A McPherson

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Introduction to protein crystallization
    Alexander McPherson
    Department of Molecular Biology and Biochemistry, University of Califonia, Irvine 560 Steinhaus Hall, Irvine, CA 92697 3900, USA
    Methods 34:254-65. 2004
  2. pmc Biophysical and atomic force microscopy characterization of the RNA from satellite tobacco mosaic virus
    Yuri G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
    Nucleic Acids Res 38:8284-94. 2010
  3. ncbi request reprint Micelle formation and crystallization as paradigms for virus assembly
    Alexander McPherson
    University of Califonia Irvine, Department of Molecular Biology and Biochemistry, Irvine, CA 92697 3900, USA
    Bioessays 27:447-58. 2005
  4. ncbi request reprint Development of an alternative approach to protein crystallization
    Alexander McPherson
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
    J Struct Funct Genomics 8:193-8. 2007
  5. ncbi request reprint Atomic force microscopy applications in macromolecular crystallography
    A McPherson
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 3900, USA
    Acta Crystallogr D Biol Crystallogr 57:1053-60. 2001
  6. doi request reprint Atomic force microscopy investigation of viruses
    Alexander McPherson
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
    Methods Mol Biol 736:171-95. 2011
  7. ncbi request reprint Some ill considered comments on the protein structure initiative
    Alex McPherson
    Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
    Structure 15:1526-7. 2007
  8. pmc A comparison of salts for the crystallization of macromolecules
    A McPherson
    Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697 3900, USA
    Protein Sci 10:418-22. 2001
  9. ncbi request reprint Macromolecular crystallization in the structural genomics era
    Alexander McPherson
    Department of Molecular Biology and Biochemistry, University of California at Irvine, 560 Steinhaus Hall, Irvine, CA 92697 3900, USA
    J Struct Biol 142:1-2. 2003
  10. ncbi request reprint Atomic force microscopy in the study of macromolecular crystal growth
    A McPherson
    Department of Molecular Biology and Biochemistry, University of California, Irvine 92697 3900, USA
    Annu Rev Biophys Biomol Struct 29:361-410. 2000

Research Grants

  1. STRUCTURE OF VIRAL RNA AND ITS ROLE IN ASSEMBLY
    Alexander McPherson; Fiscal Year: 2006

Collaborators

  • A J Malkin
  • M Plomp
  • W E Robinson
  • Min Zhang
  • HUNG Y FAN
  • Joseph D Ng
  • P D Gershon
  • D L Makino
  • Arlo Z Randall
  • MICHAEL ROSSMANN
  • P Baldi
  • Klaus Schulten
  • Steven B Larson
  • Yu G Kuznetsov
  • Yuri G Kuznetsov
  • Y G Kuznetsov
  • John S Day
  • Yurii G Kuznetsov
  • Robert Cudney
  • Robert W Lucas
  • S B Larson
  • Chieugiang Nguyen
  • A Low
  • Kristina Clemens
  • J Day
  • Yurii Kuznetsov
  • Y Kuznetsov
  • Suzanne Sandmeyer
  • Audrey Low
  • Peter L Freddolino
  • A Greenwood
  • Gary Braslawsky
  • Scott Glaser
  • Jiashu Zhou
  • Shoibal Datta
  • John Day
  • Aaron Greenwood
  • J G Victoria
  • R W Lucas
  • Kunio Nagashima
  • Liza Larsen
  • Rhonda Dasilva
  • Virginia Bilanchone
  • Adam Harned
  • Chuan Xiao
  • Didier Raoult
  • N Ban
  • P R Desjardins
  • Jeffrey J Dowell
  • Jennifer B H Martiny
  • Siyang Sun
  • Jose A Gavira
  • P Ulbrich
  • T Ruml
  • Sohail Jahid
  • S Haubova
  • Nayantara Kothari
  • Anton S Arkhipov
  • Sarah Daijogo
  • Thomas M Menees
  • Bert L Semler
  • James R Gurnon
  • James L Van Etten
  • Ana Paulina Barba de la Rosa
  • Noel T Keen
  • Mary A Canady
  • Natantara H Kothari
  • J T Kitasako
  • D M Mathews
  • J A Dodds

Detail Information

Publications65

  1. ncbi request reprint Introduction to protein crystallization
    Alexander McPherson
    Department of Molecular Biology and Biochemistry, University of Califonia, Irvine 560 Steinhaus Hall, Irvine, CA 92697 3900, USA
    Methods 34:254-65. 2004
    ..In addition, it may provide a framework in which to place the articles that follow...
  2. pmc Biophysical and atomic force microscopy characterization of the RNA from satellite tobacco mosaic virus
    Yuri G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
    Nucleic Acids Res 38:8284-94. 2010
    ..AFM images of RNA emerging from disrupted virions appear most consistent with linear arrangements of structural domains...
  3. ncbi request reprint Micelle formation and crystallization as paradigms for virus assembly
    Alexander McPherson
    University of Califonia Irvine, Department of Molecular Biology and Biochemistry, Irvine, CA 92697 3900, USA
    Bioessays 27:447-58. 2005
    ....
  4. ncbi request reprint Development of an alternative approach to protein crystallization
    Alexander McPherson
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
    J Struct Funct Genomics 8:193-8. 2007
    ..The strategy proposed here is essentially orthogonal to current approaches and has an objective of doubling the success rate of today...
  5. ncbi request reprint Atomic force microscopy applications in macromolecular crystallography
    A McPherson
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 3900, USA
    Acta Crystallogr D Biol Crystallogr 57:1053-60. 2001
    ..These are all features which are important in determining the ultimate resolution and quality of a crystal's diffraction pattern...
  6. doi request reprint Atomic force microscopy investigation of viruses
    Alexander McPherson
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
    Methods Mol Biol 736:171-95. 2011
    ..It can be applied to individual isolated virus, as well as to infected cells. AFM is still in its early development and holds great promise for further investigation of biological systems at the nanometer scale...
  7. ncbi request reprint Some ill considered comments on the protein structure initiative
    Alex McPherson
    Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
    Structure 15:1526-7. 2007
  8. pmc A comparison of salts for the crystallization of macromolecules
    A McPherson
    Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697 3900, USA
    Protein Sci 10:418-22. 2001
    ..The high success rate of sodium malonate in producing crystals was even more impressive when an overall unique success rate with individual macromolecules was considered...
  9. ncbi request reprint Macromolecular crystallization in the structural genomics era
    Alexander McPherson
    Department of Molecular Biology and Biochemistry, University of California at Irvine, 560 Steinhaus Hall, Irvine, CA 92697 3900, USA
    J Struct Biol 142:1-2. 2003
  10. ncbi request reprint Atomic force microscopy in the study of macromolecular crystal growth
    A McPherson
    Department of Molecular Biology and Biochemistry, University of California, Irvine 92697 3900, USA
    Annu Rev Biophys Biomol Struct 29:361-410. 2000
    ..The unique features of these crystals, apparently in AFM images, undoubtedly influence the diffraction properties of the crystals and the quality of the molecular images obtained by X-ray crystallography...
  11. ncbi request reprint Protein crystallization in the structural genomics era
    Alexander McPherson
    University of Califonia, Irvine, Department of Molecular Biology and Biochemistry, 560 Steinhaus Hall, Irvine, CA 92697 3900, USA
    J Struct Funct Genomics 5:3-12. 2004
    ..A brief summary is provided here of the progress in the past few years and the influence of the structural genomics project...
  12. ncbi request reprint Crystals of the beta-subunit of bovine luteinizing hormone and indicators for the involvement of proteolysis in protein crystallization
    Alexander McPherson
    Department of Molecular Biology and Biochemistry, 560 Steinhaus Hall, Irvine, CA 92697 3900, USA
    Acta Crystallogr D Biol Crystallogr 60:872-7. 2004
    ..Some indicators of when proteolysis may be a factor in crystallization, as well as some consequences, are described...
  13. ncbi request reprint Searching for silver bullets: an alternative strategy for crystallizing macromolecules
    Alexander McPherson
    University of California, Irvine, Department of Molecular Biology and Biochemistry, Room 560 Steinhaus Hall, Irvine, CA 92697 3900, USA
    J Struct Biol 156:387-406. 2006
    ..We propose that an alternate approach to crystallizing proteins might be developed, which employs a limited set of fundamental crystallization conditions combined with a broad screen of potentially useful small molecule additives...
  14. pmc Biophysical studies on the RNA cores of satellite tobacco mosaic virus
    J Day
    Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California 92697 3900, USA
    Biophys J 80:2364-71. 2001
    ..The intimate association of amino acid residues 2 through 25 with RNA likely contributes to the stability of the condensed conformation of the nucleic acid cores...
  15. ncbi request reprint Macromolecular crystal growth investigations using atomic force microscopy
    A McPherson
    University of California, Irvine Department of Molecular Biology and Biochemistry, 92697 3900, USA
    J Synchrotron Radiat 11:21-3. 2004
    ..All of these can be recorded under normal growth conditions, in native mother liquors, over time intervals ranging from minutes to days, and at the molecular level...
  16. ncbi request reprint Refined structure of satellite tobacco mosaic virus at 1.8 A resolution
    S B Larson
    Department of Biochemistry, University of California, Riverside, CA 92521, USA
    J Mol Biol 277:37-59. 1998
    ..The intimate relationship between protein and nucleic acid in STMV suggests an assembly pathway based on the cooperative and coordinated co-condensation of RNA with capsid protein dimers...
  17. ncbi request reprint Surface processes in the crystallization of turnip yellow mosaic virus visualized by atomic force microscopy
    A J Malkin
    Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, 92697 3900, USA
    J Struct Biol 127:35-43. 1999
    ..We believe this provides the first visual record of a cooperative restructuring of the surface of a supramolecular crystal...
  18. ncbi request reprint Structural transitions of satellite tobacco mosaic virus particles
    Y G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California, Irvine, Room 560, Steinhaus Hall, Irvine, California 92697 3900, USA
    Virology 284:223-34. 2001
    ..Evidence is also presented that preparations of native virus and their crystals are naturally somewhat heterogeneous and contain a variety of particles of anomalous size...
  19. ncbi request reprint Atomic force microscopy imaging of retroviruses: human immunodeficiency virus and murine leukemia virus
    Yu G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697 4800, USA
    Scanning 26:209-16. 2004
    ..Further application of AFM to viruses associated with other pathologies may ultimately have a significant impact on the diagnosis and treatment of virus-promoted diseases...
  20. ncbi request reprint Atomic force microscopy investigation of Mason-Pfizer monkey virus and human immunodeficiency virus type 1 reassembled particles
    Yu G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California, Irvine, 560 SH, Irvine, CA 92697 3900, USA
    Virology 360:434-46. 2007
    ..They exhibited left handed helical symmetry based on a p6 hexagonal net. The organization of HIV fusion proteins in the tubes is significantly different than for the protein units in the particles of M-PMV DeltaProCANC...
  21. pmc Atomic force microscopy investigation of isolated virions of murine leukemia virus
    Y G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697 3900, USA
    J Virol 79:1970-4. 2005
    ..They also permitted estimation of viral shell thickness (35 to 40 nm) and showed the presence of a distinct trough between the shell and the core surface...
  22. ncbi request reprint The structure of satellite panicum mosaic virus at 1.9 A resolution
    N Ban
    Department of Biochemistry, University of California, Riverside 92521, USA
    Nat Struct Biol 2:882-90. 1995
    ..Basic amino acid residues in contact with the nucleic acid show a considerable degree of disorder. The carboxy-terminal strand of the virus coat protein interacts with adjacent subunits, forming an additional beta-strand...
  23. ncbi request reprint Application of atomic force microscopy to studies of surface processes in virus crystallization and structural biology
    A J Malkin
    University of California, Irvine, Department of Molecular Biology and Biochemistry, Irvine, CA 92697 3900, USA
    Acta Crystallogr D Biol Crystallogr 58:1617-21. 2002
    ..High-resolution images of intact, enveloped HSV-1 and the underlying capsid structure demonstrate capabilities of AFM to probe structures of large macromolecular assemblies...
  24. ncbi request reprint Crystallization of Brome mosaic virus and T = 1 Brome mosaic virus particles following a structural transition
    R W Lucas
    Department of Molecular Biology and Biochemistry, University of California, Irvine, 92697-3900, USA
    Virology 286:290-303. 2001
    ..In some cases these aberrant particles are incorporated into growing crystals where they are frequently responsible for defect formation...
  25. ncbi request reprint Self-repair of biological fibers catalyzed by the surface of a virus crystal
    Y G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California, Irvine 92697 1931, USA
    Proteins 44:392-6. 2001
    ..The surfaces of virus crystals provide ideal workbenches for the visualization and manipulation of nanoscale objects, particularly extended structures such as these fibers...
  26. ncbi request reprint Satellite tobacco mosaic virus RNA: structure and implications for assembly
    S B Larson
    Department of Molecular Biology and Biochemistry, 560 Steinhaus Hall, University of California Irvine, Irvine, CA 92697 3900, USA
    Curr Opin Struct Biol 11:59-65. 2001
    ..Connection of the stem-loops in the most efficient manner produces a persuasive model for the encapsidated RNA. This arrangement has significant implications for virus assembly and for the essential role of RNA...
  27. ncbi request reprint Mechanisms of growth for protein and virus crystals
    A J Malkin
    University of California, Department of Biochemistry, Riverside 92521, USA
    Nat Struct Biol 2:956-9. 1995
    ..Biological macromolecules apparently utilize a more diverse range of growth mechanisms in their crystallization than any previously studied materials...
  28. pmc Atomic force microscopy investigation of vaccinia virus structure
    Y Kuznetsov
    University of California, Irvine, Department of Molecular Biology and Biochemistry, Irvine, CA 92697 3900, USA
    J Virol 82:7551-66. 2008
    ..Prolonged exposure to proteases deproteinized the DNA, leaving masses of extended, free DNA. Estimates of the interior core volume suggest moderate but not extreme compaction of the genome...
  29. ncbi request reprint Repair of impurity-poisoned protein crystal surfaces
    M Plomp
    Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697 3900, USA
    Proteins 50:486-95. 2003
    ..Growth-dissolution-growth cycles could be used to produce larger crystals that otherwise would have stopped growing because of impurity poisoning...
  30. ncbi request reprint Atomic force microscopy analysis of icosahedral virus RNA
    Yurii G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
    J Mol Biol 347:41-52. 2005
    ..RNA base sequence, therefore, may be sufficient to encode the conformation of the encapsidated RNA even in the absence of coat proteins...
  31. ncbi request reprint Investigation of RNA structure in satellite panicum mosaic virus
    D L Makino
    Department of Molecular Biology and Biochemistry, University of California Irvine, 560 Steinhaus Hall, Irvine, CA 92697, USA
    Virology 351:420-31. 2006
    ..This study further shows that analysis of viruses in crystals grown under different chemical conditions may reveal additional information regarding the structure of encapsidated RNA...
  32. ncbi request reprint Macromolecular crystal growth as revealed by atomic force microscopy
    Alexander McPherson
    Department of Molecular Biology and Biochemistry, University of California at Irvine, 560 Steinhaus Hall, Irvine, CA 92697 3900, USA
    J Struct Biol 142:32-46. 2003
    ..All of these can be recorded under normal growth conditions, in native mother liquors, over time intervals ranging from minutes to days, and at the molecular level...
  33. pmc The TY3 Gag3 spacer controls intracellular condensation and uncoating
    Kristina Clemens
    Department of Biological Chemistry, University of California, Irvine, Irvine CA 92697, USA
    J Virol 85:3055-66. 2011
    ..These interactions promote CA domain multimerization. In the third phase, a negatively charged SP domain destabilizes the remaining CA-SP shell for cDNA release...
  34. ncbi request reprint The crystallographic structure of brome mosaic virus
    Robert W Lucas
    University of California Irvine, 560 Steinhaus Hall, Irvine, CA 92697 3900, USA
    J Mol Biol 317:95-108. 2002
    ..The density cannot be attributed to cations and it was modeled as a PEG molecule...
  35. ncbi request reprint A novel strategy for the crystallization of proteins: X-ray diffraction validation
    Steven B Larson
    Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
    Acta Crystallogr D Biol Crystallogr 63:310-8. 2007
    ....
  36. ncbi request reprint Atomic force microscopy investigation of wild-type Moloney murine leukemia virus particles and virus particles lacking the envelope protein
    Y G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697 3900, USA
    Virology 323:189-96. 2004
    ..This suggests that the conformation of the envelope glycoprotein or the disposition of oligosaccharides may be different among particles, on some virions exposing the specific epitope, and others little or none...
  37. ncbi request reprint Electron microscopy of satellite tobacco mosaic virus crystals: metal-coated, negatively stained and stereo pairs
    P R Desjardins
    Department of Plant Pathology, University of California, Riverside 92521, USA
    J Electron Microsc (Tokyo) 49:509-14. 2000
    ..Conversely, knowing the exact unit cell parameters and the distribution of virions in the crystal from X-ray diffraction data aids in the further interpretation of electron micrographs of virus crystals...
  38. ncbi request reprint Combined use of AFM and X-ray diffraction to analyze crystals of an engineered, domain-deleted antibody
    Steven B Larson
    University of California, Irvine, Department of Molecular Biology and Biochemistry, Irvine, CA 92697 3900, USA
    Acta Crystallogr D Biol Crystallogr 61:416-22. 2005
    ..An approach to crystallizing proteins showing phase separation, particularly intact antibodies, that uses a preliminary detergent test set is described...
  39. ncbi request reprint Bence Jones KWR protein structures determined by X-ray crystallography
    Debora L Makino
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 3900, USA
    Acta Crystallogr D Biol Crystallogr 63:780-92. 2007
    ..The arrangement of Bence Jones dimers is also consistent with other observations regarding Bence Jones amyloid-fibril structure and current models...
  40. ncbi request reprint The structure of tomato aspermy virus by X-ray crystallography
    Robert W Lucas
    Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697 3900, USA
    J Struct Biol 139:90-102. 2002
    ..A positive ion, putatively modeled as a Mg(+)ion, lies on the quasi-threefold axis surrounded by three quasi-symmetric glutamate 175 side chains...
  41. pmc A new crystal form of bovine pancreatic RNase A in complex with 2'-deoxyguanosine-5'-monophosphate
    Steven B Larson
    Department of Molecular Biology and Biochemistry, The University of California, Irvine, CA 92697 3900, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 63:728-33. 2007
    ..Because GMP may be produced during degradation of RNA, this association could represent an inhibitor complex and thereby affect the observed enzyme kinetics...
  42. pmc Atomic force microscopy investigation of human immunodeficiency virus (HIV) and HIV-infected lymphocytes
    Y G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California 92697 3900, USA
    J Virol 77:11896-909. 2003
    ..Treatment with even low concentrations (<0.1%) of sodium dodecyl sulfate completely destroyed all virions but produced many interesting products, including aggregates of viral proteins with strands of nucleic acid...
  43. pmc Structure of bovine pancreatic ribonuclease complexed with uridine 5'-monophosphate at 1.60 A resolution
    Steven B Larson
    Department of Molecular Biology and Biochemistry, The University of California, Irvine, CA 92697 3900, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 66:113-20. 2010
    ..The structure was refined to an R factor of 0.197 and an R(free) of 0.253...
  44. ncbi request reprint Atomic force microscopy investigation of Turnip Yellow Mosaic Virus capsid disruption and RNA extrusion
    Yu G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California, Irvine, Room 560, Steinhaus Hall Irvine, CA 92697 3900, USA
    Virology 352:329-37. 2006
    ..Similar products were also obtained by heating TYMV to 70 -75 degrees C and by exposure to alkaline pH. Experiments showed the nucleic acid to have an elaborate secondary structure distributed linearly along its length...
  45. pmc Four crystal forms of a Bence-Jones protein
    Debora L Makino
    Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 3900, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:79-82. 2005
    ..This latter crystal form may shed some light on the formation of fibrils common to certain storage diseases...
  46. ncbi request reprint Crystallographic structure of the T=1 particle of brome mosaic virus
    Steven B Larson
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 3900, USA
    J Mol Biol 346:815-31. 2005
    ..In both particles crucial linkages are made about icosahedral dyads...
  47. ncbi request reprint Preliminary analysis of crystals of panicum mosaic virus (PMV) by X-ray diffraction and atomic force microscopy
    Debora L Makino
    University of California at Irvine, Department of Molecular Biology and Biochemistry, 560 Steinhaus Hall, Irvine, CA 92697 3900, USA
    Acta Crystallogr D Biol Crystallogr 61:173-9. 2005
    ..This is the first observation of such a phenomenon in macromolecular crystals...
  48. ncbi request reprint First crystallographic structure of a xylanase from glycoside hydrolase family 5: implications for catalysis
    Steven B Larson
    Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697 3900, USA
    Biochemistry 42:8411-22. 2003
    ..The first 13 N-terminal residues form one beta-strand of this domain. Residues 44, 45, and 316-322 form the linkers between this domain and the catalytic domain...
  49. ncbi request reprint Atomic force microscopy investigation of a chlorella virus, PBCV-1
    Yu G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California Irvine, 560 Steinhaus Hall, Irvine, CA 92697 3900, USA
    J Struct Biol 149:256-63. 2005
    ..Also observed upon disintegration are strands of linear dsDNA. Fibers of unknown function are also occasionally seen associated with some virions...
  50. ncbi request reprint The RNA of turnip yellow mosaic virus exhibits icosahedral order
    Steven B Larson
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 3900, USA
    Virology 334:245-54. 2005
    ..The distribution of RNA observed crystallographically appears to be in agreement with models based on biochemical data and secondary structural analyses...
  51. pmc X-ray crystallographic analyses of pig pancreatic alpha-amylase with limit dextrin, oligosaccharide, and alpha-cyclodextrin
    Steven B Larson
    Department of Molecular Biology and Biochemistry, The University of California, Irvine, California 92697 3900, USA
    Biochemistry 49:3101-15. 2010
    ..By comprehensive integration of these complexes we have constructed a model for the binding of polysaccharides having the helical character known to be present in natural substrates such as starch and glycogen...
  52. ncbi request reprint Atomic force microscopy investigation of the giant mimivirus
    Yuri G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 3900, USA
    Virology 404:127-37. 2010
    ..These are probably contained within the capsid along with the DNA bearing sac. The fibers were occasionally observed associated with toroidal protein clusters interpreted as processive enzymes modifying the fibers...
  53. doi request reprint Structural analysis of a Synechococcus myovirus S-CAM4 and infected cells by atomic force microscopy
    Yuri G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 3900, USA
    J Gen Virol 91:3095-104. 2010
    ..The capsid structure appears most closely related to that of the cyanophage Syn9 and the Bacillus subtilis phage SPO1, which may, in turn, be evolutionarily related to herpesvirus...
  54. pmc High-resolution structure of proteinase K cocrystallized with digalacturonic acid
    Steven B Larson
    Department of Molecular Biology and Biochemistry, The University of California, Irvine, 92697 3900, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 65:192-8. 2009
    ..One of the calcium-ion sites has not been reported previously. This study further illustrates the involvement of small molecules in the crystallization of macromolecules through their ability to form intermolecular lattice interactions...
  55. pmc Atomic force microscopy in imaging of viruses and virus-infected cells
    Yurii G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California, Irvine, 560 Steinhaus Hall, Irvine, CA 92697 3900, USA
    Microbiol Mol Biol Rev 75:268-85. 2011
    ..The images resemble common light photographic images and require little interpretation. The structures of viruses observed by AFM are consistent with models derived by X-ray crystallography and cryo-EM...
  56. pmc Atomic force microscopy investigation of fibroblasts infected with wild-type and mutant murine leukemia virus (MuLV)
    Yurii G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 3900, USA
    Biophys J 83:3665-74. 2002
    ..The cell surfaces, however, became covered with tubelike structures that appear to result from a failure of the virions to properly undergo morphogenesis, and to fail in budding completely from the cell's surfaces...
  57. pmc Structure of pig heart citrate synthase at 1.78 A resolution
    Steven B Larson
    Department of Molecular Biology and Biochemistry, The University of California, Irvine, 92697 3900, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 65:430-4. 2009
    ....
  58. pmc Mutation in the glycosylated gag protein of murine leukemia virus results in reduced in vivo infectivity and a novel defect in viral budding or release
    Audrey Low
    Department of Molecular Biology and Biochemistry and Cancer Research Institute, University of California, Irvine, CA 92697 3905, USA
    J Virol 81:3685-92. 2007
    ..These results indicate that gPr80gag is important for M-MuLV replication in vivo and in vitro and that the protein may be involved in a late step in viral budding or release...
  59. ncbi request reprint The structure of an antitumor C(H)2-domain-deleted humanized antibody
    Steven B Larson
    Department of Molecular Biology and Biochemistry, The University of California, Irvine, CA 92697 3900, USA
    J Mol Biol 348:1177-90. 2005
    ..3, which binds a similar epitope on TAG-72. The combining site consists of a deep cleft, heavily lined with aromatic amino acid side-chains but bounded by numerous charged groups...
  60. ncbi request reprint The incorporation of large impurities into virus crystals
    Yu G Kuznetsov
    Molecular Biology and Biochemistry, University of California, Irvine, 560 Steinhaus Hall, Irvine, CA 92697 3900, USA
    Acta Crystallogr D Biol Crystallogr 61:720-3. 2005
    ..The high solvent content, the forgiving character of the lattice and the plasticity of the virions allow these incorporations to be possible...
  61. pmc Investigation by atomic force microscopy of the structure of Ty3 retrotransposon particles
    Yurii G Kuznetsov
    Department of Molecular Biology, University of California, Irvine, California 92697 1700, USA
    J Virol 79:8032-45. 2005
    ..Ty3 VLPs did not undergo major external rearrangements during proteolytic maturation...
  62. ncbi request reprint Identification of DNA and RNA from retroviruses using ribonuclease A
    Yuri G Kuznetsov
    Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
    Scanning 28:278-81. 2006
    ..Using this approach, we obtained evidence that reverse transcription of RNA into DNA may occur within the retroviral capsid...
  63. pmc Rapid visualization at high resolution of pathogens by atomic force microscopy: structural studies of herpes simplex virus-1
    Marco Plomp
    Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697 3900, USA
    Am J Pathol 160:1959-66. 2002
    ..It is a useful technique that complements X-ray-based structure determination, cryo-electron microscopy techniques, and optical microscopies in the field of molecular pathogenesis...
  64. ncbi request reprint Unraveling the architecture of viruses by high-resolution atomic force microscopy
    Alexander J Malkin
    BioSecurity and NanoSciences Laboratory, Department of Chemistry and Materials Science, Lawrence Livermore National Laboratory, Livermore, CA, USA
    Methods Mol Biol 292:85-108. 2005
    ....
  65. ncbi request reprint Molecular dynamics simulations of the complete satellite tobacco mosaic virus
    Peter L Freddolino
    Center for Biophysics and Computational Biology, University of Illinois, Urbana Champaign, Urbana, Illinois 61801, USA
    Structure 14:437-49. 2006
    ....

Research Grants1

  1. STRUCTURE OF VIRAL RNA AND ITS ROLE IN ASSEMBLY
    Alexander McPherson; Fiscal Year: 2006
    ..This research is significant because the conformation of the nucleic acid component of no virus is currently known, nor is there any comprehensive structural basis for the processes of viral assembly and disassembly. ..