Affiliation: University of California
- The AnnoLite and AnnoLyze programs for comparative annotation of protein structuresMarc 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...
- Localization of binding sites in protein structures by optimization of a composite scoring functionAndrea 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...
- MODBASE: a database of annotated comparative protein structure models and associated resourcesUrsula 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)...
- DBAli tools: mining the protein structure spaceMarc 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...
- Neuromyelitis optica IgG does not alter aquaporin-4 water permeability, plasma membrane M1/M23 isoform content, or supramolecular assemblyAndrea 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...
- Super-resolution imaging of aquaporin-4 orthogonal arrays of particles in cell membranesAndrea 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...
- Complement-dependent cytotoxicity in neuromyelitis optica requires aquaporin-4 protein assembly in orthogonal arraysPuay 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...
- Orthogonal array formation by human aquaporin-4: examination of neuromyelitis optica-associated aquaporin-4 polymorphismsJonathan 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...
- Model of aquaporin-4 supramolecular assembly in orthogonal arrays based on heterotetrameric association of M1-M23 isoformsByung 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...
- MODBASE, a database of annotated comparative protein structure models, and associated resourcesUrsula 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)...
- A method for integrative structure determination of protein-protein complexesDina 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...
- Live-cell imaging of aquaporin-4 supramolecular assembly and diffusionA 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...
- Comprehensive search for cysteine cathepsins in the human genomeAndrea 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...
- 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...
- Light inactivation of water transport and protein-protein interactions of aquaporin-Killer Red chimerasFlorian 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...
- Post-Golgi supramolecular assembly of aquaporin-4 in orthogonal arraysAndrea Rossi
Departments of Medicine and Physiology, University of California San Francisco, CA 94143, USA
Traffic 13:43-53. 2012....
- Aquaporin-4: orthogonal array assembly, CNS functions, and role in neuromyelitis opticaAlan S Verkman
Department of Medicine, University of California, San Francisco, CA 94143 0521, USA
Acta Pharmacol Sin 32:702-10. 2011....
- Ninjurin1, a target of p53, regulates p53 expression and p53-dependent cell survival, senescence, and radiation-induced mortalitySeong 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...
- Fabs enable single particle cryoEM studies of small proteinsShenping 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...
- Aquaporin-4 Mz isoform: brain expression, supramolecular assembly and neuromyelitis optica antibody bindingAndrea Rossi
Department of Medicine, University of California, San Francisco, California 94143 0521, USA
Glia 59:1056-63. 2011....
- The structure of chagasin in complex with a cysteine protease clarifies the binding mode and evolution of an inhibitor familyStephanie 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...
- Leigh Syndrome with COX deficiency and SURF1 gene mutations: MR imaging findingsAndrea 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...