Andrea Rossi

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc The AnnoLite and AnnoLyze programs for comparative annotation of protein structures
    Marc A Marti-Renom
    Structural Genomics Unit, Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    BMC Bioinformatics 8:S4. 2007
  2. pmc Localization of binding sites in protein structures by optimization of a composite scoring function
    Andrea Rossi
    Department of Biopharmaceutical Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Research, University of California, San Francisco, California 94143 2552, USA
    Protein Sci 15:2366-80. 2006
  3. pmc MODBASE: a database of annotated comparative protein structure models and associated resources
    Ursula Pieper
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, QB3 at Mission Bay, Office 503B, University of California at San Francisco 1700 4th Street, San Francisco, CA 94158, USA
    Nucleic Acids Res 34:D291-5. 2006
  4. pmc DBAli tools: mining the protein structure space
    Marc A Marti-Renom
    Structural Genomics Unit, and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94158 2330, USA
    Nucleic Acids Res 35:W393-7. 2007
  5. pmc Neuromyelitis optica IgG does not alter aquaporin-4 water permeability, plasma membrane M1/M23 isoform content, or supramolecular assembly
    Andrea Rossi
    Department of Medicine, University of California, San Francisco, California 94143, USA
    Glia 60:2027-39. 2012
  6. pmc Super-resolution imaging of aquaporin-4 orthogonal arrays of particles in cell membranes
    Andrea Rossi
    Department of Medicine, University of California, San Francisco, CA 94143, USA
    J Cell Sci 125:4405-12. 2012
  7. pmc Complement-dependent cytotoxicity in neuromyelitis optica requires aquaporin-4 protein assembly in orthogonal arrays
    Puay Wah Phuan
    Department of Medicine and Physiology, University of California, San Francisco, California 94143, USA
    J Biol Chem 287:13829-39. 2012
  8. pmc Orthogonal array formation by human aquaporin-4: examination of neuromyelitis optica-associated aquaporin-4 polymorphisms
    Jonathan M Crane
    Department of Medicine, University of California, San Francisco, CA 94143, USA
    J Neuroimmunol 236:93-8. 2011
  9. pmc Model of aquaporin-4 supramolecular assembly in orthogonal arrays based on heterotetrameric association of M1-M23 isoforms
    Byung Ju Jin
    Department of Medicine, University of California, San Francisco, California, USA
    Biophys J 100:2936-45. 2011
  10. pmc MODBASE, a database of annotated comparative protein structure models, and associated resources
    Ursula Pieper
    Department of Biopharmaceutical Sciences, and California Institute for Quantitative Biomedical Research, Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California San Francisco, San Francisco, CA 94143 2240, USA
    Nucleic Acids Res 32:D217-22. 2004

Collaborators

Detail Information

Publications22

  1. pmc The AnnoLite and AnnoLyze programs for comparative annotation of protein structures
    Marc A Marti-Renom
    Structural Genomics Unit, Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    BMC Bioinformatics 8:S4. 2007
    ..Here we introduce two programs, AnnoLite and AnnoLyze, which use the structural alignments deposited in the DBAli database...
  2. pmc Localization of binding sites in protein structures by optimization of a composite scoring function
    Andrea Rossi
    Department of Biopharmaceutical Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Research, University of California, San Francisco, California 94143 2552, USA
    Protein Sci 15:2366-80. 2006
    ..The method is completely automated (http://salilab.org/patcher) and can be applied on a large scale in a structural genomics setting...
  3. pmc MODBASE: a database of annotated comparative protein structure models and associated resources
    Ursula Pieper
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, QB3 at Mission Bay, Office 503B, University of California at San Francisco 1700 4th Street, San Francisco, CA 94158, USA
    Nucleic Acids Res 34:D291-5. 2006
    ..org/pibase) as well as predictions of ligand binding sites, interactions between yeast proteins, and functional consequences of human nsSNPs (LS-SNP, http://salilab.org/LS-SNP)...
  4. pmc DBAli tools: mining the protein structure space
    Marc A Marti-Renom
    Structural Genomics Unit, and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94158 2330, USA
    Nucleic Acids Res 35:W393-7. 2007
    ..Thus, the DBAli tools, which are freely accessible via the World Wide Web at http://salilab.org/DBAli/, allow users to mine the protein structure space by establishing relationships between protein structures and their functions...
  5. pmc Neuromyelitis optica IgG does not alter aquaporin-4 water permeability, plasma membrane M1/M23 isoform content, or supramolecular assembly
    Andrea Rossi
    Department of Medicine, University of California, San Francisco, California 94143, USA
    Glia 60:2027-39. 2012
    ..We conclude that NMO-IgG does not: (i) inhibit AQP4 water permeability, (ii) cause preferential internalization of M1-AQP4, or (iii) cause intramembrane AQP4 clustering...
  6. pmc Super-resolution imaging of aquaporin-4 orthogonal arrays of particles in cell membranes
    Andrea Rossi
    Department of Medicine, University of California, San Francisco, CA 94143, USA
    J Cell Sci 125:4405-12. 2012
    ..OAP area was not altered by anti-AQP4 IgG autoantibodies (NMO-IgG) that cause the neurological disease neuromyelitis optica. Super-resolution imaging allowed elucidation of novel nanoscale structural and dynamic features of OAPs...
  7. pmc Complement-dependent cytotoxicity in neuromyelitis optica requires aquaporin-4 protein assembly in orthogonal arrays
    Puay Wah Phuan
    Department of Medicine and Physiology, University of California, San Francisco, California 94143, USA
    J Biol Chem 287:13829-39. 2012
    ..We conclude that AQP4 assembly in OAPs is required for CDC in NMO, establishing a new mechanism of OAP-dependent NMO pathogenesis. Disruption of AQP4 OAPs may greatly reduce NMO-IgG dependent CDC and NMO pathology...
  8. pmc Orthogonal array formation by human aquaporin-4: examination of neuromyelitis optica-associated aquaporin-4 polymorphisms
    Jonathan M Crane
    Department of Medicine, University of California, San Francisco, CA 94143, USA
    J Neuroimmunol 236:93-8. 2011
    ..NMO-associated mutations R19I and R19T in AQP4 did not affect OAP assembly, palmitoylation-dependent regulation of assembly, or NMO autoantibody binding. Residue-19 polymorphisms in AQP4 are thus unlikely to be disease relevant...
  9. pmc Model of aquaporin-4 supramolecular assembly in orthogonal arrays based on heterotetrameric association of M1-M23 isoforms
    Byung Ju Jin
    Department of Medicine, University of California, San Francisco, California, USA
    Biophys J 100:2936-45. 2011
    ..Our model of AQP4 OAPs links a molecular-level interaction of AQP4 with its supramolecular assembly in cell membranes...
  10. pmc MODBASE, a database of annotated comparative protein structure models, and associated resources
    Ursula Pieper
    Department of Biopharmaceutical Sciences, and California Institute for Quantitative Biomedical Research, Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California San Francisco, San Francisco, CA 94143 2240, USA
    Nucleic Acids Res 32:D217-22. 2004
    ..org/modweb), modeling of loops in protein structures (MODLOOP, http://salilab.org/modloop) and predicting functional consequences of single nucleotide polymorphisms (SNPWEB, http://salilab. org/snpweb)...
  11. pmc A method for integrative structure determination of protein-protein complexes
    Dina Schneidman-Duhovny
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
    Bioinformatics 28:3282-9. 2012
    ..On the other hand, computational methods for modeling assembly structures from individual components frequently suffer from high false-positive rate, rarely resulting in a unique solution...
  12. pmc Live-cell imaging of aquaporin-4 supramolecular assembly and diffusion
    A S Verkman
    Departments of Medicine and Physiology, University of California, San Francisco, San Francisco, California, USA
    Methods Enzymol 504:341-54. 2012
    ..The biophysical data afforded by live-cell imaging of AQP4 and OAPs has provided new insights in the roles of AQP4 in organ physiology and neurological disease...
  13. ncbi request reprint Comprehensive search for cysteine cathepsins in the human genome
    Andrea Rossi
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94143 2240, USA
    Biol Chem 385:363-72. 2004
    ..No expression of any of the three cathepsin L-like pseudogenes was found. Based on these results, it is likely that to date all human cysteine cathepsins are known...
  14. pmc Transient hyperckemia in the setting of neuromyelitis optica (NMO)
    Rabia Malik
    UCSF, Neurology, 505 Parnassus Avenue Box 0114 M 798, San Francisco, California, USA, 94143
    Muscle Nerve 50:859-62. 2014
    ..We report 2 patients with transient hyperCKemia associated with NMO suggesting possible skeletal muscle damage...
  15. pmc Light inactivation of water transport and protein-protein interactions of aquaporin-Killer Red chimeras
    Florian Baumgart
    Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
    J Gen Physiol 139:83-91. 2012
    ..Our data also support the utility of CALI to study protein-protein interactions as well as other membrane transporters and receptors...
  16. pmc Post-Golgi supramolecular assembly of aquaporin-4 in orthogonal arrays
    Andrea Rossi
    Departments of Medicine and Physiology, University of California San Francisco, CA 94143, USA
    Traffic 13:43-53. 2012
    ....
  17. pmc Aquaporin-4: orthogonal array assembly, CNS functions, and role in neuromyelitis optica
    Alan S Verkman
    Department of Medicine, University of California, San Francisco, CA 94143 0521, USA
    Acta Pharmacol Sin 32:702-10. 2011
    ....
  18. pmc Ninjurin1, a target of p53, regulates p53 expression and p53-dependent cell survival, senescence, and radiation-induced mortality
    Seong Jun Cho
    Comparative Oncology Laboratory, University of California, Davis, CA 95616, USA
    Proc Natl Acad Sci U S A 110:9362-7. 2013
    ..Thus, we postulate that as a membrane adhesion molecule, Ninj1 is an ideal target to regulate p53 activity via the p53-Ninj1 loop...
  19. pmc Fabs enable single particle cryoEM studies of small proteins
    Shenping Wu
    The W M Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, USA
    Structure 20:582-92. 2012
    ..Because Fabs can be readily generated against a wide range of proteins by phage display, this approach is generally applicable to study many small proteins by single particle cryoEM...
  20. pmc Aquaporin-4 Mz isoform: brain expression, supramolecular assembly and neuromyelitis optica antibody binding
    Andrea Rossi
    Department of Medicine, University of California, San Francisco, California 94143 0521, USA
    Glia 59:1056-63. 2011
    ....
  21. ncbi request reprint The structure of chagasin in complex with a cysteine protease clarifies the binding mode and evolution of an inhibitor family
    Stephanie X Wang
    Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
    Structure 15:535-43. 2007
    ..Interactions of chagasin with a target protease are reminiscent of the cystatin family inhibitors. Protein inhibitors of cysteine proteases may have evolved more than once on nonhomologous scaffolds...
  22. ncbi request reprint Leigh Syndrome with COX deficiency and SURF1 gene mutations: MR imaging findings
    Andrea Rossi
    Department of Pediatric Neuroradiology, G Gaslini Children s Research Hospital, Largo G Gaslini 5, I 16147 Genoa, Italy
    AJNR Am J Neuroradiol 24:1188-91. 2003
    ..MR imaging pattern recognition can suggest an underlying COX deficiency and should prompt investigators to search for SURF1 gene mutations...