Research Output

2007

Self-organization of treadmilling filaments

Doubrovinski, K. & Kruse, K., Nov 29 2007, In : Physical Review Letters. 99, 22, 228104.

Research output: Contribution to journalArticle

24 Scopus citations

Signal transduction pathway of TonB-dependent transporters

Ferguson, A. D., Amezcua, C. A., Halabi, N. M., Chelliah, Y., Rosen, M. K., Ranganathan, R. & Deisenhofer, J., Jan 9 2007, In : Proceedings of the National Academy of Sciences of the United States of America. 104, 2, p. 513-518 6 p.

Research output: Contribution to journalArticle

72 Scopus citations

Single-molecule fluorescence to study molecularmotors

Park, H., Toprak, E. & Selvin, P. R., Feb 1 2007, In : Quarterly Reviews of Biophysics. 40, 1, p. 87-111 25 p.

Research output: Contribution to journalReview article

59 Scopus citations

Sox15 and Fhl3 transcriptionally coactivate Foxk1 and regulate myogenic progenitor cells

Meeson, A. P., Shi, X., Alexander, M. S., Williams, R. S., Allen, R. E., Jiang, N., Adham, I. M., Goetsch, S. C., Hammer, R. E. & Garry, D. J., Apr 4 2007, In : EMBO Journal. 26, 7, p. 1902-1912 11 p.

Research output: Contribution to journalArticle

54 Scopus citations

Structural basis for conserved complement factor-like function in the antimalarial protein TEP1

Baxter, R. H. G., Chang, C. I., Chelliah, Y., Blandin, S., Levashina, E. A. & Deisenhofer, J., Jul 10 2007, In : Proceedings of the National Academy of Sciences of the United States of America. 104, 28, p. 11615-11620 6 p.

Research output: Contribution to journalArticle

62 Scopus citations

The peptidoglycan recognition proteins LCa and LCx

Chang, C. I. & Deisenhofer, J., Jun 1 2007, In : Cellular and Molecular Life Sciences. 64, 11, p. 1395-1402 8 p.

Research output: Contribution to journalReview article

4 Scopus citations

Three-dimensional particle tracking via bifocal imaging

Toprak, E., Balci, H., Blehm, B. H. & Selvin, P. R., Jul 1 2007, In : Nano Letters. 7, 7, p. 2043-2045 3 p.

Research output: Contribution to journalArticle

165 Scopus citations

Use of a cAMP BRET sensor to characterize a novel regulation of cAMP by the sphingosine 1-phosphate/G13 pathway

Jiang, L. I., Collins, J., Davis, R., Lin, K. M., DeCamp, D., Roach, T., Hsueh, R., Rebres, R. A., Ross, E. M., Taussig, R., Fraser, I. & Sternweis, P. C., Apr 6 2007, In : Journal of Biological Chemistry. 282, 14, p. 10576-10584 9 p.

Research output: Contribution to journalArticle

175 Scopus citations
2006

3D-QSAR studies of arylpyrazole antagonists of cannabinoid receptor subtypes CB1 and CB2. A combined NMR and CoMFA approach

Chen, J. Z., Han, X. W., Liu, Q., Makriyannis, A., Wang, J. & Xie, X. Q., Jan 26 2006, In : Journal of Medicinal Chemistry. 49, 2, p. 625-636 12 p.

Research output: Contribution to journalArticle

54 Scopus citations

Additional human β2-microglobulin curbs HLA-B27 misfolding and promotes arthritis and spondylitis without colitis in male HLA-B27-transgenic rats

Tran, T. M., Dorris, M. L., Satumtira, N., Richardson, J. A., Hammer, R. E., Shang, J. & Taurog, J. D., Apr 2006, In : Arthritis and rheumatism. 54, 4, p. 1317-1327 11 p.

Research output: Contribution to journalArticle

119 Scopus citations

A global analysis of cross-talk in a mammalian cellular signalling network

Natarajan, M., Lin, K. M., Hsueh, R. C., Sternweis, P. C. & Ranganathan, R., Jun 1 2006, In : Nature Cell Biology. 8, 6, p. 571-580 10 p.

Research output: Contribution to journalArticle

183 Scopus citations

ApoE Receptor 2 Controls Neuronal Survival in the Adult Brain

Beffert, U., Nematollah Farsian, F., Masiulis, I., Hammer, R. E., Yoon, S. O., Giehl, K. M. & Herz, J., Dec 19 2006, In : Current Biology. 16, 24, p. 2446-2452 7 p.

Research output: Contribution to journalArticle

57 Scopus citations

Autoinhibition regulates cellular localization and actin assembly activity of the diaphanous-related formins FRLα and mDia1

Seth, A., Otomo, C. & Rosen, M. K., Aug 28 2006, In : Journal of Cell Biology. 174, 5, p. 701-713 13 p.

Research output: Contribution to journalArticle

99 Scopus citations

Automatic atom type and bond type perception in molecular mechanical calculations

Wang, J., Wang, W., Kollman, P. A. & Case, D. A., Oct 1 2006, In : Journal of Molecular Graphics and Modelling. 25, 2, p. 247-260 14 p.

Research output: Contribution to journalArticle

2318 Scopus citations

Biochemical properties and inhibitors of (N-)WASP

Leung, D. W., Morgan, D. M. & Rosen, M. K., Jan 1 2006, In : Methods in Enzymology. 406, p. 281-296 16 p., 21.

Research output: Contribution to journalReview article

13 Scopus citations

Crystal structure of cryptochrome 3 from Arabidopsis thaliana and its implications for photolyase activity

Huang, Y., Baxter, R., Smith, B. S., Partch, C. L., Colbert, C. L. & Deisenhofer, J., Nov 21 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, 47, p. 17701-17706 6 p.

Research output: Contribution to journalArticle

88 Scopus citations

Defocused orientation and position imaging (DOPI) of myosin V

Toprak, E., Enderlein, J., Syed, S., McKinney, S. A., Petschek, R. G., Ha, T., Goldman, Y. E. & Selvin, P. R., Apr 25 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, 17, p. 6495-6499 5 p.

Research output: Contribution to journalArticle

166 Scopus citations

Essential roles for the FE65 amyloid precursor protein-interacting proteins in brain development

Guénette, S., Chang, Y., Hiesberger, T., Richardson, J. A., Eckman, C. B., Eckman, E. A., Hammer, R. E. & Herz, J., Jan 25 2006, In : EMBO Journal. 25, 2, p. 420-431 12 p.

Research output: Contribution to journalArticle

113 Scopus citations

Evolutionary potential of a duplicated repressor-operator pair: Simulating pathways using mutation data

Poelwijk, F. J., Kiviet, D. J. & Tans, S. J., May 2006, In : PLoS Computational Biology. 2, 5, p. 467-475 9 p.

Research output: Contribution to journalArticle

36 Scopus citations

Functional dissection of Reelin signaling by site-directed disruption of disabled-1 adaptor binding to apolipoprotein E receptor 2: Distinct roles in development and synaptic plasticity

Beffert, U., Durudas, A., Weeber, E. J., Stolt, P. C., Giehl, K. M., Sweatt, J. D., Hammer, R. E. & Herz, J., Feb 15 2006, In : Journal of Neuroscience. 26, 7, p. 2041-2052 12 p.

Research output: Contribution to journalArticle

93 Scopus citations

Genetic algorithm-optimized QSPR models for bioavailability, protein binding, and urinary excretion

Wang, J., Krudy, G., Xie, X. Q., Wu, C. & Holland, G., Nov 1 2006, In : Journal of Chemical Information and Modeling. 46, 6, p. 2674-2683 10 p.

Research output: Contribution to journalArticle

58 Scopus citations

Genetic analysis of Mint/X11 proteins: Essential presynaptic functions of a neuronal adaptor protein family

Ho, A., Morishita, W., Atasoy, D., Liu, X., Tabuchi, K., Hammer, R. E., Malenka, R. C. & Südhof, T. C., Dec 13 2006, In : Journal of Neuroscience. 26, 50, p. 13089-13101 13 p.

Research output: Contribution to journalArticle

69 Scopus citations

Gβγinhibits Gα GTPase-activating proteins by inhibition of Gα-GTP binding during stimulation by receptor

Tang, W., Tu, Y., Nayak, S. K., Woodson, J., Jehl, M. & Ross, E. M., Feb 24 2006, In : Journal of Biological Chemistry. 281, 8, p. 4746-4753 8 p.

Research output: Contribution to journalArticle

23 Scopus citations

Helix-to-coil transitions in proteins: Helicity resonance in ultrafast electron diffraction

Lin, M. M., Shorokhov, D. & Zewail, A. H., Mar 10 2006, In : Chemical Physics Letters. 420, 1-3, p. 1-7 7 p.

Research output: Contribution to journalArticle

15 Scopus citations

Heritable and stable gene knockdown in rats

Dann, C. T., Alvarado, A. L., Hammer, R. E. & Garbers, D. L., Jul 25 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, 30, p. 11246-11251 6 p.

Research output: Contribution to journalArticle

63 Scopus citations

Knowledge-based potentials in protein design

Poole, A. M. & Ranganathan, R., Aug 1 2006, In : Current Opinion in Structural Biology. 16, 4, p. 508-513 6 p.

Research output: Contribution to journalReview article

67 Scopus citations
31 Scopus citations

Mutation of β-glucosidase 2 causes glycolipid storage disease and impaired male fertility

Yildiz, Y., Matern, H., Thompson, B., Allegood, J. C., Warren, R. L., Ramirez, D. M. O., Hammer, R. E., Hamra, F. K., Matern, S. & Russell, D. W., Nov 1 2006, In : Journal of Clinical Investigation. 116, 11, p. 2985-2994 10 p.

Research output: Contribution to journalArticle

165 Scopus citations

New-generation Amber united-atom force field

Yang, L., Tan, C. H., Hsieh, M. J., Wang, J., Duan, Y., Cieplak, P., Caldwell, J., Kollman, P. A. & Luo, R., Jul 6 2006, In : Journal of Physical Chemistry B. 110, 26, p. 13166-13176 11 p.

Research output: Contribution to journalArticle

151 Scopus citations

NMR structures of the selenoproteins Sep15 and SelM reveal redox activity of a new thioredoxin-like family

Ferguson, A. D., Labunskyy, V. M., Fomenko, D. E., Araç, D., Chelliah, Y., Amezcua, C. A., Rizo-Rey, J., Gladyshev, V. N. & Deisenhofer, J., Feb 10 2006, In : Journal of Biological Chemistry. 281, 6, p. 3536-3543 8 p.

Research output: Contribution to journalArticle

142 Scopus citations

Noise resistance in the spindle assembly checkpoint

Doncic, A., Ben-Jacob, E. & Barkai, N., May 16 2006, In : Molecular Systems Biology. 2, p. 2006.0027 msb4100070.

Research output: Contribution to journalArticle

13 Scopus citations

Polarization effect on position accuracy of fluorophore localization

Enderlein, J., Toprak, E. & Selvin, P. R., Jan 1 2006, In : Optics Express. 14, 18, p. 8111-8120 10 p.

Research output: Contribution to journalArticle

126 Scopus citations
63 Scopus citations

Recent advances in computational prediction of drug absorption and permeability in drug discovery

Hou, T., Wang, J., Zhang, W., Wang, W. & Xu, X., Sep 1 2006, In : Current Medicinal Chemistry. 13, 22, p. 2653-2667 15 p.

Research output: Contribution to journalReview article

142 Scopus citations

Recent advances in free energy calculations with a combination of molecular mechanics and continuum models

Wang, J. M., Hou, T. & Xu, X., Sep 1 2006, In : Current Computer-Aided Drug Design. 2, 3, p. 287-306 20 p.

Research output: Contribution to journalReview article

206 Scopus citations

Redundant functions of RIM1α and RIM2α in Ca 2+-triggered neurotransmitter release

Schoch, S., Mittelstaedt, T., Kaeser, P. S., Padgett, D., Feldmann, N., Chevaleyre, V., Castillo, P. E., Hammer, R. E., Han, W., Schmitz, F., Lin, W. & Südhof, T. C., Dec 13 2006, In : EMBO Journal. 25, 24, p. 5852-5863 12 p.

Research output: Contribution to journalArticle

94 Scopus citations

Robustness analysis of biochemical network models

Kim, J., Bates, D. G., Postlethwaite, I., Ma, L. & Iglesias, P. A., May 1 2006, In : IEE Proceedings: Systems Biology. 153, 3, p. 96-104 9 p.

Research output: Contribution to journalArticle

62 Scopus citations

Secreted PCSK9 decreases the number of LDL receptors in hepatocytes and in livers of parabiotic mice

Lagace, T. A., Curtis, D. E., Garuti, R., McNutt, M. C., Sahng, W. P., Prather, H. B., Anderson, N. N., Ho, Y. K., Hammer, R. E. & Horton, J. D., Nov 1 2006, In : Journal of Clinical Investigation. 116, 11, p. 2995-3005 11 p.

Research output: Contribution to journalArticle

426 Scopus citations

Specific patterns of Cdc42 activity are related to distinct elements of T cell polarization

Tskvitaria-Fuller, I., Seth, A., Mistry, N., Gu, H., Rosen, M. K. & Wülfing, C., Aug 1 2006, In : Journal of Immunology. 177, 3, p. 1708-1720 13 p.

Research output: Contribution to journalArticle

Open Access
43 Scopus citations

Structural and computational characterization of the SHV-1 β-lactamase-β-lactamase inhibitor protein interface

Reynolds, K. A., Thomson, J. M., Corbett, K. D., Bethel, C. R., Berger, J. M., Kirsch, J. F., Bonomo, R. A. & Handel, T. M., Sep 8 2006, In : Journal of Biological Chemistry. 281, 36, p. 26745-26753 9 p.

Research output: Contribution to journalArticle

40 Scopus citations

Structural determinants for phosphatidic acid regulation of phospholipase C-β1

Ross, E. M., Mateu, D., Gomes, A. V., Arana, C., Tran, T. & Litosch, I., Nov 3 2006, In : Journal of Biological Chemistry. 281, 44, p. 33087-33094 8 p.

Research output: Contribution to journalArticle

29 Scopus citations
2005

Abnormal development of the apical ectodermal ridge and polysyndactyly in Megf7-deficient mice

Johnson, E. B., Hammer, R. E. & Herz, J., Nov 15 2005, In : Human molecular genetics. 14, 22, p. 3523-3538 16 p.

Research output: Contribution to journalArticle

97 Scopus citations

Acidic region tyrosines provide access points for allosteric activation of the autoinhibited Vav1 Db1 homology domain

Amarasinghe, G. K. & Rosen, M. K., Nov 22 2005, In : Biochemistry. 44, 46, p. 15257-15268 12 p.

Research output: Contribution to journalArticle

27 Scopus citations

A novel mechanism of actin filament processive capping by formin: Solution of the rotation paradox

Shemesh, T., Otomo, T., Rosen, M. K., Bershadsky, A. D. & Kozlov, M. M., Sep 12 2005, In : Journal of Cell Biology. 170, 6, p. 889-893 5 p.

Research output: Contribution to journalArticle

42 Scopus citations

A plausible model for the digital response of p53 to DNA damage

Ma, L., Wagner, J., Rice, J. J., Hu, W., Levine, A. J. & Stolovitzky, G. A., Oct 4 2005, In : Proceedings of the National Academy of Sciences of the United States of America. 102, 40, p. 14266-14271 6 p.

Research output: Contribution to journalArticle

241 Scopus citations

Characterization of flavonoids by aluminum complexation and collisionally activated dissociation

Zhang, J., Wang, J. & Brodbelt, J. S., Mar 1 2005, In : Journal of Mass Spectrometry. 40, 3, p. 350-363 14 p.

Research output: Contribution to journalArticle

41 Scopus citations

C-terminal ECFP fusion impairs synaptotagmin 1 function: Crowding out synaptotagmin 1

Han, W., Rhee, J. S., Maximov, A., Lin, W., Hammer, R. E., Rosenmund, C. & Südhof, T. C., Feb 11 2005, In : Journal of Biological Chemistry. 280, 6, p. 5089-5100 12 p.

Research output: Contribution to journalArticle

25 Scopus citations

Decreased plasma cholesterol and hypersensitivity to statins in mice lacking Pcsk9

Rashid, S., Curtis, D. E., Garuti, R., Anderson, N. H., Bashmakov, Y., Ho, Y. K., Hammer, R. E., Moon, Y. A. & Horton, J. D., Apr 12 2005, In : Proceedings of the National Academy of Sciences of the United States of America. 102, 15, p. 5374-5379 6 p.

Research output: Contribution to journalArticle

488 Scopus citations

Erratum: Development and testing of a general amber force field (Journal of Computational Chemistry (2004) 25 (1157))

Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A., Jan 15 2005, In : Journal of Computational Chemistry. 26, 1, 1 p.

Research output: Contribution to journalComment/debate

119 Scopus citations

Evaluating putative mechanisms of the mitotic spindle checkpoint

Doncic, A., Ben-Jacob, E. & Barkai, N., May 3 2005, In : Proceedings of the National Academy of Sciences of the United States of America. 102, 18, p. 6332-6337 6 p.

Research output: Contribution to journalArticle

57 Scopus citations