JAMES BOWIE

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Crystal structure of Proteus mirabilis lipase, a novel lipase from the Proteus/psychrophilic subfamily of lipase family I.1
    Tyler P Korman
    Department of Chemistry and Biochemisty, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS ONE 7:e52890. 2012
  2. pmc Rampant exchange of the structure and function of extramembrane domains between membrane and water soluble proteins
    Hyun Jun Nam
    Department of Life Science, Division of IT Convergence Engineering, School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Korea
    PLoS Comput Biol 9:e1002997. 2013
  3. pmc Dieselzymes: development of a stable and methanol tolerant lipase for biodiesel production by directed evolution
    Tyler P Korman
    Department of Chemistry and Biochemisty, UCLA DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, USA
    Biotechnol Biofuels 6:70. 2013
  4. pmc Native interface of the SAM domain polymer of TEL
    Hoang H Tran
    Department of Chemistry and Biochemistry, UCLA Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, 90095 1570, USA
    BMC Struct Biol 2:5. 2002
  5. pmc Dimerization of the transmembrane domain of amyloid precursor proteins and familial Alzheimer's disease mutants
    Paul M Gorman
    Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 2M9, Canada
    BMC Neurosci 9:17. 2008
  6. ncbi request reprint Helix packing angle preferences
    J U Bowie
    Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA
    Nat Struct Biol 4:915-7. 1997
  7. pmc Membrane proteins: a new method enters the fold
    James U Bowie
    Dept of Chemistry and Biochemistry, UCLA Dept of Energy Center for Genomics and Proteomics, Molecular Biology Institute, University of California Los Angeles, Boyer Hall, 611 Charles E Young Drive East, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 101:3995-6. 2004
  8. pmc Membrane protein folding: how important are hydrogen bonds?
    James U Bowie
    Department of Chemistry and Biochemistry, UCLA DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, USA
    Curr Opin Struct Biol 21:42-9. 2011
  9. ncbi request reprint Solving the membrane protein folding problem
    James U Bowie
    Department of Chemistry and Biochemistry, UCLA DOE Center for Genomics and Proteomics, Molecular Biology Institute, Boyer Hall, UCLA, 611 Charles E Young Drive E, Los Angeles, California 90095 1570, USA
    Nature 438:581-9. 2005
  10. ncbi request reprint Stabilizing membrane proteins
    J U Bowie
    Department of Chemistry and Biochemistry, and UCLA DOE Laboratory of Structural Biology and Molecular Medicine, Boyer Hall, 611 Charles E Young Drive East, Los Angeles, CA 90095 1570, USA
    Curr Opin Struct Biol 11:397-402. 2001

Research Grants

  1. STRUCTURE/FUNCTION OF SAM DOMAINS
    JAMES BOWIE; Fiscal Year: 1999
  2. Membrane Protein Stability
    JAMES BOWIE; Fiscal Year: 2006
  3. Generation of Membrane Protein Production Strains
    JAMES BOWIE; Fiscal Year: 2006
  4. Formulatrix Automated Protein Crystallization System
    JAMES BOWIE; Fiscal Year: 2007
  5. STRUCTURE/FUNCTION OF SAM DOMAINS
    JAMES BOWIE; Fiscal Year: 2007
  6. FASEB Summer Conference on Molecular Biophysics of Cellular Membranes
    JAMES BOWIE; Fiscal Year: 2007
  7. Generation of Membrane Protein Production Strains(RMI)
    JAMES BOWIE; Fiscal Year: 2007
  8. Membrane Protein Stability
    JAMES BOWIE; Fiscal Year: 2007
  9. Improving membrane protein crystallization
    JAMES BOWIE; Fiscal Year: 2007
  10. Generation of Membrane Protein Production Strains
    JAMES BOWIE; Fiscal Year: 2009

Collaborators

Detail Information

Publications63

  1. pmc Crystal structure of Proteus mirabilis lipase, a novel lipase from the Proteus/psychrophilic subfamily of lipase family I.1
    Tyler P Korman
    Department of Chemistry and Biochemisty, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS ONE 7:e52890. 2012
    ..A distinct mechanism for Ca²⁺ coordination may explain how these lipases can fold without specific chaperones...
  2. pmc Rampant exchange of the structure and function of extramembrane domains between membrane and water soluble proteins
    Hyun Jun Nam
    Department of Life Science, Division of IT Convergence Engineering, School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Korea
    PLoS Comput Biol 9:e1002997. 2013
    ..A database of predicted structural and functional relationships for proteins in the human genome is provided at sbi.postech.ac.kr/emdmp...
  3. pmc Dieselzymes: development of a stable and methanol tolerant lipase for biodiesel production by directed evolution
    Tyler P Korman
    Department of Chemistry and Biochemisty, UCLA DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, USA
    Biotechnol Biofuels 6:70. 2013
    ..However, since the Proteus mirabilis lipase is only moderately stable and methanol tolerant, these properties need to be improved before the enzyme can be used industrially...
  4. pmc Native interface of the SAM domain polymer of TEL
    Hoang H Tran
    Department of Chemistry and Biochemistry, UCLA Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, 90095 1570, USA
    BMC Struct Biol 2:5. 2002
    ..In previous work, we determined the structure of a mutant TEL-SAM polymer bearing a Val to Glu substitution in center of the subunit interface. It remained unclear how much the mutation affected the architecture of the polymer, however...
  5. pmc Dimerization of the transmembrane domain of amyloid precursor proteins and familial Alzheimer's disease mutants
    Paul M Gorman
    Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 2M9, Canada
    BMC Neurosci 9:17. 2008
    ..The transmembrane domain (TM) of APP contains the known dimerization motif GXXXA. We have investigated the dimerization of both wild type and FAD mutant APP transmembrane domains...
  6. ncbi request reprint Helix packing angle preferences
    J U Bowie
    Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA
    Nat Struct Biol 4:915-7. 1997
    ..Here I show that much of the apparent preference for particular angles is due to statistical bias and that true packing angle preferences are not well described by regular packing models...
  7. pmc Membrane proteins: a new method enters the fold
    James U Bowie
    Dept of Chemistry and Biochemistry, UCLA Dept of Energy Center for Genomics and Proteomics, Molecular Biology Institute, University of California Los Angeles, Boyer Hall, 611 Charles E Young Drive East, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 101:3995-6. 2004
  8. pmc Membrane protein folding: how important are hydrogen bonds?
    James U Bowie
    Department of Chemistry and Biochemistry, UCLA DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, USA
    Curr Opin Struct Biol 21:42-9. 2011
    ..Thus, just like water soluble proteins, evolution can drive the creation of potent hydrogen bonds in membrane proteins where necessary, but mitigating forces in their environment must still be overcome...
  9. ncbi request reprint Solving the membrane protein folding problem
    James U Bowie
    Department of Chemistry and Biochemistry, UCLA DOE Center for Genomics and Proteomics, Molecular Biology Institute, Boyer Hall, UCLA, 611 Charles E Young Drive E, Los Angeles, California 90095 1570, USA
    Nature 438:581-9. 2005
    ..Our enhanced view of the structure universe, combined with an increasingly quantitative understanding of fold determination, engenders optimism that a solution to the folding problem for membrane proteins can be achieved...
  10. ncbi request reprint Stabilizing membrane proteins
    J U Bowie
    Department of Chemistry and Biochemistry, and UCLA DOE Laboratory of Structural Biology and Molecular Medicine, Boyer Hall, 611 Charles E Young Drive East, Los Angeles, CA 90095 1570, USA
    Curr Opin Struct Biol 11:397-402. 2001
    ..One way to alleviate this problem is to find more stable mutants of a membrane protein of interest. This approach is made tractable by the finding that stability-enhancing mutations appear to be relatively common in membrane proteins...
  11. pmc Helix-bundle membrane protein fold templates
    J U Bowie
    Department of Chemistry and Biochemistry and DOE Laboratory of Structural Biology and Molecular Medicine, UCLA, Los Angeles, California 90095 1570, USA
    Protein Sci 8:2711-9. 1999
    ..The generated folds could serve as templates for fold recognition or as starting points for conformational searches that are well distributed throughout conformation space...
  12. ncbi request reprint The SAM domain of polyhomeotic forms a helical polymer
    Chongwoo A Kim
    Department of Chemistry and Biochemistry, Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, UCLA, 611 Charles E Young Drive East, Los Angeles, California 90095 1570, USA
    Nat Struct Biol 9:453-7. 2002
    ..The formation of these polymer structures by SAM domains in two divergent repressors suggests a conserved mode of repression involving a higher order chromatin structure...
  13. ncbi request reprint The many faces of SAM
    Feng Qiao
    U S Department of Energy UCLA DOE Institute of Genomics and Proteomics, Molecular Biology Institute, Department of Chemistry and Biochemistry, UCLA, CA 90095, USA
    Sci STKE 2005:re7. 2005
    ..In this review, we describe the structural basis of SAM domain interactions and highlight their roles in the scaffolding of protein complexes in normal and pathological processes...
  14. ncbi request reprint Structural organization of a Sex-comb-on-midleg/polyhomeotic copolymer
    Chongwoo A Kim
    Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
    J Biol Chem 280:27769-75. 2005
    ..The copolymer model suggests that polymeric Scm complexes could extend beyond the local domains of polymeric Ph complexes on chromatin, possibly playing a role in long range repression...
  15. pmc Polymer-driven crystallization
    Sehat Nauli
    UCLA DOE Institute of Genomics and Proteomics, University of California, Los Angeles 90095 1570, USA
    Protein Sci 16:2542-51. 2007
    ..The crystal structures of two fusion proteins show that the TELSAM polymer is responsible for the majority of contacts in the crystal lattice. The results suggest that biological polymers could be designed as crystallization modules...
  16. pmc A novel cytoplasmic tail MXXXL motif mediates the internalization of prostate-specific membrane antigen
    Sigrid A Rajasekaran
    Department of Pathology and Laboratory Medicine, Molecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
    Mol Biol Cell 14:4835-45. 2003
    ..We also show that dominant negative micro2 of the adaptor protein (AP)-2 complex strongly inhibits the internalization of PSMA, indicating that AP-2 is involved in the internalization of PSMA mediated by the MXXXL motif...
  17. ncbi request reprint SAM domains can utilize similar surfaces for the formation of polymers and closed oligomers
    Ranjini Ramachander
    Department of Chemistry and Biochemistry, UCLA DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095 1570, USA
    J Mol Biol 342:1353-8. 2004
    ..These results indicate that SAM domains can create a variety of oligomeric architectures utilizing common binding surfaces...
  18. ncbi request reprint An architectural framework that may lie at the core of the postsynaptic density
    Marisa K Baron
    Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California, Los Angeles, 611 Charles E Young Drive East, Los Angeles, CA 90095 1570, USA
    Science 311:531-5. 2006
    ..Zn2+, which is found in high concentrations in the PSD, binds tightly to Shank3 and may regulate assembly. Sheets of the Shank protein could form a platform for the construction of the PSD complex...
  19. pmc Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins
    Nathan Hyunjoong Joh
    Department of Chemistry and Biochemistry, UCLA DOE Center for Genomics and Proteomics, Molecular Biology Institute, USA
    Nature 453:1266-70. 2008
    ..Weak hydrogen-bonding should be reflected in considerations of membrane protein folding, dynamics, design, evolution and function...
  20. pmc HotPatch: a statistical approach to finding biologically relevant features on protein surfaces
    Frank K Pettit
    UCLA DOE Institute for Genomics and Proteomics, Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
    J Mol Biol 369:863-79. 2007
    ..The program can be accessed online (at http://hotpatch.mbi.ucla.edu)...
  21. pmc Analysis of side-chain rotamers in transmembrane proteins
    Aaron K Chamberlain
    Department of Chemistry and Biochemistry, UCLA DOE Center for Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, California 90095 1570, USA
    Biophys J 87:3460-9. 2004
    ..Our results demonstrate how the membrane environment influences protein structures, providing information that will be useful in the structure prediction and design of transmembrane proteins...
  22. doi request reprint Regulation of enzyme localization by polymerization: polymer formation by the SAM domain of diacylglycerol kinase delta1
    Bryan T Harada
    Molecular Biology Institute, University of California, Los Angeles, Boyer Hall, Los Angeles, CA 90095 1570, USA
    Structure 16:380-7. 2008
    ..Thus, polymerization of DGK delta regulates the activity of the enzyme by sequestering DGK delta in an inactive cellular location. Regulation by dynamic polymerization is an emerging theme in signal transduction...
  23. pmc Mae inhibits Pointed-P2 transcriptional activity by blocking its MAPK docking site
    Feng Qiao
    UCLA DOE Institute of Genomics and Proteomics, Los Angeles, CA, USA
    EMBO J 25:70-9. 2006
    ....
  24. ncbi request reprint Derepression by depolymerization; structural insights into the regulation of Yan by Mae
    Feng Qiao
    UCLA DOE Institute of Genomics and Proteomics, Molecular Biology Institute, Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA
    Cell 118:163-73. 2004
    ..Depolymerization of Yan by Mae represents a novel mechanism of transcriptional control that sensitizes Yan for regulation by receptor tyrosine kinases...
  25. ncbi request reprint A simple method for modeling transmembrane helix oligomers
    Sanguk Kim
    Department of Chemistry and Biochemistry and UCLA DOE Center for Genomics and Proteomics, Boyer Hall, University of California Los Angeles, 611 Charles E Young Drive E, Room 655, Los Angeles, CA 90095 1570, USA
    J Mol Biol 329:831-40. 2003
    ..Our method should be useful for obtaining structural models of transmembrane domains, improving our understanding of structure/function relationships for particular membrane proteins...
  26. ncbi request reprint SAM domains: uniform structure, diversity of function
    Chongwoo A Kim
    Department of Chemistry and Biochemistry, UCLA DOE Center for Genomics and Proteomics, Molecular Biology Institute, Boyer Hall, 611 Charles E Young Drive E, UCLA, Los Angeles, CA 90095 1570, USA
    Trends Biochem Sci 28:625-8. 2003
    ..Such functional diversity within a homologous protein family presents a significant challenge for bioinformatic function assignment...
  27. ncbi request reprint Side-chain contributions to membrane protein structure and stability
    Salem Faham
    Department of Chemistry and Biochemistry, UCLA DOE Center for Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, CA 90095 1570, USA
    J Mol Biol 335:297-305. 2004
    ..4) We find little energetic difference, on average, in the burial of apolar surface or polar surface area, implying that van der Waals packing is the dominant force that drives membrane protein folding...
  28. ncbi request reprint Oligomerization-dependent association of the SAM domains from Schizosaccharomyces pombe Byr2 and Ste4
    Ranjini Ramachander
    Department of Chemistry and Biochemistry, Molecular Biology Institute, and the UCLA DOE Laboratory of Structural Biology and Molecular Medicine, University of California, Los Angeles, California 90095, USA
    J Biol Chem 277:39585-93. 2002
    ..The fact that high affinity binding occurs only with the addition of an oligomerization domain suggests that it may be necessary to include ancillary oligomerization modules when searching for binding partners of SAM domains...
  29. doi request reprint Methods for measuring the thermodynamic stability of membrane proteins
    Heedeok Hong
    Department of Chemistry and Biochemistry, UCLA DOE Center for Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, California, USA
    Methods Enzymol 455:213-36. 2009
    ....
  30. pmc Identifying polymer-forming SAM domains
    Alejandro D Meruelo
    Medical Scientist Training Program, UCLA DOE Institute for Genomics and Proteomics, Molecular Biology Institute, UCLA, Los Angeles, California 90095 1570, USA
    Proteins 74:1-5. 2009
    ..Of 2901 SAM family members, we find 694 that score above the threshold and are likely polymers, including SAM domains from the proteins Lethal Malignant Brain Tumor, Bicaudal-C, Liprin-beta, Adenylate Cyclase, and Atherin...
  31. pmc Structural imperatives impose diverse evolutionary constraints on helical membrane proteins
    Amit Oberai
    Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 106:17747-50. 2009
    ....
  32. pmc Method to measure strong protein-protein interactions in lipid bilayers using a steric trap
    Heedeok Hong
    Department of Chemistry and Biochemistry, University of California, Los Angeles Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 107:19802-7. 2010
    ..Thus, steric trapping can open new biological systems to experimental scrutiny in natural bilayer environments...
  33. pmc Similar energetic contributions of packing in the core of membrane and water-soluble proteins
    Nathan H Joh
    Department of Chemistry and Biochemistry, UCLA DOE Center for Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
    J Am Chem Soc 131:10846-7. 2009
    ..We observed little difference in the packing energetics of water and membrane soluble proteins. Our results imply that other mechanisms are employed to stabilize the structure of membrane proteins...
  34. pmc Protein unfolding with a steric trap
    Tracy M Blois
    Department of Chemistry and Biochemistry, UCLA DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
    J Am Chem Soc 131:13914-5. 2009
    ..The steric trap method provides a simple method for studying aspects of protein folding and stability in native solvent conditions, could be used to specifically unfold selected domains, and could be applicable to membrane proteins...
  35. pmc Genetic selection system for improving recombinant membrane protein expression in E. coli
    Elizabeth Massey-Gendel
    Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
    Protein Sci 18:372-83. 2009
    ..The EXP strains also improve the expression of other membrane proteins that were not the target of selection, in one case roughly 90-fold...
  36. pmc A limited universe of membrane protein families and folds
    Amit Oberai
    Department of Chemistry and Biochemistry, UCLA DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095 1570, USA
    Protein Sci 15:1723-34. 2006
    ..While apparently a finite and reachable goal, we estimate that it will likely take more than three decades to obtain the structures needed for 90% residue coverage, if current trends continue...
  37. ncbi request reprint Transmembrane domain of myelin protein zero can form dimers: possible implications for myelin construction
    Megan L Plotkowski
    Department of Chemistry and Biochemistry, Molecular Biology Institute, and University of California at Los Angeles, USA
    Biochemistry 46:12164-73. 2007
    ..By combining our new results with prior work, we suggest a new model for an MPZ lattice that may form during the construction of myelin...
  38. pmc Transmembrane glycine zippers: physiological and pathological roles in membrane proteins
    Sanguk Kim
    Department of Chemistry and Biochemistry and UCLA DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 102:14278-83. 2005
    ..Our findings highlight an important structural motif in a wide variety of normal and pathological processes...
  39. ncbi request reprint Snorkeling preferences foster an amino acid composition bias in transmembrane helices
    Aaron K Chamberlain
    Department of Chemistry and Biochemistry, UCLA DOE Center for Genomics and Proteomics, Molecular Biology Institute, Boyer Hall, 611 Charles E Young Drive E, Los Angeles, CA 90095 1570, USA
    J Mol Biol 339:471-9. 2004
    ....
  40. ncbi request reprint Evaluation of C-H cdots, three dots, centered O hydrogen bonds in native and misfolded proteins
    Aaron K Chamberlain
    Department of Chemistry and Biochemistry, UCLA DOE Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, University of California, Boyer Hall, 611 Charles E Young Drive E, 90095 1570, Los Angeles, CA, USA
    J Mol Biol 322:497-503. 2002
    ..Taken collectively, however, C(alpha)-H cdots, three dots, centered Y bonds provide a weakly cohesive force that stabilizes proteins...
  41. pmc Membrane channel structure of Helicobacter pylori vacuolating toxin: role of multiple GXXXG motifs in cylindrical channels
    Sanguk Kim
    Department of Chemistry and Biochemistry, University of California Los Angeles Department of Energy Center for Genomics and Proteomics, Molecular Biology Institute, Boyer Hall, University of California, Los Angeles, CA 90095 1570, USA
    Proc Natl Acad Sci U S A 101:5988-91. 2004
    ..Our model suggests that the same design of two anion-selective channels was achieved by two different evolutionary paths and provides insight into the mechanism of VacA function...
  42. ncbi request reprint A C alpha-H...O hydrogen bond in a membrane protein is not stabilizing
    Sarah Yohannan
    Department of Chemistry and Biochemistry, UCLA DOE Center for Genomics and Proteomics, Molecular Biology Institute, 655 Boyer Hall, University of California, Los Angeles, Los Angeles, California 90095 1570, USA
    J Am Chem Soc 126:2284-5. 2004
    ..Thus, Thr24 appears to destabilize the protein rather than stabilize. Our results suggest that Calpha-H...O bonds are not a major contributor to protein stability...
  43. ncbi request reprint Proline substitutions are not easily accommodated in a membrane protein
    Sarah Yohannan
    Department of Chemistry and Biochemistry, DOE Center for Genomics and Proteomics, Molecular Biology Institute, 655 Boyer Hall, 611 Charles E Young Dr E, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    J Mol Biol 341:1-6. 2004
    ..Our results indicate that proline is not easily accommodated in transmembrane helices and that the tolerance to proline substitution is dependent, in a complex way, on the position in the structure...
  44. pmc Crystallization of bacteriorhodopsin from bicelle formulations at room temperature
    Salem Faham
    Department of Chemistry and Biochemistry, UCLA DOE Center for Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, California 90095 1570, USA
    Protein Sci 14:836-40. 2005
    ..The ability to grow crystals at room temperature significantly expands the applicability of bicelle crystallization...
  45. pmc Post-translational modifications of integral membrane proteins resolved by top-down Fourier transform mass spectrometry with collisionally activated dissociation
    Christopher M Ryan
    The Pasarow Mass Spectrometry Laboratory, The Neuropsychiatric Institute NPI Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90024, USA
    Mol Cell Proteomics 9:791-803. 2010
    ....
  46. pmc The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors
    Sarah Yohannan
    Department of Chemistry and Biochemistry, UCLA DOE Institute for Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 101:959-63. 2004
    ..Our analysis allows us to predict kink positions with >90% reliability. Kink prediction indicates that different G protein-coupled receptor proteins have different kink patterns and therefore different structures...
  47. ncbi request reprint Construction of helix-bundle membrane proteins
    Aaron K Chamberlain
    Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
    Adv Protein Chem 63:19-46. 2003
  48. pmc Asymmetric amino acid compositions of transmembrane beta-strands
    Aaron K Chamberlain
    Department of Chemistry and Biochemistry, University of California, Los Angeles Department of Energy Center for Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, California 90095 1570, USA
    Protein Sci 13:2270-4. 2004
    ....
  49. ncbi request reprint Bicelle crystallization: a new method for crystallizing membrane proteins yields a monomeric bacteriorhodopsin structure
    Salem Faham
    Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 1570, USA
    J Mol Biol 316:1-6. 2002
    ..0 A resolution. In all previous bR structures the protein is organized as a parallel trimer, but in the crystals grown from bicelles, the individual bR subunits are arranged in an antiparallel fashion...
  50. pmc A model of the closed form of the nicotinic acetylcholine receptor m2 channel pore
    Sanguk Kim
    Department of Chemistry and Biochemistry and UCLA Department of Energy Center for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California 90095, USA
    Biophys J 87:792-9. 2004
    ..This model agrees well with experimental results from solid-state NMR, chemical reactivity, and mutagenesis experiments. The model depicts the channel pore, the channel gate, and the residues responsible for cation specificity...
  51. pmc Janus model of the Na,K-ATPase beta-subunit transmembrane domain: distinct faces mediate alpha/beta assembly and beta-beta homo-oligomerization
    Sonali P Barwe
    Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
    J Mol Biol 365:706-14. 2007
    ..These results provide a structural basis for understanding how Na,K-beta links ion transport and cell-cell adhesion...
  52. pmc Antagonistic regulation of Yan nuclear export by Mae and Crm1 may increase the stringency of the Ras response
    Haiyun Song
    Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
    Genes Dev 19:1767-72. 2005
    ..After activation, transcriptional up-regulation of Mae apparently leads to complete depolymerization and export of Yan...
  53. ncbi request reprint A transmembrane segment mimic derived from Escherichia coli diacylglycerol kinase inhibits protein activity
    Anthony W Partridge
    Division of Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
    J Biol Chem 278:22056-60. 2003
    ....
  54. ncbi request reprint Transmembrane domain helix packing stabilizes integrin alphaIIbbeta3 in the low affinity state
    Anthony W Partridge
    The Department of Medicine, University of California San Diego, La Jolla, California 92093 0726, USA
    J Biol Chem 280:7294-300. 2005
    ..Therefore, we propose that helical packing of the alpha and beta TM domains forms a clasp that regulates integrin activation...
  55. ncbi request reprint Secondary structure and backbone dynamics of Escherichia coli diacylglycerol kinase, as revealed by site-directed solid-state 13C NMR
    Satoru Yamaguchi
    Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo 678 1297, Japan
    Biochim Biophys Acta 1698:97-105. 2004
    ....
  56. ncbi request reprint Cell biology: border crossing
    James U Bowie
    Nature 433:367-9. 2005
  57. ncbi request reprint The affinity of GXXXG motifs in transmembrane helix-helix interactions is modulated by long-range communication
    Roman A Melnyk
    Division of Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
    J Biol Chem 279:16591-7. 2004
    ....
  58. ncbi request reprint Flip-flopping membrane proteins
    James U Bowie
    Nat Struct Mol Biol 13:94-6. 2006
  59. ncbi request reprint How to prepare membrane proteins for solid-state NMR: A case study on the alpha-helical integral membrane protein diacylglycerol kinase from E. coli
    Mark Lorch
    Centre for Biomolecular Magnetic Resonance and Institut für Biophysikalische Chemie, J W Goethe Universitat, Marie Curie Strasse 9, 60439 Frankfurt, Germany
    Chembiochem 6:1693-700. 2005
    ..However, reconstitution is the method of choice for biophysical studies by solid-state NMR. In addition, we discuss the identification of lipids bound to membrane-protein crystals by 31P-MAS NMR...
  60. pmc The Database of Interacting Proteins: 2004 update
    Lukasz Salwinski
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, 90095 1570, USA
    Nucleic Acids Res 32:D449-51. 2004
    ....
  61. ncbi request reprint Pivotal role of the glycine-rich TM3 helix in gating the MscS mechanosensitive channel
    Michelle D Edwards
    School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK
    Nat Struct Mol Biol 12:113-9. 2005
    ..Introduction of glycine at Ala106 validated this model by acting as a powerful suppressor of defects seen with mutations at Gly104 and Gly108...
  62. pmc Point mutations in membrane proteins reshape energy landscape and populate different unfolding pathways
    K Tanuj Sapra
    Biotechnology Center, University of Technology, Tatzberg 47, 01307 Dresden, Germany
    J Mol Biol 376:1076-90. 2008
    ..This is the first experimental proof showing that point mutations can reshape the free energy landscape of a membrane protein and force single proteins to populate certain unfolding pathways over others...
  63. ncbi request reprint A role for zinc in postsynaptic density asSAMbly and plasticity?
    Eckart D Gundelfinger
    Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Brenneckestrasse 6, 39118 Magdeburg, Germany
    Trends Biochem Sci 31:366-73. 2006
    ..Based on these observations, we propose a new model of synaptic plasticity in which Zn2+ influx directly and instantly modulates the structure and function of the postsynaptic density...

Research Grants34

  1. STRUCTURE/FUNCTION OF SAM DOMAINS
    JAMES BOWIE; Fiscal Year: 1999
    ..We plan to characterize SAM domain mediated oligomerization in the Eph receptors, identify residues important for the interaction and examine the biological consequences of mutants that do not oligomerize. ..
  2. Membrane Protein Stability
    JAMES BOWIE; Fiscal Year: 2006
    ..IV. Develop hydrogen exchange as a means to probe the unfolded state of bR. ..
  3. Generation of Membrane Protein Production Strains
    JAMES BOWIE; Fiscal Year: 2006
    ..This project is an effort to reduce this problem by converting bacteria into membrane protein production factories. ..
  4. Formulatrix Automated Protein Crystallization System
    JAMES BOWIE; Fiscal Year: 2007
    ....
  5. STRUCTURE/FUNCTION OF SAM DOMAINS
    JAMES BOWIE; Fiscal Year: 2007
    ..We have developed protein inhibitors of TEL-SAM polymerization and plan to test whether these inhibitors can block cell transformation by the TEL oncogenes. ..
  6. FASEB Summer Conference on Molecular Biophysics of Cellular Membranes
    JAMES BOWIE; Fiscal Year: 2007
    ..There are 32 confirmed speakers. Funding is also requested for the tenth conference in the series to held in the summer of 2008. ..
  7. Generation of Membrane Protein Production Strains(RMI)
    JAMES BOWIE; Fiscal Year: 2007
    ..This project is an effort to reduce this problem by converting bacteria into membrane protein production factories. ..
  8. Membrane Protein Stability
    JAMES BOWIE; Fiscal Year: 2007
    ..IV. Develop hydrogen exchange as a means to probe the unfolded state of bR. ..
  9. Improving membrane protein crystallization
    JAMES BOWIE; Fiscal Year: 2007
    ..This proposal seeks to increase the rate at which we can obtain this critical structural information. ..
  10. Generation of Membrane Protein Production Strains
    JAMES BOWIE; Fiscal Year: 2009
    ..This project is an effort to reduce this problem by converting bacteria into membrane protein production factories. ..
  11. Improving membrane protein crystallization
    JAMES BOWIE; Fiscal Year: 2009
    ..This proposal seeks to increase the rate at which we can obtain this critical structural information. ..
  12. SAM Domains
    James U Bowie; Fiscal Year: 2010
    ..Thus, this project could illuminate the mechanisms of diverse disease states. ..
  13. STRUCTURE/FUNCTION OF SAM DOMAINS
    JAMES BOWIE; Fiscal Year: 2006
    ..We have developed protein inhibitors of TEL-SAM polymerization and plan to test whether these inhibitors can block cell transformation by the TEL oncogenes. ..
  14. Biacore T100
    JAMES BOWIE; Fiscal Year: 2006
    ..SPR is an extremely important technique for measuring these interactions ..
  15. STRUCTURE/FUNCTION OF SAM DOMAINS
    JAMES BOWIE; Fiscal Year: 2000
    ..We plan to characterize SAM domain mediated oligomerization in the Eph receptors, identify residues important for the interaction and examine the biological consequences of mutants that do not oligomerize. ..
  16. Membrane Protein Stability
    JAMES BOWIE; Fiscal Year: 2001
    ..We have devised a strategy for stability mutant screening that does not depend on a rapid activity assay. This method could bring the benefits of high stability to essentially any membrane protein of interest. ..
  17. STRUCTURE/FUNCTION OF SAM DOMAINS
    JAMES BOWIE; Fiscal Year: 2001
    ..We plan to characterize SAM domain mediated oligomerization in the Eph receptors, identify residues important for the interaction and examine the biological consequences of mutants that do not oligomerize. ..
  18. STRUCTURE/FUNCTION OF SAM DOMAINS
    JAMES BOWIE; Fiscal Year: 2002
    ..We plan to characterize SAM domain mediated oligomerization in the Eph receptors, identify residues important for the interaction and examine the biological consequences of mutants that do not oligomerize. ..
  19. Membrane Protein Stability
    JAMES BOWIE; Fiscal Year: 2002
    ..We have devised a strategy for stability mutant screening that does not depend on a rapid activity assay. This method could bring the benefits of high stability to essentially any membrane protein of interest. ..
  20. STRUCTURE/FUNCTION OF SAM DOMAINS
    JAMES BOWIE; Fiscal Year: 2003
    ..We have developed protein inhibitors of TEL-SAM polymerization and plan to test whether these inhibitors can block cell transformation by the TEL oncogenes. ..
  21. Membrane Protein Stability
    JAMES BOWIE; Fiscal Year: 2003
    ..We have devised a strategy for stability mutant screening that does not depend on a rapid activity assay. This method could bring the benefits of high stability to essentially any membrane protein of interest. ..
  22. ACT Database: Protein Structure-Function Relationships
    JAMES BOWIE; Fiscal Year: 2003
    ..Linking ACT more closely to other databases, such as the Database of Interacting Proteins (DIP), based here at UCLA. ..
  23. STRUCTURE/FUNCTION OF SAM DOMAINS
    JAMES BOWIE; Fiscal Year: 2004
    ..We have developed protein inhibitors of TEL-SAM polymerization and plan to test whether these inhibitors can block cell transformation by the TEL oncogenes. ..
  24. Membrane Protein Stability
    JAMES BOWIE; Fiscal Year: 2004
    ..We have devised a strategy for stability mutant screening that does not depend on a rapid activity assay. This method could bring the benefits of high stability to essentially any membrane protein of interest. ..
  25. ACT Database: Protein Structure-Function Relationships
    JAMES BOWIE; Fiscal Year: 2004
    ..Linking ACT more closely to other databases, such as the Database of Interacting Proteins (DIP), based here at UCLA. ..
  26. STRUCTURE/FUNCTION OF SAM DOMAINS
    JAMES BOWIE; Fiscal Year: 2005
    ..We have developed protein inhibitors of TEL-SAM polymerization and plan to test whether these inhibitors can block cell transformation by the TEL oncogenes. ..
  27. ACT Database: Protein Structure-Function Relationships
    JAMES BOWIE; Fiscal Year: 2005
    ..Linking ACT more closely to other databases, such as the Database of Interacting Proteins (DIP), based here at UCLA. ..
  28. Membrane Protein Stability
    JAMES BOWIE; Fiscal Year: 2005
    ..IV. Develop hydrogen exchange as a means to probe the unfolded state of bR. ..
  29. Generation of Membrane Protein Production Strains(RMI)
    JAMES BOWIE; Fiscal Year: 2005
    ..This project is an effort to reduce this problem by converting bacteria into membrane protein production factories. ..
  30. Membrane Protein Stability
    James U Bowie; Fiscal Year: 2010
    ..We are working to understand how the large class of proteins that float in cell membranes manage to assemble so that we can learn how to intervene in folding diseases. ..