Dimitar B Nikolov

Summary

Affiliation: Memorial Sloan-Kettering Cancer Center
Country: USA

Publications

  1. pmc Eph/ephrin recognition and the role of Eph/ephrin clusters in signaling initiation
    Dimitar B Nikolov
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA Electronic address
    Biochim Biophys Acta 1834:2160-5. 2013
  2. pmc Crystal structure of the human ephrin-A5 ectodomain
    Dimitar Nikolov
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Protein Sci 16:996-1000. 2007
  3. pmc Architecture of Eph receptor clusters
    Juha P Himanen
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
    Proc Natl Acad Sci U S A 107:10860-5. 2010
  4. ncbi request reprint Structures of axon guidance molecules and their neuronal receptors
    William A Barton
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Adv Protein Chem 68:65-106. 2004
  5. pmc Insights into Eph receptor tyrosine kinase activation from crystal structures of the EphA4 ectodomain and its complex with ephrin-A5
    Kai Xu
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Proc Natl Acad Sci U S A 110:14634-9. 2013
  6. ncbi request reprint Neural migration. Structures of netrin-1 bound to two receptors provide insight into its axon guidance mechanism
    Kai Xu
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Science 344:1275-9. 2014
  7. ncbi request reprint Crystal structures of the Tie2 receptor ectodomain and the angiopoietin-2-Tie2 complex
    William A Barton
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
    Nat Struct Mol Biol 13:524-32. 2006
  8. ncbi request reprint Crystal structure of the ephrin-B1 ectodomain: implications for receptor recognition and signaling
    Dimitar B Nikolov
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Biochemistry 44:10947-53. 2005
  9. pmc Host cell recognition by the henipaviruses: crystal structures of the Nipah G attachment glycoprotein and its complex with ephrin-B3
    Kai Xu
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 105:9953-8. 2008
  10. ncbi request reprint Repelling class discrimination: ephrin-A5 binds to and activates EphB2 receptor signaling
    Juha Pekka Himanen
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nat Neurosci 7:501-9. 2004

Collaborators

Detail Information

Publications38

  1. pmc Eph/ephrin recognition and the role of Eph/ephrin clusters in signaling initiation
    Dimitar B Nikolov
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA Electronic address
    Biochim Biophys Acta 1834:2160-5. 2013
    ..This article is part of a Special Issue entitled: Emerging recognition and activation mechanisms of receptor tyrosine kinases. ..
  2. pmc Crystal structure of the human ephrin-A5 ectodomain
    Dimitar Nikolov
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Protein Sci 16:996-1000. 2007
    ..The results of this study further emphasize the importance of the G-H loop for receptor recognition and selectivity, and could serve as a starting point for the development of structure-based Eph antagonists...
  3. pmc Architecture of Eph receptor clusters
    Juha P Himanen
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
    Proc Natl Acad Sci U S A 107:10860-5. 2010
    ..Structure-function analysis, by using site-directed mutagenesis and cell-based signaling assays, confirms the importance of the identified oligomerization interfaces for Eph clustering...
  4. ncbi request reprint Structures of axon guidance molecules and their neuronal receptors
    William A Barton
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Adv Protein Chem 68:65-106. 2004
  5. pmc Insights into Eph receptor tyrosine kinase activation from crystal structures of the EphA4 ectodomain and its complex with ephrin-A5
    Kai Xu
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Proc Natl Acad Sci U S A 110:14634-9. 2013
    ....
  6. ncbi request reprint Neural migration. Structures of netrin-1 bound to two receptors provide insight into its axon guidance mechanism
    Kai Xu
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Science 344:1275-9. 2014
    ..The differences result from different lengths of the linker connecting receptor domains fibronectin type III domain 4 (FN4) and FN5, which differs among DCC and neogenin splice variants, providing a basis for diverse signaling outcomes. ..
  7. ncbi request reprint Crystal structures of the Tie2 receptor ectodomain and the angiopoietin-2-Tie2 complex
    William A Barton
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
    Nat Struct Mol Biol 13:524-32. 2006
    ..Analysis of the structures and structure-based mutagenesis provide insight into the mechanism of receptor activation and support the hypothesis that all angiopoietins interact with Tie2 in a structurally similar manner...
  8. ncbi request reprint Crystal structure of the ephrin-B1 ectodomain: implications for receptor recognition and signaling
    Dimitar B Nikolov
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Biochemistry 44:10947-53. 2005
    ..The implications of the ephrin-B1 structure, in context of available ephrin-B1 mutagenesis data, for the mechanism of Eph-ephrin recognition and signaling initiation are discussed...
  9. pmc Host cell recognition by the henipaviruses: crystal structures of the Nipah G attachment glycoprotein and its complex with ephrin-B3
    Kai Xu
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 105:9953-8. 2008
    ..The structures further suggest that the NiV-G/ephrin interactions can be effectively targeted to disrupt viral entry and provide the foundation for structure-based antiviral drug design...
  10. ncbi request reprint Repelling class discrimination: ephrin-A5 binds to and activates EphB2 receptor signaling
    Juha Pekka Himanen
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nat Neurosci 7:501-9. 2004
    ..The structural data reveal the molecular basis for EphB2-ephrin-A5 signaling and provide a framework for understanding the complexities of functional interactions and crosstalk between A- and B-subclass Eph receptors and ephrins...
  11. pmc Ligand recognition by A-class Eph receptors: crystal structures of the EphA2 ligand-binding domain and the EphA2/ephrin-A1 complex
    Juha P Himanen
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    EMBO Rep 10:722-8. 2009
    ..Finally, the structure of the unligated receptor reveals a homodimer assembly that might represent EphA2-specific homotypic cell adhesion interactions...
  12. ncbi request reprint Eph signaling: a structural view
    Juha Pekka Himanen
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Trends Neurosci 26:46-51. 2003
    ..Of particular importance is the insight into how approximation of ligand-expressing and receptor-expressing cells could lead to the formation and activation of highly ordered signaling centers at cell-cell interfaces...
  13. doi request reprint Ganglioside mediate the interaction between Nogo receptor 1 and LINGO-1
    Nayanendu Saha
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, NY 10021, USA
    Biochem Biophys Res Commun 413:92-7. 2011
    ..Moreover, the tripartite complex comprising of NgR1, LINGO-1 and ganglioside exhibits stronger binding to Nogo-A (Nogo-54) in the presence of p75, suggesting the gangliosides modulate the myelin inhibitor-receptor signaling...
  14. pmc Crystal structure of the ligand-binding domain of the promiscuous EphA4 receptor reveals two distinct conformations
    Nikhil Singla
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
    Biochem Biophys Res Commun 399:555-9. 2010
    ..Our results suggest that the ligand promiscuity of the Ephs is directly correlated with the structural flexibility of the ligand-binding surface of the receptor...
  15. pmc Crystal structure of the Nogo-receptor-2
    Mariya Semavina
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York 10065, USA
    Protein Sci 20:684-9. 2011
    ..We also present the crystal structure of the LRR and part of the stalk regions of NgR2 and compare it to the previously reported NgR1 structure with respect to the distinct signaling properties of the two receptor isoforms...
  16. pmc A semisynthetic Eph receptor tyrosine kinase provides insight into ligand-induced kinase activation
    Nikhil Singla
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Chem Biol 18:361-71. 2011
    ..To our knowledge, this work represents the first reported semisynthesis of a receptor tyrosine kinase and provides a potentially general method for producing single-pass membrane proteins for structural and biochemical characterization...
  17. pmc New insights into the Hendra virus attachment and entry process from structures of the virus G glycoprotein and its complex with Ephrin-B2
    Kai Xu
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
    PLoS ONE 7:e48742. 2012
    ..In addition, our data indicates that conformational rearrangements of the G glycoprotein head domain upon receptor binding may be the trigger leading to the activation of the viral F fusion glycoprotein during virus infection...
  18. pmc Cell-cell signaling via Eph receptors and ephrins
    Juha Pekka Himanen
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
    Curr Opin Cell Biol 19:534-42. 2007
    ....
  19. pmc Structural and functional features of the Escherichia coli hydroperoxide resistance protein OsmC
    Jacob Lesniak
    Joan and Sanford I Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10021, USA
    Protein Sci 12:2838-43. 2003
    ....
  20. pmc Structure and axon outgrowth inhibitor binding of the Nogo-66 receptor and related proteins
    William A Barton
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    EMBO J 22:3291-302. 2003
    ..The NgR structure analysis, as well as a comparison of NgR surface residues not conserved in NgR2 and NgR3, identifies potential protein interaction sites important in the assembly of a functional signaling complex...
  21. pmc Structural basis for angiopoietin-1-mediated signaling initiation
    Xuehong Yu
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 110:7205-10. 2013
    ....
  22. ncbi request reprint Structure of the angiopoietin-2 receptor binding domain and identification of surfaces involved in Tie2 recognition
    William A Barton
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
    Structure 13:825-32. 2005
    ..The structure reveals a fibrinogen fold with a unique C-terminal P domain. Conservation analysis and structure-based mutagenesis identify a groove on the Ang2 molecular surface that mediates receptor recognition...
  23. pmc Ephrin-B2 and ephrin-B3 as functional henipavirus receptors
    Kai Xu
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Semin Cell Dev Biol 23:116-23. 2012
    ..We review recent progress in the study of henipavirus entry, particularly the identification of ephrins as their entry receptors, and the structural characterization of the ephrin/Henipa-G interactions...
  24. pmc Toward the semisynthesis of multidomain transmembrane receptors: modification of Eph tyrosine kinases
    Nikhil Singla
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Protein Sci 17:1740-7. 2008
    ....
  25. pmc Crystal structure of the Hendra virus attachment G glycoprotein bound to a potent cross-reactive neutralizing human monoclonal antibody
    Kai Xu
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
    PLoS Pathog 9:e1003684. 2013
    ..4, and serves as a blueprint for further optimization of m102.4 as a therapeutic agent and for the development of entry inhibitors and vaccines. ..
  26. pmc Crystal structures of Lgr4 and its complex with R-spondin1
    Kai Xu
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Structure 21:1683-9. 2013
    ..The molecular details of ligand/receptor recognition provide insight into receptor activation and could serve as template for stem-cell-based regenerative therapeutics development...
  27. ncbi request reprint Purification, crystallization and preliminary characterization of an Eph-B2/ephrin-B2 complex
    Juha P Himanen
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Acta Crystallogr D Biol Crystallogr 58:533-5. 2002
    ..The structure of the complex will elucidate the chemical nature of the interactions between Eph receptors and ephrins, which would create the possibility of using them as targets for structure-based anticancer-drug development...
  28. ncbi request reprint Structure of the semaphorin-3A receptor binding module
    Alexander Antipenko
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Neuron 39:589-98. 2003
    ....
  29. ncbi request reprint GABARAP: lessons for synaptogenesis
    Joseph E Coyle
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Neuroscientist 9:205-16. 2003
    ..Currently, a more general role is emerging for GABARAP, including shipping GABAA receptors to and from the cell surface, organizing them into postsynaptic clusters, and regulating the steady-state receptor density...
  30. pmc Expanding pyrimidine diphosphosugar libraries via structure-based nucleotidylyltransferase engineering
    William A Barton
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 99:13397-402. 2002
    ..In aggregate, our results provide valuable blueprints for altering nucleotidylyltransferase specificity by design, which is the first step toward in vitro glycorandomization...
  31. ncbi request reprint Structure of GABARAP in two conformations: implications for GABA(A) receptor localization and tubulin binding
    Joseph E Coyle
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Neuron 33:63-74. 2002
    ..9 A resolution and documents that GABARAP can self-associate in a head-to-tail manner. The structural details of this oligomerization reveal how GABARAP can both promote tubulin polymerization and facilitate GABA(A) receptor clustering...
  32. ncbi request reprint Eph receptors and ephrins
    Juha Pekka Himanen
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Int J Biochem Cell Biol 35:130-4. 2003
    ..The elucidation of the structural details of Eph-ephrin recognition and binding should yield insight into the future development of novel therapeutic agents targeting cardiovascular function, nerve regeneration, and cancer...
  33. pmc Highly efficient selenomethionine labeling of recombinant proteins produced in mammalian cells
    William A Barton
    Department of Biochemistry, Virginia Commonwealth University, Richmond, 23298, USA
    Protein Sci 15:2008-13. 2006
    ....
  34. ncbi request reprint Adam meets Eph: an ADAM substrate recognition module acts as a molecular switch for ephrin cleavage in trans
    Peter W Janes
    Department of Biochemistry and Molecular Biology, PO Box 13D, Monash University, Victoria 3800, Australia
    Cell 123:291-304. 2005
    ..Our data suggest a simple mechanism for regulating ADAM10-mediated ephrin proteolysis, which ensures that only Eph bound ephrins are recognized and cleaved...
  35. ncbi request reprint Three distinct molecular surfaces in ephrin-A5 are essential for a functional interaction with EphA3
    Bryan Day
    Queensland Institute of Medical Research, P O Royal Brisbane Hospital 4029, Queensland, Australia
    J Biol Chem 280:26526-32. 2005
    ....
  36. pmc Kinetic analysis of the binding of monomeric and dimeric ephrins to Eph receptors: correlation to function in a growth cone collapse assay
    Kumar B Pabbisetty
    Department of Pharmaceutical Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
    Protein Sci 16:355-61. 2007
    ..Our kinetic analysis and correlation of binding affinity with function helped us better understand the interactions between ephrins and Eph receptors and should be useful in the design of inhibitors that interfere with the interactions...
  37. ncbi request reprint Structure-based enzyme engineering and its impact on in vitro glycorandomization
    Jon S Thorson
    Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, University of Wisconsin Madison, Madison, WI 53705, USA
    Chembiochem 5:16-25. 2004
  38. pmc Structural and functional characterization of the Pseudomonas hydroperoxide resistance protein Ohr
    Jacob Lesniak
    Joan and Sanford I Weill Graduate School of Medical Sciences of Cornell University, New York City, NY 10021, USA
    EMBO J 21:6649-59. 2002
    ..We propose that the Ohr catalytic mechanism is similar to that of the structurally unrelated peroxiredoxins, directly utilizing highly reactive cysteine thiol groups to elicit hydroperoxide reduction...

Research Grants19

  1. Structural Study of Semaphorins, Neuropilins and Plexins
    Dimitar Nikolov; Fiscal Year: 2009
    ..abstract_text> ..
  2. STRUCTURAL STUDY OF EPH RECEPTORS AND EPHRINS
    Dimitar Nikolov; Fiscal Year: 2000
    ..The kinetics and thermodynamics of these interactions will also be determined. ..
  3. Novel Small-Molecule Inhibitors of the Tie2/Angiopoietin Interactions and Signali
    Dimitar Nikolov; Fiscal Year: 2007
    ....
  4. Structure Study of Angiopoietins and the Tie2 Receptor
    Dimitar Nikolov; Fiscal Year: 2007
    ....
  5. STRUCTURAL STUDY OF EPH RECEPTORS AND EPHRINS
    Dimitar Nikolov; Fiscal Year: 2007
    ..abstract_text> ..
  6. Structural Study of Semaphorins, Neuropilins and Plexins
    Dimitar Nikolov; Fiscal Year: 2007
    ....
  7. Structure Study of Angiopoietins and the Tie2 Receptor
    Dimitar Nikolov; Fiscal Year: 2006
    ....
  8. STRUCTURAL STUDY OF EPH RECEPTORS AND EPHRINS
    Dimitar Nikolov; Fiscal Year: 2006
    ..abstract_text> ..
  9. STRUCTURAL STUDY OF EPH RECEPTORS AND EPHRINS
    Dimitar Nikolov; Fiscal Year: 2005
    ..abstract_text> ..
  10. Structure Study of Angiopoietins and the Tie2 Receptor
    Dimitar Nikolov; Fiscal Year: 2005
    ....
  11. Structure Study of Angiopoietins and the Tie2 Receptor
    Dimitar Nikolov; Fiscal Year: 2004
    ....
  12. STRUCTURAL STUDY OF EPH RECEPTORS AND EPHRINS
    Dimitar Nikolov; Fiscal Year: 2003
    ..The kinetics and thermodynamics of these interactions will also be determined. ..
  13. STRUCTURAL STUDY OF EPH RECEPTORS AND EPHRINS
    Dimitar Nikolov; Fiscal Year: 2002
    ..The kinetics and thermodynamics of these interactions will also be determined. ..
  14. STRUCTURAL STUDY OF EPH RECEPTORS AND EPHRINS
    Dimitar Nikolov; Fiscal Year: 2001
    ..The kinetics and thermodynamics of these interactions will also be determined. ..
  15. STRUCTURAL STUDY OF EPH RECEPTORS AND EPHRINS
    Dimitar B Nikolov; Fiscal Year: 2010
    ..Structural and biophysical characterization of the Eph/ephrin/ADAM interactions and cleavage;3. Production, structural and functional characterization of full-length (transmembrane) Eph receptors. ..
  16. Structural Study of Semaphorins, Neuropilins and Plexins
    Dimitar Nikolov; Fiscal Year: 2006
    ....