Research Output 1979 2019

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Article
2015
13 Citations (Scopus)
Treponema pallidum
Spirochaetales
Flavin-Adenine Dinucleotide
Protein Transport
Syphilis
13 Citations (Scopus)

Evolutionary conservation of complexins: From choanoflagellates to mice

Yang, X., Pei, J., Kaeser-Woo, Y. J., Bacaj, T., Grishin, N. V. & Südhof, T. C., Oct 1 2015, In : EMBO Reports. 16, 10, p. 1308-1317 10 p.

Research output: Contribution to journalArticle

Choanoflagellata
Synaptotagmins
Exocytosis
Conservation
Synaptic Vesicles
24 Citations (Scopus)

Fitting two- and three-site binding models to isothermal titration calorimetric data

Brautigam, C. A., Apr 1 2015, In : Methods. 76, p. 124-136 13 p.

Research output: Contribution to journalArticle

Calorimetry
Titration
Binding Sites
Isotherms
Thermodynamics
396 Citations (Scopus)

Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins

Lin, Y., Protter, D. S. W., Rosen, M. K. & Parker, R., Oct 15 2015, In : Molecular Cell. 60, 2, p. 208-219 12 p.

Research output: Contribution to journalArticle

RNA-Binding Proteins
RNA
Salts
Fluorescence Recovery After Photobleaching
Eukaryotic Cells
44 Citations (Scopus)

High-precision, automated integration of multiple isothermal titration calorimetric thermograms: New features of NITPIC

Scheuermann, T. H. & Brautigam, C. A., Apr 1 2015, In : Methods. 76, p. 87-98 12 p.

Research output: Contribution to journalArticle

Calorimetry
Titration
Preclinical Drug Evaluations
Thermodynamics
Isotherms
9 Citations (Scopus)
Treponema pallidum
Membrane Potentials
Lipoproteins
Membranes
Disulfides
27 Citations (Scopus)

Isoform-Selective and Stereoselective Inhibition of Hypoxia Inducible Factor-2

Scheuermann, T. H., Stroud, D., Sleet, C. E., Bayeh, L., Shokri, C., Wang, H., Caldwell, C. G., Longgood, J., MacMillan, J. B., Bruick, R. K., Gardner, K. H. & Tambar, U. K., Jul 30 2015, In : Journal of Medicinal Chemistry. 58, 15, p. 5930-5941 12 p.

Research output: Contribution to journalArticle

Protein Isoforms
Transcription Factors
Oxygen
Protein Conformation
Homeostasis
26 Citations (Scopus)

KDM4/JMJD2 Histone Demethylase Inhibitors Block Prostate Tumor Growth by Suppressing the Expression of AR and BMYB-Regulated Genes

Duan, L., Rai, G., Roggero, C., Zhang, Q. J., Wei, Q., Ma, S. H., Zhou, Y., Santoyo, J., Martinez, E. D., Xiao, G., Raj, G., Jadhav, A., Simeonov, A., Maloney, D. J., Rizo-Rey, J., Hsieh, J-T. & Liu, Z-P., Apr 11 2015, In : Chemistry and Biology. 22, 9, p. 1185-1196 12 p.

Research output: Contribution to journalArticle

Histone Demethylases
Androgen Receptors
Tumors
Prostate
Genes
104 Citations (Scopus)

Large-scale determination of previously unsolved protein structures using evolutionary information

Ovchinnikov, S., Kinch, L., Park, H., Liao, Y., Pei, J., Kim, D. E., Kamisetty, H., Grishin, N. V. & Baker, D., Sep 3 2015, In : eLife. 4, September, e09248.

Research output: Contribution to journalArticle

Proteins
Model structures
Set theory
10 Citations (Scopus)

Ligand-induced folding of a two-component signaling receiver domain

Ocasio, V. J., Corrêa, F. & Gardner, K. H., Feb 17 2015, In : Biochemistry. 54, 6, p. 1353-1363 11 p.

Research output: Contribution to journalArticle

Phosphorylation
Ligands
Phosphoric Monoester Hydrolases
Histidine
Sphingomonadaceae
13 Citations (Scopus)

Manual classification strategies in the ECOD database

Cheng, H., Liao, Y., Schaeffer, R. D. & Grishin, N. V., Jul 1 2015, In : Proteins: Structure, Function and Bioinformatics. 83, 7, p. 1238-1251 14 p.

Research output: Contribution to journalArticle

Protein Databases
Proteins
Databases
Protein Domains
Computational Biology
25 Citations (Scopus)

Methyl labeling and TROSY NMR spectroscopy of proteins expressed in the eukaryote Pichia pastoris

Clark, L., Zahm, J. A., Ali, R., Kukula, M., Bian, L., Patrie, S. M., Gardner, K. H., Rosen, M. & Rosenbaum, D. M., May 30 2015, (Accepted/In press) In : Journal of Biomolecular NMR.

Research output: Contribution to journalArticle

Biomolecular Nuclear Magnetic Resonance
Pichia
Eukaryota
Labeling
Nuclear magnetic resonance spectroscopy
32 Citations (Scopus)

Nuclear export inhibitors avert progression in preclinical models of inflammatory demyelination

Haines, J. D., Herbin, O., De La Hera, B., Vidaurre, O. G., Moy, G. A., Sun, Q., Fung, H. Y. J., Albrecht, S., Alexandropoulos, K., McCauley, D., Chook, Y. M., Kuhlmann, T., Kidd, G. J., Shacham, S. & Casaccia, P., Apr 28 2015, In : Nature Neuroscience. 18, 4, p. 511-520 10 p.

Research output: Contribution to journalArticle

Cell Nucleus Active Transport
Demyelinating Diseases
Gene Knockdown Techniques
Neurons
Kainic Acid
50 Citations (Scopus)

Nuclear localization signals for four distinct Karyopherin-β nuclear import systems

Soniat, M. & Chook, Y. M., Jun 15 2015, In : Biochemical Journal. 468, 3, p. 353-362 10 p.

Research output: Contribution to journalArticle

Karyopherins
Nuclear Localization Signals
Cell Nucleus Active Transport
Proline
Tyrosine
28 Citations (Scopus)

Real-time resolution of point mutations that cause phenovariance in mice

Wang, T., Zhan, X., Bua, C. H., Lyona, S., Pratta, D., Hildebrand, S., Choi, J. H., Zhang, Z., Zeng, M., Wang, K. W., Turer, E. E., Chen, Z., Zhang Ph.D., D-W., Yue, T., Wang, Y., Shi, H-X., Wang, J., Sun, L., SoRelle, J., McAlpine, W. & 28 others, Hutchins, N., Zhan, X., Fin, M., Gobert, R., Quan, J., Kreutzer, M., Arnett, S., Hawkins, K., Leach, A., Tate, C., Daniel, C., Reyna, C., Prince, L., Davis, S., Purrington, J., Bearden, R., Weatherly, J., White, D., Russell, J. L., Sun, Q., Tang, M., Li, X., Scott, L., Moresco, E. M. Y., McInerney, G. M., Karlsson Hedestam, G. B., Xie, Y. & Beutler, B. A., Feb 3 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 5, p. E440-E449

Research output: Contribution to journalArticle

Point Mutation
Mutation
Ethylnitrosourea
Phenotype
High-Throughput Nucleotide Sequencing
2 Citations (Scopus)

Refinement by shifting secondary structure elements improves sequence alignments

Tong, J., Pei, J., Otwinowski, Z. & Grishin, N. V., Mar 1 2015, In : Proteins: Structure, Function and Bioinformatics. 83, 3, p. 411-427 17 p.

Research output: Contribution to journalArticle

Sequence Alignment
Benchmarking
Proteins
Servers
227 Citations (Scopus)

Sampling the conformational space of the catalytic subunit of human g-secretase

Bai, X. C., Rajendra, E., Yang, G., Shi, Y. & Scheres, S. H. W., Dec 1 2015, In : eLife. 4, December2015, e11182.

Research output: Contribution to journalArticle

Amyloid Precursor Protein Secretases
Catalytic Domain
Presenilins
Sampling
Conformations
5 Citations (Scopus)
Rho Guanine Nucleotide Exchange Factors
PDZ Domains
Binding Sites
Ligands
Guanine Nucleotide Exchange Factors
63 Citations (Scopus)

Sensitivity-Enhanced NMR Reveals Alterations in Protein Structure by Cellular Milieus

Frederick, K. K., Michaelis, V. K., Corzilius, B., Ong, T. C., Jacavone, A. C., Griffin, R. G. & Lindquist, S., Oct 22 2015, In : Cell. 163, 3, p. 620-628 9 p.

Research output: Contribution to journalArticle

Cellular Structures
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance
Polarization
Proteins

SFESA: A web server for pairwise alignment refinement by secondary structure shifts

Tong, J., Pei, J. & Grishin, N. V., Sep 3 2015, In : BMC Bioinformatics. 16, 1, 282.

Research output: Contribution to journalArticle

Web Server
Secondary Structure
Pairwise
Alignment
Refinement
19 Citations (Scopus)

Skipper genome sheds light on unique phenotypic traits and phylogeny

Cong, Q., Borek, D., Otwinowski, Z. & Grishin, N. V., Aug 27 2015, In : BMC Genomics. 16, 1, 639.

Research output: Contribution to journalArticle

Lepidoptera
Phylogeny
Butterflies
Genome
Moths
45 Citations (Scopus)

Structural Basis and IP6 Requirement for Pds5-Dependent Cohesin Dynamics

Ouyang, Z., Zheng, G., Tomchick, D. R., Luo, X. & Yu, H., Nov 16 2015, (Accepted/In press) In : Molecular Cell.

Research output: Contribution to journalArticle

Chromosomes
Chromosome Segregation
DNA Repair
cohesins
Phytic Acid
27 Citations (Scopus)

Structural determinants of nuclear export signal orientation in binding to exportin CRM1

Fung, H. Y. J., Fu, S. C., Brautigam, C. A. & Chook, Y. M., Sep 8 2015, In : eLife. 4, September 2015, e10034.

Research output: Contribution to journalArticle

Nuclear Export Signals
Karyopherins
Chromosomes
Maintenance
Protein Sorting Signals
66 Citations (Scopus)

Structural organization of nuclear lamins A, C, B1, and B2 revealed by superresolution microscopy

Shimia, T., Kittisopikul, M., Tran, J., Goldman, A. E., Adam, S. A., Zheng, Y., Jaqaman, K. & Goldman, R. D., Nov 5 2015, In : Molecular Biology of the Cell. 26, 22, p. 4075-4086 12 p.

Research output: Contribution to journalArticle

Nuclear Lamina
Lamins
Lamin Type A
Microscopy
Protein Isoforms
53 Citations (Scopus)

Structure of a Yeast 40S-eIF1-eIF1A-eIF3-eIF3j initiation complex

Aylett, C. H. S., Boehringer, D., Erzberger, J. P., Schaefer, T. & Ban, N., Jan 1 2015, In : Nature Structural and Molecular Biology. 22, 3, p. 269-271 3 p.

Research output: Contribution to journalArticle

Eukaryotic Small Ribosome Subunits
Saccharomycetales
Ribosomes
Yeasts
Proteins
30 Citations (Scopus)

Structure of the apoptosome: Mechanistic insights into activation of an initiator caspase from Drosophila

Pang, Y., Bai, X. C., Yan, C., Hao, Q., Chen, Z., Wang, J. W., Scheres, S. H. W. & Shi, Y., Jan 1 2015, In : Genes and Development. 29, 3, p. 277-287 11 p.

Research output: Contribution to journalArticle

Apoptosomes
Initiator Caspases
Drosophila
Caspase 9
Enzyme Precursors
227 Citations (Scopus)

Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution

Yan, Z., Bai, X. C., Yan, C., Wu, J., Li, Z., Xie, T., Peng, W., Yin, C. C., Li, X., Scheres, S. H. W., Shi, Y. & Yan, N., Jan 1 2015, In : Nature. 517, 7532, p. 50-55 6 p.

Research output: Contribution to journalArticle

Ryanodine Receptor Calcium Release Channel
Allosteric Regulation
Rabbits
Ion Channels
Tacrolimus Binding Protein 1A
64 Citations (Scopus)

Syntaxin opening by the MUN domain underlies the function of Munc13 in synaptic-vesicle priming

Yang, X., Wang, S., Sheng, Y., Zhang, M., Zou, W., Wu, L., Kang, L., Rizo-Rey, J., Zhang, R., Xu, T. & Ma, C., Jul 9 2015, In : Nature Structural and Molecular Biology. 22, 7, p. 547-554 8 p.

Research output: Contribution to journalArticle

Qa-SNARE Proteins
SNARE Proteins
Synaptic Vesicles
Syntaxin 1
Mutation
123 Citations (Scopus)

The architecture of the spliceosomal U4/U6.U5 tri-snRNP

Nguyen, T. H. D., Galej, W. P., Bai, X. C., Savva, C. G., Newman, A. J., Scheres, S. H. W. & Nagai, K., Jul 1 2015, In : Nature. 523, 7558, p. 47-52 6 p.

Research output: Contribution to journalArticle

U5 Small Nuclear Ribonucleoproteins
Small Nuclear Ribonucleoproteins
Spliceosomes
Catalytic Domain
U2 Small Nuclear Ribonucleoproteins
30 Citations (Scopus)

The Cdc20-binding Phe box of the spindle checkpoint protein BubR1 maintains the mitotic checkpoint complex during mitosis

Diaz-Martinez, L. A., Tian, W., Li, B., Warrington, R., Jia, L., Brautigam, C. A., Luo, X. & Yu, H., Jan 23 2015, In : Journal of Biological Chemistry. 290, 4, p. 2431-2443 13 p.

Research output: Contribution to journalArticle

Anaphase-Promoting Complex-Cyclosome
M Phase Cell Cycle Checkpoints
Mitosis
Ligases
Chromosomes
11 Citations (Scopus)

The complete mitochondrial genome of Papilio glaucus and its phylogenetic implications

Shen, J., Cong, Q. & Grishin, N. V., Sep 1 2015, In : Meta Gene. 5, p. 68-83 16 p.

Research output: Contribution to journalArticle

Lepidoptera
Mitochondrial Genome
Genetic Speciation
Genome
Butterflies
132 Citations (Scopus)

The Synaptic Vesicle Release Machinery

Rizo-Rey, J. & Xu, J., Jun 22 2015, In : Annual Review of Biophysics. 44, p. 339-367 29 p.

Research output: Contribution to journalArticle

SNARE Proteins
Synaptic Vesicles
Syntaxin 1
Machinery
Fusion reactions
41 Citations (Scopus)

Tiger Swallowtail Genome Reveals Mechanisms for Speciation and Caterpillar Chemical Defense

Cong, Q., Borek, D., Otwinowski, Z. & Grishin, N. V., Feb 17 2015, In : Cell Reports. 10, 6, p. 910-919 10 p.

Research output: Contribution to journalArticle

Genes
Genome
Mutation
Circadian Clocks
Terpenes
23 Citations (Scopus)

Type VI Secretion System Toxins Horizontally Shared between Marine Bacteria

Salomon, D., Klimko, J. A., Trudgian, D. C., Kinch, L. N., Grishin, N. V., Mirzaei, H. & Orth, K., Aug 1 2015, In : PLoS Pathogens. 11, 8, e1005128.

Research output: Contribution to journalArticle

Vibrio alginolyticus
Bacteria
Horizontal Gene Transfer
Vibrio
Poisons
4 Citations (Scopus)

Using homology relations within a database markedly boosts protein sequence similarity search

Tong, J., Sadreyev, R. I., Pei, J., Kinch, L. N. & Grishin, N. V., Jun 2 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 22, p. 7003-7008 6 p.

Research output: Contribution to journalArticle

Databases
Amino Acid Sequence Homology
Proteins
Search Engine
Sequence Alignment
2014
51 Citations (Scopus)

Actin cytoskeleton reorganization by syk regulates fcγ receptor responsiveness by increasing its lateral mobility and clustering

Jaumouillé, V., Farkash, Y., Jaqaman, K., Das, R., Lowell, C. A. & Grinstein, S., Jun 9 2014, In : Developmental Cell. 29, 5, p. 534-546 13 p.

Research output: Contribution to journalArticle

Fc Receptors
Actin Cytoskeleton
Phagocytosis
Cluster Analysis
Actins
131 Citations (Scopus)

An optogenetic gene expression system with rapid activation and deactivation kinetics

Motta-Mena, L. B., Reade, A., Mallory, M. J., Glantz, S., Weiner, O. D., Lynch, K. W. & Gardner, K. H., Mar 2014, In : Nature Chemical Biology. 10, 3, p. 196-202 7 p.

Research output: Contribution to journalArticle

Optogenetics
Gene Expression
Light
Zebrafish
Transcriptional Activation
117 Citations (Scopus)

Antibacterial membrane attack by a pore-forming intestinal C-type lectin

Mukherjee, S., Zheng, H., Derebe, M. G., Callenberg, K. M., Partch, C. L., Rollins, D., Propheter, D. C., Rizo-Rey, J., Grabe, M., Jiang, Q. X. & Hooper, L. V., 2014, In : Nature. 505, 7481, p. 103-107 5 p.

Research output: Contribution to journalArticle

C-Type Lectins
Bacteria
Membranes
Symbiosis
Peptidoglycan
82 Citations (Scopus)

A plug release mechanism for membrane permeation by MLKL

Su, L., Quade, B., Wang, H., Sun, L., Wang, X. & Rizo-Rey, J., Sep 13 2014, In : Structure. 22, 10, p. 1489-1500 12 p.

Research output: Contribution to journalArticle

Membranes
Phosphorylation
Fluorescence Spectrometry
Liposomes
Phosphotransferases
127 Citations (Scopus)

Architecture of the large subunit of the mammalian mitochondrial ribosome

Greber, B. J., Boehringer, D., Leitner, A., Bieri, P., Voigts-Hoffmann, F., Erzberger, J. P., Leibundgut, M., Aebersold, R. & Ban, N., Jan 10 2014, In : Nature. 505, 7484, p. 515-519 5 p.

Research output: Contribution to journalArticle

Mitochondria
Cryoelectron Microscopy
Ribosomal RNA
Ribosomal Proteins
Oxidative Phosphorylation
47 Citations (Scopus)

A tethered delivery mechanism explains the catalytic action of a microtubule polymerase

Ayaz, P., Munyoki, S., Geyer, E. A., Piedra, F. A., Vu, E. S., Bromberg, R., Otwinowski, Z., Grishin, N. V., Brautigam, C. A. & Rice, L. M., 2014, In : eLife. 3, p. e03069

Research output: Contribution to journalArticle

Tubulin
Microtubules
Microtubule Proteins
Yeast
Conformations
58 Citations (Scopus)

Atomic basis of CRM1-cargo recognition, release and inhibition

Fung, H. Y. J. & Chook, Y. M., 2014, In : Seminars in Cancer Biology. 27, p. 52-61 10 p.

Research output: Contribution to journalArticle

Cell Nucleus Active Transport
Cytoplasm
Short Interspersed Nucleotide Elements
Nuclear Export Signals
Neoplasms
17 Citations (Scopus)

Bimodal-hybrid heterocyclic amine targeting oxidative pathways and copper mis-regulation in Alzheimer's disease

Gonzalez, P., Da Costa, V. C. P., Hyde, K., Wu, Q., Annunziata, O., Rizo-Rey, J., Akkaraju, G. & Green, K. N., Nov 1 2014, In : Metallomics. 6, 11, p. 2072-2082 11 p.

Research output: Contribution to journalArticle

Amyloid
Amines
Copper
Alzheimer Disease
Metals
11 Citations (Scopus)

Chemically functionalized carbon films for single molecule imaging

Llaguno, M. C., Xu, H., Shi, L., Huang, N., Zhang, H., Liu, Q. & Jiang, Q. X., Mar 2014, In : Journal of Structural Biology. 185, 3, p. 405-417 13 p.

Research output: Contribution to journalArticle

Carbon
Gi-Go GTP-Binding Protein alpha Subunits
RNA
Ligands
Macromolecular Substances
128 Citations (Scopus)

Chloride sensing by WNK1 involves inhibition of autophosphorylation

Piala, A. T., Moon, T. M., Akella, R., He, H., Cobb, M. H. & Goldsmith, E. J., May 6 2014, In : Science Signaling. 7, 324, ra41.

Research output: Contribution to journalArticle

Chlorides
Sodium Chloride
Phosphorylation
Phosphotransferases
Potassium Chloride
23 Citations (Scopus)
Stachybotrys
Trichothecenes
Multigene Family
Fungi
Genome
117 Citations (Scopus)

Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine

Wong, W., Bai, X. C., Brown, A., Fernandez, I. S., Hanssen, E., Condron, M., Tan, Y. H., Baum, J. & Scheres, S. H. W., Jan 1 2014, In : eLife. 3

Research output: Contribution to journalArticle

Emetine
Plasmodium falciparum
Ribosomes
Parasites
Antimalarials
88 Citations (Scopus)

ECOD: An Evolutionary Classification of Protein Domains

Cheng, H., Schaeffer, R. D., Liao, Y., Kinch, L. N., Pei, J., Shi, S., Kim, B. H. & Grishin, N. V., Dec 1 2014, In : PLoS Computational Biology. 10, 12

Research output: Contribution to journalArticle

Proteins
Protein
protein
proteins
Protein Structure
40 Citations (Scopus)

Ena/VASP proteins cooperate with the WAVE complex to regulate the actin cytoskeleton

Chen, X. J., Squarr, A. J., Stephan, R., Chen, B., Higgins, T. E., Barry, D. J., Martin, M. C., Rosen, M. K., Bogdan, S. & Way, M., Sep 8 2014, In : Developmental Cell. 30, 5, p. 569-584 16 p.

Research output: Contribution to journalArticle

Actin Cytoskeleton
Actins
Polymerization
Cell Movement
Pseudopodia
5 Citations (Scopus)

Erratum: Retromer Binding to FAM21 and the WASH Complex Is Perturbed by the Parkinson Disease-Linked VPS35(D620N) Mutation (Current Biology (2014) 24 (1670-1676))

McGough, I. J., Steinberg, F., Jia, D., Barbuti, P. A., McMillan, K. J., Heesom, K. J., Whone, A. L., Caldwell, M. A., Billadeau, D. D., Rosen, M. K. & Cullen, P. J., Jul 21 2014, In : Current Biology. 24, 14, p. 1678 1 p.

Research output: Contribution to journalArticle