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Figure 2.10: Overlap between manual and computer annotated datasets Although the Hinge Atlas and computer annotated set have a significant overlap, they are statistically different sets. Importantly, the hinge residues within these sets are different from each other, despite sharing 106 residues. 94
samples 1800 1600 1400 1200 1000 800 600 400 200 0 Glycine content by resampling 2.5% 7.5% 12.5% 17.5% 22.5% %GLY Figure 2.11: Resampling of glycine occurrence in hinge vs. non-hinge residues Histogram of blue trace) and ! ! 95 NON-hinge Hinge f ˜ " j (aGLY ) (sample frequency of glycine among NON-hinge residues, " f j (aGLY )(sample frequency of glycine among hinge residues, dashed red trace). The sample frequency of glycine residues among NON-hinge residues in bins containing 1/8th of all Hinge Atlas proteins was found to average 0.078. The sample frequency of glycine among hinge residues in bins containing 1/8th of all Hinge Atlas proteins was found to average 0.124. The standard deviation was considerably larger for the hinge set, since this is a small subset of the Hinge Atlas.
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Abstract Flexibility and domain dyn
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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
Page 43 and 44: Figure 1.3: Conformational change a
Page 45 and 46: particular, we found that hinges te
Page 47 and 48: and the holo. In this case it is po
Page 49 and 50: Our molecular motions database serv
Page 51 and 52: We first made a simple GOR(Garnier-
Page 53 and 54: The morph trajectory was sterically
Page 55 and 56: protein in the Jmol window to his/h
Page 57 and 58: of the hinge was otherwise unclear,
Page 59 and 60: Catalytic Sites Atlas (nonredundant
Page 61 and 62: ! ! ! ! ! h c = number of times res
Page 63 and 64: ! ! ! ! µ h " d c D # H . It is eq
Page 65 and 66: As mentioned earlier, the fact that
Page 67 and 68: STRIDE[50] recognizes secondary str
Page 69 and 70: ! ! alignment at this position[24,
Page 71 and 72: To test this idea, we decided to ca
Page 73 and 74: GOR method is useful for predicting
Page 75 and 76: ! HI active"site (i) as 0.4 for res
Page 77 and 78: lowered, and the area under the cur
Page 79 and 80: would be preferable to the other, o
Page 81 and 82: Discussion Correlations were found
Page 83 and 84: Sequence in the immediate neighborh
Page 85 and 86: 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: completely random predictor, with a
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 and 138: Figure 3.2: Results for individual
Page 139 and 140: a. 139
Page 141 and 142: Figure 3.3: Folylpolyglutamate Synt
Page 143 and 144: . c. 143
Page 145 and 146:
a. 145
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Figure 3.5: Lir-1 (closed) Morph ID
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. c. 149
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a. 151
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Figure 3.7: Ribose binding protein
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. c. 155
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Tables GNM 157 Single-cut predictor
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Chapter 4: HingeMaster: normal mode
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The problem of hinge prediction is
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Translation Libration Screw Motion
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! [ K] = [ U] " [ ] 2 [ U] T Where
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generated one ROC curve for each mo
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! ! 1 (l " k) A(k,l) = 2 % ' $ C(i,
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however, since we found that the Co
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A key part of this analysis involve
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describe its net vibrational displa
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! Because it cuts the backbone at t
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! ! x HingeMaster = x" # y . [6] 2
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different values of ! " * and gener
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manually select domains and color p
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E. coli resides in the periplasmic
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The results for this protein are sh
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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
Page 197 and 198:
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
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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
Page 237 and 238:
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
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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
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Figures Figure 5.1: Assignment of r
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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
Page 281 and 282:
9. M Gerstein RJ, T Johnson, J Tsai
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28. Wriggers W, Schulten K: Protein
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45. Dumontier M, Yao R, Feldman HJ,
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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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