Research Output

2005

Natural-like function in artificial WW domains

Russ, W. P., Lowery, D. M., Mishra, P., Yaffe, M. B. & Ranganathan, R., Sep 22 2005, In : Nature. 437, 7058, p. 579-583 5 p.

Research output: Contribution to journalArticle

175 Scopus citations

Neuropeptide B-deficient mice demonstrate hyperalgesia in response to inflammatory pain

Kelly, M. A., Beuckmann, C. T., Williams, S. C., Sinton, C. M., Motoike, T., Richardson, J. A., Hammer, R. E., Garry, M. G. & Yanagisawa, M., Jul 12 2005, In : Proceedings of the National Academy of Sciences of the United States of America. 102, 28, p. 9942-9947 6 p.

Research output: Contribution to journalArticle

45 Scopus citations

NMR analyses of the activation of the Arp2/3 complex by neuronal Wiskott-Aldrich syndrome protein

Kreishman-Deitrick, M., Goley, E. D., Burdine, L., Denison, C., Egile, C., Li, R., Murali, N., Kodadek, T. J., Welch, M. D. & Rosen, M. K., Nov 22 2005, In : Biochemistry. 44, 46, p. 15247-15256 10 p.

Research output: Contribution to journalArticle

39 Scopus citations

p53-Mdm2 loop controlled by a balance of its feedback strength and effective dampening using ATM and delayed feedback

Wagner, J., Ma, L., Rice, J. J., Hu, W., Levine, A. J. & Stolovitzky, G. A., Sep 1 2005, In : IEE Proceedings Systems Biology. 152, 3, p. 109-117 9 p.

Research output: Contribution to journalArticle

69 Scopus citations

Q & A. Elliott Ross.

Ross, E., Dec 6 2005, In : Current biology : CB. 15, 23, p. R942-943

Research output: Contribution to journalArticle

Robustness analysis of biochemical networks using μ-analysis and hybrid optimisation

Kim, J., Bates, D. G., Postlethwaite, I., Ma, L. & Iglesias, P. A., Dec 1 2005, Proceedings of the 44th IEEE Conference on Decision and Control, and the European Control Conference, CDC-ECC '05. p. 6234-6239 6 p. 1583160. (Proceedings of the 44th IEEE Conference on Decision and Control, and the European Control Conference, CDC-ECC '05; vol. 2005).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Schoenheimer effect explained - Feedback regulation of cholesterol synthesis in mice mediated by Insig proteins

Engelking, L., Liang, G., Hammer, R. E., Takaishi, K., Kuriyama, H., Evers, B. M., Li, W. P., Horton, J. D., Goldstein, J. L. & Brown, M. S., Sep 1 2005, In : Journal of Clinical Investigation. 115, 9, p. 2489-2498 10 p.

Research output: Contribution to journalArticle

158 Scopus citations

Self renewal, expansion, and transfection of rat spermatogonial stem cells in culture

Hamra, F. K., Chapman, K. M., Nguyen, D. M., Williams-Stephens, A. A., Hammer, R. E. & Garbers, D. L., Nov 29 2005, In : Proceedings of the National Academy of Sciences of the United States of America. 102, 48, p. 17430-17435 6 p.

Research output: Contribution to journalArticle

165 Scopus citations

Spinophilin regulates Ca2+ signalling by binding the N-terminal domain of RGS2 and the third intracellular loop of G-protein-coupled receptors

Wang, X., Zeng, W., Syombo, A. A., Tang, W., Ross, E. M., Barnes, A. P., Milgram, S. L., Penninger, J. M., Allen, P. B., Greengard, P. & Muallem, S., Apr 1 2005, In : Nature Cell Biology. 7, 4, p. 405-411 7 p.

Research output: Contribution to journalArticle

122 Scopus citations

Stochastic model for Soj relocation dynamics in Bacillus subtilis

Doubrovinski, K. & Howard, M., Jul 12 2005, In : Proceedings of the National Academy of Sciences of the United States of America. 102, 28, p. 9808-9813 6 p.

Research output: Contribution to journalArticle

28 Scopus citations

Structural basis of actin filament nucleation and processive capping by a formin homology 2 domain

Otomo, T., Tomchick, D. R., Otomo, C., Panchal, S. C., Machius, M. & Rosen, M. K., Feb 3 2005, In : Nature. 433, 7025, p. 488-494 7 p.

Research output: Contribution to journalArticle

251 Scopus citations

Structural basis of Rho GTPase-mediated activation of the formin mDia1

Otomo, T., Otomo, C., Tomchick, D. R., Machius, M. & Rosen, M. K., Apr 29 2005, In : Molecular cell. 18, 3, p. 273-281 9 p.

Research output: Contribution to journalArticle

176 Scopus citations

Structure and function of Formin homology 2 domain

Otomo, T. & Rosen, M. K., Aug 2005, In : Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme. 50, 9, p. 1088-1093 6 p.

Research output: Contribution to journalReview article

1 Scopus citations

Structure of the ectodomain of Drosophila peptidoglycan-recognition protein LCa suggests a molecular mechanism for pattern recognition

Chang, C. I., Ihara, K., Chelliah, Y., Mengin-Lecreulx, D., Wakatsuki, S. & Deisenhofer, J., Jul 19 2005, In : Proceedings of the National Academy of Sciences of the United States of America. 102, 29, p. 10279-10284 6 p.

Research output: Contribution to journalArticle

64 Scopus citations

The homeodomain protein PDX1 is required at mid-pancreatic development for the formation of the exocrine pancreas

Hale, M. A., Kagami, H., Shi, L., Holland, A. M., Elsässer, H. P., Hammer, R. E. & MacDonald, R. J., Oct 1 2005, In : Developmental Biology. 286, 1, p. 225-237 13 p.

Research output: Contribution to journalArticle

76 Scopus citations
44 Scopus citations

The photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis

Deisenhofer, J. & Michel, H., Aug 2005, In : Bioscience reports. 24, 4-5, p. 323-361 39 p.

Research output: Contribution to journalArticle

6 Scopus citations

Threshold dissociation and molecular modeling of transition metal complexes of flavonoids

Zhang, J., Brodbelt, J. S. & Wang, J., Feb 1 2005, In : Journal of the American Society for Mass Spectrometry. 16, 2, p. 139-151 13 p.

Research output: Contribution to journalArticle

47 Scopus citations
2004

A Drosophila pattern recognition receptor contains a peptidoglycan docking groove and unusual L,D-carboxypeptidase activity

Chang, C. I., Pili-Floury, S., Hervé, M., Parquet, C., Chelliah, Y., Lemaitre, B., Mengin-Lecreulx, D. & Deisenhofer, J., Sep 1 2004, In : PLoS biology. 2, 9

Research output: Contribution to journalArticle

76 Scopus citations

A two-state allosteric model for autoinhibition rationalizes WASP signal integration and targeting

Buck, M., Xu, W. & Rosen, M. K., Apr 23 2004, In : Journal of Molecular Biology. 338, 2, p. 271-285 15 p.

Research output: Contribution to journalArticle

44 Scopus citations

Chemical inhibition of N-WASP by stabilization of a native autoinhibited conformation

Peterson, J. R., Bickford, L. C., Morgan, D., Kim, A. S., Ouerfelli, O., Kirschner, M. W. & Rosen, M. K., Aug 1 2004, In : Nature Structural and Molecular Biology. 11, 8, p. 747-755 9 p.

Research output: Contribution to journalArticle

135 Scopus citations

Chemoattractant-induced phosphatidylinositol 3,4,5-trisphosphate accumulation is spatially amplified and adapts, independent of the actin cytoskeleton

Janetopoulos, C., Ma, L., Devreotes, P. N. & Iglesias, P. A., Jun 15 2004, In : Proceedings of the National Academy of Sciences of the United States of America. 101, 24, p. 8951-8956 6 p.

Research output: Contribution to journalArticle

176 Scopus citations

Critical roles of the guanylyl cyclase B receptor in endochondral ossification and development of female reproductive organs

Tamura, N., Doolittle, L. K., Hammer, R. E., Shelton, J. M., Richardson, J. A. & Garbers, D. L., Dec 7 2004, In : Proceedings of the National Academy of Sciences of the United States of America. 101, 49, p. 17300-17305 6 p.

Research output: Contribution to journalArticle

194 Scopus citations

Defining the spermatogonial stem cell

Hamra, F. K., Schultz, N., Chapman, K. M., Grellhesl, D. M., Cronkhite, J. T., Hammer, R. E. & Garbers, D. L., May 15 2004, In : Developmental Biology. 269, 2, p. 393-410 18 p.

Research output: Contribution to journalArticle

114 Scopus citations

Development and testing of a general Amber force field

Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A., Jul 15 2004, In : Journal of Computational Chemistry. 25, 9, p. 1157-1174 18 p.

Research output: Contribution to journalArticle

7841 Scopus citations

Discovery, Modeling, and Human Pharmacokinetics of N-(2-Acetyl-4,6-dimethylphenyl)-3-(3,4-dimethylisoxazol-5-ylsulfamoyl) -thiophene-2-carboxamide (TBC3711), a Second Generation, ETA Selective, and Orally Bioavailable Endothelin Antagonist

Wu, C., Decker, E. R., Blok, N., Bui, H., You, T. J., Wang, J., Bourgoyne, A. R., Knowles, V., Berens, K. L., Holland, G. W., Brock, T. A. & Dixon, R. A. F., Apr 8 2004, In : Journal of Medicinal Chemistry. 47, 8, p. 1969-1986 18 p.

Research output: Contribution to journalArticle

92 Scopus citations

Disregulated glyceroneogenesis: PCK1 as a candidate diabetes and obesity gene

Beale, E. G., Hammer, R. E., Antoine, B. & Forest, C., Apr 2004, In : Trends in Endocrinology and Metabolism. 15, 3, p. 129-135 7 p.

Research output: Contribution to journalReview article

80 Scopus citations

Double-knockout mice for α- and β-synucleins: Effect on synaptic functions

Chandra, S., Fornai, F., Kwon, H. B., Yazdani, U., Atasoy, D., Liu, X., Hammer, R. E., Battaglia, G., German, D. C., Castillo, P. E. & Südhof, T. C., Oct 12 2004, In : Proceedings of the National Academy of Sciences of the United States of America. 101, 41, p. 14966-14971 6 p.

Research output: Contribution to journalArticle

287 Scopus citations

Expression of a Poly-Glutamine-Ataxin-3 Transgene in Orexin Neurons Induces Narcolepsy-Cataplexy in the Rat

Beuckmann, C. T., Sinton, C. M., Williams, S. C., Richardson, J. A., Hammer, R. E., Sakurai, T. & Yanagisawa, M., May 5 2004, In : Journal of Neuroscience. 24, 18, p. 4469-4477 9 p.

Research output: Contribution to journalArticle

140 Scopus citations

Expression of the poly-glutamine-ataxin-3 transgene causes loss of orexin expression: A rat model of narcolepsy

Beuckmann, C. T., Sinton, C. M., Williams, S. C., Richardson, J. A., Hammer, R. E., Sakurai, T. & Yanagisawa, M., May 1 2004, In : Sleep and Biological Rhythms. 2, SUPPL. 1, p. S44

Research output: Contribution to journalArticle

Local complexity of amino acid interactions in a protein core

Jain, R. K. & Ranganathan, R., Jan 1 2004, In : Proceedings of the National Academy of Sciences of the United States of America. 101, 1, p. 111-116 6 p.

Research output: Contribution to journalArticle

35 Scopus citations

Metal Import through Microbial Membranes

Ferguson, A. D. & Deisenhofer, J., Jan 9 2004, In : Cell. 116, 1, p. 15-24 10 p.

Research output: Contribution to journalReview article

101 Scopus citations

Normal Development and Fertility of Knockout Mice Lacking the Tumor Suppressor Gene LRP1b Suggest Functional Compensation by LRP1

Marschang, P., Brich, J., Weeber, E. J., Sweatt, J. D., Shelton, J. M., Richardson, J. A., Hammer, R. E. & Herz, J., May 1 2004, In : Molecular and cellular biology. 24, 9, p. 3782-3793 12 p.

Research output: Contribution to journalArticle

45 Scopus citations
Open Access
193 Scopus citations

Paradigms for computational nucleic acid design

Dirks, R. M., Lin, M., Winfree, E. & Pierce, N. A., Jul 14 2004, In : Nucleic acids research. 32, 4, p. 1392-1403 12 p.

Research output: Contribution to journalArticle

140 Scopus citations

Responding to Directional Cues: A Tale of Two Cells

Paliwal, S., Ma, L., Krishnan, J., Levchenko, A. & Iglesias, P. A., Aug 2004, In : IEEE Control Systems. 24, 4, p. 77-90 14 p.

Research output: Contribution to journalArticle

9 Scopus citations

Structural determinants of allosteric ligand activation in RXR heterodimers

Shulman, A. I., Larson, C., Mangelsdorf, D. J. & Ranganathan, R., Feb 6 2004, In : Cell. 116, 3, p. 417-429 13 p.

Research output: Contribution to journalArticle

252 Scopus citations

Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana

Brautigam, C. A., Smith, B. S., Ma, Z., Palnitkar, M., Tomchick, D. R., Machius, M. & Deisenhofer, J., Aug 17 2004, In : Proceedings of the National Academy of Sciences of the United States of America. 101, 33, p. 12142-12147 6 p.

Research output: Contribution to journalArticle

214 Scopus citations

Tetramerization and ATP Binding by a Protein Comprising the A, B, and C Domains of Rat Synapsin I

Brautigam, C. A., Chelliah, Y. & Deisenhofer, J., Mar 19 2004, In : Journal of Biological Chemistry. 279, 12, p. 11948-11956 9 p.

Research output: Contribution to journalArticle

22 Scopus citations

Two complementary, local excitation, global inhibition mechanisms acting in parallel can explain the chemoattractant-induced regulation of PI(3,4,5)P 3 response in Dictyostelium cells

Ma, L., Janetopoulos, C., Yang, L., Devreotes, P. N. & Iglesias, P. A., Dec 2004, In : Biophysical journal. 87, 6, p. 3764-3774 11 p.

Research output: Contribution to journalArticle

114 Scopus citations

Uncoupling conformational change from GTP hydrolysis in a heterotrimetric G protein α-subunit

Thomas, C. J., Du, X., Li, P., Wang, Y., Ross, E. M. & Sprang, S. R., May 18 2004, In : Proceedings of the National Academy of Sciences of the United States of America. 101, 20, p. 7560-7565 6 p.

Research output: Contribution to journalArticle

23 Scopus citations
2003

A conserved amphipathic helix in WASP/scar proteins is essential for activation of Arp2/3 complex

Panchal, S. C., Kaiser, D. A., Torres, E., Pollard, T. D. & Rosen, M. K., Aug 1 2003, In : Nature Structural Biology. 10, 8, p. 591-598 8 p.

Research output: Contribution to journalArticle

118 Scopus citations

Allosteric determinants in guanine nucleotide-binding proteins

Hatley, M. E., Lockless, S. W., Gibson, S. K., Gilman, A. G. & Ranganathan, R., Nov 25 2003, In : Proceedings of the National Academy of Sciences of the United States of America. 100, SUPPL. 2, p. 14445-14450 6 p.

Research output: Contribution to journalArticle

105 Scopus citations

A matter of life or death

Ranganathan, R., Mar 14 2003, In : Science. 299, 5613, p. 1677-1679 3 p.

Research output: Contribution to journalReview article

10 Scopus citations

A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed-Phase Quantum Mechanical Calculations

Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J. & Kollman, P., Dec 1 2003, In : Journal of Computational Chemistry. 24, 16, p. 1999-2012 14 p.

Research output: Contribution to journalArticle

3179 Scopus citations

A role for Mints in transmitter release: Mint 1 knockout mice exhibit impaired GABAergic synaptic transmission

Ho, A., Morishita, W., Hammer, R. E., Malenka, R. C. & Südhof, T. C., Feb 4 2003, In : Proceedings of the National Academy of Sciences of the United States of America. 100, 3, p. 1409-1414 6 p.

Research output: Contribution to journalArticle

73 Scopus citations

Cardiomyocyte-Specific Endothelin A Receptor Knockout Mice Have Normal Cardiac Function and an Unaltered Hypertrophic Response to Angiotensin II and Isoproterenol

Kedzierski, R. M., Grayburn, P. A., Kisanuki, Y. Y., Williams, C. S., Hammer, R. E., Richardson, J. A., Schneider, M. D. & Yanagisawa, M., Nov 1 2003, In : Molecular and cellular biology. 23, 22, p. 8226-8232 7 p.

Research output: Contribution to journalArticle

63 Scopus citations

Cell-autonomous and nonautonomous actions of endothelin-A receptor signaling in craniofacial and cardiovascular development

Clouthier, D. E., Williams, S. C., Hammer, R. E., Richardson, J. A. & Yanagisawa, M., Sep 15 2003, In : Developmental Biology. 261, 2, p. 506-519 14 p.

Research output: Contribution to journalArticle

45 Scopus citations

Conditional expression of mutant M-line titins results in cardiomyopathy with altered sarcomere structure

Gotthardt, M., Hammer, R. E., Hübner, N., Monti, J., Witt, C. C., McNabb, M., Richardson, J. A., Granzier, H., Labeit, S. & Herz, J., Feb 21 2003, In : Journal of Biological Chemistry. 278, 8, p. 6059-6065 7 p.

Research output: Contribution to journalArticle

102 Scopus citations

Contingent phosphorylation/dephosphorylation provides a mechanism of molecular memory in WASP

Torres, E. & Rosen, M. K., May 1 2003, In : Molecular cell. 11, 5, p. 1215-1227 13 p.

Research output: Contribution to journalArticle

131 Scopus citations