Research Output 1967 2020

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2015

Product formation by the promiscuous lanthipeptide synthetase ProcM is under kinetic control

Yu, Y., Mukherjee, S. & Van Der Donk, W. A., Apr 22 2015, In : Journal of the American Chemical Society. 137, 15, p. 5140-5148 9 p.

Research output: Contribution to journalArticle

Cyclization
Ligases
Regioselectivity
kinetics
Kinetics

Rate and Equilibrium Constants for an Enzyme Conformational Change during Catalysis by Orotidine 5′-Monophosphate Decarboxylase

Goryanova, B., Goldman, L. M., Ming, S., Amyes, T. L., Gerlt, J. A. & Richard, J. P., Jul 28 2015, In : Biochemistry. 54, 29, p. 4555-4564 10 p.

Research output: Contribution to journalArticle

Decarboxylation
Carboxy-Lyases
Equilibrium constants
Catalysis
Rate constants

Reconstitution and structure of a bacterial Pnkp1-Rnl-Hen1 RNA repair complex

Wang, P., Selvadurai, K. & Huang, R. H., Apr 17 2015, In : Nature communications. 6, 6876.

Research output: Contribution to journalArticle

Bacterial Structures
immunity
Repair
rhomboids
RNA

Redox potential tuning through differential quinone binding in the photosynthetic reaction center of Rhodobacter sphaeroides

Vermaas, J. V., Taguchi, A. T., Dikanov, S. A., Wraight, C. A. & Tajkhorshid, E., Mar 31 2015, In : Biochemistry. 54, 12, p. 2104-2116 13 p.

Research output: Contribution to journalArticle

Photosynthetic Reaction Center Complex Proteins
Rhodobacter sphaeroides
Quinones
Ubiquinone
Oxidation-Reduction

Restored physiology in protein-deficient yeast by a small molecule channel

Cioffi, A. G., Hou, J., Grillo, A. S., Diaz, K. A. & Burke, M. D., Aug 19 2015, In : Journal of the American Chemical Society. 137, 32, p. 10096-10099 4 p.

Research output: Contribution to journalArticle

Fungal Proteins
Physiology
yeast
physiology
Proteins

Retrograde NGF axonal transport - Motor coordination in the unidirectional motility regime

Chowdary, P. D., Che, D. L., Zhang, K. & Cui, B., Jun 3 2015, In : Biophysical journal. 108, 11, p. 2691-2703 13 p., 6557.

Research output: Contribution to journalArticle

Axonal Transport
Endosomes
Nerve Growth Factor
Kinesin
Dyneins

Small-angle scattering determination of the shape and localization of human cytochrome P450 embedded in a phospholipid nanodisc environment

Skar-Gislinge, N., Kynde, S. A. R., Denisov, I. G., Ye, X., Lenov, I., Sligar, S. & Arleth, L., Jan 1 2015, In : Acta Crystallographica Section D: Biological Crystallography. 71, p. 2412-2421 10 p.

Research output: Contribution to journalArticle

Small Angle Scattering
Cytochrome P-450 CYP3A
Cytochrome P-450 Enzyme System
Phospholipids
Membrane Proteins

Structural Basis for Specificity and Flexibility in a Plant 4-Coumarate:CoA Ligase

Li, Z. & Nair, S. K., Nov 3 2015, In : Structure. 23, 11, p. 2032-2042 11 p.

Research output: Contribution to journalArticle

Coenzyme A Ligases
Adenosine Monophosphate
Tobacco
Protein Isoforms
Adenosine Triphosphate

Structural determinants of the mechanical stability of α-Catenin

Li, J., Newhall, J., Ishiyama, N., Gottardi, C., Ikura, M., Leckband, D. E. & Tajkhorshid, E., Jul 31 2015, In : Journal of Biological Chemistry. 290, 31, p. 18890-18903 14 p.

Research output: Contribution to journalArticle

Catenins
Mechanical stability
Cell adhesion
Molecular Dynamics Simulation
Cell Adhesion

Structure, Function and Inhibition of the Phosphoethanolamine Methyltransferases of the Human Malaria Parasites Plasmodium vivax and Plasmodium knowlesi

Garg, A., Lukk, T., Kumar, V., Choi, J. Y., Augagneur, Y., Voelker, D. R., Nair, S. & Mamoun, C. B., 2015, In : Scientific reports. 5, 9064.

Research output: Contribution to journalArticle

Plasmodium knowlesi
Vivax Malaria
Antimalarials
Parasites
Phosphatidylcholines

Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB

Ortega, M. A., Hao, Y., Zhang, Q., Walker, M. C., van der Donk, W. A. & Nair, S. K., Jan 22 2015, In : Nature. 517, 7535, p. 509-512 4 p.

Research output: Contribution to journalArticle

Hydro-Lyases
Bacteriocins
Transfer RNA
Dehydration
Nisin

Structure-Function Relationship of the Interaction between Tissue Factor and Factor VIIa

Gajsiewicz, J. M. & Morrissey, J. H., Sep 26 2015, In : Seminars in Thrombosis and Hemostasis. 41, 7, p. 682-690 9 p.

Research output: Contribution to journalArticle

Factor VIIa
Thromboplastin
Membrane Proteins
Proteins
Protein Folding

Structure-guided design and biosynthesis of a novel FR-900098 analogue as a potent Plasmodium falciparum 1-deoxy-d-xylulose-5-phosphate reductoisomerase (Dxr) inhibitor

Cobb, R. E., Bae, B., Li, Z., Desieno, M. A., Nair, S. K. & Zhao, H., Feb 14 2015, In : Chemical Communications. 51, 13, p. 2526-2528 3 p.

Research output: Contribution to journalArticle

Biosynthesis
Phosphates
Antimalarials
Derivatives
xylulose-5-phosphate

Studies of the TLR4-associated protein MD-2 using yeast-display and mutational analyses

Mattis, D. M., Chervin, A. S., Ranoa, D. R., Kelley, S. L., Tapping, R. I. & Kranz, D. M., May 8 2015, In : Molecular Immunology. 68, 2, p. 203-212 10 p.

Research output: Contribution to journalArticle

Toll-Like Receptor 4
Lipopolysaccharides
Yeasts
Proteins
Immune System

Substrate control in stereoselective lanthionine biosynthesis

Tang, W., Jiménez-Osés, G., Houk, K. N. & Van Der Donk, W. A., Jan 1 2015, In : Nature Chemistry. 7, 1, p. 57-64 8 p.

Research output: Contribution to journalArticle

Biosynthesis
Enzymes
Substrates
Stereoselectivity
Cyclization

Synergistic binding of the leader and core peptides by the lantibiotic synthetase HalM2

Thibodeaux, G. N., McClerren, A. L., Ma, Y., Gancayco, M. R. & van der Donk, W. A., Apr 17 2015, In : ACS chemical biology. 10, 4, p. 970-977 8 p.

Research output: Contribution to journalArticle

Peptide Synthases
Bacteriocins
Ligases
Protein Sorting Signals
Peptides

Synthesis of many different types of organic small molecules using one automated process

Li, J., Ballmer, S. G., Gillis, E. P., Fujii, S., Schmidt, M. J., Palazzolo, A. M. E., Lehmann, J. W., Morehouse, G. F. & Burke, M. D., Mar 13 2015, In : Science. 347, 6227, p. 1221-1226 6 p.

Research output: Contribution to journalArticle

Biological Products

Systematic Profiling of Poly(A)+ Transcripts Modulated by Core 3’ End Processing and Splicing Factors Reveals Regulatory Rules of Alternative Cleavage and Polyadenylation

Li, W., You, B., Hoque, M., Zheng, D., Luo, W., Ji, Z., Park, J. Y., Gunderson, S. I., Kalsotra, A., Manley, J. L. & Tian, B., Apr 1 2015, In : PLoS genetics. 11, 4, e1005166.

Research output: Contribution to journalArticle

Polyadenylation
Poly A
3' untranslated regions
cleavage
introns

Task-related differential expression of four cytochrome P450 genes in honeybee appendages

Mao, W., Schuler, M. A. & Berenbaum, M. R., Oct 1 2015, In : Insect Molecular Biology. 24, 5, p. 582-588 7 p.

Research output: Contribution to journalArticle

appendages
cytochrome P-450
Cytochrome P-450 Enzyme System
honey bees
Leg

The atypical occurrence of two biotin protein ligases in Francisella novicida is due to distinct roles in virulence and biotin metabolism

Feng, Y., Chin, C. Y., Chakravartty, V., Gao, R., Crispell, E. K., Weiss, D. S. & Cronan, J. E., Jun 9 2015, In : mBio. 6, 3

Research output: Contribution to journalArticle

Francisella
Ligases
Biotin
Virulence
Proteins

The conserved modular elements of the acyl carrier proteins of lipid synthesis are only partially interchangeable

Zhu, L. & Cronan, J. E., May 29 2015, In : Journal of Biological Chemistry. 290, 22, p. 13791-13799 9 p.

Research output: Contribution to journalArticle

Acyl Carrier Protein
Lactococcus lactis
Escherichia coli
Lipids
Proteins

The Dual Characteristics of Light-Induced Cryptochrome 2, Homo-oligomerization and Heterodimerization, for Optogenetic Manipulation in Mammalian Cells

Che, D. L., Duan, L., Zhang, K. & Cui, B., Oct 16 2015, In : ACS synthetic biology. 4, 10, p. 1124-1135 12 p.

Research output: Contribution to journalArticle

Cryptochromes
Optogenetics
Oligomerization
Hominidae
Cells

The enterococcal cytolysin synthetase has an unanticipated lipid kinase fold

Dong, S. H., Tang, W., Lukk, T., Yu, Y., Nair, S. K. & van der donk, W. A., Jul 30 2015, In : eLife. 4, JULY2015, e07607.

Research output: Contribution to journalArticle

Perforin
Ligases
Dehydration
Phosphotransferases
Lipids

The phosphoenolpyruvate: Sugar phosphotransferase system is involved in sensitivity to the glucosylated bacteriocin sublancin

Garcia De Gonzalo, C. V., Denham, E. L., Mars, R. A. T., Stülke, J., Van Der Donk, W. A. & Van Dijl, J. M., Nov 1 2015, In : Antimicrobial Agents and Chemotherapy. 59, 11, p. 6844-6854 11 p.

Research output: Contribution to journalArticle

Phosphoenolpyruvate Sugar Phosphotransferase System
Bacteriocins
Bacillus
Phosphotransferases
Gram-Positive Bacteria
Streptomyces coelicolor
Escherichia coli
Ligases
Enzymes
Adenosine Monophosphate

The two transmembrane helices of CcoP are sufficient for assembly of the cbb3-type heme-copper oxygen reductase from Vibrio cholerae

Ahn, Y. O., Lee, H. J., Kaluka, D., Yeh, S. R., Rousseau, D. L., Ädelroth, P. & Gennis, R. B., Jul 13 2015, In : Biochimica et Biophysica Acta - Bioenergetics. 1847, 10, p. 1231-1239 9 p.

Research output: Contribution to journalArticle

Vibrio cholerae
Heme
Copper
Oxidoreductases
Oxygen

Tissue Factor Residues That Modulate Magnesium-Dependent Rate Enhancements of the Tissue Factor/Factor VIIa Complex

Gajsiewicz, J. M., Nuzzio, K. M., Rienstra, C. M. & Morrissey, J. H., Aug 4 2015, In : Biochemistry. 54, 30, p. 4665-4671 7 p.

Research output: Contribution to journalArticle

Factor VIIa
Factor X
Thromboplastin
Magnesium
Ions

U0126 protects cells against oxidative stress independent of its function as a MEK inhibitor

Ong, Q., Guo, S., Zhang, K. & Cui, B., Jan 21 2015, In : ACS Chemical Neuroscience. 6, 1, p. 130-137 8 p.

Research output: Contribution to journalArticle

Oxidative stress
Mitogen-Activated Protein Kinase Kinases
Oxidative Stress
MAP Kinase Signaling System
Reactive Oxygen Species

Uncovering RNA binding proteins associated with age and gender during liver maturation

Chaturvedi, P., Neelamraju, Y., Arif, W., Kalsotra, A. & Janga, S. C., Mar 2015, In : Scientific reports. 5, 9512.

Research output: Contribution to journalArticle

RNA-Binding Proteins
Liver
Protein Interaction Maps
Gene Expression
Cluster Analysis

Unveiling the crucial intermediates in androgen production

Mak, P. J., Gregory, M. C., Denisov, I. G., Sligar, S. G. & Kincaid, J. R., Dec 29 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 52, p. 15856-15861 6 p.

Research output: Contribution to journalArticle

Androgens
Lyases
Carbon
17-alpha-Hydroxypregnenolone
Pregnenolone

Visualizing directional rab7 and trka cotrafficking in axons by ptirf microscopy

Zhang, K., Chowdary, P. D. & Cui, B., Jan 1 2015, In : Methods in Molecular Biology. 1298, p. 319-329 11 p.

Research output: Contribution to journalArticle

Endosomes
Axons
Microscopy
Nerve Growth Factor
trkA Receptor
2014

A catalytic role for methionine revealed by a combination of computation and experiments on phosphite dehydrogenase

Ranaghan, K. E., Hung, J. E., Bartlett, G. J., Mooibroek, T. J., Harvey, J. N., Woolfson, D. N., Van Der Donk, W. A. & Mulholland, A. J., Jun 2014, In : Chemical Science. 5, 6, p. 2191-2199 9 p.

Research output: Contribution to journalArticle

Molecular mechanics
Quantum theory
Methionine
Norleucine
Phosphites

Active site proton delivery and the lyase activity of human CYP17A1

Khatri, Y., Gregory, M. C., Grinkova, Y. V., Denisov, I. G. & Sligar, S., Jan 3 2014, In : Biochemical and Biophysical Research Communications. 443, 1, p. 179-184 6 p.

Research output: Contribution to journalArticle

Lyases
Human Activities
Protons
Catalytic Domain
Carbon

Affinity-based design of a synthetic universal reversal agent for heparin anticoagulants

Shenoi, R. A., Kalathottukaren, M. T., Travers, R. J., Lai, B. F. L., Creagh, A. L., Lange, D., Yu, K., Weinhart, M., Chew, B. H., Du, C., Brooks, D. E., Carter, C. J., Morrissey, J. H., Haynes, C. A. & Kizhakkedathu, J. N., Oct 29 2014, In : Science Translational Medicine. 6, 260, 260ra150.

Research output: Contribution to journalArticle

Anticoagulants
Heparin
Antidotes
Hemorrhage
Polymers

Affinity-based design of a synthetic universal reversal agent for heparin anticoagulants

Shenoi, R. A., Kalathottukaren, M. T., Travers, R. J., Lai, B. F. L., Creagh, A. L., Lange, D., Yu, K., Weinhart, M., Chew, B. H., Du, C., Brooks, D. E., Carter, C. J., Morrissey, J. H., Haynes, C. A. & Kizhakkedathu, J. N., Oct 29 2014, In : Science Translational Medicine. 6, 260, 260ra150.

Research output: Contribution to journalArticle

Open Access
Anticoagulants
Heparin
Antidotes
Hemorrhage
Polymers

A Francisella virulence factor catalyses an essential reaction of biotin synthesis

Feng, Y., Napier, B. A., Manandhar, M., Henke, S. K., Weiss, D. S. & Cronan, J. E., Jan 1 2014, In : Molecular Microbiology. 91, 2, p. 300-314 15 p.

Research output: Contribution to journalArticle

Francisella
Virulence Factors
Biotin
Virulence
Escherichia

A highly tilted membrane configuration for the prefusion state of synaptobrevin

Blanchard, A. E., Arcario, M. J., Schulten, K. & Tajkhorshid, E., Nov 4 2014, In : Biophysical journal. 107, 9, p. 2112-2121 10 p.

Research output: Contribution to journalArticle

R-SNARE Proteins
Membranes
SNARE Proteins
Exocytosis
Lipid Bilayers

Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development

Giudice, J., Xia, Z., Wang, E. T., Scavuzzo, M. A., Ward, A. J., Kalsotra, A., Wang, W., Wehrens, X. H. T., Burge, C. B., Li, W. & Cooper, T. A., Apr 22 2014, In : Nature communications. 5, 3603.

Research output: Contribution to journalArticle

splicing
Alternative Splicing
Cardiac Myocytes
genes
Genes

A mechanically-induced colon cancer cell population shows increased metastatic potential

Tang, X., Kuhlenschmidt, T. B., Li, Q., Ali, S., Lezmi, S., Chen, H., Pires-Alves, M., Laegreid, W. W., Saif, T. A. & Kuhlenschmidt, M. S., May 29 2014, In : Molecular Cancer. 13, 1, 131.

Research output: Contribution to journalArticle

Colonic Neoplasms
Population
Neoplasm Metastasis
Anoikis
Tumor Microenvironment

A microscopic view of phospholipid insertion into biological membranes

Vermaas, J. V. & Tajkhorshid, E., Feb 20 2014, In : Journal of Physical Chemistry B. 118, 7, p. 1754-1764 11 p.

Research output: Contribution to journalArticle

Biological membranes
Phospholipids
insertion
membranes
Membranes

A microscopic view of the mechanisms of active transport across the cellular membrane

Enkavi, G., Li, J., Wen, P., Thangapandian, S., Moradi, M., Jiang, T., Han, W. & Tajkhorshid, E., Jan 1 2014, In : Annual Reports in Computational Chemistry. 10, p. 77-125 49 p.

Research output: Contribution to journalArticle

Membrane
Proteins
Membranes
Protein
Substrate

Amphotericin forms an extramembranous and fungicidal sterol sponge

Anderson, T. M., Clay, M. C., Cioffi, A. G., Diaz, K. A., Hisao, G. S., Tuttle, M. D., Nieuwkoop, A. J., Comellas, G., Maryum, N., Wang, S., Uno, B. E., Wildeman, E. L., Gonen, T., Rienstra, C. M. & Burke, M. D., May 2014, In : Nature chemical biology. 10, 5, p. 400-406 7 p.

Research output: Contribution to journalArticle

Porifera
Amphotericin B
Sterols
Yeasts
Lipid Bilayers
Fatty Acid Synthesis Inhibitors
Fatty Acids
Bacteria
Anhydrides
Infection
Succinic Acid
Escherichia coli
Growth
Succinate Dehydrogenase
Ligases

A novel T cell receptor single-chain signaling complex mediates antigen-specific T cell activity and tumor control

Stone, J. D., Harris, D. T., Soto, C. M., Chervin, A. S., Aggen, D. H., Roy, E. J. & Kranz, D. M., Jan 1 2014, In : Cancer Immunology, Immunotherapy. 63, 11, p. 1163-1176 14 p.

Research output: Contribution to journalArticle

T-Cell Antigen Receptor
T-Lymphocytes
Antigens
Neoplasms
Immunoglobulin Fragments
Ligases
Substrate Specificity
substrate
kinetics
Kinetics

Archaeal Elp3 catalyzes tRNA wobble uridine modification at C5 via a radical mechanism

Selvadurai, K., Wang, P., Seimetz, J. & Huang, R. H., Oct 1 2014, In : Nature chemical biology. 10, 10, p. 810-812 3 p.

Research output: Contribution to journalArticle

Archaeal Proteins
Acetyl Coenzyme A
Uridine
Transfer RNA

Assembly of an activated rhodopsin-transducin complex in nanoscale lipid bilayers

D'Antona, A. M., Xie, G., Sligar, S. G. & Oprian, D. D., Jan 14 2014, In : Biochemistry. 53, 1, p. 127-134 8 p.

Research output: Contribution to journalArticle

Transducin
Lipid bilayers
Rhodopsin
Lipid Bilayers
Stoichiometry

A third subunit in ancestral cytochrome c-dependent nitric oxide reductases

Bricio, C., Alvarez, L., San Martin, M., Schurig-Briccio, L. A., Gennis, R. B. & Berenguer, J., Aug 2014, In : Applied and environmental microbiology. 80, 16, p. 4871-4878 8 p.

Research output: Contribution to journalArticle

cytochrome c
nitric oxide
Cytochromes c
cytochrome
Thermus thermophilus

Atomistic models of general anesthetics for use in in silico biological studies

Arcario, M. J., Mayne, C. G. & Tajkhorshid, E., Oct 23 2014, In : Journal of Physical Chemistry B. 118, 42, p. 12075-12086 12 p.

Research output: Contribution to journalArticle

anesthetics
Anesthetics
General Anesthetics
Computer Simulation
membranes