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Figure 1.3: Conformational change and functional grouping. Example plots of the distribution of maximum Cα displacement of the mobile component (2nd core) in structures annotated with Gene Ontology terms (‘DNA binding’, 17 morphs – top; ‘metabolism’,17 morphs – centre), compared with the reference morph dataset (200 canonical morphs - bottom). Red bars indicate morphs whose 2nd core max. Cα displacement falls below the median, while green bars indicate those above. 43
Page 1 and 2: Abstract Flexibility and domain dyn
Page 3 and 4: Flexibility and domain dynamics of
Page 5 and 6: Table of Contents Table of figures
Page 7 and 8: Can hinges be predicted by a simple
Page 9 and 10: FlexOracle (FO1, FO1M, FO) 176 Defi
Page 11 and 12: Conclusions 279 References 281 Tabl
Page 13 and 14: Table of tables Table 2.1: Amino ac
Page 15 and 16: Acknowledgements Committee: Mark Ge
Page 17 and 18: Introduction The problem of predict
Page 19 and 20: Ab initio methods attempt to model
Page 21 and 22: potential for simplification, motio
Page 23 and 24: Chapter 1: The molecular motions da
Page 25 and 26: MolMovDB is a resource for studying
Page 27 and 28: voids in proteins, helix-helix pack
Page 29 and 30: A full-feature version of FIRST5 wi
Page 31 and 32: gradual transition from the initial
Page 33 and 34: energy. Thus the first residue list
Page 35 and 36: activity, DNA-directed DNA polymera
Page 37 and 38: homology table to an entry in the C
Page 39 and 40: Highlight active sites from the CSA
Page 44 and 45: Chapter 2: Hinge Atlas: relating pr
Page 46 and 47: Background Motions play an essentia
Page 48 and 49: (Structural Classification of Prote
Page 50 and 51: esidues were differentially represe
Page 52 and 53: Methods Preparation of computer ann
Page 54 and 55: manual culling too stringent would
Page 56 and 57: that could be used in motion predic
Page 58 and 59: esidues, provided an accurate measu
Page 60 and 61: ! ! Method for analyzing relative f
Page 62 and 63: ! ! The argument of the log is the
Page 64 and 65: ! h c H < d c D , h( a) then we rej
Page 66 and 67: C = distance from the nearest activ
Page 68 and 69: Are hinge residues conserved in evo
Page 70 and 71: ! ! ! Our dataset was no longer the
Page 72 and 73: Are hinge residues more likely to o
Page 74 and 75: ! ! Hinge prediction by combining s
Page 76 and 77: the predictor by means of ROC (Rece
Page 78 and 79: We also sought to determine whether
Page 80 and 81: significant information can be extr
Page 82 and 83: hinge residues to be hypermutable.
Page 84 and 85: site residues were found to coincid
Page 86 and 87: .0026 Figure 2.2: Distance from act
Page 88 and 89: Figure 2.4: Physicochemical propert
Page 90 and 91: Figure 2.6: Conservation: enzymes d
Page 92 and 93:
last two bins (lowest 40% ASA) are
Page 94 and 95:
Figure 2.10: Overlap between manual
Page 96 and 97:
Tables Occurrence Occurrence p- Res
Page 98 and 99:
Secondary Hinge All Hinge structure
Page 100 and 101:
Conservation score bin Active site
Page 102 and 103:
Number of hinge points 1 76 2 75 3
Page 104 and 105:
Counts in PDB Counts in Hinge Atlas
Page 106 and 107:
Chapter 3: FlexOracle: predicting f
Page 108 and 109:
or subunits.[3, 25] They can be fur
Page 110 and 111:
Numerous valuable contributions hav
Page 112 and 113:
location graph should have minima a
Page 114 and 115:
Single-cut predictor (FoldX version
Page 116 and 117:
hinges is to make not one but two c
Page 118 and 119:
To identify and deal with the vario
Page 120 and 121:
and were not used in the Statistica
Page 122 and 123:
predictor results. Some of these di
Page 124 and 125:
where the hypergeometric function g
Page 126 and 127:
esidues (loose criterion). When a g
Page 128 and 129:
Under either scheme, only one chain
Page 130 and 131:
AMPA-bound structure. Domain 2 is a
Page 132 and 133:
emoving ligands from the structure
Page 134 and 135:
coordinate neighbors in a very stab
Page 136 and 137:
Figures Figure 3.1: Fragmenting the
Page 138 and 139:
scale at the top of the figure. Lab
Page 140 and 141:
. c. d. 140
Page 142 and 143:
a. 142
Page 144 and 145:
Figure 3.4: AMPA Receptor GluR2 (cl
Page 146 and 147:
. c. 146
Page 148 and 149:
a. 148
Page 150 and 151:
Figure 3.6: cAMP-dependent protein
Page 152 and 153:
. c. 152
Page 154 and 155:
a. 154
Page 156 and 157:
Figure 3.8: Calmodulin (open, calci
Page 158 and 159:
Test result Number of Success 24 Pa
Page 160 and 161:
structure-based hinge predictors (T
Page 162 and 163:
In this work we first introduce hNM
Page 164 and 165:
! We begin our development with the
Page 166 and 167:
The string will have a nodal point
Page 168 and 169:
! ! ! ! 2" 3kBT #Ri $ #R j = (%&1 N
Page 170 and 171:
! hNMc goes through the same proced
Page 172 and 173:
The hinge locations themselves were
Page 174 and 175:
However, this restriction was ignor
Page 176 and 177:
Hinge Atlas Gold. We have chosen to
Page 178 and 179:
! ! ! ! ! ! ! C = { StoneHinge,FO1,
Page 180 and 181:
! ! while the set of residues in th
Page 182 and 183:
the associated PDB-deposited struct
Page 184 and 185:
Select up to three hinge points usi
Page 186 and 187:
169±1, and 190±1. The false posit
Page 188 and 189:
After completing the calculations,
Page 190 and 191:
With regard to the p-value, the rea
Page 192 and 193:
and hNMb both completely failed to
Page 194 and 195:
primary inter-domain flexibility. T
Page 196 and 197:
is reasonably successful in these c
Page 198 and 199:
The ROC curve is simply a plot of t
Page 200 and 201:
NME is a variation of this method t
Page 202 and 203:
f926644-25628), and the apo structu
Page 204 and 205:
have unusually high temperature fac
Page 206 and 207:
As in the case of Glutamine Binding
Page 208 and 209:
the structure, which are near the h
Page 210 and 211:
is controlled by the periplasmic pe
Page 212 and 213:
mucous secretions. It has broad spe
Page 214 and 215:
Figures Figure 4.1: ROC curve for h
Page 216 and 217:
216
Page 218 and 219:
a. b. c. 218
Page 220 and 221:
Figure 4.4: Glutamine Binding Prote
Page 222 and 223:
222
Page 224 and 225:
found for this hinge, as lactoferri
Page 226 and 227:
attracts biological interest, not o
Page 228 and 229:
member NMR ensemble. The structure
Page 230 and 231:
Figure 4.8: MurA (open form) Morph
Page 232 and 233:
x c * " c predicted Standard c ! 1
Page 234 and 235:
StoneHinge TLSMD hNMb hNMd FO Succe
Page 236 and 237:
Inorganic pyrophosphatase f044577-
Page 238 and 239:
of applying an euler rotation to on
Page 240 and 241:
proteins shows that the lowest orde
Page 242 and 243:
interpenetrating domains. This prob
Page 244 and 245:
otations, and the choice of interme
Page 246 and 247:
ligand) is then put into standard o
Page 248 and 249:
Angle calculation We calculate the
Page 250 and 251:
D3RMSD_aligned is not to be confuse
Page 252 and 253:
Display of results We used jmol to
Page 254 and 255:
The motion of GlnBP (see Chapter 4,
Page 256 and 257:
! distorted domains, and does not r
Page 258 and 259:
Upon binding ATP, M rotates approxi
Page 260 and 261:
statement as to the quality of this
Page 262 and 263:
Although we only explored the appli
Page 264 and 265:
ensemble generated by the Conformat
Page 266 and 267:
266
Page 268 and 269:
268
Page 270 and 271:
Figure 5.5: Results for Ribose Bind
Page 272 and 273:
Figure 5.7: Results for MurA Good q
Page 274 and 275:
Protein Conformation Explorer ID Ri
Page 276 and 277:
Supplementary figures Supplementary
Page 278 and 279:
Conclusions At the beginning of thi
Page 280 and 281:
References 1. Taverna DM, Goldstein
Page 282 and 283:
19. Thorpe MF, Lei M, Rader AJ, Jac
Page 284 and 285:
36. Swindells MB: A procedure for d
Page 286 and 287:
54. Lee B, Richards FM: The interpr
Page 288 and 289:
71. Means AR, Tash JS, Chafouleas J
Page 290 and 291:
89. Maiorov V, Abagyan R: Energy st
Page 292 and 293:
107. Sun Y-J, Rose J, Wang B-C, Hsi
Page 294:
Proteins and Protein Complexes: A S
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