FRED COHEN

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc JEvTrace: refinement and variations of the evolutionary trace in JAVA
    Marcin P Joachimiak
    Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA 94143 0450, USA
    Genome Biol 3:RESEARCH0077. 2002
  2. ncbi request reprint Therapeutic approaches to protein-misfolding diseases
    Fred E Cohen
    University of California at San Francisco, Department of Cellular and Molecular Pharmacology, Genentech Hall, 600 16th Street N472J, San Francisco, California 94107, USA
    Nature 426:905-9. 2003
  3. ncbi request reprint Protein misfolding and prion diseases
    F E Cohen
    Departments of Cellular and Molecular Pharmacology and Medicine, University of California, San Francisco, CA 94143 0450, USA
    J Mol Biol 293:313-20. 1999
  4. ncbi request reprint Folding of prion protein to its native alpha-helical conformation is under kinetic control
    I V Baskakov
    Institute for Neurodegenerative Diseases, Department of Neurology, University of California, San Francisco, California 94143, USA
    J Biol Chem 276:19687-90. 2001
  5. pmc Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems
    F Horn
    Department of Cellular and Molecular Pharmacology, UCSF, Box 0450, San Francisco, CA 94143 0450, USA
    Nucleic Acids Res 29:346-9. 2001
  6. ncbi request reprint Helix-helix packing angle preferences for finite helix axes
    D Walther
    Department of Cellular and Molecular Pharmacology, University of California at San Francisco, 94143 0450, USA
    Proteins 33:457-9. 1998
  7. ncbi request reprint Pathologic conformations of prion proteins
    F E Cohen
    Department of Biochemistry and Biophysics, University of California, San Francisco 94143, USA
    Annu Rev Biochem 67:793-819. 1998
  8. ncbi request reprint Cryptic epitopes in N-terminally truncated prion protein are exposed in the full-length molecule: dependence of conformation on pH
    Y Matsunaga
    Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94143 0446, USA
    Proteins 44:110-8. 2001
  9. pmc Bayesian statistical analysis of protein side-chain rotamer preferences
    R L Dunbrack
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco 94143 0450, USA
    Protein Sci 6:1661-81. 1997
  10. ncbi request reprint Engineering the prion protein using chemical synthesis
    H L Ball
    Institute for Neurodegenerative Diseases and Department of Neurology, University of California at San Francisco, 94143 0518, USA
    J Pept Res 58:357-74. 2001

Collaborators

Detail Information

Publications71

  1. pmc JEvTrace: refinement and variations of the evolutionary trace in JAVA
    Marcin P Joachimiak
    Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA 94143 0450, USA
    Genome Biol 3:RESEARCH0077. 2002
    ..We wish to facilitate the graphical interpretation of disparate data types through the creation of flexible software implementations...
  2. ncbi request reprint Therapeutic approaches to protein-misfolding diseases
    Fred E Cohen
    University of California at San Francisco, Department of Cellular and Molecular Pharmacology, Genentech Hall, 600 16th Street N472J, San Francisco, California 94107, USA
    Nature 426:905-9. 2003
    ..Molecules are now emerging that link our biophysical insights with our therapeutic aspirations...
  3. ncbi request reprint Protein misfolding and prion diseases
    F E Cohen
    Departments of Cellular and Molecular Pharmacology and Medicine, University of California, San Francisco, CA 94143 0450, USA
    J Mol Biol 293:313-20. 1999
    ..These concepts can be generalized to gain insight into other disorders of protein aggregation and deposition such as Alzheimer's disease...
  4. ncbi request reprint Folding of prion protein to its native alpha-helical conformation is under kinetic control
    I V Baskakov
    Institute for Neurodegenerative Diseases, Department of Neurology, University of California, San Francisco, California 94143, USA
    J Biol Chem 276:19687-90. 2001
    ..Our data demonstrate that the folding of the prion protein to its native alpha-helical monomeric conformation is under kinetic control...
  5. pmc Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems
    F Horn
    Department of Cellular and Molecular Pharmacology, UCSF, Box 0450, San Francisco, CA 94143 0450, USA
    Nucleic Acids Res 29:346-9. 2001
    ..The NucleaRDB was started recently as an application of the concept for the generalization of this technology. The GPCRDB is available via the WWW at http://www.gpcr.org/7tm/ and the NucleaRDB at http://www.receptors.org/NR/...
  6. ncbi request reprint Helix-helix packing angle preferences for finite helix axes
    D Walther
    Department of Cellular and Molecular Pharmacology, University of California at San Francisco, 94143 0450, USA
    Proteins 33:457-9. 1998
    ..Here, we complement Bowie's analysis by consideration of the more realistic case where helices are of finite length. As a result, the statistical bias toward near perpendicular packings appears to be even stronger...
  7. ncbi request reprint Pathologic conformations of prion proteins
    F E Cohen
    Department of Biochemistry and Biophysics, University of California, San Francisco 94143, USA
    Annu Rev Biochem 67:793-819. 1998
    ..Finally, we explore the phenomenologic constraints on models of prion replication with a specific emphasis on biophysical studies of prion protein structures...
  8. ncbi request reprint Cryptic epitopes in N-terminally truncated prion protein are exposed in the full-length molecule: dependence of conformation on pH
    Y Matsunaga
    Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94143 0446, USA
    Proteins 44:110-8. 2001
    ..A similar pH dependence for a monoclonal antibody reactive to the central region identified an acidic region incorporating Glu152 as a significant participant...
  9. pmc Bayesian statistical analysis of protein side-chain rotamer preferences
    R L Dunbrack
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco 94143 0450, USA
    Protein Sci 6:1661-81. 1997
    ..The new library is suitable for use in homology modeling, protein folding simulations, and the refinement of X-ray and NMR structures...
  10. ncbi request reprint Engineering the prion protein using chemical synthesis
    H L Ball
    Institute for Neurodegenerative Diseases and Department of Neurology, University of California at San Francisco, 94143 0518, USA
    J Pept Res 58:357-74. 2001
    ....
  11. ncbi request reprint Solution structure of Syrian hamster prion protein rPrP(90-231)
    H Liu
    Department of Pharmaceutical Chemistry, University of California, San Francisco 94143, USA
    Biochemistry 38:5362-77. 1999
    ..Comparison of the structure with previous reports suggests sequence-dependent features that may be reflected in a species barrier to prion disease transmission...
  12. pmc Solid-state NMR studies of the secondary structure of a mutant prion protein fragment of 55 residues that induces neurodegeneration
    D D Laws
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 98:11686-90. 2001
    ..Studies of an analogous peptide from Syrian hamster PrP verify that sequence alterations in residues 101-117 affect the conformation of aggregated forms of the peptides...
  13. pmc Conformational propagation with prion-like characteristics in a simple model of protein folding
    P M Harrison
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143, USA
    Protein Sci 10:819-35. 2001
    ....
  14. ncbi request reprint A synthetic peptide initiates Gerstmann-Sträussler-Scheinker (GSS) disease in transgenic mice
    K Kaneko
    Institute for Neurodegenerative Diseases, Department of Neurology, University of California, San Francisco, 94143, USA
    J Mol Biol 295:997-1007. 2000
    ..We conclude that a chemically synthesized peptide refolded into the appropriate conformation can accelerate or possibly initiate prion disease...
  15. pmc Solution structure of a 142-residue recombinant prion protein corresponding to the infectious fragment of the scrapie isoform
    T L James
    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 94:10086-91. 1997
    ..Conformational heterogeneity of rPrP at the N terminus may be key to the transformation of PrPC into PrPSc, whereas the discontinuous epitope near the C terminus controls this transition...
  16. pmc Branched polyamines cure prion-infected neuroblastoma cells
    S Supattapone
    Institute for Neurodegenerative Diseases, University of California at San Francisco, San Francisco, California 94143, USA
    J Virol 75:3453-61. 2001
    ..Branched polyamines are the first class of compounds shown to cure prion infection in living cells and may prove useful as therapeutic, disinfecting, and strain-typing reagents for prion diseases...
  17. ncbi request reprint Heritable disorder resembling neuronal storage disease in mice expressing prion protein with deletion of an alpha-helix
    T Muramoto
    Department of Neurology, University of California, San Francisco 94143, USA
    Nat Med 3:750-5. 1997
    ..Whether children with the human counterpart of this malady will be found remains to be determined...
  18. ncbi request reprint Pairwise sequence alignment below the twilight zone
    J D Blake
    Department of Cellular and Molecular Pharmacology, University of California, Box 0450, San Francisco, CA 94143, USA
    J Mol Biol 307:721-35. 2001
    ..Using this method, we have identified a potential homologue to one additional previously unassigned open reading frame from the H. pylori genome...
  19. pmc Acridine and phenothiazine derivatives as pharmacotherapeutics for prion disease
    C Korth
    Institute for Neurodegenerative Diseases, University of California, San Francisco 94143, USA
    Proc Natl Acad Sci U S A 98:9836-41. 2001
    ....
  20. ncbi request reprint Binding of neural cell adhesion molecules (N-CAMs) to the cellular prion protein
    G Schmitt-Ulms
    Institute for Neurodegenerative Diseases, Department of Neurology, University of California, San Francisco, 94143, USA
    J Mol Biol 314:1209-25. 2001
    ..1, SEM) days, arguing that N-CAM is not involved in PrP(Sc) replication. Our findings raise the possibility that N-CAM may join with PrP(C) in carrying out some as yet unidentified physiologic cellular function...
  21. ncbi request reprint High-level expression and characterization of a purified 142-residue polypeptide of the prion protein
    I Mehlhorn
    Department of Neurology, University of California, San Francisco 94143, USA
    Biochemistry 35:5528-37. 1996
    ..The high levels of purified rPrP which can now be obtained should facilitate determination of the multiple tertiary structures that Prp can adopt...
  22. ncbi request reprint Evolutionary, mechanistic, and predictive analyses of the hydroxymethyldihydropterin pyrophosphokinase family of proteins
    D L Gerloff
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, 94143, USA
    Biochem Biophys Res Commun 254:70-6. 1999
    ..This prediction report illustrates the importance of non-computational approaches to structure prediction at its present frontier, which is to obtain medium resolution models of tertiary structure...
  23. ncbi request reprint Separation of scrapie prion infectivity from PrP amyloid polymers
    H Wille
    Department of Neurology, University of California, San Francisco 94143, USA
    J Mol Biol 259:608-21. 1996
    ..The results also demonstrate that the specific beta-sheet-rich structures required for prion infectivity can be differentiated from those needed for amyloid formation as determined by Congo red binding...
  24. ncbi request reprint Structure prediction in a post-genomic environment: a secondary and tertiary structural model for the initiation factor 5A family
    D L Gerloff
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, 94143, USA
    Biochem Biophys Res Commun 251:173-81. 1998
    ..We place the pair of predictions in the public domain before an experimental structure is known. This example illustrates the impact of genome sequencing projects on structure prediction from sequence alignments...
  25. pmc Evidence for protein X binding to a discontinuous epitope on the cellular prion protein during scrapie prion propagation
    K Kaneko
    Department of Neurology, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 94:10069-74. 1997
    ..Our findings seem to explain the protective effects of basic polymorphic residues in PrP of humans and sheep and suggest therapeutic and prophylactic approaches to prion diseases...
  26. pmc Strain-specified relative conformational stability of the scrapie prion protein
    D Peretz
    Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94143, USA
    Protein Sci 10:854-63. 2001
    ..Based on these results, the eight prion strains segregated into four distinct groups. Our results support the unorthodox proposal that distinct PrP(Sc) conformers encipher the biological properties of prion strains...
  27. ncbi request reprint Prion propagation in mice expressing human and chimeric PrP transgenes implicates the interaction of cellular PrP with another protein
    G C Telling
    Department of Neurology, University of California, San Francisco 94143, USA
    Cell 83:79-90. 1995
    ..Protein X might function as a molecular chaperone in the formation of PrPSc...
  28. ncbi request reprint Eight prion strains have PrP(Sc) molecules with different conformations
    J Safar
    Department of Neurology, University of California, San Francisco 94143 0518, USA
    Nat Med 4:1157-65. 1998
    ....
  29. ncbi request reprint Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors
    J T Nguyen
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA
    Science 282:2088-92. 1998
    ..The mechanism can be exploited: screening a series of ligands in which key prolines were replaced by nonnatural N-substituted residues yielded a ligand that selectively bound the Grb2 SH3 domain with 100 times greater affinity...
  30. pmc A protease-resistant 61-residue prion peptide causes neurodegeneration in transgenic mice
    S Supattapone
    Institute for Neurodegenerative Diseases, University of California at San Francisco, San Francisco, California 94143, USA
    Mol Cell Biol 21:2608-16. 2001
    ..PrP61 may be a useful model for deciphering the mechanism by which PrP molecules acquire protease resistance and become neurotoxic...
  31. ncbi request reprint Prion protein gene variation among primates
    H M Schätzl
    Department of Neurology, University of California, San Francisco 94143, USA
    J Mol Biol 245:362-74. 1995
    ..Alignment of primate and other mammalian PrP sequences suggests that codons between 90 and 130 have a profound influence on the transmissibility of prions from one species to another...
  32. ncbi request reprint Prion protein of 106 residues creates an artifical transmission barrier for prion replication in transgenic mice
    S Supattapone
    Department of Neurology and Institute for Neurodegenerative Diseases, University of California, San Francisco 94143 0518, USA
    Cell 96:869-78. 1999
    ..The unique features of RML106 prions offer insights into the mechanism of prion replication, and the small size of PrP(Sc)106 should facilitate structural analysis...
  33. ncbi request reprint X-ray diffraction of scrapie prion rods and PrP peptides
    J T Nguyen
    Department of Neurology, University of California, San Francisco 94143, USA
    J Mol Biol 252:412-22. 1995
    ..15 A for the peptide SHa 90-145. The intersheet distance of PrP 27-30 was thus within the observed range for the peptides, and suggests that the amyloidogenic core of PrP is closely modeled by the peptide SHa 90-145...
  34. ncbi request reprint Identification of candidate proteins binding to prion protein
    F Yehiely
    Department of Neurology, University of California, San Francisco, California, 94143, USA
    Neurobiol Dis 3:339-55. 1997
    ..Four of the isolated clones are expressed preferentially in the mouse brain and encode a similar motif...
  35. pmc Identification of two prion protein regions that modify scrapie incubation time
    S Supattapone
    Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94143, USA
    J Virol 75:1408-13. 2001
    ..These data provide evidence that the N terminus of MoPrP and the chimeric region of MHM2 PrP (residues 108 through 111) both influence the inherent efficiency of prion propagation...
  36. ncbi request reprint A conformational transition at the N terminus of the prion protein features in formation of the scrapie isoform
    D Peretz
    Department of Neurology, School of Pharmacy, University of California, San Francisco, CA 94143, USA
    J Mol Biol 273:614-22. 1997
    ..Denaturation of PrP 27-30 exposed the epitopes of the N-terminal domain. We argue from our findings that the major conformational change underlying PrPSc formation occurs within the N-terminal segment of PrP 27-30...
  37. ncbi request reprint Leishmania major: molecular modeling of cysteine proteases and prediction of new nonpeptide inhibitors
    P M Selzer
    Department of Pathology, University of California, San Francisco 94143, USA
    Exp Parasitol 87:212-21. 1997
    ..Three inhibitors were identified which were not only effective against the L. major protease but also inhibited parasite growth at 5-50 microM...
  38. ncbi request reprint Structure-activity relationship study of prion inhibition by 2-aminopyridine-3,5-dicarbonitrile-based compounds: parallel synthesis, bioactivity, and in vitro pharmacokinetics
    Barnaby C H May
    Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, California 94158, USA
    J Med Chem 50:65-73. 2007
    ....
  39. ncbi request reprint Synthetic mammalian prions
    Giuseppe Legname
    Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143, USA
    Science 305:673-6. 2004
    ..Neuropathological findings suggest that a novel prion strain was created. Our results provide compelling evidence that prions are infectious proteins...
  40. pmc Evidence for assembly of prions with left-handed beta-helices into trimers
    Cedric Govaerts
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 101:8342-7. 2004
    ..Moreover, the parallel left-handed beta-helical model for PrP(Sc) may provide important clues to the structure of filaments found in some other neurodegenerative diseases...
  41. ncbi request reprint Directed evolution of an anti-prion protein scFv fragment to an affinity of 1 pM and its structural interpretation
    Beatrice Luginbühl
    Biochemisches Institut, Universitat Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    J Mol Biol 363:75-97. 2006
    ..Structural interpretation of the affinity improvement was performed based on the crystal structure of the original prion binder in complex with the BoPrP (95-104) peptide by modeling the corresponding mutations...
  42. ncbi request reprint Prions: so many fibers, so little infectivity
    Barnaby C H May
    Institute for Neurodegenerative Diseases, University of California San Francisco, 513 Parnassus Avenue, HSE 774, San Francisco, CA 94143 0518, USA
    Trends Biochem Sci 29:162-5. 2004
  43. pmc Strain-specified characteristics of mouse synthetic prions
    Giuseppe Legname
    Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 102:2168-73. 2005
    ..8 M. The incubation times, neuropathological lesion profiles, and Gdn1/2 values indicate that MoSP1 prions differ from RML and many other prion strains derived from sheep with scrapie and cattle with bovine spongiform encephalopathy...
  44. ncbi request reprint Developing therapeutics for the diseases of protein misfolding
    Barnaby C H May
    Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143 2240, USA
    Neurology 66:S118-22. 2006
    ..Due to the underlying molecular basis of this disease class, many of the therapeutic approaches used to target prion misfolding have parallels in other misfolding diseases...
  45. ncbi request reprint Structure-activity relationship study of 9-aminoacridine compounds in scrapie-infected neuroblastoma cells
    Barnaby C H May
    Institute for Neurodegenerative Diseases, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143, USA
    Bioorg Med Chem Lett 16:4913-6. 2006
    ..The efficacy of compounds against PrP(Sc) accumulation was influenced by both substituents of the distal tertiary amine and acridine heterocycle, while cellular cytotoxicity was encoded in the acridine heterocycle substituents...
  46. pmc Searching for new antimalarial therapeutics amongst known drugs
    Jennifer L Weisman
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158 2542, USA
    Chem Biol Drug Des 67:409-16. 2006
    ..The findings we report here indicate that this is an effective strategy to identify novel scaffolds and therefore aid in antimalarial drug discovery efforts...
  47. pmc Continuum of prion protein structures enciphers a multitude of prion isolate-specified phenotypes
    Giuseppe Legname
    Institute for Neurodegenerative Diseases, Department of Neurology, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 103:19105-10. 2006
    ..The biophysical explanation for the unprecedented plasticity of PrP(Sc) remains to be determined...
  48. pmc Automatic extraction of protein point mutations using a graph bigram association
    Lawrence C Lee
    Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 3:e16. 2007
    ..73. We believe the graph bigram search metric to be a significant improvement over previous search metrics for point mutation extraction and to be applicable to text-mining application requiring the association of words...
  49. pmc Bis-acridines as lead antiparasitic agents: structure-activity analysis of a discrete compound library in vitro
    Conor R Caffrey
    Sandler Center for Basic Research in Parasitic Diseases, BH508, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158 2330, USA
    Antimicrob Agents Chemother 51:2164-72. 2007
    ..Our approach illustrates the usefulness of screening focused compound libraries against multiple parasite targets. Some of the bis-acridines identified here may represent useful starting points for further lead optimization...
  50. ncbi request reprint Discriminating between cellular and misfolded prion protein by using affinity to 9-aminoacridine compounds
    Puay Wah Phuan
    Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
    J Gen Virol 88:1392-401. 2007
    ....
  51. pmc Cell division modulates prion accumulation in cultured cells
    Sina Ghaemmaghami
    Institute for Neurodegenerative Diseases and Department of Neurology, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 104:17971-6. 2007
    ..Our results suggest that the apparent effectiveness of antiprion compounds in culture may be strongly influenced by the growth phase of the target cells...
  52. ncbi request reprint Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors
    Florence Horn
    Department of Cellular and Molecular Pharmacology, University of California of San Francisco, 94143, USA
    Bioinformatics 20:557-68. 2004
    ..3% of the GPCR point mutations with a specificity of 87.9%, and 64.5% of the NR point mutations with a specificity of 85.8%. MuteXt routinely analyzes 100 electronic articles in approximately 1 h...
  53. pmc Mutant PrPSc conformers induced by a synthetic peptide and several prion strains
    Patrick Tremblay
    Institute for Neurodegenerative Diseases and Department of Neurology, University of California, San Francisco, California 94143, USA
    J Virol 78:2088-99. 2004
    ....
  54. pmc Dominant-negative inhibition of prion replication in transgenic mice
    Veronique Perrier
    Institute for Neurodegenerative Diseases and Departments of Pathology, Biochemistry and Biophysics, Cellular and Molecular Pharmacology, Medicine, and Neurology, University of California, San Francisco, CA 94143 0518, USA
    Proc Natl Acad Sci U S A 99:13079-84. 2002
    ..However, expression of dominant-negative PrP alone had no deleterious effects on the mice and did not support prion propagation...
  55. ncbi request reprint Screening of acyl hydrazide proteinase inhibitors for antiparasitic activity against Trypanosoma brucei
    Conor R Caffrey
    Department of Pathology, Tropical Disease Research Unit, University of California San Francisco, San Francisco, CA 94143, USA
    Int J Antimicrob Agents 19:227-31. 2002
    ..Nevertheless, the data support the potential of acyl hydrazides as antitrypanosomal chemotherapeutic agents for treatment of sleeping sickness...
  56. ncbi request reprint Pathway complexity of prion protein assembly into amyloid
    Ilia V Baskakov
    Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94143, USA
    J Biol Chem 277:21140-8. 2002
    ....
  57. pmc Structural studies of the scrapie prion protein by electron crystallography
    Holger Wille
    Department of Neurology, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 99:3563-8. 2002
    ..These low-resolution projection maps and models have implications for understanding prion propagation and the pathogenesis of neurodegeneration...
  58. ncbi request reprint Differences between the prion protein and its homolog Doppel: a partially structured state with implications for scrapie formation
    Eric M Nicholson
    Department of Molecular and Cell Biology, University of California, 229 Stanley Hall, Berkeley, CA 94720, USA
    J Mol Biol 316:807-15. 2002
    ..This suggests that the partially structured state of PrP encompassing portions of the B and C helices, may be a significant factor in the ability of PrP to convert from PrP(C) to PrP(Sc)...
  59. pmc Potent inhibition of scrapie prion replication in cultured cells by bis-acridines
    Barnaby C H May
    Department of Cellular and Molecular Pharmacology, Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 100:3416-21. 2003
    ..Our data suggest that bis-acridine analogs may provide a potent alternative to the acridine-based compound quinacrine, which is currently under clinical evaluation for the treatment of prion disease...
  60. ncbi request reprint New local potential useful for genome annotation and 3D modeling
    John Marc Chandonia
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143 2240, USA
    J Mol Biol 332:835-50. 2003
    ..JThread is applied to predicted open reading frames (ORFs) from the genomes of Mycoplasma genitalium and Drosophila melanogaster, identifying 20 new structural annotations in the former and 801 in the latter...
  61. ncbi request reprint Toward the synthesis of artificial proteins: the discovery of an amphiphilic helical peptoid assembly
    Timothy S Burkoth
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
    Chem Biol 9:647-54. 2002
    ..Inspired by nature's process of sequence variation and natural selection, we identified rare abiological sequence-specific heteropolymers that begin to mimic the structure and functional properties of their biological counterparts...
  62. pmc Electron crystallography of the scrapie prion protein complexed with heavy metals
    Holger Wille
    Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143, USA Department of Neurology, University of California, San Francisco, CA 94143, USA
    Arch Biochem Biophys 467:239-48. 2007
    ..Differential staining also confirmed the location of the internal deletion of PrP(Sc)106 at or near these densities...
  63. ncbi request reprint CoMFA and HQSAR of acylhydrazide cruzain inhibitors
    Carlos R Rodrigues
    LASSBio, Faculdade de Farmacia, Universidade Federal do Rio de Janeiro, 21944 970, Brazil
    Bioorg Med Chem Lett 12:1537-41. 2002
    ..689). Based upon the information derived from CoMFA and HQSAR, we have identified some key features that may be used to design new acylhydrazide derivatives that may be more potent cruzain inhibitors...
  64. ncbi request reprint Time-controlled transcardiac perfusion cross-linking for the study of protein interactions in complex tissues
    Gerold Schmitt-Ulms
    Institute for Neurodegenerative Disease, San Francisco, California 94143, USA
    Nat Biotechnol 22:724-31. 2004
    ..Many of these proteins have been implicated in cell adhesion/neuritic outgrowth, and harbor immunoglobulin C2 and fibronectin type III-like motifs...
  65. ncbi request reprint Synthesis and structure-activity relationship study of potent trypanocidal thio semicarbazone inhibitors of the trypanosomal cysteine protease cruzain
    Xiaohui Du
    Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94143, USA
    J Med Chem 45:2695-707. 2002
    ..The nonpeptide nature of this series, small size, and extremely low cost of production suggest this is a promising direction for the development of new antitrypanosome chemotherapy...
  66. ncbi request reprint Co-evolutionary analysis reveals insights into protein-protein interactions
    Chern Sing Goh
    Program in Biological and Medical Informatics, University of California, San Francisco, CA 94143, USA
    J Mol Biol 324:177-92. 2002
    ....
  67. pmc Apolipoprotein (apo) E4 enhances amyloid beta peptide production in cultured neuronal cells: apoE structure as a potential therapeutic target
    Shiming Ye
    Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158, USA
    Proc Natl Acad Sci U S A 102:18700-5. 2005
    ..These findings provide insights into why apoE4 is associated with increased risk for Alzheimer's disease and may represent a potential target for drug development...
  68. pmc GPCRDB information system for G protein-coupled receptors
    Florence Horn
    Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, California, USA
    Nucleic Acids Res 31:294-7. 2003
    ..The GPCRDB is updated automatically once every 4-5 months and is freely accessible at http://www.gpcr.org/7tm/...
  69. ncbi request reprint Molecular phylogeny and evolution of the plant-specific seven-transmembrane MLO family
    Alessandra Devoto
    Sainsbury Laboratory, John Innes Centre, Colney, Norwich NR4 7UH, UK
    J Mol Evol 56:77-88. 2003
    ..This revealed evidence for concerted evolution of all three cytoplasmic domains with each other and the C-terminal cytoplasmic tail, suggesting interplay of all intracellular domains for MLO function...
  70. pmc Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray
    Zbynek Bozdech
    Department of Biochemistry and Biophysics, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143 0448, USA
    Genome Biol 4:R9. 2003
    ..The P. falciparum sequencing project has brought new opportunities for identifying molecular targets for antimalarial drug and vaccine development...
  71. pmc Genes contributing to prion pathogenesis
    GULTEKIN TAMGUNEY
    Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
    J Gen Virol 89:1777-88. 2008
    ....

Research Grants15

  1. COMPUTER ANALYSIS AND PREDICTION OF PROTEIN STRUCTURE
    FRED COHEN; Fiscal Year: 1993
    ..An exploration of the possibility of grafting the active site of one enzyme onto the structural scaffold provided by another protein will be studied in collaboration with Dr. Craik at UCSF and Dr. Wells at Genentech...
  2. COMPUTER ANALYSIS PREDICTION OF PROTEIN STRUCTURE
    FRED COHEN; Fiscal Year: 1991
    ..With Drs. Kuntz, Stewler and Arnaud at UCSF, the structure of PTH and chemical variants of PTH will be characterized. It is hoped that structural modelling will lead to the design of pharmacologically relevant mutant proteins...
  3. COMPUTER ANALYSIS & PREDICTION OF PROTEIN STRUCTURE
    FRED COHEN; Fiscal Year: 1999
    ..This provides a natural way to circumvent the gap penalty problem that plagues current structure alignment algorithms. ..
  4. COMPUTER ANALYSIS AND PREDICTION OF PROTEIN STRUCTURE
    FRED COHEN; Fiscal Year: 2003
    ..Finally, work on the design of a novel class of abiologic sturctured heteropolymers is described that builds on our recent results with N-alkylated glycines. ..