K I Varughese

Summary

Affiliation: The Scripps Research Institute
Country: USA

Publications

  1. ncbi Platinum-induced space-group transformation in crystals of the platelet glycoprotein Ib alpha N-terminal domain
    Kottayil I Varughese
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
    Acta Crystallogr D Biol Crystallogr 60:405-11. 2004
  2. pmc Conformational changes of Spo0F along the phosphotransfer pathway
    Kottayil I Varughese
    Division of Cellular Biology, Department of Molecular and Experimental Medicine, MEM 116, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Bacteriol 187:8221-7. 2005
  3. pmc Rebuttal: beryllofluoride binding mimics phosphorylation of aspartate in response regulators
    Kottayil I Varughese
    Division of Cellular Biology, Department of Molecular and Experimental Medicine, MEM 116, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Bacteriol 187:8231. 2005
  4. ncbi Formation of a novel four-helix bundle and molecular recognition sites by dimerization of a response regulator phosphotransferase
    K I Varughese
    Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, California 92037, USA
    Mol Cell 2:485-93. 1998
  5. pmc The crystal structure of beryllofluoride Spo0F in complex with the phosphotransferase Spo0B represents a phosphotransfer pretransition state
    Kottayil I Varughese
    Division of Cellular Biology, Department of Molecular and Experimental Medicine, MEM 116, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Bacteriol 188:4970-7. 2006
  6. ncbi Molecular recognition of bacterial phosphorelay proteins
    Kottayil Iype Varughese
    Division of Cellular Biology, Department of Molecular and Experimental Medicine, MEM 116, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Curr Opin Microbiol 5:142-8. 2002
  7. ncbi A response regulatory protein with the site of phosphorylation blocked by an arginine interaction: crystal structure of Spo0F from Bacillus subtilis
    M Madhusudan
    Department of Biology, University of California at San Diego, La Jolla, California 92093 0359, USA
    Biochemistry 36:12739-45. 1997
  8. ncbi Crystal structure of a phosphatase-resistant mutant of sporulation response regulator Spo0F from Bacillus subtilis
    - Madhusudan
    Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
    Structure 4:679-90. 1996
  9. ncbi A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction
    J Zapf
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
    Structure 8:851-62. 2000
  10. ncbi Crystal structure of the von Willebrand factor modulator botrocetin
    U Sen
    Roon Research Center for Arteriosclerosis and Thrombosis, Division of Experimental Hemostasis and Thrombosis, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
    Biochemistry 40:345-52. 2001

Collaborators

Detail Information

Publications22

  1. ncbi Platinum-induced space-group transformation in crystals of the platelet glycoprotein Ib alpha N-terminal domain
    Kottayil I Varughese
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
    Acta Crystallogr D Biol Crystallogr 60:405-11. 2004
    ..The tetragonal crystal structure was subsequently solved using molecular-replacement techniques using the monoclinic structure as the search model and was refined with 1.7 A resolution data...
  2. pmc Conformational changes of Spo0F along the phosphotransfer pathway
    Kottayil I Varughese
    Division of Cellular Biology, Department of Molecular and Experimental Medicine, MEM 116, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Bacteriol 187:8221-7. 2005
    ..This commentary deals with the conformational fluctuations of the molecule as it moves from an apo-state to a metal-coordinated state, to a phosphorylated state, and then to a phosphoryl-transferring state...
  3. pmc Rebuttal: beryllofluoride binding mimics phosphorylation of aspartate in response regulators
    Kottayil I Varughese
    Division of Cellular Biology, Department of Molecular and Experimental Medicine, MEM 116, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Bacteriol 187:8231. 2005
  4. ncbi Formation of a novel four-helix bundle and molecular recognition sites by dimerization of a response regulator phosphotransferase
    K I Varughese
    Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, California 92037, USA
    Mol Cell 2:485-93. 1998
    ..It is apparent that different surfaces of response regulators may be involved in recognition of the protein partners to which they are paired...
  5. pmc The crystal structure of beryllofluoride Spo0F in complex with the phosphotransferase Spo0B represents a phosphotransfer pretransition state
    Kottayil I Varughese
    Division of Cellular Biology, Department of Molecular and Experimental Medicine, MEM 116, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Bacteriol 188:4970-7. 2006
    ..In order to visualize the autophosphorylation of the histidine kinase, KinA, and the subsequent phosphoryl transfer to Spo0F, we generated in silico models representing these reaction steps...
  6. ncbi Molecular recognition of bacterial phosphorelay proteins
    Kottayil Iype Varughese
    Division of Cellular Biology, Department of Molecular and Experimental Medicine, MEM 116, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Curr Opin Microbiol 5:142-8. 2002
    ....
  7. ncbi A response regulatory protein with the site of phosphorylation blocked by an arginine interaction: crystal structure of Spo0F from Bacillus subtilis
    M Madhusudan
    Department of Biology, University of California at San Diego, La Jolla, California 92093 0359, USA
    Biochemistry 36:12739-45. 1997
    ..This observation suggests that a small molecule with a shape complementary to the active site and having a guanidinium group might inhibit phosphotransfer between response regulators and their cognate histidine kinases...
  8. ncbi Crystal structure of a phosphatase-resistant mutant of sporulation response regulator Spo0F from Bacillus subtilis
    - Madhusudan
    Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
    Structure 4:679-90. 1996
    ....
  9. ncbi A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction
    J Zapf
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
    Structure 8:851-62. 2000
    ..Information at the molecular level on the interaction between response regulators and phosphohistidine domains is necessary to develop a rationale for how phospho-signaling fidelity is maintained in two-component systems...
  10. ncbi Crystal structure of the von Willebrand factor modulator botrocetin
    U Sen
    Roon Research Center for Arteriosclerosis and Thrombosis, Division of Experimental Hemostasis and Thrombosis, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
    Biochemistry 40:345-52. 2001
    ..A distinctive feature of botrocetin is the presence of a negatively charged surface that may play a role in the association with the vWF A1 domain...
  11. ncbi Altered structural and mechanistic properties of mutant dihydropteridine reductases
    P M Kiefer
    University of California at San Diego, La Jolla, California 92093 0317, USA
    J Biol Chem 271:3437-44. 1996
    ..This is of little value to dihydropteridine reductase but may be significant in the sequentially analogous short chain dehydrogenases/reductases, where a serine is the amino acid of choice for this position...
  12. ncbi Modulation of alpha-thrombin function by distinct interactions with platelet glycoprotein Ibalpha
    Reha Celikel
    Roon Research Center for Arteriosclerosis and Thrombosis, Division of Experimental Thrombosis and Hemostasis, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Science 301:218-21. 2003
    ..These interactions may modulate alpha-thrombin function by mediating GpIbalpha clustering and cleavage of protease-activated receptors, which promote platelet activation, while limiting fibrinogen clotting through blockade of exosite I...
  13. ncbi Metals in the sporulation phosphorelay: manganese binding by the response regulator Spo0F
    Debashis Mukhopadhyay
    Division of Cellular Biology, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
    Acta Crystallogr D Biol Crystallogr 60:638-45. 2004
    ..It is proposed that the existence of a deep pocket which extends from the surface to the metal site could attract and direct the metal, thereby facilitating the metal binding of the complex...
  14. ncbi Crystal structure of NMC-4 fab anti-von Willebrand factor A1 domain
    R Celikel
    Roon Research Center for Arteriosclerosis and Thrombosis, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
    Blood Cells Mol Dis 23:123-34. 1997
    ..Thus, the structural information obtained with NMC-4 may prove relevant to understand the stereochemical bases of the GP Ib alpha-vWF interaction essential for thrombus formation at sites of vascular lesion...
  15. pmc Crystal structure of the transcriptional repressor PagR of Bacillus anthracis
    Haiyan Zhao
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
    Microbiology 156:385-91. 2010
    ..In the crystal lattice four PagR dimers pack together to form an inactive octamer. Model-building studies suggest that the dimer binds to a DNA duplex with a bend of around 4 degrees...
  16. ncbi Structure and function of the von Willebrand factor A1 domain
    Kottayil I Varughese
    Roon Research Center for Arteriosclerosis and Thrombosis, Division of Experimental Hemostasis and Thrombosis, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
    Curr Protein Pept Sci 3:301-12. 2002
    ..In this review, we present the current knowledge on the structural features of the VWF A1 domain that support its functions...
  17. ncbi A computational analysis on the specificity of interactions between histidine kinases and response regulators
    Debashis Mukhopadhyay
    Division of Cellular Biology, Department of Molecular and Experimental Medicine, MEM 116, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    J Biomol Struct Dyn 22:555-62. 2005
    ..The observed pattern suggests that the chances for cross talk between non-partner proteins are extremely low, but cross talk could take place in special cases...
  18. pmc The crystal structure of YycH involved in the regulation of the essential YycFG two-component system in Bacillus subtilis reveals a novel tertiary structure
    Hendrik Szurmant
    Division of Cellular Biology, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
    Protein Sci 15:929-34. 2006
    ..3 A data to an R-factor of 25.2%. The molecule is made up of three domains, and has a novel three-dimensional structure. The N-terminal domain features a calcium binding site and the central domain contains two conserved loop regions...
  19. ncbi DNA complexed structure of the key transcription factor initiating development in sporulating bacteria
    Haiyan Zhao
    Division of Cellular Biology, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
    Structure 10:1041-50. 2002
    ..The protein:protein and protein:DNA interfaces revealed in the crystal provide a basis for interpreting the transcription activation process and for the design of drugs to counter infections by these bacteria...
  20. ncbi Role of aspartate-37 in determining cofactor specificity and binding in rat liver dihydropteridine reductase
    D A Matthews
    Agouron Pharmaceuticals Inc, La Jolla, California 92037
    Arch Biochem Biophys 287:234-9. 1991
    ..The results indicate that the DHPR cofactor binding site is similar to typical dinucleotide requiring dehydrogenases such as lactic acid and liver alcohol dehydrogenase...
  21. ncbi A single amino acid change in the binding pocket alters specificity of an anti-integrin antibody AP7.4 as revealed by its crystal structure
    Sona Vasudevan
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
    Blood Cells Mol Dis 32:176-81. 2004
    ..Hence, the flexibility of the RGD-carrying loop observed in the crystal structure may stem from the fact that the antibody molecule mimics the function of these cell adhesion molecules...
  22. ncbi Structure of pteridine reductase (PTR1) from Leishmania tarentolae
    Haiyan Zhao
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Acta Crystallogr D Biol Crystallogr 59:1539-44. 2003
    ..The functional enzyme is a tetramer and the crystallographic asymmetric unit contains a tetramer with 222 point-group symmetry...