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276 J.D. Watson and J.M. ThorntonTable 11.1 Summary of functional predictions and their origins for large-scale analyses. The table shows a summary of the examples discussed in reviewswhich attempt to address the effectiveness of structure-based function prediction using structural genomics targets. For each of the proteins in the articlesdescribed in Section 11.3, a simple summary of the analysis performed is given along with crosses in the appropriate columns indicating which of the structure-basedapproaches was most informativeStudy Protein DescriptionKim et al. (2003) MJ0882 Putative methyltransferase through fold similarity– later experimentally verified.Watson et al.(2007)Adams et al.(2007)MJ0577 Bound ATP suggested an ATP hydrolysis function.TM841 Bound palmitate molecule demonstrated fattyacid binding.MJ0226 Novel fold but weak similarity to nucleotidebinding proteins and HAM1 protein.MJ0285 Multimeric assembly forms a hollow spherewith “windows”. Prompted question as tothe nature of action.MPN625 Two conserved cysteine residues found to lie inthe cleft of a putative active site. This siteresembles those in the 2-cysteine peroxiredoxinfamily.BioH Novel carboxylesterase. Enzyme active-sitetemplate search identifies the catalytic triadIsdG Fold comparison and reverse templates methodsindicate a monooxygenase function.ChuS Three of the four conserved histidine residuesfound adjacent to or pointing into one oftwo large clefts. Shows unusual haem coordination.Fold or assembly(see Chapter 6)XXXKey analyses providing functional cluesSurface/cleft (seeChapter 7)X XXXTemplate (seeChapter 8) Bound ligandXXX
11 Function Predictions of Structural Genomics Results 277YgiN Fold similarity to ActVA-Orf6, a monooxygenasefamily member. Identification of twoprior reports in the literature lent additionalsupportive evidence.YjjX Fold similar to nucleotide binding proteins.Closer inspection of the active sitesrevealed significant similarities that suggesteda novel ITPase/XTPase function.YhhW Fold similarity to family with broad functionalrange. Local similarities in molecular surfacesidentified a deep charged pocket nextto a metal binding site. Shows significantsimilarity to quercetin 2,3-dioxygenase.z3393 Global structural and local molecular surfacecomparisons suggest gentisate 1,2-dioxygenaseactivity.XX XX XX X
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Daniel John RigdenEditorFrom Protei
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ContentsSection I Generating and In
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Contentsxi4.2.1 Alpha-Helical Bundl
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Contentsxiii7.4.2 Predicting Bindin
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Contentsxv12.3 Accuracy and Added V
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4 J. Lee et al.about 5.3 million pr
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6 J. Lee et al.Table 1.1 A list of
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8 J. Lee et al.2000; Sorin and Pand
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10 J. Lee et al.Although most knowl
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12 J. Lee et al.Fig. 1.3 Two exampl
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14 J. Lee et al.rugged containing m
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16 J. Lee et al.1.3.4 Mathematical
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18 J. Lee et al.potentials, each re
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20 J. Lee et al.viewpoint of struct
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22 J. Lee et al.Hsieh MJ, Luo R (20
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24 J. Lee et al.Sippl MJ (1990) Cal
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Chapter 2Fold RecognitionLawrence A
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2 Fold Recognition 29It has long be
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2 Fold Recognition 31Fig. 2.2 Graph
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2 Fold Recognition 33distribute the
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2 Fold Recognition 35Table 2.1 (a)
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2 Fold Recognition 37dependent on t
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2 Fold Recognition 39based on the r
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2 Fold Recognition 41The idea of co
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2 Fold Recognition 43query sequence
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2 Fold Recognition 452.3.4 Consensu
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2 Fold Recognition 472.4 Alignment
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2 Fold Recognition 49statistical me
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2 Fold Recognition 51methods (e.g.
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2 Fold Recognition 53Berman HM, Wes
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2 Fold Recognition 55Tress ML, Jone
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58 A. Fiserwith more than 50% seque
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60 A. FiserIn contrast to ab initio
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62 A. FiserTable 3.1 (continued)SWI
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64 A. Fiserbetween fold recognition
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66 A. FiserFig. 3.1 Comparing accur
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68 A. Fiserinto conserved core regi
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70 A. Fiseralignments are built and
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72 A. Fiserfold, such as the hyperv
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74 A. Fiserfunctions delivers impro
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76 A. Fiserfrom efforts of genome s
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78 A. FiserA rigorous statistical e
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80 A. Fiser(Clore et al. 1993). Cha
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82 A. FiserImproved and new methods
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84 A. FiserClaessens M, Van Cutsem
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86 A. FiserHavel TF, Snow ME (1991)
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88 A. FiserPetrey D, Xiang Z, Tang
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90 A. Fiservan Vlijmen HW, Karplus
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92 T. Nugent and D.T. Jones4.2 Stru
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94 T. Nugent and D.T. JonesFig. 4.2
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96 T. Nugent and D.T. JonesTable 4.
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98 T. Nugent and D.T. Jones2000), d
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100 T. Nugent and D.T. JonesTable 4
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102 T. Nugent and D.T. JonesFig. 4.
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104 T. Nugent and D.T. JonesFig. 4.
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106 T. Nugent and D.T. Jonessubdivi
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108 T. Nugent and D.T. Jonescomplex
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110 T. Nugent and D.T. JonesMartell
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Chapter 5Bioinformatics Approaches
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5 Structure and Function of Intrins
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Chapter 6Function Diversity Within
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6 Function Diversity Within Folds a
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Chapter 7Predicting Protein Functio
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7 Predicting Protein Function from
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Table 7.1 Online resources and tool
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Chapter 83D MotifsElaine C. Meng, B
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8 3D Motifs 189clustering similar s
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8 3D Motifs 191To improve the signa
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8 3D Motifs 193structures together.
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8 3D Motifs 195Table 8.1 (continued
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8 3D Motifs 1978.3.1 User-Defined M
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8 3D Motifs 199Fig. 8.3 The FFF mot
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8 3D Motifs 2018.3.2 Motif Discover
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8 3D Motifs 203In addition to SITE
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8 3D Motifs 205folds; they shared a
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8 3D Motifs 207from a training set
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8 3D Motifs 209Table 8.3 Web server
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8 3D Motifs 211its greater overall
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8 3D Motifs 213Ideally, a 3D motif
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8 3D Motifs 215Ivanisenko VA, Pintu
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Chapter 9Protein Dynamics: From Str
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9 Protein Dynamics: From Structure
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Page 276 and 277: 270 R.A. LaskowskiReferencesAltschu
Page 278 and 279: 272 R.A. LaskowskiXenarios I, Salwi
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Page 298 and 299: Chapter 12Prediction of Protein Fun
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Page 324 and 325: 320 IndexConsensus templates, 205Co
Page 326 and 327: 322 IndexLigand-binding templates,
Page 328: 324 IndexStructure-function linkage
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