Robert Stroud

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc X-ray structures of the signal recognition particle receptor reveal targeting cycle intermediates
    Christopher L Reyes
    Graduate Group in Biophysics, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California, United States of America
    PLoS ONE 2:e607. 2007
  2. pmc Crystal structure of the aquaglyceroporin PfAQP from the malarial parasite Plasmodium falciparum
    Zachary E R Newby
    Department of Chemistry, Genentech Hall, School of Medicine, University of California in San Francisco, 600 16th Street, San Francisco, California 94158 2517, USA
    Nat Struct Mol Biol 15:619-25. 2008
  3. pmc The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs
    Nadine Czudnochowski
    Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA, ProLynx, 455 Mission Bay Blvd, Suite 145, San Francisco, CA 94158, USA and Faculty of Biology, Technion Israel Institute of Technology, Technion City, Haifa 320003, Israel
    Nucleic Acids Res 42:2037-48. 2014
  4. pmc New tools in membrane protein determination
    Robert Michael Stroud
    Department of Biochemistry and Biophysics, University of California San Francisco, S 412C Genentech Hall, 600 16th Street, San Francisco, CA 94158 2517 USA
    F1000 Biol Rep 3:8. 2011
  5. pmc Crystal structure of a eukaryotic phosphate transporter
    Bjørn P Pedersen
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA
    Nature 496:533-6. 2013
  6. pmc Structural basis for alternating access of a eukaryotic calcium/proton exchanger
    Andrew B Waight
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA
    Nature 499:107-10. 2013
  7. pmc Architecture and selectivity in aquaporins: 2.5 a X-ray structure of aquaporin Z
    David F Savage
    Department of Biochemistry and Biophysics, University of California School of Medicine, San Francisco, California, USA
    PLoS Biol 1:E72. 2003
  8. pmc Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1
    Alexei V Korennykh
    Howard Hughes Medical Institute, University of California, San Francisco, 600 16th Street, Room S272, Box 0724, San Francisco, CA 94158, USA
    BMC Biol 9:48. 2011
  9. pmc Structural and functional basis for RNA cleavage by Ire1
    Alexei V Korennykh
    Howard Hughes Medical Institute, University of California, San Francisco, Genentech Hall, 600 16th Street, San Francisco, CA 94158, USA
    BMC Biol 9:47. 2011
  10. pmc Transmembrane transporters: an open and closed case
    Robert M Stroud
    Department of Biochemistry and Biophysics, University of California, Genentech Hall, 600 16th Street, San Francisco, CA 94158 2517, USA
    Proc Natl Acad Sci U S A 104:1445-6. 2007

Research Grants

  1. STRUCTURE BASED DRUG DESIGN
    Robert Stroud; Fiscal Year: 2001
  2. SIGNAL SEQUENCE RECOGNITION AND PROTEIN TARGETING
    Robert Stroud; Fiscal Year: 2003
  3. RNA MODIFICATION ENZYMES:METHYLTRANFERASES/PSI SYNTHASES
    Robert Stroud; Fiscal Year: 2003
  4. RNA Modification Enzymes: Methyltransferase/psi-synthase
    Robert M Stroud; Fiscal Year: 2010
  5. STRUCTURE/FUNCTION OF PROTEINS AT MOLECULAR LEVEL
    Robert Stroud; Fiscal Year: 1999
  6. SIGNAL SEQUENCE RECOGNITION AND PROTEIN TARGETING
    Robert Stroud; Fiscal Year: 2006
  7. Molecular Basis for Transmembrane Conduction & Signaling
    Robert Stroud; Fiscal Year: 2006
  8. RNA Modification Enzymes: Methyltransferase/psi-synthase
    Robert Stroud; Fiscal Year: 2009
  9. STRUCTURE BASED DRUG DESIGN
    Robert Stroud; Fiscal Year: 2000
  10. Molecular Basis for Transmembrane Conduction & Signaling
    Robert Stroud; Fiscal Year: 2007

Collaborators

Detail Information

Publications86

  1. pmc X-ray structures of the signal recognition particle receptor reveal targeting cycle intermediates
    Christopher L Reyes
    Graduate Group in Biophysics, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California, United States of America
    PLoS ONE 2:e607. 2007
    ..We propose that these structural changes represent discrete conformational states assumed by FtsY during targeting complex formation and dissociation...
  2. pmc Crystal structure of the aquaglyceroporin PfAQP from the malarial parasite Plasmodium falciparum
    Zachary E R Newby
    Department of Chemistry, Genentech Hall, School of Medicine, University of California in San Francisco, 600 16th Street, San Francisco, California 94158 2517, USA
    Nat Struct Mol Biol 15:619-25. 2008
    ..The two Asn-Pro-Ala (NPA) regions of PfAQP, which bear rare substitutions to Asn-Leu-Ala (NLA) and Asn-Pro-Ser (NPS), participate in preserving the orientation of the selectivity filter asparagines in the center of the channel...
  3. pmc The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs
    Nadine Czudnochowski
    Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA, ProLynx, 455 Mission Bay Blvd, Suite 145, San Francisco, CA 94158, USA and Faculty of Biology, Technion Israel Institute of Technology, Technion City, Haifa 320003, Israel
    Nucleic Acids Res 42:2037-48. 2014
    ..On the basis of the covalent bond between enzyme and isomerized 5-FU we propose a Michael addition mechanism for pseudouridine formation that is consistent with all experimental data. ..
  4. pmc New tools in membrane protein determination
    Robert Michael Stroud
    Department of Biochemistry and Biophysics, University of California San Francisco, S 412C Genentech Hall, 600 16th Street, San Francisco, CA 94158 2517 USA
    F1000 Biol Rep 3:8. 2011
    ..My goal here is to summarize some of the most recent advances that have enhanced our prospects for understanding membrane proteins at the level of atomic structure...
  5. pmc Crystal structure of a eukaryotic phosphate transporter
    Bjørn P Pedersen
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA
    Nature 496:533-6. 2013
    ..The PiPT structure demonstrates and expands on principles of substrate transport by the MFS transporters and illuminates principles of phosphate uptake in particular...
  6. pmc Structural basis for alternating access of a eukaryotic calcium/proton exchanger
    Andrew B Waight
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA
    Nature 499:107-10. 2013
    ....
  7. pmc Architecture and selectivity in aquaporins: 2.5 a X-ray structure of aquaporin Z
    David F Savage
    Department of Biochemistry and Biophysics, University of California School of Medicine, San Francisco, California, USA
    PLoS Biol 1:E72. 2003
    ....
  8. pmc Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1
    Alexei V Korennykh
    Howard Hughes Medical Institute, University of California, San Francisco, 600 16th Street, Room S272, Box 0724, San Francisco, CA 94158, USA
    BMC Biol 9:48. 2011
    ..In this study, we investigated how the binding of cofactors to the kinase domain of Ire1 modulates its RNase activity...
  9. pmc Structural and functional basis for RNA cleavage by Ire1
    Alexei V Korennykh
    Howard Hughes Medical Institute, University of California, San Francisco, Genentech Hall, 600 16th Street, San Francisco, CA 94158, USA
    BMC Biol 9:47. 2011
    ..Here, we experimentally define the active site of Ire1 RNase and quantitatively evaluate the contribution of the key active site residues to catalysis...
  10. pmc Transmembrane transporters: an open and closed case
    Robert M Stroud
    Department of Biochemistry and Biophysics, University of California, Genentech Hall, 600 16th Street, San Francisco, CA 94158 2517, USA
    Proc Natl Acad Sci U S A 104:1445-6. 2007
  11. pmc Significance of structural changes in proteins: expected errors in refined protein structures
    R M Stroud
    Department of Biochemistry and Biophysics, University of California San Francisco 94143 0448, USA
    Protein Sci 4:2392-404. 1995
    ..Structure change in a macromolecule can thus be referenced to the expected uncertainty in atomic position as reflected in the variance between otherwise identical structures with the observed values of correlated parameters...
  12. pmc 2007 annual progress report synopsis of the Center for Structures of Membrane Proteins
    Robert M Stroud
    The Center for Structures of Membrane Proteins CSMP, UCSF, San Francisco, CA 94158 2517, USA
    J Struct Funct Genomics 10:193-208. 2009
    ..A synopsis of the 2007 annual progress report for the Center for Structures of Membrane Proteins, a specialized center of the Protein Structure Initiative...
  13. ncbi request reprint Selectivity and conductance among the glycerol and water conducting aquaporin family of channels
    Robert M Stroud
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143 2240, USA
    FEBS Lett 555:79-84. 2003
    ..Water molecules form a single hydrogen bonded file throughout the 28 A long channel in AqpZ. The basis for absolute exclusion of proton or hydronium ion conductance through the line of water is explored using simulations...
  14. ncbi request reprint Glycerol facilitator GlpF and the associated aquaporin family of channels
    Robert M Stroud
    Department of Biochemistry and Biophysics, School of Medicine, 600 16th Street, University of California San Francisco, CA 94143 2240, USA
    Curr Opin Struct Biol 13:424-31. 2003
    ..The structure also suggests the mechanism behind the selectivity of aquaglyceroporins for glycerol, the basis for enantioselectivity among alditols, and the basis for the prevention of any leakage of the electrochemical gradient...
  15. pmc Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: a model for viral DNA binding
    J C Chen
    Departments of Biochemistry and Biophysics, Laboratory Medicine, and Internal Medicine, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 97:8233-8. 2000
    ..The crystal structure of the isolated catalytic core domain (residues 52-210), independently determined at 1.6-A resolution, is identical to the core domain within the two-domain 52-288 structure...
  16. ncbi request reprint Signal sequence recognition and protein targeting
    R M Stroud
    S 960 Department of Biochemistry and Biophysics, School of Medicine, University of California, San Francisco CA 94143 0448, USA
    Curr Opin Struct Biol 9:754-9. 1999
    ..The structure of signal peptidase suggests how it releases functional proteins...
  17. ncbi request reprint Ion-channel-forming colicins
    R M Stroud
    Department of Biochemistry and Biophysics, University of California, San Francisco School of Medicine 94143 0448, USA
    Curr Opin Struct Biol 8:525-33. 1998
    ....
  18. ncbi request reprint Binding of the anticancer drug ZD1694 to E. coli thymidylate synthase: assessing specificity and affinity
    E E Rutenber
    Department of Biochemistry and Biophysics, University of California at San Francisco, 94143 0448, USA
    Structure 4:1317-24. 1996
    ..Attempts to abolish toxicity in human patients while preserving potency against the target enzyme, have led to the development of ZD1694, which has already shown significant activity against colorectal tumours...
  19. pmc On the mechanism of sensing unfolded protein in the endoplasmic reticulum
    Joel J Credle
    Howard Hughes Medical Institute, Departments of Biochemistry and Biophysics and Medicine, University of California, San Francisco, CA 94143 2200, USA
    Proc Natl Acad Sci U S A 102:18773-84. 2005
    ..The changes in the ER lumen in turn position Ire1 kinase domains in the cytoplasm optimally for autophosphorylation to initiate the UPR...
  20. ncbi request reprint Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A
    Shahram Khademi
    Department of Biochemistry and Biophysics, S412C Genentech Hall, University of California San Francisco, 600 16th Street, San Francisco, CA 94143 2240, USA
    Science 305:1587-94. 2004
    ..Favorable interactions for NH3 are seen within the channel and use conserved histidines. Reconstitution of AmtB into vesicles shows that AmtB conducts uncharged NH3...
  21. ncbi request reprint The first structure of an RNA m5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate
    Paul G Foster
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94148, USA
    Structure 11:1609-20. 2003
    ..Docking of this stem loop RNA into the structure followed by molecular mechanics shows that the Fmu structure is consistent with binding to the folded RNA substrate...
  22. ncbi request reprint Crystal structure of the priming beta-ketosynthase from the R1128 polyketide biosynthetic pathway
    Hu Pan
    Department of Biophysics and Biochemistry, University of California San Francisco, San Francisco, CA 94143, USA
    Structure 10:1559-68. 2002
    ..Selectivity and primer unit size appear to involve the side chains of three residues on the loops close to the dimer interface that constitute the bottom of the substrate binding pocket...
  23. ncbi request reprint The structure of Cryptococcus neoformans thymidylate synthase suggests strategies for using target dynamics for species-specific inhibition
    Janet S Finer-Moore
    Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, Room S412B, San Francisco, CA 94143 2240, USA
    Acta Crystallogr D Biol Crystallogr 61:1320-34. 2005
    ..These observations highlight the critical need to incorporate multiple target conformations in any computational attempt to facilitate drug discovery...
  24. ncbi request reprint The glycerol facilitator GlpF its aquaporin family of channels, and their selectivity
    Robert M Stroud
    Department of Biochemistry and Biophysics, School of Medicine, University of California, San Francisco, California 94143, USA
    Adv Protein Chem 63:291-316. 2003
  25. ncbi request reprint Targeting proteins to membranes: structure of the signal recognition particle
    Pascal F Egea
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
    Curr Opin Struct Biol 15:213-20. 2005
    ....
  26. ncbi request reprint A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function
    Tom T Lee
    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
    Cell 120:599-611. 2005
    ..Active collaboration of RNA in catalysis leads us to conclude that RumA and its substrate RNA may reflect features from the earliest RNA-protein era...
  27. pmc Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry
    Feixia Chu
    Mass Spectrometry Facility, University of California, San Francisco 94143 0046, USA
    Proc Natl Acad Sci U S A 101:16454-9. 2004
    ..FtsY interface in the complex...
  28. pmc Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases
    Akram Alian
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158 2517, USA
    Proc Natl Acad Sci U S A 105:6876-81. 2008
    ..Loop residues other than the target U54 make more than half of their hydrogen bonds to the protein via sugar-phosphate moieties, accounting, in part, for the broad consensus sequence for TrmA substrates...
  29. ncbi request reprint Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase
    Tom T Lee
    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94107 USA
    Structure 12:397-407. 2004
    ..The iron-sulfur cluster may be involved in the correct folding of the protein or may have a role in RNA binding...
  30. ncbi request reprint Crystal structure of the first KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.7 A
    Zhihua Du
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143 2280, USA
    J Biol Chem 280:38823-30. 2005
    ..Interaction of PCBP2 KH1 with the C-rich strand of human telomeric DNA suggests that PCBPs may participate in mechanisms involved in the regulation of telomere/telomerase functions...
  31. pmc The role of protein dynamics in thymidylate synthase catalysis: variants of conserved 2'-deoxyuridine 5'-monophosphate (dUMP)-binding Tyr-261
    Zachary Newby
    University of California at San Francisco, San Francisco, California 94143 0448, USA
    Biochemistry 45:7415-28. 2006
    ..Changes to atomic vibrations in crystals of a ternary complex of Escherichia coli Tyr261Trp are associated with a greater than 2000-fold drop in kcat/Km. These results underline the important contribution of dynamics to catalysis in TS...
  32. ncbi request reprint Substrate recognition by RNA 5-methyluridine methyltransferases and pseudouridine synthases: a structural perspective
    Sun Hur
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
    J Biol Chem 281:38969-73. 2006
  33. pmc Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome
    Akram Alian
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158 2517, USA
    J Mol Biol 388:785-800. 2009
    ..Residues whose side chains contact rearranged bases in the bound stem-loop, while conserved among RluFs, are not conserved between RluFs and RluBs, suggesting that RluB does not bind to the rearranged stem loop...
  34. pmc X-ray crystallographic and NMR studies of protein-protein and protein-nucleic acid interactions involving the KH domains from human poly(C)-binding protein-2
    Zhihua Du
    Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158 2517, USA
    RNA 13:1043-51. 2007
    ....
  35. ncbi request reprint Water and glycerol permeation through the glycerol channel GlpF and the aquaporin family
    John K Lee
    Department of Biochemistry and Biophysics, School of Medicine, University of California, San Francisco, CA 94143 2240, USA
    J Synchrotron Radiat 11:86-8. 2004
    ..This result reveals the great possibility of emulating and deciphering the function of other aquaporins with GlpF via mutagenesis and investigation of structure and function...
  36. pmc A general protocol for the crystallization of membrane proteins for X-ray structural investigation
    Zachary E R Newby
    Department of Biochemistry and Biophysics, University of California in San Francisco, 600 16th Street, San Francisco, California 94158 2517, USA
    Nat Protoc 4:619-37. 2009
    ..The process of protein crystallization is highly variable, and obtaining diffraction quality crystals can require weeks to months or even years in some cases...
  37. ncbi request reprint Structure of human pro-chymase: a model for the activating transition of granule-associated proteases
    K Kinkead Reiling
    Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94143, USA
    Biochemistry 42:2616-24. 2003
    ..The zymogen positioning of both the 180s and autolysis loops are synergistic structural elements that appear to prevent premature proteolysis by chymase and, quite possibly, by other dipeptide zymogens...
  38. pmc Structural context shapes the aquaporin selectivity filter
    David F Savage
    Graduate Group in Biophysics, Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158 2517, USA
    Proc Natl Acad Sci U S A 107:17164-9. 2010
    ....
  39. pmc Structural basis for conductance by the archaeal aquaporin AqpM at 1.68 A
    John K Lee
    Macromolecular Structure Group, Department of Biochemistry and Biophysics, University of California, S 412C Genentech Hall, 600 16th Street, San Francisco, CA 94143 2240, USA
    Proc Natl Acad Sci U S A 102:18932-7. 2005
    ..As a result of this and other side-chain substituents in the walls of the channel, the channel is intermediate in size and exhibits differentially tuned electrostatics when compared with the other subfamilies...
  40. pmc Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes
    Pascal F Egea
    Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 107:17182-7. 2010
    ..In vivo, a 15 amino acid truncation of the cytoplasmic C-terminal helix of SecY fails to rescue a secY-deficient strain, supporting the essential role of this helix as suggested from the structure...
  41. pmc How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA
    Sun Hur
    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
    Mol Cell 26:189-203. 2007
    ....
  42. ncbi request reprint Lessons and conclusions from dissecting the mechanism of a bisubstrate enzyme: thymidylate synthase mutagenesis, function, and structure
    Janet S Finer-Moore
    S 960 Department of Biochemistry and Biophysics, University of California in San Francisco, San Francisco, California 94143 0448, USA
    Biochemistry 42:248-56. 2003
  43. pmc The channel architecture of aquaporin 0 at a 2.2-A resolution
    William E C Harries
    Macromolecular Structure Group, Department of Biochemistry and Biophysics, University of California, S 412C Genentech Hall, 600 16th Street, San Francisco, CA 94143 2240, USA
    Proc Natl Acad Sci U S A 101:14045-50. 2004
    ..In addition, our structure illustrates the basis for formation of certain types of cataracts that are the result of mutations...
  44. ncbi request reprint Anisotropic dynamics of the JE-2147-HIV protease complex: drug resistance and thermodynamic binding mode examined in a 1.09 A structure
    K Kinkead Reiling
    Department of Biochemistry and Biophysics, Graduate Group in Biophysics, University of California at San Francisco, San Francisco, California 94143, USA
    Biochemistry 41:4582-94. 2002
    ....
  45. pmc Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit
    Hu Pan
    Department of Biophysics and Biochemistry, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 100:12648-53. 2003
    ....
  46. pmc Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination
    Franklin A Hays
    Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158 2517, USA
    J Struct Funct Genomics 10:9-16. 2009
    ..A screen of 384 rationally selected eukaryotic IMPs in baker's yeast Saccharomyces cerevisiae is outlined to demonstrate the results expected when applying this discovery-oriented pipeline to whole-organism membrane proteomes...
  47. ncbi request reprint Tryptophan 80 and leucine 143 are critical for the hydride transfer step of thymidylate synthase by controlling active site access
    Timothy A Fritz
    Macromolecular Structure Group, Department of Biochemistry and Biophysics, The University of California San Francisco, San Francisco, California 94143 0448, USA
    Biochemistry 41:7021-9. 2002
    ....
  48. pmc The unfolded protein response signals through high-order assembly of Ire1
    Alexei V Korennykh
    Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
    Nature 457:687-93. 2009
    ..Activation of Ire1 through oligomerization expands the mechanistic repertoire of kinase-based signalling receptors...
  49. pmc Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening
    Min Li
    Membrane Protein Expression Center, University of California at San Francisco, San Francisco, CA 94158 2517, USA
    J Mol Biol 385:820-30. 2009
    ..This discovery-oriented pipeline provides an efficient way to select proteins from particular membrane protein classes, families, or organisms that may be more suited to structure analysis than others...
  50. pmc Structural and biochemical insights into the dicing mechanism of mouse Dicer: a conserved lysine is critical for dsRNA cleavage
    Zhihua Du
    Departments of Pharmaceutical Chemistry and Biochemistry and Biophysics, University of California, San Francisco, CA 94158 2517, USA
    Proc Natl Acad Sci U S A 105:2391-6. 2008
    ..N-terminal residues of this alpha-helix have the potential to engage in minor groove interaction with dsRNA substrates...
  51. ncbi request reprint Characterization of the 23 S ribosomal RNA m5U1939 methyltransferase from Escherichia coli
    Sanjay Agarwalla
    Department of Biochemistry, University of California at San Francisco, San Francisco, California 94143 0448, USA
    J Biol Chem 277:8835-40. 2002
    ..We propose to name this gene rumA and accordingly name the protein product as RumA for RNA uridine methyltransferase...
  52. ncbi request reprint Conformational dynamics along an enzymatic reaction pathway: thymidylate synthase, "the movie"
    Robert M Stroud
    S 960 Department of Biochemistry and Biophysics, University of California in San Francisco, San Francisco, California 94143 0448, USA
    Biochemistry 42:239-47. 2003
  53. pmc Structures of SRP54 and SRP19, the two proteins that organize the ribonucleic core of the signal recognition particle from Pyrococcus furiosus
    Pascal F Egea
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
    PLoS ONE 3:e3528. 2008
    ....
  54. pmc Structures of the signal recognition particle receptor from the archaeon Pyrococcus furiosus: implications for the targeting step at the membrane
    Pascal F Egea
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
    PLoS ONE 3:e3619. 2008
    ..Based on previous structures of two sub-complexes, we propose a model of the core of archeal and eukaryotic SRP*SR targeting complexes...
  55. pmc Crystal structure of the third KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.6 A resolution
    Sebastian Fenn
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143 2280, USA
    Nucleic Acids Res 35:2651-60. 2007
    ..A nucleotide platform, an interesting feature found in some RNA molecules, was identified, evidently for the first time in DNA...
  56. pmc Structural basis of aquaporin inhibition by mercury
    David F Savage
    Graduate Group in Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
    J Mol Biol 368:607-17. 2007
    ..Thus, we elucidate a steric inhibition mechanism for this important class of channels by mercury...
  57. ncbi request reprint Substrate twinning activates the signal recognition particle and its receptor
    Pascal F Egea
    Department of Biochemistry and Biophysics, University of California at San Francisco, California 94143 2240, USA
    Nature 427:215-21. 2004
    ..This unique circle of twinned interactions is severed twice on hydrolysis, leading to complex dissociation after cargo delivery...
  58. pmc The crystal structure of E. coli rRNA pseudouridine synthase RluE
    Hu Pan
    Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143, USA
    J Mol Biol 367:1459-70. 2007
    ..The stem alone is not a good RluE substrate, suggesting RluE makes additional interactions with other regions in the ribosome...
  59. pmc Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies
    Sanjay Agarwalla
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94107, USA
    J Biol Chem 279:34123-9. 2004
    ..Sequence data base searches revealed that RumA homologs are widespread in various kingdoms of life and contain a conserved and unique iron-sulfur cluster binding motif, CX(5)CGGC...
  60. pmc Mechanism of association and reciprocal activation of two GTPases
    Shu ou Shan
    Department of Biochemistry and Biophysics, University of California, San Francisco, USA
    PLoS Biol 2:e320. 2004
    ..Each stage provides a potential control point in the targeting reaction at which regulation by additional components can be exerted, thus ensuring the binding and release of cargo at the appropriate time...
  61. ncbi request reprint The structure of a ketoreductase determines the organization of the beta-carbon processing enzymes of modular polyketide synthases
    Adrian T Keatinge-Clay
    Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16 th Street, San Francisco, California 94107, USA
    Structure 14:737-48. 2006
    ....
  62. pmc Function of human Rh based on structure of RhCG at 2.1 A
    Franz Gruswitz
    Department of Biochemistry and Biophysics, S412C Genentech Hall, Center for the Structure of Membrane Proteins, and Membrane Protein Expression Center, University of California, San Francisco, CA 94158, USA
    Proc Natl Acad Sci U S A 107:9638-43. 2010
    ..Models of the erythrocyte Rh complex based on our RhCG structure suggest that the erythrocytic Rh complex is composed of stochastically assembled heterotrimers of RhAG, RhD, and RhCE...
  63. pmc Pyrrolidine carboxamides as a novel class of inhibitors of enoyl acyl carrier protein reductase from Mycobacterium tuberculosis
    Xin He
    Department of Pharmaceutical Chemistry, University of California, 600 16 Street, San Francisco, California 94158 2517, USA
    J Med Chem 49:6308-23. 2006
    ..Resolution of racemic mixtures of several inhibitors indicate that only one enantiomer is active as an inhibitor of InhA...
  64. pmc Cell-free complements in vivo expression of the E. coli membrane proteome
    David F Savage
    Graduate Group in Biophysics, University of California at San Francisco, San Francisco, California 94158 2517, USA
    Protein Sci 16:966-76. 2007
    ..We conclude that CF is a novel, robust expression system capable of expressing more proteins than an in vivo system and suitable for production of membrane proteins at the milligram level...
  65. pmc Crystal structure of bovine mitochondrial factor B at 0.96-A resolution
    John K Lee
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158 2517, USA
    Proc Natl Acad Sci U S A 105:13379-84. 2008
    ..Identification of a bound Mg(2+) ion reveals that FB is a metalloprotein. We also report the cocrystal structures of FB bound with phenylarsine oxide and Cd(2+), two known inhibitors of the FB coupling activity...
  66. pmc Crystal structure of human aquaporin 4 at 1.8 A and its mechanism of conductance
    Joseph D Ho
    Graduate Program in Chemistry and Chemical Biology and Department of Biochemistry and Biophysics, Genentech Hall, University of California, 600 16th Street, San Francisco, CA 94158 2517, USA
    Proc Natl Acad Sci U S A 106:7437-42. 2009
    ....
  67. pmc De novo design of an IL-4 antagonist and its structure at 1.9 A
    Sherry L Laporte
    Department of Biochemistry and Biophysics, University of California, 600 16th Street, Box 2240, San Francisco, CA 94143 2240, USA
    Proc Natl Acad Sci U S A 102:1889-94. 2005
    ....
  68. pmc Catalytically-active complex of HIV-1 integrase with a viral DNA substrate binds anti-integrase drugs
    Akram Alian
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
    Proc Natl Acad Sci U S A 106:8192-7. 2009
    ..This novel complex may help define substrate interactions and delineate the mechanism of action of known integration inhibitors...
  69. pmc A survey of integral alpha-helical membrane proteins
    Libusha Kelly
    Graduate Group in Bioinformatics, University of California at San Francisco, San Francisco, CA, USA
    J Struct Funct Genomics 10:269-80. 2009
    ....
  70. ncbi request reprint Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA:ACP transacylase
    Adrian T Keatinge-Clay
    Graduate Group in Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
    Structure 11:147-54. 2003
    ..Macromolecular docking simulations with actinorhodin ACP suggest that the majority of the ACP docking surface is formed by a helical flap. These results should help to engineer polyketide synthases (PKSs) that produce novel polyketides...
  71. ncbi request reprint TARP auxiliary subunits switch AMPA receptor antagonists into partial agonists
    Karen Menuz
    Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA 94143, USA
    Science 318:815-7. 2007
    ..Our results demonstrate that the presence of an auxiliary subunit can determine whether a compound functions as an agonist or antagonist...
  72. ncbi request reprint The Amt/MEP/Rh family: structure of AmtB and the mechanism of ammonia gas conduction
    Shahram Khademi
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
    Physiology (Bethesda) 21:419-29. 2006
    ..The reprotonation of NH(3) on the receiving side raises the pH on that side in the absence of metabolism of NH(3), and there is no transfer of protons through the protein...
  73. ncbi request reprint An antibiotic factory caught in action
    Adrian T Keatinge-Clay
    Graduate Group in Biophysics, University of California San Francisco, San Francisco, California 94107 2240, USA
    Nat Struct Mol Biol 11:888-93. 2004
    ..We provide evidence that the first cyclization of the polyketide occurs within the KS-CLF tunnel. The mechanistic details of this central PKS polymerase could guide biosynthetic chemists in designing new pharmaceuticals and polymers...
  74. ncbi request reprint The only active mutant of thymidylate synthase D169, a residue far from the site of methyl transfer, demonstrates the exquisite nature of enzyme specificity
    David L Birdsall
    Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143 0448, USA
    Protein Eng 16:229-40. 2003
    ..Changes to partitioning among productive and non-productive conformations of reaction intermediates may contribute as much, if not more, to the diminished activity of this mutant than reduced stabilization of transition states...
  75. ncbi request reprint Insights into channel architecture and substrate specificity from crystal structures of two macrocycle-forming thioesterases of modular polyketide synthases
    Shiou Chuan Tsai
    Department of Chemical Engineering, Stanford University, Stanford, California 94305 5025, USA
    Biochemistry 41:12598-606. 2002
    ..A series of high-resolution snapshots of a protein channel at different pHs is presented alongside analysis of channel residues, which could help in the redesign of the protein channel architecture...
  76. ncbi request reprint The structural roles of conserved Pro196, Pro197 and His199 in the mechanism of thymidylate synthase
    Dolores Gonzalez-Pacanowska
    Department of Biochemistry and Biophysics, S412 B, University of California San Francisco, San Francisco, CA 94143 0448, USA
    Protein Eng 16:607-14. 2003
    ..The small effects of Pro196 or Pro197 mutations on enzyme kinetics suggest that the conformational restrictions encoded by the Pro-Pro sequence are largely maintained when either member of the pair is mutated...
  77. ncbi request reprint Control of the selectivity of the aquaporin water channel family by global orientational tuning
    Emad Tajkhorshid
    Theoretical Biophysics Group, Beckman Institute, University of Illinois at Urbana Champaign, 405 North Mathews, Urbana, IL 61801, USA
    Science 296:525-30. 2002
    ..Both simulations and observations revealed a more regular distribution of channel water and an increased water permeability for the W48F/F200T mutant...
  78. ncbi request reprint Phylogenetic classification of protozoa based on the structure of the linker domain in the bifunctional enzyme, dihydrofolate reductase-thymidylate synthase
    Robert H O'Neil
    Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA
    J Biol Chem 278:52980-7. 2003
    ..Furthermore, the structure of C. hominis DHFR-TS calls into question surface electrostatic channeling as the universal means of dihydrofolate transport between TS and DHFR in the bifunctional enzyme...
  79. ncbi request reprint Crystal structure of an Acyl-ACP dehydrogenase from the FK520 polyketide biosynthetic pathway: insights into extender unit biosynthesis
    Kenji Watanabe
    Department of Chemical Engineering, Stanford University, Stanford, CA 94305 5025, USA
    J Mol Biol 334:435-44. 2003
    ..A biochemical mechanism for the role of FkbI in the biosynthesis of methoxymalonyl-ACP is proposed...
  80. ncbi request reprint Structure-based studies on species-specific inhibition of thymidylate synthase
    M Paola Costi
    Dipartimento di Scienze Farmaceutiche, Universita di Modena e Reggio Emilia, Via G Campi n 183, 41100, Modena, Italy
    Biochim Biophys Acta 1587:206-14. 2002
    ..The role of structural and computational studies in the discovery of nonanalog antifolate inhibitors of bacterial TS, naphthalein and dansyl derivatives, and in the understanding of their biological activity profile, are discussed...
  81. pmc Structural basis for mobility in the 1.1 A crystal structure of the NG domain of Thermus aquaticus Ffh
    Ursula D Ramirez
    Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Medical School, 303 E Chicago Avenue, MC S215, Chicago, IL 60611 3008, USA
    J Mol Biol 320:783-99. 2002
    ..Our data allows us to propose a structural explanation for the functional significance of sequence elements conserved at the N/G interface...
  82. ncbi request reprint Crystal structure and molecular modeling of 17-DMAG in complex with human Hsp90
    Joseph M Jez
    Kosan Biosciences, Inc, 3832 Bay Center Place, Hayward, CA 94545, USA
    Chem Biol 10:361-8. 2003
    ..We speculate that 17-DMAG analogs constrained to a cis-amide in the ground state could provide a significant increase in affinity for Hsp90...
  83. ncbi request reprint The crystal structure of dihydrofolate reductase-thymidylate synthase from Cryptosporidium hominis reveals a novel architecture for the bifunctional enzyme
    Robert H O'Neil
    Department of Chemistry, Dartmouth College, Burke Laboratories, Hanover, NH 03755, USA
    J Eukaryot Microbiol 50:555-6. 2003
  84. ncbi request reprint Mechanistic diversity of cytokine receptor signaling across cell membranes
    Robert M Stroud
    Department of Biochemistry and Biophysics, UCSF Genentech Hall, 600 16th Street, University of California, San Francisco, CA 94143 2240, USA
    Sci STKE 2004:re7. 2004
    ..The principles uncovered nevertheless illustrate the basis for high specificity and fidelity in cytokine-mediated signaling...
  85. pmc Inhibitory complex of the transmembrane ammonia channel, AmtB, and the cytosolic regulatory protein, GlnK, at 1.96 A
    Franz Gruswitz
    Department of Biochemistry and Biophysics, Genentech Hall, School of Medicine, University of California, 600 16th Street, San Francisco, CA 94158 2517, USA
    Proc Natl Acad Sci U S A 104:42-7. 2007
    ..ATP and Mg(2+) augment the interaction of GlnK. The hydrolyzed product, adenosine 5'-diphosphate orients the surface of GlnK for AmtB blockade. 2-Oxoglutarate diminishes AmtB/GlnK association, and sites for 2-oxoglutarate are evaluated...
  86. pmc Profile of Robert M. Stroud
    Tinsley H Davis
    Proc Natl Acad Sci U S A 103:5256-8. 2006

Research Grants62

  1. STRUCTURE BASED DRUG DESIGN
    Robert Stroud; Fiscal Year: 2001
    ..Public domain access to the structures of therapeutic targets and technology will encourage their use by major pharmaceutical companies for the better design of therapeutics. ..
  2. SIGNAL SEQUENCE RECOGNITION AND PROTEIN TARGETING
    Robert Stroud; Fiscal Year: 2003
    ..Components of the membrane pore are to be prepared and characterized for structural approaches to translocation. ..
  3. RNA MODIFICATION ENZYMES:METHYLTRANFERASES/PSI SYNTHASES
    Robert Stroud; Fiscal Year: 2003
    ..Finally, the work seeks to isolate and characterize a host enzyme that may be a novel target for HIV. ..
  4. RNA Modification Enzymes: Methyltransferase/psi-synthase
    Robert M Stroud; Fiscal Year: 2010
    ..The importance of synthase activity is underlined by disorders such as sideroplastic anemia. The RNA MTase is a potential new drug target for anti-HIV therapy. ..
  5. STRUCTURE/FUNCTION OF PROTEINS AT MOLECULAR LEVEL
    Robert Stroud; Fiscal Year: 1999
    ....
  6. SIGNAL SEQUENCE RECOGNITION AND PROTEIN TARGETING
    Robert Stroud; Fiscal Year: 2006
    ..These will instruct in the mechanism of replacing the role of RNA by protein, and therefore in the essence of the dynamic roles of SRP RNA and cpSRP43. ..
  7. Molecular Basis for Transmembrane Conduction & Signaling
    Robert Stroud; Fiscal Year: 2006
    ..A further aim is to improve crystals of the Acetylcholine receptor as a means of three-dimensional structure determination of an archetype of gating mechanisms in an archetype of neuroreceptor superfamilies. ..
  8. RNA Modification Enzymes: Methyltransferase/psi-synthase
    Robert Stroud; Fiscal Year: 2009
    ..The importance of synthase activity is underlined by disorders such as sideroplastic anemia. The RNA MTase is a potential new drug target for anti-HIV therapy. ..
  9. STRUCTURE BASED DRUG DESIGN
    Robert Stroud; Fiscal Year: 2000
    ..Public domain access to the structures of therapeutic targets and technology will encourage their use by major pharmaceutical companies for the better design of therapeutics. ..
  10. Molecular Basis for Transmembrane Conduction & Signaling
    Robert Stroud; Fiscal Year: 2007
    ..The structures of these proteins will establish their mechanism of action and provide templates for drug discovery aimed at those of particular therapeutic advantage, and the essential elements to understand their selectivity. ..
  11. SIGNAL SEQUENCE RECOGNITION AND PROTEIN TARGETING
    Robert Stroud; Fiscal Year: 2001
    ..Components of the membrane pore are to be prepared and characterized for structural approaches to translocation. ..
  12. THYMIDYLATE SYNTHASE
    Robert Stroud; Fiscal Year: 2001
    ..b>Robert Stroud, UCSF...
  13. RNA MODIFICATION ENZYMES:METHYLTRANFERASES/PSI SYNTHASES
    Robert Stroud; Fiscal Year: 2001
    ..Finally, the work seeks to isolate and characterize a host enzyme that may be a novel target for HIV. ..
  14. 2005 Mechanisms of Membrane Transport Gordon Conference
    Robert Stroud; Fiscal Year: 2005
    ..abstract_text> ..
  15. SIGNAL SEQUENCE RECOGNITION AND PROTEIN TARGETING
    Robert Stroud; Fiscal Year: 2005
    ..These will instruct in the mechanism of replacing the role of RNA by protein, and therefore in the essence of the dynamic roles of SRP RNA and cpSRP43. ..
  16. SIGNAL SEQUENCE RECOGNITION AND PROTEIN TARGETING
    Robert Stroud; Fiscal Year: 2004
    ..These will instruct in the mechanism of replacing the role of RNA by protein, and therefore in the essence of the dynamic roles of SRP RNA and cpSRP43. ..
  17. STRUCTURE AND FUNCTION OF PROTEINS AT MOLECULAR LEVEL
    Robert Stroud; Fiscal Year: 1990
    ....
  18. STRUCTURE AND FUNCTION OF PROTEINS AT MOLECULAR LEVEL
    Robert Stroud; Fiscal Year: 1980
    ..Preliminary crystallization of a large extra loop (type III) tRNA, which diffracts to approximately 8 A and of tRNA charging enzyme complexes will be pursued in the hope of understanding tRNA plus charging enzyme recognition. ..
  19. STRUCTURE AND FUNCTION OF PROTEINS AT MOLECULAR LEVEL
    Robert Stroud; Fiscal Year: 1992
    ....
  20. STRUCTURE BASED DRUG DESIGN
    Robert Stroud; Fiscal Year: 2004
    ..Public domain access to the structures of therapeutic targets and technology will encourage their use by major pharmaceutical companies for the better design of therapeutics. ..
  21. STRUCTURE BASED DRUG DESIGN
    Robert Stroud; Fiscal Year: 1999
    ..Public domain access to the structures of therapeutic targets and technology will encourage their use by major pharmaceutical companies for the better design of therapeutics. ..
  22. RNA Modification Enzymes: Methyltransferase/psi-synthase
    Robert Stroud; Fiscal Year: 2004
    ..This is a required enzyme in HIV replication, and as such it may represent a new target for anti-HIV drugs. ..
  23. STRUCTURE BASED DRUG DESIGN
    Robert Stroud; Fiscal Year: 2003
    ..Public domain access to the structures of therapeutic targets and technology will encourage their use by major pharmaceutical companies for the better design of therapeutics. ..
  24. Molecular Basis for Transmembrane Conduction & Signaling
    Robert Stroud; Fiscal Year: 2003
    ..A further aim is to improve crystals of the Acetylcholine receptor as a means of three-dimensional structure determination of an archetype of gating mechanisms in an archetype of neuroreceptor superfamilies. ..
  25. SIGNAL SEQUENCE RECOGNITION AND PROTEIN TARGETING
    Robert Stroud; Fiscal Year: 2000
    ..Components of the membrane pore are to be prepared and characterized for structural approaches to translocation. ..
  26. STRUCTURE/FUNCTION OF PROTEINS AT MOLECULAR LEVEL
    Robert Stroud; Fiscal Year: 2000
    ....
  27. STRUCTURE/FUNCTION OF PROTEINS AT MOLECULAR LEVEL
    Robert Stroud; Fiscal Year: 2001
    ....
  28. STRUCTURE/FUNCTION OF PROTEINS AT MOLECULAR LEVEL
    Robert Stroud; Fiscal Year: 2002
    ....
  29. RNA MODIFICATION ENZYMES:METHYLTRANFERASES/PSI SYNTHASES
    Robert Stroud; Fiscal Year: 2002
    ..Finally, the work seeks to isolate and characterize a host enzyme that may be a novel target for HIV. ..
  30. STRUCTURE BASED DRUG DESIGN
    Robert Stroud; Fiscal Year: 2002
    ..Public domain access to the structures of therapeutic targets and technology will encourage their use by major pharmaceutical companies for the better design of therapeutics. ..
  31. STRUCTURE AND FUNCTION OF PROTEINS AT MOLECULAR LEVEL
    Robert Stroud; Fiscal Year: 1993
    ....
  32. SIGNAL SEQUENCE RECOGNITION AND PROTEIN TARGETING
    Robert Stroud; Fiscal Year: 2007
    ..These will instruct in the mechanism of replacing the role of RNA by protein, and therefore in the essence of the dynamic roles of SRP RNA and cpSRP43. ..
  33. RNA MODIFICATION ENZYMES:METHYLTRANFERASES/PSI SYNTHASES
    Robert Stroud; Fiscal Year: 2000
    ..Finally, the work seeks to isolate and characterize a host enzyme that may be a novel target for HIV. ..
  34. SIGNAL SEQUENCE RECOGNITION AND PROTEIN TARGETING
    Robert Stroud; Fiscal Year: 2002
    ..Components of the membrane pore are to be prepared and characterized for structural approaches to translocation. ..
  35. STRUCTURE AND FUNCTION OF PROTEINS AT MOLECULAR LEVEL
    Robert Stroud; Fiscal Year: 1991
    ....