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scale at the top of the figure. Labels give the structure ID for viewing on our server, the name of the protein, the conformation (open or closed), and the outcome (success, partial success, failure) according to the loose criterion described in the text. There is a clear tendency for FlexOracle predictions to align with the annotated hinge location and to correctly discriminate between single and double stranded hinges. The predictor was clearly less successful with triple stranded hinges (cAMP dependent protein kinase,Troponin C). 138
a. 139
Page 1 and 2:
Abstract Flexibility and domain dyn
Page 3 and 4:
Flexibility and domain dynamics of
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Table of Contents Table of figures
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Can hinges be predicted by a simple
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FlexOracle (FO1, FO1M, FO) 176 Defi
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Conclusions 279 References 281 Tabl
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Table of tables Table 2.1: Amino ac
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Acknowledgements Committee: Mark Ge
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Introduction The problem of predict
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Ab initio methods attempt to model
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potential for simplification, motio
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Chapter 1: The molecular motions da
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MolMovDB is a resource for studying
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voids in proteins, helix-helix pack
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A full-feature version of FIRST5 wi
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gradual transition from the initial
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energy. Thus the first residue list
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activity, DNA-directed DNA polymera
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homology table to an entry in the C
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Highlight active sites from the CSA
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Figure 1.3: Conformational change a
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particular, we found that hinges te
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and the holo. In this case it is po
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Our molecular motions database serv
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We first made a simple GOR(Garnier-
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The morph trajectory was sterically
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protein in the Jmol window to his/h
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of the hinge was otherwise unclear,
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Catalytic Sites Atlas (nonredundant
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! ! ! ! ! h c = number of times res
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! ! ! ! µ h " d c D # H . It is eq
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As mentioned earlier, the fact that
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STRIDE[50] recognizes secondary str
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! ! alignment at this position[24,
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To test this idea, we decided to ca
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GOR method is useful for predicting
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! HI active"site (i) as 0.4 for res
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lowered, and the area under the cur
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would be preferable to the other, o
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Discussion Correlations were found
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Sequence in the immediate neighborh
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Figures p-value 0.5 0.25 0 .01 PHE
Page 87 and 88: Figure 2.3: Secondary structure Res
Page 89 and 90: Figure 2.5: Conservation: full set
Page 91 and 92: Figure 2.7: Solvent accessible surf
Page 93 and 94: completely random predictor, with a
Page 95 and 96: samples 1800 1600 1400 1200 1000 80
Page 97 and 98: m = distance from nearest residues
Page 99 and 100: Hinge All Hinge Residues residues R
Page 101 and 102: in hinge residues HI p-value 1 277
Page 103 and 104: Total resid. in Hinge Atlas 54839 H
Page 105 and 106: Chi- Computer annotated set Hinge A
Page 107 and 108: BMC: Bioinformatics, we present the
Page 109 and 110: hinges. Kundu et al. use the lowest
Page 111 and 112: Domains can move relative to each o
Page 113 and 114: The quantity ! E(i) represents the
Page 115 and 116: Identification of local minima As w
Page 117 and 118: compute FoldX_energy (stability of
Page 119 and 120: energy element of each cluster was
Page 121 and 122: At least two sets of atomic coordin
Page 123 and 124: ! FN (false negatives): Number of r
Page 125 and 126: We observed qualitatively (figures
Page 127 and 128: pairs of structures used to generat
Page 129 and 130: coordinate set does not significant
Page 131 and 132: The LIR family is composed of eight
Page 133 and 134: CaM is a major calcium-binding prot
Page 135 and 136: The results of running FlexOracle a
Page 137: Figure 3.2: Results for individual
Page 141 and 142: Figure 3.3: Folylpolyglutamate Synt
Page 143 and 144: . c. 143
Page 145 and 146: a. 145
Page 147 and 148: Figure 3.5: Lir-1 (closed) Morph ID
Page 149 and 150: . c. 149
Page 151 and 152: a. 151
Page 153 and 154: Figure 3.7: Ribose binding protein
Page 155 and 156: . c. 155
Page 157 and 158: Tables GNM 157 Single-cut predictor
Page 159 and 160: Chapter 4: HingeMaster: normal mode
Page 161 and 162: The problem of hinge prediction is
Page 163 and 164: Translation Libration Screw Motion
Page 165 and 166: ! [ K] = [ U] " [ ] 2 [ U] T Where
Page 167 and 168: generated one ROC curve for each mo
Page 169 and 170: ! ! 1 (l " k) A(k,l) = 2 % ' $ C(i,
Page 171 and 172: however, since we found that the Co
Page 173 and 174: A key part of this analysis involve
Page 175 and 176: describe its net vibrational displa
Page 177 and 178: ! Because it cuts the backbone at t
Page 179 and 180: ! ! x HingeMaster = x" # y . [6] 2
Page 181 and 182: different values of ! " * and gener
Page 183 and 184: manually select domains and color p
Page 185 and 186: E. coli resides in the periplasmic
Page 187 and 188: The results for this protein are sh
Page 189 and 190:
esidues (62). As is customary we al
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FlexOracle (FO) The FlexOracle algo
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extra breakpoints based on visual i
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hinge, it is usually predicted by a
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Supplementary methods Statistical t
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! ! ! eigenvector. The resulting re
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TNC induces a conformational change
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possibility that unexpected results
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UDP-N-acetylglucosamine enolpyruvyl
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predicted both hinges, again with m
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Most predictors (including FO, Ston
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FO, hNMb, and hNMd were completely
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HingeMaster makes a strong predicti
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Figure 4.2: ROC curves for HingeMas
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Figure 4.3: HingeMaster results for
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d. e. 219
Page 221 and 222:
221
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Figure 4.5: Human lactoferrin (open
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Figure 4.6: Troponin C (TNC) Morph
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Figure 4.7: Calmodulin, calcium fre
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229
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Tables Predictor Basis Max. hinge p
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test true c positive positive sensi
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235 Closed Metal bound # of hinge p
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Chapter 5: The Conformation Explore
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ending, which involves a rigid regi
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lengths and angles)[89]. The equili
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for holo as well as apo forms, but
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queried using the “?” button. O
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coordinate. This phenomenon is know
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! At the end of each equilibration
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aborted. This marked the correspond
Page 253 and 254:
sRMSD has a major limitation that m
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with respect to the starting struct
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generated structure with respect to
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Ribose Binding Protein (RBP) As des
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strikingly similar both to the holo
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energy minimization. The minimizati
Page 265 and 266:
Figures Figure 5.1: Assignment of r
Page 267 and 268:
Figure 5.3: Results for glutamine b
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Figure 5.4: Results for biotin carb
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Figure 5.6: Results for Adenylate K
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close to the holo. The structure wi
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Table 5.1: MolMovDB ID, PDB ID, fre
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with sRMSD; however its main utilit
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morph server, and left confident th
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9. M Gerstein RJ, T Johnson, J Tsai
Page 283 and 284:
28. Wriggers W, Schulten K: Protein
Page 285 and 286:
45. Dumontier M, Yao R, Feldman HJ,
Page 287 and 288:
62. Thorpe MF, D.J. Jacobs, M.V. Ch
Page 289 and 290:
81. Winn MD, Isupov MN, Murshudov G
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98. Morris GM, Goodsell DS, Hallida
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115. Miyazawa T: Normal Vibrations
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