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94 T. Nugent and D.T. JonesFig. 4.2 A canonical beta-barrel protein, the monomeric porin OmpG from Escherichia coli,viewed from the side. Porins are transmembrane proteins with hollow centres through which smallmolecules can diffuse. PDB code 2f1c4.3 Membrane Proteins Are Difficult to CrystalliseTM proteins, which have both hydrophobic and hydrophilic regions on their surfaces,are much more difficult to isolate than water-soluble proteins, as the nativemembrane surrounding the protein must be disrupted and replaced with detergentmolecules without causing any denaturation. Despite considerable efforts, relativelyfew TM proteins have yielded crystals that diffract to high resolution. Whileit is thought that TM proteins comprise approximately 30% of a proteome, they aresignificantly under-represented in structural databases such as the Protein DataBank (Bernstein et al. 1977) where they comprise only about 1% of total depositedstructures (White 2004). Tables 4.1 and 4.2 summarise the alpha-helical and betabarrelcrystal structures currently available (Lomize et al. 2006b). However, withadvanced technologies such as synchrotron X-ray microscopy becoming available,it is now possible to determine X-ray structures from ever-smaller protein crystals.Combined with novel crystallisation methods such as the use of antibodies to solubiliseproteins, and lipidic phases as crystallisation media, the rate at which TMprotein structures are elucidated should increase over the coming years.4.4 DatabasesA number of databases now exist that serve as repositories for the sequences andstructures of TM proteins. OPM (Lomize et al. 2006b), PDB_TM (Tusnády et al.2005b), CGDB (Sansom et al. 2008), MPDB (Raman et al. 2006) and Stephen White’s
4 Membrane Protein Structure Prediction 95Table 4.1 Alpha-helical transmembrane protein superfamilies, taken from the OPM database(Lomize et al. 2006b)FunctionSuperfamilyLight absorption-driven transportersRhodopsin-like proteinsOxidoreduction-driven transportersPhotosynthetic reaction centers and photosystemsElectrochemical potential-driven transporters Light-harvesting complexesP-P-bond hydrolysis-driven transporters Transmembrane cytochrome b likePorters (uniporters, symporters, antiporters) Cytochrome c oxidasesChannels including ion channelsMulti-heme cytochromesEnzymesProton or Sodium translocating F/V/A-typeATPasesProteins with alpha-helical transmembrane P-type ATPase (P-ATPase)anchorsVitamine B12 transporter-like ABCtransportersSingle-helix ATPase regulatorsLipid flippase-like ABC transportersMolybdate uptake ABC transporterGeneral secretory pathway (Sec)Mitochondrial Carrier (MC)Major Facilitator Superfamily (MFS)Resistance-nodulation-cell divisionDicarboxylate/amino acid:Cation Symporter(DAACS)Monovalent cation/proton antiporter (CPA)Neurotransmitter sodium symporterAmmonia transporter (Amt)Drug/Metabolite Transporter (DMT)Voltage-gated channel likeLarge conductance mechanosensitive ionchannel (MscL)Small conductance mechanosensitive ionchannel (MscS)CorA Metal Ion Transporters (MIT)Ligand-gated ion channel (LIC) of neurotransmitterreceptorsChloride Channel (ClC)Outer membrane auxiliary proteinsEpithelial sodium channel (EnaC)Magnesium ion transporter-E (MgtE)Major Intrinsic Protein (MIP)Methane monooxygenaseRhomboid proteinsDisulfide bond oxidoreductase-B (DsbB)T cell receptor transmembrane dimerizationdomainSteryl-sulfate sulfohydrolase(continued)
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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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Page 70 and 71: 60 A. FiserIn contrast to ab initio
Page 72 and 73: 62 A. FiserTable 3.1 (continued)SWI
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Page 122 and 123: Chapter 5Bioinformatics Approaches
Page 124 and 125: 5 Structure and Function of Intrins
Page 150 and 151: 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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252 R.A. LaskowskiConsequently, man
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254 R.A. Laskowskiucla.edu, and Pro
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256 R.A. LaskowskiFig. 10.2 Gene On
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258 R.A. Laskowski10.2.5 Protein In
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260 R.A. LaskowskiFig. 10.4 Schemat
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262 R.A. Laskowskiaccessibility and
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264 R.A. LaskowskiFig. 10.6 A ligan
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266 R.A. LaskowskiGly97Gly99Tyr98Ty
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268 R.A. LaskowskiFig. 10.8 Example
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270 R.A. LaskowskiReferencesAltschu
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272 R.A. LaskowskiXenarios I, Salwi
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274 J.D. Watson and J.M. ThorntonTh
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276 J.D. Watson and J.M. ThorntonTa
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278 J.D. Watson and J.M. Thorntonva
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280 J.D. Watson and J.M. Thorntonfo
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282 J.D. Watson and J.M. Thorntonin
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284 J.D. Watson and J.M. Thorntonan
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286 J.D. Watson and J.M. ThorntonFi
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288 J.D. Watson and J.M. ThorntonPD
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290 J.D. Watson and J.M. ThorntonKi
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Chapter 12Prediction of Protein Fun
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12 Prediction of Protein Function f
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320 IndexConsensus templates, 205Co
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322 IndexLigand-binding templates,
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324 IndexStructure-function linkage
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