`5Xb Xb0 @@@ @@@@X :ubXbXb@ EN DB XbP     & ./ \J L{s lC 7  51 Acton2003 Albermann1997 Almo199990 Arrowmith2003 Arrowsmith20011 Baase1992 Bader2000 Bader2001$ Bader2002 Bader2003( Bairoch2002) Bairoch2002! Baron20000 Beasley2003 Beisser2002 Berendzen1999 Berendzen2002 Bertone20011 Bertone2003 Betel2003( Bienvenut2002 Bogan2000 Bonanno1999$ Boone2002$ Brannetti2002. Breiman2001/ Breiman2002 Brinen20022 Broger1994) Bucher20022 Burley1999# Cagney2000 Canaves2002 Capel1999$ Castagnoli2002) Cerutti2002$Cesareni20022 Chance19999" Chiba2001 Christendat20015Chung Submittedt Cohen2000 Cohen2002 Cohen2002# Conover2000 D'Arcy1994 Dale19940 Das2003, Dash1997 Deacon2002 Donaldson20011 Douglas2003$ Drees2002 Duan2001 Duan20024 Dyson19993 Dyson20021 Echols2003 Edwards20010 Edwards2003! Eisenberg2000  Eisenberg2001 Eisenberg2002 Elsliger20020*Engelman1986$ Evangelista20020 Evdokimova20033) Falquet2002Federhen1996  Fernandez2001$ Ferracuti2002# Fields20000$ Fields20022Frishman1998Frishman1999Frishman2000Frishman2002 Gaasterland1999 Garcia-Bustos1991( Gasteiger2002(Gattiker2002)Gattiker2002 Geier2000Gerstein200100Gerstein200301Gerstein200305Gerstein Submitted%Gierasch1989# Giot2000# Godwin2000l Godzik2002 Goh2000 Goh2002 Goh20021 Goh20035Goh Submittede* Goldman1986 Gruber20000 Guda20020Guldener2002 Haase2000 Hall19919 Hani19988" Hattori2001 Heinz1992 Heitman1991 Heumann1997 Heumann1999 Higney20020 Hodgson2002 Hogue2000 Hogue2001$ Hogue2002 Hogue2003 Hol2000) Hulo20020" Ito2001  Jaroszewski2002 Joachimiak2000#Johnston2000# Judson20000# Kalbfleisch2000Kalderon1984 Kaps19999 Kaps200000 Khachatryan2003 Kim2002 Kim2002 Klock2002 Kluger20011# Knight20000 Koonin19977- Koonin19977 Kreusch2002 Kuhn20020 Lan20010 Lan20031 Lan2003 Langen1994 Lemcke20000 Lesley2001  Lesley2002# Li2000-  Lichtarge2002 Liebl1997 Lin1999 Liong2002 Lipman19977- Lipman19977, Liu1997#Lockshon200005Luscombe Submitted1 Ma20030 Mannhaupt2000 Mannhaupt2002# Mansfield2000!Marcotte20000 Marcotte20011 Mathews2002Matthews1992 Mayer1999 Mayer2002 McMullan2002  McPhillips2002 Mewes1997 Mewes1998 Mewes1999 Mewes2000 Mewes2002 Michelson20021 Milburn2003 Miller20022 Miller20022  Mirny2001 Mokrejs2002 Montelione200111 Montelione2003 Morgenstern2002 Munsterkotter2002# Narayan2000$Nardelli2002$ Nelson200200 Northey2003 Ouellette2001" Ozawa2001) Pagni2002$ Paoluzi2002 Park20020 Pavlova2003 Pawson20010 Pearson1999Pedelacq2002Pfeiffer19977Pfeiffer1998Pfeiffer1999Pfeiffer20000 Piltch20020# Pochart2000  Quinlan1987+ Quinlan1993$ Quondam2002# Qureshi-Emili2000'Rapoport1992 Rho2002! Rice20002 Richardson1984 Robb20020 Roberts1984#Rothberg2000 Rudd2002t" Sakaki20011 Sali1999n! Salwinski2000  Salwinski2001 Salwinski20020 Savchenko2003 Scheibe2002Schuller20000 Schultz2002 Selby20020 Semesi20033 Service2002  Shakhnovich2001 Shin20022) Sigrist20020 Skarina2003 Skinner1996 Smith1984 Sowa2002 Spraggon2002# Srinivasan2000Standish1999* Steitz19868 Stevens2002 Stocker1999 Stocker2000 Stuber1994 Studier1999 Swaminathan1999 Tatusov1997- Tatusov1997 Taylor20020 Terwilliger1996 Terwilliger1999 Terwilliger2002 Thompson20011$ Tong2002# Uetz2000# Vijayadamodar2000 Vincent2002& von Heijne1990 Waldo1999 Waldo2002 Walther2000 Weil20000 Weil2002t Wilson20022 Wolting2001  Wood1999 Wooley20020 Wootton19964 Wright19993 Wright20021 Wunderlich2003!Xenarios2000 Xenarios2001Xenarios20021 Xiao20030# Yang2000o Yee20010 Yee20032Yokoyama2003" Yoshida20015 Yu Submitted Zheng20011 Zheng20035Zhu Submittedi$ Zucconi2002    AuthorsJournals Keywords                                pbX  Acton, T. Albermann, K. Almo, S. C.Arrowmith, C. H.Arrowsmith, C. H. Baase, W. A. Bader, G. D. Bairoch, A. Baron, M. K. Beasley, S.Beisser, P. S. Berendzen, J. Bertone, P. Betel, D.Bienvenut, W. V. Bogan, A. A.Bonanno, J. B. Boone, C. Brannetti, B. Breiman, Leo Brinen, L. S. Broger, C. Bucher, P. Burley, S. K. Cagney, G.Canaves, J. M. Capel, M.Castagnoli, L. Cerutti, L. Cesareni, G. Chance, M. R. Chiba, T.Christendat, D. Chung, S. Cohen, F. E. Conover, D. D'Arcy, A. Dale, G. E. Das, R. Dash, MDash, M and Liu, H Deacon, A. M. Donaldson, I.Douglas, S. M. Drees, B. Duan, X. J. Dyson, H. J. Echols, N.Edwards, A. M. Eisenberg, D.Elsliger, M. A.Engelman, D. M.Evangelista, M.Evdokimova, E. Falquet, L. Federhen, S. Fernandez, E. Ferracuti, S. Fields, S. Frishman, D.Gaasterland, T.Garcia-Bustos, J. Gasteiger, E. Gattiker, A. Geier, B. Gerstein, M.Gierasch, L. M. Giot, L. Godwin, B. Godzik, A. Goh, C. S. Goh, C.-S. Goldman, A. Gruber, C. Guda, C. Guldener, U. Haase, D. Hall, M. N. Hani, J. Hattori, M. Heinz, D. W. Heitman, J. Heumann, K. Higney, P.Hodgson, K. O. Hogue, C. W. Hol, W. G. Hulo, N. Ito, T.Jaroszewski, L.Joachimiak, M. Johnston, M. Judson, R. S.Kalbfleisch, T. Kalderon, D. Kaps, A.Khachatryan, A. Kim, C. Y. Kim, S. M. Klock, H. E. Kluger, Y. Knight, J. R. Koonin, E. V. Kreusch, A. Kuhn, P. Lan, N. Langen, H. Lemcke, K. Lesley, S. A. Li, Y. Lichtarge, O. Liebl, S. Lin, D. Liong, E. C. Lipman, D. J. Liu, H Lockshon, D.Luscombe, N.M. Ma, L. C. Mannhaupt, G.Mansfield, T. A.Marcotte, E. M. Mathews, I.Matthews, B. W. Mayer, K. McMullan, D.McPhillips, T. M. Mewes, H. W. Michelson, S. Milburn, D. Miller, M. A. Miller, M. D. Mirny, L. Mokrejs, M.Montelione, G. T.Morgenstern, B.Munsterkotter, M. Narayan, V. Nardelli, G. Nelson, B. Northey, J.Ouellette, B. F. Ozawa, R. Pagni, M. Paoluzi, S. Park, M. S. Pavlova, M. Pawson, T.Pearson, W. R.Pedelacq, J. D. Pfeiffer, F. Piltch, E. Pochart, P. Quinlan, J.R. Quondam, M.Qureshi-Emili, A.Rapoport, T. A. Rho, B. S. Rice, D. W.Richardson, W. D. Robb, A.Roberts, B. L.Rothberg, J. M. Rudd, S. Sakaki, Y. Sali, A. Salwinski, L. Savchenko, A. Scheibe, D. Schuller, C.Schultz, P. G. Selby, T. L. Semesi, A.Service, R. F.Shakhnovich, E. Shin, T.Sigrist, C. J. Skarina, T.Skinner, M. M. Smith, A. E. Sowa, M. E. Spraggon, G.Srinivasan, M.Standish, B. M. Steitz, T. A.Stevens, R. C. Stocker, S. Stuber, D.Studier, F. W.Swaminathan, S.Tatusov, R. L. Taylor, S. S.Terwilliger, T. C.Thompson, M. J. Tong, A. H. Uetz, P.Vijayadamodar, G. Vincent, J.von Heijne, G. Waldo, G. S. Walther, D. Weil, B. Wilson, I. A. Wolting, C. Wood, T. C. Wooley, J.Wootton, J. C. Wright, P. E.Wunderlich, Z. Xenarios, I. Xiao, R. Yang, M. Yee, A. Yokoyama, S. Yoshida, M. Yu, H. Zheng, D. Zhu, X. Zucconi, A.  $ Annu Rev Biophys Biophys Chem BiochemistryBiochim Biophys ActaBioinformaticsBrief BioinformCellCurr Opin Cell BiolCurr Opin Chem BiolCurr Opin Struct Biol Curr Top Microbiol ImmunolGenome ResearchInt. J. Man-Machine Stud.Intelligent Data Anal. J Mol BiolMachine LearningMethods EnzymolNat Biotechnol Nat GenetNat Struct Biol NatureNucleic Acids ResProc Natl Acad Sci U S A Protein EngProtein Expr Purif Proteins Proteomics Science         x*Amino Acid Sequence*Base Sequence*Binding, Competitive*Computational Biology*Conserved Sequence *Databases*Databases, Factual*Databases, Genetic*Databases, Protein*Evolution, Molecular*Genes, Archaeal*Genes, Bacterial*Genes, Fungal*Genes, Structural *Genes, Viral *Genome*Genome, Bacterial*Genome, Fungal*Genome, Human*Genomics/methods/trends *Ligands*Lipid Bilayers83*Luminescent Proteins/chemistry/genetics/metabolism*Macromolecular Systems*Membrane Proteins*Multigene Family *Phylogeny*Protein Binding*Protein Conformation*Protein Engineering*Protein Folding,'*Protein Processing, Post-Translational *Proteome *Software$ *Structure-Activity RelationshipAcademies and InstitutesAlanine/chemistry AlgorithmsAmino Acid MotifsAmino Acid Sequence Animal(#Antigens, Polyomavirus Transforming$ Antigens, Viral, Tumor/*geneticsArabidopsis/genetics Archaeal Proteins/chemistryD>Archaeal Proteins/chemistry/classification/genetics/physiology4/Archaeal Proteins/chemistry/genetics/metabolismAutomatic Data Processing Bacteria/chemistry/genetics Bacterial Proteins/*chemistryD?Bacterial Proteins/*chemistry/genetics/isolation & purificationD?Bacterial Proteins/chemistry/classification/genetics/physiology Bacterial Proteins/metabolism Base Sequence beta-Galactosidase/genetics Binding SitesBinding Sites/*physiologyBiological Transport Biological Transport, Active$ Caenorhabditis elegans/chemistry Catalytic Domain/physiology Cell Cycle Cell LineCell Nucleus/*metabolismCell Nucleus/metabolismCell PhysiologyCercopithecus aethiops$Chemokines/chemistry/metabolismChloroplasts/metabolismChromosome DeletionCloning, MolecularColiphages/chemistryComparative Study$Computational Biology/*methods Computational Biology/*trends(%Computational Biology/methods/*trends$Computer Communication NetworksComputer Graphics ComputersConsensus SequenceConserved SequenceCrystallizationCrystallography, X-Ray$Crystallography, X-Ray/*methodsCytoplasm/metabolismDatabases, FactualDatabases, GeneticDatabases, ProteinDecision Trees Directed Molecular EvolutionDNA Restriction Enzymes$DNA-Binding Proteins/*chemistry$DNA-Binding Proteins/physiologyDNA/*chemistryDNA/chemistry/metabolismDNA/genetics/metabolismElectrophysiology(%Endoplasmic Reticulum/*ultrastructureHEEscherichia coli Proteins/chemistry/genetics/isolation & purification(%Escherichia coli/genetics/*metabolism Escherichia coli/metabolismEukaryotic Cells Eukaryotic Cells/*metabolismEvolution, MolecularExpressed Sequence Tags,&Ferritin/chemistry/genetics/metabolism Fluorescence$Fluorescent Antibody TechniqueFolic Acid Antagonists ForecastingFourier Analysis Fungal Proteins/*metabolism@ 95% of the total recombinant protein accumulated in inclusion bodies. Furthermore, as a result of an internal start of translation, a truncated derivative of the enzyme that copurified with the full-length enzyme was produced. We were able to increase the expression level 20-fold by changing 18 N-terminal codons and to eliminate the internal start of translation. In addition, through molecular modelling and subsequent site-directed mutagenesis to replace two amino acids, we constructed a biochemically similar but soluble derivative of the type S1 DHFR that, after production in E.coli, resulted in a 264-fold increase in DHFR activity. The highly overproduced enzyme was purified to homogeneity, characterized biochemically and crystallized.'4.F. Hoffmann-La Roche Ltd., Basel, Switzerland.>7Dale, G. E. Broger, C. Langen, H. D'Arcy, A. Stuber, D.u 0269-2139 Journal Articlep Protein EngnBacterial Proteins/*chemistry Base Sequence Crystallization Escherichia coli/metabolism Folic Acid Antagonists Models, Molecular Molecular Sequence Data Mutagenesis, Site-Directed Protein Conformation *Protein Engineering Recombinant Fusion Proteins/*chemistry Solubility Staphylococcus aureus/*enzymology Tetrahydrofolate Dehydrogenase/*chemistry Trimethoprim/pharmacology Trimethoprim Resistanceijdhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7971955 *Sequence11437590222  2001 Julf^XHigh-throughput proteomics: protein expression and purification in the postgenomic world 159-64D=Proteomics has become a major focus as researchers attempt to understand the vast amount of genomic information. Protein complexity makes identifying and understanding gene function inherently difficult. The challenge of studying proteins in a global way is driving the development of new technologies for systematic and comprehensive analysis of protein structure and function. Protein expression and purification are key processes in these studies, but have typically only been applied on a case-by-case basis to proteins of interest. Researchers are addressing the challenge of parallel expression and purification of large numbers of gene products through the principles of high-throughput screening technologies commonly used in pharmaceutical development. Some of the issues relevant to these approaches are discussed here.o'~xGenomics Institute, Novartis Research Foundation, 3115 Merryfield Row, San Diego, California, 92121, USA. lesley@gnf.org Lesley, S. A.811046-5928 Journal Article Review Review, TutorialProtein Expr Purif*Genome, Human Genomics/instrumentation/*methods/*trends Human Protein Engineering/instrumentation/*methods/*trends Proteome/*biosynthesis/genetics/*isolation & purification Recombinant Proteins/*biosynthesis/genetics/*isolation & purificationlehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11437590 121936469918 2002 Sep 3.yStructural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline11664-9h<6Structural genomics is emerging as a principal approach to define protein structure-function relationships. To apply this approach on a genomic scale, novel methods and technologies must be developed to determine large numbers of structures. We describe the design and implementation of a high-throughput structural genomics pipeline and its application to the proteome of the thermophilic bacterium Thermotoga maritima. By using this pipeline, we successfully cloned and attempted expression of 1,376 of the predicted 1,877 genes (73%) and have identified crystallization conditions for 432 proteins, comprising 23% of the T. maritima proteome. Representative structures from TM0423 glycerol dehydrogenase and TM0449 thymidylate synthase-complementing protein are presented as examples of final outputs from the pipeline.'Joint Center for Structural Genomics, Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA. lesley@gnf.orgtmLesley, S. A. Kuhn, P. Godzik, A. Deacon, A. M. Mathews, I. Kreusch, A. Spraggon, G. Klock, H. E. McMullan, D. Shin, T. Vincent, J. Robb, A. Brinen, L. S. Miller, M. D. McPhillips, T. M. Miller, M. A. Scheibe, D. Canaves, J. M. Guda, C. Jaroszewski, L. Selby, T. L. Elsliger, M. A. Wooley, J. Taylor, S. S. Hodgson, K. O. Wilson, I. A. Schultz, P. G. Stevens, R. C. 0027-8424 Journal ArticleProc Natl Acad Sci U S ACloning, Molecular *Genome, Bacterial Models, Molecular Open Reading Frames Protein Conformation *Proteome Support, U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S. Thermotoga maritima/*genetics/metabolismlehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12193646  v LigandsMacromolecular SystemsMembrane Fusion$!Membrane Glycoproteins/physiology4/Membrane Proteins/chemistry/genetics/physiology Methanobacterium/chemistry$ Methanococcus/chemistry/geneticsMicrobodies/metabolismMitochondria/metabolism$Mitochondrial Proteins/geneticsModels, MolecularModels, StatisticalMolecular BiologyMolecular Sequence DataMultigene Family($Muramidase/chemistry/*ultrastructure Mutagenesis, Site-Directed MutationMutation/genetics Neurospora crassa/genetics,(Nuclear Magnetic Resonance, Biomolecular41Nuclear Magnetic Resonance, Biomolecular/*methods4.Nuclear Proteins/*analysis/genetics/metabolism$!Nucleic Acids/genetics/metabolismOpen Reading FramesPeptide Library Peptides/chemistry/metabolism0,Phosphoglycerate Kinase/chemistry/metabolism Phylogeny PlasmidsPoint MutationPrecipitin TestsPrions/chemistry ProbabilityProcollagen/chemistryProtein Binding Protein Binding/*physiologyProtein Conformation84Protein Engineering/instrumentation/*methods/*trendsProtein Folding Protein Interaction Mapping("Protein Sorting Signals/*chemistry0,Protein Sorting Signals/*genetics/physiology0,Protein Sorting Signals/chemistry/metabolism Protein Structure, TertiaryProteins/*chemistry$Proteins/*chemistry/*metabolism0,Proteins/*chemistry/classification/*genetics<7Proteins/*chemistry/classification/genetics/*metabolism Proteins/*chemistry/genetics,'Proteins/*chemistry/genetics/metabolismProteins/*metabolism Proteins/chemistry/*genetics$Proteins/chemistry/*metabolism,)Proteins/chemistry/*metabolism/physiology<6Proteins/chemistry/classification/*genetics/physiology,'Proteins/chemistry/genetics/*metabolism Proteins/chemistry/metabolism Proteins/genetics/metabolismProteome/*analysis<9Proteome/*biosynthesis/genetics/*isolation & purification Proteome/*chemistry/geneticsProteomics/*methodsPyruvate Kinase/genetics,)Receptors, Chemokine/chemistry/metabolism,&Recombinant Fusion Proteins/*chemistry40Recombinant Fusion Proteins/chemistry/metabolismHERecombinant Proteins/*biosynthesis/genetics/*isolation & purificationRegression Analysis Reproducibility of ResultsResearch Design Ribonucleoproteins/physiologyRibosomes/metabolismRNA/genetics/metabolism RoboticsDASaccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism("Saccharomyces cerevisiae/*genetics($Saccharomyces cerevisiae/*metabolism("Saccharomyces cerevisiae/chemistry0+Saccharomyces cerevisiae/chemistry/genetics$!Saccharomyces cerevisiae/genetics0-Saccharomyces cerevisiae/genetics/*metabolismSequence Alignment Sequence Alignment/methods Sequence Homology, Amino Acid Signal Recognition ParticleSignal TransductionSimian virus 40/*genetics Software SolubilitySpecies Specificitysrc Homology Domains$!Staphylococcus aureus/*enzymology Statistics$Structure-Activity RelationshipSubstrate SpecificitySupport, Non-U.S. Gov't$Support, U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S.T-Phages/*enzymology Temperature,)Tetrahydrofolate Dehydrogenase/*chemistryThermodynamicsThermotoga maritima,(Thermotoga maritima/*genetics/metabolism Trans-Activation (Genetics)Transcription, Genetic TransfectionTranslation, GeneticTrimethoprim ResistanceTrimethoprim/pharmacology Two-Hybrid System TechniquesUser-Computer InterfaceViral Proteins/*chemistryViral Proteins/*genetics$!Wiskott-Aldrich Syndrome/geneticsYeasts/geneticsZinc Fingers/physiology"@ 1570293t899 1992 May 1mFolding and function of a T4 lysozyme containing 10 consecutive alanines illustrate the redundancy of information in an amino acid sequence 3751-5Single and multiple Xaa----Ala substitutions were constructed in the alpha-helix comprising residues 39-50 in bacteriophage T4 lysozyme. The variant with alanines at 10 consecutive positions (A40-49) folds normally and has activity essentially the same as wild type, although it is less stable. The crystal structure of this polyalanine mutant displays no significant change in the main-chain atoms of the helix when compared with the wild-type structure. The individual substitutions of the solvent-exposed residues Asn-40, Ser-44, and Glu-45 with alanine tend to increase the thermostability of the protein, whereas replacements of the buried or partially buried residues Lys-43 and Leu-46 are destabilizing. The melting temperature of the lysozyme in which Lys-43 and Leu-46 are retained and positions 40, 44, 45, 47, and 48 are substituted with alanine (i.e., A40-42/44-45/47-49) is increased by 3.1 degrees C relative to wild type at pH 3.0, but reduced by 1.6 degrees C at pH 6.7. In the case of the charged amino acids Glu-45 and Lys-48, the changes in melting temperature indicate that the putative salt bridge between these two residues contributes essentially nothing to the stability of the protein. The results clearly demonstrate that there is considerable redundancy in the sequence information in the polypeptide chain; not every amino acid is essential for folding. Also, further evidence is provided that the replacement of fully solvent-exposed residues within alpha-helices with alanines may be a general way to increase protein stability. The general approach may permit a simplification of the protein folding problem by retaining only amino acids proven to be essential for folding and replacing the remainder with alanine.w'jdInstitute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene 97403.0)Heinz, D. W. Baase, W. A. Matthews, B. W.c 0027-8424 Journal ArticleeProc Natl Acad Sci U S AAlanine/chemistry Amino Acid Sequence Models, Molecular Molecular Sequence Data Muramidase/chemistry/*ultrastructure Mutagenesis, Site-Directed Protein Conformation Structure-Activity Relationship T-Phages/*enzymologyAjdhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1570293111040017 Suppl5 2000 Nov2+Structural genomics for science and society. 964-6F|uThe field of robotics is affecting structural biology, enabling the era of structural genomics. The potential impact on protein fold prediction, biology, protein engineering and medicine is immense. Unraveling mysteries in the protein structure universe will require a dedicated effort for decades to come with computational toxicology as possibly a century long challenge.o'University of Washington, Biomolecular Structural Center and the Howard Hughes Medical Institute, Seattle 98195-7742, USA. hol@gouda.bmsc.washington.edu Hol, W. G. 1072-8368 Journal Article Nat Struct BiolRCell Physiology Computational Biology/methods/*trends Computers Crystallography, X-Ray *Genomics/methods/trends Nuclear Magnetic Resonance, Biomolecular Protein Conformation Proteins/*chemistry/genetics/metabolism Robotics Structure-Activity Relationshiplehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11104001i11283351988o 2001 Apr 10RLA comprehensive two-hybrid analysis to explore the yeast protein interactome4569-74v>7Protein-protein interactions play crucial roles in the execution of various biological functions. Accordingly, their comprehensive description would contribute considerably to the functional interpretation of fully sequenced genomes, which are flooded with novel genes of unpredictable functions. We previously developed a system to examine two-hybrid interactions in all possible combinations between the approximately 6,000 proteins of the budding yeast Saccharomyces cerevisiae. Here we have completed the comprehensive analysis using this system to identify 4,549 two-hybrid interactions among 3,278 proteins. Unexpectedly, these data do not largely overlap with those obtained by the other project [Uetz, P., et al. (2000) Nature (London) 403, 623-627] and hence have substantially expanded our knowledge on the protein interaction space or interactome of the yeast. Cumulative connection of these binary interactions generates a single huge network linking the vast majority of the proteins. Bioinformatics-aided selection of biologically relevant interactions highlights various intriguing subnetworks. They include, for instance, the one that had successfully foreseen the involvement of a novel protein in spindle pole body function as well as the one that may uncover a hitherto unidentified multiprotein complex potentially participating in the process of vesicular transport. Our data would thus significantly expand and improve the protein interaction map for the exploration of genome functions that eventually leads to thorough understanding of the cell as a molecular system.p'Division of Genome Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-0934, Japan. titolab@kenroku.kanazawa-u.ac.jpD>Ito, T. Chiba, T. Ozawa, R. Yoshida, M. Hattori, M. Sakaki, Y. 0027-8424 Journal ArticleyProc Natl Acad Sci U S AFungal Proteins/*metabolism Genome, Fungal Protein Binding Saccharomyces cerevisiae/genetics/*metabolism Support, Non-U.S. Gov't Two-Hybrid System Techniqueslehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11283351609600739 3 Pt 2 1984 DecB/=0.878, and only nine had correlation coefficients r80 organisms; the vast majority from yeast, Helicobacter pylori and human. Tools have been developed that allow users to analyze, visualize and integrate their own experimental data with the information about protein-protein interactions available in the DIP database.'UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, PO Box 951570, UCLA, Los Angeles, CA 90095-1570, USA.PJXenarios, I. Salwinski, L. Duan, X. J. Higney, P. Kim, S. M. Eisenberg, D. 1362-4962 Journal ArticleBNucleic Acids ResiVPAnimal Bacterial Proteins/metabolism Computer Graphics *Databases, Protein Forecasting Fungal Proteins/metabolism Helicobacter pylori/metabolism Human Information Storage and Retrieval Internet *Macromolecular Systems Protein Structure, Tertiary Proteins/chemistry/*metabolism Support, U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S.lehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11752321 12547425711u 2003 FebrHAProtein expression systems for structural genomics and proteomicsi 39-43cOne of the key steps of structural genomics and proteomics is high-throughput expression of many target proteins. Gene cloning, especially by ligation-independent cloning techniques, and recombinant protein expression using microbial hosts such as Escherichia coli and the yeast Pichia pastoris are well optimized and further robotized. Cell-free protein synthesis systems have been developed for large-scale production of protein samples for NMR (stable-isotope labeling) and X-ray crystallography (selenomethionine substitution). Protein folding is still a major bottleneck in protein expression. Cell-based and cell-free methods for screening of suitable samples for structure determination have been developed for achieving a high success rate.'\URIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, 230-0045, Yokohama, Japan' Yokoyama, S. 1367-5931 Journal ArticlegCurr Opin Chem BiolPlehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12547425nF?Yu, H. Luscombe, N.M. Zhu, X. Chung, S. Goh, C.-S. Gerstein, M.p SubmitteduAnnotation transfer for genomics: assessing the transferability of protein-protein and protein-DNA interactions between organismsGenome ResearchO %l(*3,|Dash, M Liu, H 1997*$Feature Selection for ClassificationIntelligent Data Anal.1131-156-11839490121r 2002 Feb,@9Coupling of folding and binding for unstructured proteinsd 54-60iThere are now numerous examples of proteins that are unstructured or only partially structured under physiological conditions and yet are nevertheless functional. Such proteins are especially prevalent in eukaryotes. In many cases, intrinsically disordered proteins adopt folded structures upon binding to their biological targets. Many new examples of coupled folding and binding events have been reported recently, providing new insights into mechanisms of molecular recognition.i'Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. dyson@scripps.edu Dyson, H. J. Wright, P. E.810959-440x Journal Article Review Review, TutorialbCurr Opin Struct BiolsAnimal DNA-Binding Proteins/physiology Eukaryotic Cells Human Protein Binding/*physiology *Protein Folding Signal Transduction Support, U.S. Gov't, P.H.S. Zinc Fingers/physiologylehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11839490l3521657o15 1986\VIdentifying nonpolar transbilayer helices in amino acid sequences of membrane proteins 321-530)Engelman, D. M. Steitz, T. A. Goldman, A.e& 0883-9182 Journal Article Review$Annu Rev Biophys Biophys Chem-|vAmino Acid Sequence *Lipid Bilayers *Membrane Proteins Protein Conformation Support, U.S. Gov't, P.H.S. Thermodynamicsjdhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35216572004116 10711 1991 Mar 7"Nuclear protein localization 83-101'D=Department of Biochemistry, University of Basel, Switzerland.f0)Garcia-Bustos, J. Heitman, J. Hall, M. N.810006-3002 Journal Article Review Review, AcademicsBiochim Biophys ActaAmino Acid Sequence Animal Biological Transport, Active Cell Nucleus/metabolism Cytoplasm/metabolism Human Molecular Sequence Data Nuclear Proteins/*analysis/genetics/metabolism Protein Sorting Signals/chemistry/metabolism Support, Non-U.S. Gov'tjdhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2004116124223602n10 2002 OctdjcFindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification}1435-44{,&FindPept (http://www.expasy.org/tools/findpept.html) is a software tool designed to identify the origin of peptide masses obtained by peptide mass fingerprinting which are not matched by existing protein identification tools. It identifies masses resulting from unspecific proteolytic cleavage, missed cleavage, protease autolysis or keratin contaminants. It also takes into account post-translational modifications derived from the annotation of the SWISS-PROT database or supplied by the user, and chemical modifications of peptides. Based on a number of experimental examples, we show that the commonly held rules for the specificity of tryptic cleavage are an oversimplification, mainly because of effects of neighboring residues, experimental conditions, and contaminants present in the enzyme sample.'>7Swiss Institute of Bioinformatics, Geneva, Switzerland.y>7Gattiker, A. Bienvenut, W. V. Bairoch, A. Gasteiger, E.o 1615-9853 Journal Articlev Proteomicslehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12422360-2653440S283l 1989 Feb 7tSignal sequences 923-30'f_Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas 75235-9041.nGierasch, L. M. 810006-2960 Journal Article Review Review, Academict BiochemistryAmino Acid Sequence Molecular Sequence Data Mutation *Protein Processing, Post-Translational Protein Sorting Signals/*genetics/physiology Support, Non-U.S. Gov't Support, U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S.bjdhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=265344010860738 2992 2000 Jun 2>8Co-evolution of proteins with their interaction partners 283-93The divergent evolution of proteins in cellular signaling pathways requires ligands and their receptors to co-evolve, creating new pathways when a new receptor is activated by a new ligand. However, information about the evolution of binding specificity in ligand-receptor systems is difficult to glean from sequences alone. We have used phosphoglycerate kinase (PGK), an enzyme that forms its active site between its two domains, to develop a standard for measuring the co-evolution of interacting proteins. The N-terminal and C-terminal domains of PGK form the active site at their interface and are covalently linked. Therefore, they must have co-evolved to preserve enzyme function. By building two phylogenetic trees from multiple sequence alignments of each of the two domains of PGK, we have calculated a correlation coefficient for the two trees that quantifies the co-evolution of the two domains. The correlation coefficient for the trees of the two domains of PGK is 0. 79, which establishes an upper bound for the co-evolution of a protein domain with its binding partner. The analysis is extended to ligands and their receptors, using the chemokines as a model. We show that the correlation between the chemokine ligand and receptor trees' distances is 0.57. The chemokine family of protein ligands and their G-protein coupled receptors have co-evolved so that each subgroup of chemokine ligands has a matching subgroup of chemokine receptors. The matching subfamilies of ligands and their receptors create a framework within which the ligands of orphan chemokine receptors can be more easily determined. This approach can be applied to a variety of ligand and receptor systems.'b\Program in Medical Information Sciences, University of California, San Francisco 94143, USA.F?Goh, C. S. Bogan, A. A. Joachimiak, M. Walther, D. Cohen, F. E. 0022-2836 Journal Article J Mol BiolChemokines/chemistry/metabolism *Evolution, Molecular Human *Ligands Models, Molecular Phosphoglycerate Kinase/chemistry/metabolism Phylogeny Protein Binding Protein Structure, Tertiary Proteins/chemistry/*metabolism Receptors, Chemokine/chemistry/metabolism Reproducibility of Results Sequence Alignment Statistics Substrate Specificity Support, Non-U.S. Gov't Support, U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S.lehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10860738