Russell Doolittle

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Correlating structure and function during the evolution of fibrinogen-related domains
    Russell F Doolittle
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 0314, USA
    Protein Sci 21:1808-23. 2012
  2. doi request reprint The protochordate Ciona intestinalis has a protein like full-length vertebrate fibrinogen
    Russell F Doolittle
    Department of Chemistry and Biochemistry, University of California, San Diego, Calif, USA
    J Innate Immun 4:219-22. 2012
  3. ncbi request reprint Evolutionary anomalies among the aminoacyl-tRNA synthetases
    R F Doolittle
    Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093 0634, USA
    Curr Opin Genet Dev 8:630-6. 1998
  4. ncbi request reprint Evolutionary aspects of whole-genome biology
    Russell F Doolittle
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093 0314, USA
    Curr Opin Struct Biol 15:248-53. 2005
  5. ncbi request reprint Natively unfolded regions of the vertebrate fibrinogen molecule
    Russell F Doolittle
    Division of Biological Sciences, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 0634, USA
    Proteins 63:391-7. 2006
  6. ncbi request reprint Binding of synthetic B knobs to fibrinogen changes the character of fibrin and inhibits its ability to activate tissue plasminogen activator and its destruction by plasmin
    Russell F Doolittle
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 0314, USA
    Biochemistry 45:2657-67. 2006
  7. ncbi request reprint Differences in binding specificity for the homologous gamma- and beta-chain "holes" on fibrinogen: exclusive binding of Ala-His-Arg-Pro-amide by the beta-chain hole
    Russell F Doolittle
    Department of Chemistry and Biochemistry and Division of Biology, University of California at San Diego, La Jolla, California 92093 0314, USA
    Biochemistry 45:13962-9. 2006
  8. ncbi request reprint Probing the beta-chain hole of fibrinogen with synthetic peptides that differ at their amino termini
    Russell F Doolittle
    Department of Chemistry and Biochemistry and Division of Biology, University of California, San Diego, La Jolla, California 92093 0314, USA
    Biochemistry 46:10033-8. 2007
  9. doi request reprint Genomic evidence for a simpler clotting scheme in jawless vertebrates
    Russell F Doolittle
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 0314, USA
    J Mol Evol 66:185-96. 2008
  10. ncbi request reprint Searching for differences between fibrinogen and fibrin that affect the initiation of fibrinolysis
    Russell F Doolittle
    Depts of Chemistry and Biochemistry and Molecular Biology, University of California, San Diego, La Jolla, CA 92093 0314, USA
    Cardiovasc Hematol Agents Med Chem 6:181-9. 2008

Research Grants

  1. STRUCTURAL STUDIES ON FIBRINOGEN AND FIBRIN
    Russell Doolittle; Fiscal Year: 2003
  2. STRUCTURAL STUDIES ON FIBRINOGEN AND FIBRIN
    Russell Doolittle; Fiscal Year: 2000
  3. Characterization of the flexible portions of fibrinogen
    Russell Doolittle; Fiscal Year: 2007

Collaborators

Detail Information

Publications33

  1. pmc Correlating structure and function during the evolution of fibrinogen-related domains
    Russell F Doolittle
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 0314, USA
    Protein Sci 21:1808-23. 2012
    ..The unbalanced style of change was also observed in FReDs from non-chordates, many of which have been implicated in innate immunity...
  2. doi request reprint The protochordate Ciona intestinalis has a protein like full-length vertebrate fibrinogen
    Russell F Doolittle
    Department of Chemistry and Biochemistry, University of California, San Diego, Calif, USA
    J Innate Immun 4:219-22. 2012
    ..In fact, 3 consecutive genes exist, the translated versions of which are homologous to individual vertebrate fibrinogen chains. The circulating form is likely a 6-chain covalent dimer, just as occurs in vertebrates...
  3. ncbi request reprint Evolutionary anomalies among the aminoacyl-tRNA synthetases
    R F Doolittle
    Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093 0634, USA
    Curr Opin Genet Dev 8:630-6. 1998
    ..The question arises - is this mainly the result of promiscuous exchange, or is the confusion really a reflection of the differential loss of past duplications? Phylogenetic analysis may yet provide the answer...
  4. ncbi request reprint Evolutionary aspects of whole-genome biology
    Russell F Doolittle
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093 0314, USA
    Curr Opin Struct Biol 15:248-53. 2005
    ..Still, some fundamental phylogenetic problems remain, including determining the root--if there is one--of the historical relationship between Archaea, Bacteria and Eukarya...
  5. ncbi request reprint Natively unfolded regions of the vertebrate fibrinogen molecule
    Russell F Doolittle
    Division of Biological Sciences, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 0634, USA
    Proteins 63:391-7. 2006
    ..Although it has long been realized that a large portion of the fibrinogen alpha chain has little if any defined structure, the physiological significance of this flexible appendage remains mysterious...
  6. ncbi request reprint Binding of synthetic B knobs to fibrinogen changes the character of fibrin and inhibits its ability to activate tissue plasminogen activator and its destruction by plasmin
    Russell F Doolittle
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 0314, USA
    Biochemistry 45:2657-67. 2006
    ....
  7. ncbi request reprint Differences in binding specificity for the homologous gamma- and beta-chain "holes" on fibrinogen: exclusive binding of Ala-His-Arg-Pro-amide by the beta-chain hole
    Russell F Doolittle
    Department of Chemistry and Biochemistry and Division of Biology, University of California at San Diego, La Jolla, California 92093 0314, USA
    Biochemistry 45:13962-9. 2006
    ....
  8. ncbi request reprint Probing the beta-chain hole of fibrinogen with synthetic peptides that differ at their amino termini
    Russell F Doolittle
    Department of Chemistry and Biochemistry and Division of Biology, University of California, San Diego, La Jolla, California 92093 0314, USA
    Biochemistry 46:10033-8. 2007
    ..In lampreys, GPRPYam is a significantly better inhibitor, but in humans, it is less effective than GPRPam, indicating that in the lamprey system the same tyrosine-arginine interaction can also occur in the gamma-chain setting...
  9. doi request reprint Genomic evidence for a simpler clotting scheme in jawless vertebrates
    Russell F Doolittle
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 0314, USA
    J Mol Evol 66:185-96. 2008
    ....
  10. ncbi request reprint Searching for differences between fibrinogen and fibrin that affect the initiation of fibrinolysis
    Russell F Doolittle
    Depts of Chemistry and Biochemistry and Molecular Biology, University of California, San Diego, La Jolla, CA 92093 0314, USA
    Cardiovasc Hematol Agents Med Chem 6:181-9. 2008
    ..Although some conformational changes have been found by X-ray crystallography, the structural changes leading to the exposure of sites thought to bind t-PA and/or plasminogen remain to be demonstrated...
  11. doi request reprint Step-by-step evolution of vertebrate blood coagulation
    R F Doolittle
    Department of Chemistry and Biochemistry and Molecular Biology, University of California, San Diego, La Jolla, CA 92093 0314, USA
    Cold Spring Harb Symp Quant Biol 74:35-40. 2009
    ..The full complement of factors known to be operating in humans does not occur until pouched marsupials (opossum), at least one key factor still absent in egg-laying mammals such as platypus...
  12. doi request reprint Coagulation in vertebrates with a focus on evolution and inflammation
    Russell F Doolittle
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 0314, USA
    J Innate Immun 3:9-16. 2011
    ..Although the roots of both systems may extend to protochordates, they arose quite independently...
  13. ncbi request reprint Some comments on John Ferry's most enduring paper
    Russell F Doolittle
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0634, USA
    Biophys Chem 112:177-80. 2004
    ..In this brief memoir, I reflect on the great insight John Ferry exhibited in his extremely influential 1952 paper on the mechanism of fibrinogen being changed into fibrin...
  14. ncbi request reprint Determining the crystal structure of fibrinogen
    R F Doolittle
    Center for Molecular Genetics, University of California, San Diego, La Jolla, CA 92093 0634, USA
    J Thromb Haemost 2:683-9. 2004
    ..Like those authors, I have tried to capture some of the excitement-as well as the disappointments-that occurred along the way to a long-term goal...
  15. ncbi request reprint X-ray crystallographic studies on fibrinogen and fibrin
    R F Doolittle
    Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093 0634, USA
    J Thromb Haemost 1:1559-65. 2003
    ..Although these studies have thrown much light on the details of the fibrinogen to fibrin conversion, much remains to be found out...
  16. ncbi request reprint Crystal structure studies on fibrinogen and fibrin
    R F Doolittle
    Center for Molecular Genetics, Rm 206, University of California, San Diego, La Jolla, CA 92093 0634, USA
    Ann N Y Acad Sci 936:31-43. 2001
    ..Nonetheless, when all the structural data are considered together, it is possible to construct a realistic model not only of a fibrinogen molecule but also of a fibrin protofibril...
  17. ncbi request reprint Structural basis of the fibrinogen-fibrin transformation: contributions from X-ray crystallography
    Russell F Doolittle
    Center for Molecular Genetics, University of California, San Diego, La Jolla 92093, USA
    Blood Rev 17:33-41. 2003
    ..In the end, although crystal structures have added greatly to our understanding of fibrin formation, much still needs to be unraveled about how clots form...
  18. ncbi request reprint Bacterial actins? An evolutionary perspective
    Russell F Doolittle
    Center for Molecular Genetics, University of California, San Diego, La Jolla 92093 0634, USA
    Bioessays 24:293-6. 2002
    ..Sequence comparisons reveal that eukaryotic actin and the bacterialhomolog (mreB protein), unlike many other proteins common to eukaryotes and Bacteria, have very different and more highly extended evolutionary histories...
  19. ncbi request reprint Some notes on crystallizing fibrinogen and fibrin fragments
    Russell F Doolittle
    Center for Molecular Genetics, Room 206, University of California, San Diego, La Jolla, CA 92093 0634, USA
    Biophys Chem 100:307-13. 2003
    ..The history of my interest in fibrinogen and its crystallization can be traced back in part to some early interactions with John Edsall...
  20. ncbi request reprint Searching for the common ancestor
    R F Doolittle
    Center for Molecular Genetics, University of California, San Diego, La Jolla 92093 0634, USA
    Res Microbiol 151:85-9. 2000
    ..F. Doolittle, P. Gogarten, R. Gupta, H. Hartman, O. Kandler, E. Koonin, J. Lake, W. Martin, M. Sogin, and C. Woese, inter alia. I hope they will forgive me if my depiction of events does not do full justice to their contributions...
  21. ncbi request reprint Three-dimensional structural studies on fragments of fibrinogen and fibrin
    R F Doolittle
    Center for Molecular Genetics University of California San Diego La Jolla CA 92093 0634 USA
    Curr Opin Struct Biol 8:792-8. 1998
    ..These include structures of a 30 kDa recombinant gammaC domain, an 86 kDa fragment D from human fibrinogen and a cross-linked double-D fragment from fibrin...
  22. ncbi request reprint The crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface
    Zhe Yang
    Center for Molecular Genetics, University of California at San Diego, La Jolla, CA 92093 0634, USA
    Biochemistry 41:15610-7. 2002
    ..These observations show that double-D structures are linked in a way that is sufficiently flexible to accommodate different D-D interfaces under different circumstances...
  23. doi request reprint Two families of synthetic peptides that enhance fibrin turbidity and delay fibrinolysis by different mechanisms
    Leela Pandi
    Department of Chemistry and Biochemistry and Division of Biology, University of California at San Diego, La Jolla, California 92093 0314, USA
    Biochemistry 48:7201-8. 2009
    ....
  24. ncbi request reprint Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide
    Zhe Yang
    Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093 0634, USA
    Biochemistry 41:10218-24. 2002
    ..The most significant differences between the lamprey and human structures occur in connecting loops at the entryways to the beta-chain and gamma-chain binding pockets...
  25. pmc The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes
    Yong Jiang
    Center for Molecular Genetics, University of California at San Diego, La Jolla, CA 92093 0634, USA
    Proc Natl Acad Sci U S A 100:7527-32. 2003
    ..A search of the genome of a urochordate, the sea squirt, Ciona intestinalis, did not turn up any genuine orthologs for these 26 factors, although paralogs and/or constituent domains were evident for virtually all of them...
  26. pmc Phylogeny determined by protein domain content
    Song Yang
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 102:373-8. 2005
    ..During the course of the study, it emerged that there is a core set of approximately 50 folds that is found in all 174 genomes and a single fold diagnostic of all Archaea...
  27. doi request reprint Crystal structure of human fibrinogen
    Justin M Kollman
    Department of Chemistry and Biochemistry and Division of Biology, University of California at San Diego, La Jolla, California 92093 0314, USA
    Biochemistry 48:3877-86. 2009
    ..As was the case for native chicken fibrinogen, no resolvable electron density could be associated with alphaC domains...
  28. ncbi request reprint The occurrence of type S1A serine proteases in sponge and jellyfish
    Ana Rojas
    Center for Molecular Genetics, University of California, San Diego, La Jolla, CA 92093 0624, USA
    J Mol Evol 55:790-4. 2006
    ..We now report the existence of Group S1A serine proteases in a sponge (phylum Porifera) and a jellyfish (phylum Cnidaria), making it safe to conclude that all animal groups possess these enzymes...
  29. ncbi request reprint Unusual non-crystallographic symmetry in crystals of a 420 kDa crustacean clottable protein
    Justin M Kollman
    Center for Molecular Genetics, University of California, San Diego, La Jolla, CA 92093 0634, USA
    Acta Crystallogr D Biol Crystallogr 61:485-9. 2005
    ..The orthorhombic crystals have a single dimer per asymmetric unit. Attempts to phase the data are currently under way...
  30. ncbi request reprint Martin David Kamen (27 August 1913 - 31 August 2002)
    Russell F Doolittle
    University of California, San Diego
    Proc Am Philos Soc 148:499-503. 2004
  31. ncbi request reprint Biodiversity: microbial genomes multiply
    Russell F Doolittle
    Nature 416:697-700. 2002
  32. ncbi request reprint The grand assault
    Russell F Doolittle
    Nature 419:493-4. 2002
  33. ncbi request reprint Molecular cloning of a new cDNA and expression of 3-hydroxy-3-methylglutaryl-CoA synthase gene from Hevea brasiliensis
    Nualpun Sirinupong
    Biochemistry Department, Faculty of Science, Prince of Songkla University, Hat Yai, 90112, Thailand
    Planta 221:502-12. 2005
    ..Therefore, a possible secondary structure of HMGS could be predicted based on the Protein Data Bank information of ACP synthase III...

Research Grants16

  1. STRUCTURAL STUDIES ON FIBRINOGEN AND FIBRIN
    Russell Doolittle; Fiscal Year: 2003
    ..Combined with the full structures of the native molecules at high resolution, these results should dispel much of the mystery of fibrin formation. ..
  2. STRUCTURAL STUDIES ON FIBRINOGEN AND FIBRIN
    Russell Doolittle; Fiscal Year: 2000
    ..Finally, there are evolutionary connections between these structures and other proteins (e.g., tenascin) that we plan to exploit. ..
  3. Characterization of the flexible portions of fibrinogen
    Russell Doolittle; Fiscal Year: 2007
    ..These studies are aimed at determining the degree of specificity involved in the assembly of fibrin units and protofibrils as well as the relative locations of the regions involved. ..