10 2010 In : Journal of the American Chemical Society. 132, 44, p. 15565-15572 8 p.

Research output: Contribution to journalArticle

Carbon Monoxide
Nitrites
Carbon monoxide
Copper
Molecules

Helix propensities calcualtions for amino acids in alanine based peptides using Jarzynski's equality

Echeverria, I. & Mario Amzel, L. 2010 In : Proteins. 78, 5, p. 1302-1310 9 p.

Research output: Contribution to journalArticle

Alanine
Trajectories
Amino Acids
Peptides
Free energy

How much binding affinity can be gained by filling a cavity?

Kawasaki, Y., Chufan, E. E., Lafont, V., Hidaka, K., Kiso, Y., Mario Amzel, L. & Freire, E. Feb 2010 In : Chemical Biology and Drug Design. 75, 2, p. 143-151 9 p.

Research output: Contribution to journalArticle

Thermodynamics
Enthalpy
Entropy
Hydrogen Bonding
Guidelines

Mutation of Asn28 disrupts the dimerization and enzymatic activity of SARS 3CLpro

Barrila, J., Gabelli, S. B., Bacha, U., Amzel, L. M. & Freire, E. May 25 2010 In : Biochemistry®. 49, 20, p. 4308-4317 10 p.

Research output: Contribution to journalArticle

Dimerization
Coronavirus
Mutation
Respiratory Tract Infections
Coronavirus Infections
Phosphatidylinositols
Amino Acids
His-His-His-His-His-His
Mutation
Antiporters

Somatic mutations in PI3Kα: Structural basis for enzyme activation and drug design

Gabelli, S. B., Mandelker, D., Schmidt-Kittler, O., Vogelstein, B. & Amzel, L. M. Mar 2010 In : Biochimica et Biophysica Acta - Proteins and Proteomics. 1804, 3, p. 533-540 8 p.

Research output: Contribution to journalArticle

Enzyme Activation
Drug Design
Phosphatidylinositol 3-Kinases
Chemical activation
Mutation

Structural effects of oncogenic PI3Kα mutations

Gabelli, S. B., Huang, C. H., Mandelker, D., Schmidt-Kittler, O., Vogelstein, B. & Amzel, L. M. 2010 In : Current Topics in Microbiology and Immunology. 347, 1, p. 43-53 11 p.

Research output: Contribution to journalArticle

Mutation
Membranes
Enzymes
Neoplasms
tyrosine receptor

Structural insights into maize viviparous14, a key enzyme in the biosynthesis of the phytohormone abscisic acid

Messing, S. A. J., Mario Amzel, L., Gabelli, S. B., Echeverria, I., Vogel, J. T., Guan, J. C., Tan, B. C., Klee, H. J. & McCarty, D. R. Sep 2010 In : Plant Cell. 22, 9, p. 2970-2980 11 p.

Research output: Contribution to journalArticle

Abscisic Acid
Plant Growth Regulators
plant hormones
Zea mays
abscisic acid