Research Output 1969 2017

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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: Research - peer-reviewArticle

Ligases
Ubiquitin
Neoplasms
Ubiquitin-Protein Ligases
Immune System Diseases

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: Research - peer-reviewArticle

Phosphatidylinositol 3-Kinase
Allosteric Site
Binding Sites
X Ray Crystallography
Libraries

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: Research - peer-reviewArticle

Phosphatidylinositols
Catalysis
Phosphotransferases
Kinetics
Substrates
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: Research - peer-reviewArticle

Sodium Channels
Calmodulin
Calcium
Electric potential
Mutation

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: Research - peer-reviewArticle

Adenosine Diphosphate Ribose
Hydrolases
Mycobacterium tuberculosis
Enzymes
Catalysis

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: Research - peer-reviewArticle

Mixed Function Oxygenases
calponin
Actins
Enzymes
Actin Depolymerizing Factors

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

Cations
Permeability
vanilloid receptor subtype 1
Capsaicin
Phenotype

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: Research - peer-reviewArticle

Growth Disorders
sodium-iodide symporter
Cell membranes
Genes
Thyroid Hormones

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: Research - peer-reviewArticle

Nucleoside Diphosphate Sugars
Hydrolases
Enzymes
Bdellovibrio bacteriovorus
nucleosides
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: Research - peer-reviewArticle

Mutation
Phosphotransferases
Enzymes
Phosphatidylinositols
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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

calmodulin
Calmodulin
activation
Chemical activation
titration

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

src Homology Domains
Lipids
Phosphotransferases
Binding Sites
Enzymes
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: Research - peer-reviewArticle

Symporters
Cell membranes
Defects
Cell Membrane
Biosynthesis

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: Research - peer-reviewArticle

Peptidoglycan
Biosynthesis
Enzymes
uridine 5'-diphospho-2,3-diacetamido-2,3-dideoxyglucopyranuronic acid
Streptococcus pneumoniae

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: Research - peer-reviewArticle

Peroxides
peptidylglycine monooxygenase
Copper
Hydroxylation
Hydrogen Peroxide

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: Research - peer-reviewArticle

Phosphorylation
Proteins
Membranes
C2 Domains
PTEN Phosphohydrolase

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: Research - peer-reviewArticle

Aminopeptidases
Methionine
Structure-Activity Relationship
Pharmaceutical Chemistry
Eukaryota

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

free energy
trajectories
Free energy
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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

Toxicity
polyglutamine
Proteins
Aptitude
Poisons

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

Galectin 1
Disaccharides
Proteins
Binding Sites
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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

Cytidine Diphosphate Choline
Cytidine Diphosphate
Pyrophosphatases
Enzymes
nudix hydrolases
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: Research - peer-reviewArticle

Carbon Monoxide
Nitrites
Copper
peptidylglycine monooxygenase
Carbon monoxide

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

Dimerization
Mutation
Coronavirus
Respiratory Tract Infections
Enzymes
Phosphatidylinositols
Amino Acids
Mutation
Lipids
Serum

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: Research - peer-reviewArticle

Enzyme Activation
Drug Design
Phosphatidylinositol 3-Kinases
Mutation
Chemical activation

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

plant hormones
abscisic acid
biosynthesis
corn
enzymes

Structure and specificity of a binary tandem domain F-Lectin from striped bass (Morone saxatilis)

Bianchet, M. A., Odom, E. W., Vasta, G. R. & Amzel, L. M. Aug 2010 In : Journal of Molecular Biology. 401, 2, p. 239-252 14 p.

Research output: Research - peer-reviewArticle

Bass
Lectins
Carbohydrates
Polysaccharides
Ligands