S S Sidhu

Summary

Affiliation: Genentech Inc
Country: USA

Publications

  1. ncbi Tyrosine plays a dominant functional role in the paratope of a synthetic antibody derived from a four amino acid code
    Frederic A Fellouse
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    J Mol Biol 357:100-14. 2006
  2. ncbi Activation of the proapoptotic death receptor DR5 by oligomeric peptide and antibody agonists
    Bing Li
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    J Mol Biol 361:522-36. 2006
  3. ncbi Phage display in pharmaceutical biotechnology
    S S Sidhu
    Department of Protein Engineering, Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Curr Opin Biotechnol 11:610-6. 2000
  4. ncbi Engineering M13 for phage display
    S S Sidhu
    Department of Protein Engineering, Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Biomol Eng 18:57-63. 2001
  5. ncbi Synthetic therapeutic antibodies
    Sachdev S Sidhu
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Nat Chem Biol 2:682-8. 2006
  6. ncbi Exploring and designing protein function with restricted diversity
    Sachdev S Sidhu
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Curr Opin Chem Biol 11:347-54. 2007
  7. ncbi Phage display for engineering and analyzing protein interaction interfaces
    Sachdev S Sidhu
    Department of Protein Engineering, Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Curr Opin Struct Biol 17:481-7. 2007
  8. ncbi Functional genomics of intracellular peptide recognition domains with combinatorial biology methods
    Sachdev S Sidhu
    Department of Protein Engineering, Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Curr Opin Chem Biol 7:97-102. 2003
  9. ncbi Exploring protein-protein interactions with phage display
    Sachdev S Sidhu
    Department of Protein Engineering, Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Chembiochem 4:14-25. 2003
  10. ncbi Convergent and divergent ligand specificity among PDZ domains of the LAP and zonula occludens (ZO) families
    Yingnan Zhang
    Department of Protein Engineering, Genentech, Inc, South San Francisco, California 94080, USA
    J Biol Chem 281:22299-311. 2006

Collaborators

Detail Information

Publications50

  1. ncbi Tyrosine plays a dominant functional role in the paratope of a synthetic antibody derived from a four amino acid code
    Frederic A Fellouse
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    J Mol Biol 357:100-14. 2006
    ..The results show that the chemical nature of Tyr endows the amino acid with a privileged role in antigen recognition, and this likely explains the high abundance of Tyr in natural antigen-binding sites...
  2. ncbi Activation of the proapoptotic death receptor DR5 by oligomeric peptide and antibody agonists
    Bing Li
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    J Mol Biol 361:522-36. 2006
    ..These phage-derived ligands may be useful for elucidating DR5 activation at the molecular level and for creating synthetic agonists of proapoptotic death receptors...
  3. ncbi Phage display in pharmaceutical biotechnology
    S S Sidhu
    Department of Protein Engineering, Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Curr Opin Biotechnol 11:610-6. 2000
    ..In addition, phage-display methods have been developed for the rapid determination of binding energetics at protein-protein interfaces...
  4. ncbi Engineering M13 for phage display
    S S Sidhu
    Department of Protein Engineering, Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Biomol Eng 18:57-63. 2001
    ..These improvements expand the utility of phage display as a powerful tool in modern biotechnology...
  5. ncbi Synthetic therapeutic antibodies
    Sachdev S Sidhu
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Nat Chem Biol 2:682-8. 2006
  6. ncbi Exploring and designing protein function with restricted diversity
    Sachdev S Sidhu
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Curr Opin Chem Biol 11:347-54. 2007
    ..These studies shed light on the underlying principles governing molecular recognition, and provide rapid yet quantitative alternatives to conventional biophysical methods for exploring protein structure and function...
  7. ncbi Phage display for engineering and analyzing protein interaction interfaces
    Sachdev S Sidhu
    Department of Protein Engineering, Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Curr Opin Struct Biol 17:481-7. 2007
    ....
  8. ncbi Functional genomics of intracellular peptide recognition domains with combinatorial biology methods
    Sachdev S Sidhu
    Department of Protein Engineering, Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Curr Opin Chem Biol 7:97-102. 2003
    ..In addition, libraries of phage-displayed PDZ and SH3 domains have been used to identify the residues responsible for ligand recognition, and also to engineer domains with altered specificities...
  9. ncbi Exploring protein-protein interactions with phage display
    Sachdev S Sidhu
    Department of Protein Engineering, Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Chembiochem 4:14-25. 2003
    ..With further optimization and automation, it may soon be possible to study hundreds of different proteins in parallel with efforts comparable to those currently expended on the analysis of individual proteins...
  10. ncbi Convergent and divergent ligand specificity among PDZ domains of the LAP and zonula occludens (ZO) families
    Yingnan Zhang
    Department of Protein Engineering, Genentech, Inc, South San Francisco, California 94080, USA
    J Biol Chem 281:22299-311. 2006
    ..These findings show that subtle changes in binding specificity can significantly alter the range of biological partners for PDZ domains, and the insights enhance our understanding of this diverse family of peptide-binding modules...
  11. ncbi Phage display for selection of novel binding peptides
    S S Sidhu
    Department of Protein Engineering, Genentech, Inc, South San Francisco, California 94080, USA
    Methods Enzymol 328:333-63. 2000
  12. ncbi The Erbin PDZ domain binds with high affinity and specificity to the carboxyl termini of delta-catenin and ARVCF
    Richard P Laura
    Department of Molecular Oncology, Genentech, Inc, 1 DNA Way, South San Francisco, California 94080, USA
    J Biol Chem 277:12906-14. 2002
    ..They also demonstrate that C-terminal phage-display technology can be used to predict physiologically relevant ligands for PDZ domains...
  13. doi The functional capacity of the natural amino acids for molecular recognition
    Sara Birtalan
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Mol Biosyst 6:1186-94. 2010
    ..Moreover, our findings illuminate the fundamental principles underlying protein-protein interactions and provide valuable guidelines for engineering synthetic binding proteins with functions beyond the scope of natural proteins...
  14. ncbi High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries
    Frederic A Fellouse
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    J Mol Biol 373:924-40. 2007
    ....
  15. ncbi Comprehensive analysis of the factors contributing to the stability and solubility of autonomous human VH domains
    Pierre A Barthelemy
    Department of Protein Engineering, Genentech, Incorporated, South San Francisco, California 94080, USA
    J Biol Chem 283:3639-54. 2008
    ..These findings should enable the development of libraries of synthetic V(H) domains with CDR3 diversities unconstrained by structural demands...
  16. pmc Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3
    Steven T Runyon
    Department of Medicinal Chemistry, Genetech, Inc, South San Francisco, CA 94080, USA
    Protein Sci 16:2454-71. 2007
    ..Such a mechanism is well suited to proteases evolved for the recognition and degradation of misfolded proteins...
  17. ncbi Comprehensive functional maps of the antigen-binding site of an anti-ErbB2 antibody obtained with shotgun scanning mutagenesis
    Felix F Vajdos
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    J Mol Biol 320:415-28. 2002
    ..The results validate shotgun scanning as a rapid and accurate method for determining the functional contributions of individual side-chains involved in protein-protein interactions...
  18. ncbi Rapid identification of small binding motifs with high-throughput phage display: discovery of peptidic antagonists of IGF-1 function
    Kurt Deshayes
    Department of Protein Engineering, Genentech, South San Francisco, CA 94080, USA
    Chem Biol 9:495-505. 2002
    ..NMR analysis revealed that the peptide is highly structured in the absence of IGF-1, and peptides that preorganize the binding elements were selected during the sorting...
  19. pmc Structural and functional analysis of the ligand specificity of the HtrA2/Omi PDZ domain
    Yingnan Zhang
    Department of Protein Engineering, Genentech, Inc, South San Francisco, California 94080, USA
    Protein Sci 16:1738-50. 2007
    ..The findings are less consistent with, but do not exclude, a role for the PDZ domain in targeting the protease to specific substrates during apoptosis...
  20. ncbi High-affinity human antibodies from phage-displayed synthetic Fab libraries with a single framework scaffold
    Chingwei V Lee
    Department of Protein Engineering, Genentech Inc 1 DNA Way, South San Francisco, CA 94080, USA
    J Mol Biol 340:1073-93. 2004
    ..The results demonstrated that high-affinity human antibodies can be generated from libraries with completely synthetic CDRs displayed on a single scaffold...
  21. ncbi Origins of PDZ domain ligand specificity. Structure determination and mutagenesis of the Erbin PDZ domain
    Nicholas J Skelton
    Department of Protein Engineering, Genentech, Inc, South San Francisco, California 94080, USA
    J Biol Chem 278:7645-54. 2003
    ....
  22. doi Rapid evolution of functional complexity in a domain family
    Andreas Ernst
    Department of Protein Engineering, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
    Sci Signal 2:ra50. 2009
    ..Our results show that ligand binding is hardwired in the PDZ fold and suggest that this flexibility may facilitate the rapid evolution of complex protein interaction networks...
  23. ncbi Contributions of CDR3 to V H H domain stability and the design of monobody scaffolds for naive antibody libraries
    Christopher J Bond
    Departments of Medicinal Chemistry, 1 DNA Way, South San Francisco, CA 94080, USA
    J Mol Biol 332:643-55. 2003
    ..In addition, they shed light on the relationships between CDR3 sequence diversity and the structural stability of the V(H)H domain fold...
  24. doi Inhibition of Wnt signaling by Dishevelled PDZ peptides
    Yingnan Zhang
    Department of Protein Engineering, Genentech, Inc, South San Francisco, California, USA
    Nat Chem Biol 5:217-9. 2009
    ..These peptide ligands inhibit Wnt/beta-catenin signaling in cells, showing that Dishevelled PDZ domains are potential targets for small-molecule cancer therapeutics...
  25. ncbi Comparative structural analysis of the Erbin PDZ domain and the first PDZ domain of ZO-1. Insights into determinants of PDZ domain specificity
    Brent A Appleton
    Department of Protein Engineering, Genentech, Inc, South San Francisco, California 94080, USA
    J Biol Chem 281:22312-20. 2006
    ..We propose a model for ligand recognition that accounts for interactions extending across the entire binding site but that highlights several key specificity switches within the PDZ domain fold...
  26. pmc Synthetic antibodies from a four-amino-acid code: a dominant role for tyrosine in antigen recognition
    Frederic A Fellouse
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Proc Natl Acad Sci U S A 101:12467-72. 2004
    ..The findings shed light on the basic principles governing the evolution of natural immune repertoires and should also aid the development of improved synthetic antibody libraries...
  27. ncbi A minimized M13 coat protein defines the requirements for assembly into the bacteriophage particle
    Tomer A Roth
    Department of Protein Engineering, Genentech Inc, South San Francisco, CA 94080, USA
    J Mol Biol 322:357-67. 2002
    ..The results suggest possible mechanisms of natural viral evolution and establish guidelines for the artificial evolution of improved coat proteins for phage display technology...
  28. ncbi Phage-displayed antibody libraries of synthetic heavy chain complementarity determining regions
    Sachdev S Sidhu
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, Mailstop 27, South San Francisco, CA 94080, USA
    J Mol Biol 338:299-310. 2004
    ....
  29. doi The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies
    Sara Birtalan
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    J Mol Biol 377:1518-28. 2008
    ..Results of such studies should illuminate the basic principles underlying natural protein-protein interactions and should aid the design of synthetic binding proteins with functions beyond the scope of natural proteins...
  30. ncbi A structure-based database of antibody variable domain diversity
    Christopher J Bond
    Department of Medicinal Chemistry, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    J Mol Biol 348:699-709. 2005
    ....
  31. doi Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies
    Kim Newton
    Department of Physiological Chemistry, Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Cell 134:668-78. 2008
    ..Polyubiquitin editing may therefore be a general mechanism for attenuating innate immune signaling...
  32. ncbi Bivalent antibody phage display mimics natural immunoglobulin
    Chingwei V Lee
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    J Immunol Methods 284:119-32. 2004
    ..Bivalent antibody phage display should be useful for many applications. In particular, the technology should aid in the production of antibodies against difficult antigens, and also, in selections that require dimerization for activity...
  33. pmc Improving therapeutic efficacy of a complement receptor by structure-based affinity maturation
    Bing Li
    Department of Antibody Engineering, South San Francisco, California 94080, USA
    J Biol Chem 284:35605-11. 2009
    ....
  34. doi Structure of the complex between HER2 and an antibody paratope formed by side chains from tryptophan and serine
    Robert D Fisher
    Department of Protein Engineering, Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    J Mol Biol 402:217-29. 2010
    ..The crystal lattice contains an unprecedented trimeric arrangement of HER2 closely related to previously observed homodimers of the related epidermal growth factor receptor...
  35. ncbi Molecular recognition by a binary code
    Frederic A Fellouse
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    J Mol Biol 348:1153-62. 2005
    ..Furthermore, these results demonstrate that molecular recognition can evolve from even the simplest chemical diversity...
  36. ncbi M13 bacteriophage coat proteins engineered for improved phage display
    Sachdev S Sidhu
    Department of Protein Engineering, Genentech Inc, South San Francisco, CA, USA
    Methods Mol Biol 352:205-19. 2007
    ..Experimental methods are presented for the design, construction, and screening of phage-displayed libraries for improved protein display...
  37. ncbi Comprehensive mutational analysis of the M13 major coat protein: improved scaffolds for C-terminal phage display
    Heike A Held
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    J Mol Biol 340:587-97. 2004
    ..These finding provide information on the requirements for filamentous phage coat assembly, and provide improved scaffolds for phage display technology...
  38. ncbi Comprehensive mutagenesis of the C-terminal domain of the M13 gene-3 minor coat protein: the requirements for assembly into the bacteriophage particle
    Gregory A Weiss
    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    J Mol Biol 332:777-82. 2003
    ..These findings shed light on the functional and structural requirements for filamentous phage assembly, and they may provide guidelines for the engineering of improved coat proteins as scaffolds for phage display technology...
  39. ncbi Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning
    Gabor Pal
    Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, Cummings Life Sciences Center, University of Chicago, Illinois 60637, USA
    J Biol Chem 281:22378-85. 2006
    ..The compilation of analogous data bases from studies of other protein-protein interactions should greatly aid the development of computational methods for explaining and designing molecular recognition...
  40. ncbi The functional binding epitope of a high affinity variant of human growth hormone mapped by shotgun alanine-scanning mutagenesis: insights into the mechanisms responsible for improved affinity
    Gabor Pal
    Department of Biochemistry and Molecular Biology, University of Chicago, Cummings Life Sciences Center, Chicago, IL 60637, USA
    J Mol Biol 332:195-204. 2003
    ..Thus, it appears that the improved binding affinity of hGH(v) site 1 was not achieved through minor adjustments to the wt interface, but rather, results from a wholesale reconfiguration of many of the original binding elements...
  41. pmc A specificity map for the PDZ domain family
    Raffi Tonikian
    Terrence Donnelly Center for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    PLoS Biol 6:e239. 2008
    ..These findings indicate that many viruses produce PDZ ligands that disrupt host protein complexes for their own benefit, and that highly pathogenic strains target PDZ domains involved in cell polarity and growth...
  42. pmc A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces
    Ryan N Gilbreth
    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
    J Mol Biol 381:407-18. 2008
    ....
  43. doi Submitting antibodies to binding arbitration
    Stephen W Michnick
    D├ępartement de Biochimie and Robert Cedergren Centre, Bioinformatique and Genomics, Universite de Montreal, C P 6128, Succursale Centre Ville, Montreal, Quebec H3C 3J7, Canada
    Nat Chem Biol 4:326-9. 2008
    ....
  44. pmc Synthetic antibodies for specific recognition and crystallization of structured RNA
    Jing Dong Ye
    Department of Chemistry, Howard Hughes Medical Institute, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 105:82-7. 2008
    ..These findings yield valuable insights for engineering of Fabs as RNA-binding modules and facilitate further development of Fabs as possible therapeutic drugs and biochemical tools to explore RNA biology...
  45. ncbi Definition of the consensus motif recognized by gamma-adaptin ear domains
    Rafael Mattera
    Cell Biology and Metabolism Branch, NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 279:8018-28. 2004
    ..These findings shed light on the mechanism of accessory protein recruitment to trans-Golgi network and endosomal clathrin coats...
  46. ncbi Intramolecular cooperativity in a protein binding site assessed by combinatorial shotgun scanning mutagenesis
    Gabor Pal
    Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, Cummings Life Sciences Center, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
    J Mol Biol 347:489-94. 2005
    ..The results reveal that hGH site 1 behaves in a highly additive manner and suggest that shotgun scanning should be useful for assessing cooperative effects in other protein-protein interactions...
  47. pmc The type III effector EspF coordinates membrane trafficking by the spatiotemporal activation of two eukaryotic signaling pathways
    Neal M Alto
    Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
    J Cell Biol 178:1265-78. 2007
    ..Thus, our findings suggest that the EspF-dependent assembly of SNX9 and N-WASP represents a novel form of signaling mimicry used to promote EPEC pathogenesis and gastrointestinal disease...
  48. pmc Alternative views of functional protein binding epitopes obtained by combinatorial shotgun scanning mutagenesis
    Gabor Pal
    Dept of Biochemistry and Molecular Biology, Cummings Life Sciences Center, University of Chicago, IL 60637, USA
    Protein Sci 14:2405-13. 2005
    ..The serine and homolog-scanning results expand upon and complement the alanine-scanning results and provide additional data on the robustness of the high affinity receptor-binding site of hGH...
  49. ncbi Full-length antibodies on display
    Sachdev S Sidhu
    Nat Biotechnol 25:537-8. 2007
  50. ncbi Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries
    Raffi Tonikian
    Department of Molecular and Medical Genetics, University of Toronto, 4398 Medical Sciences Building, 1 King s College Circle, University of Toronto, Toronto, Ontario, Canada M5S 1A8
    Nat Protoc 2:1368-86. 2007
    ..The affinity selection process described thereafter enables a single researcher to efficiently probe the recognition profiles of numerous PRMs in a 1 week time period...