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FRODA. a) initial atomic positions; b) ghost templates; c) random atomic displacement; d) fitting of ghost templates to atoms; e) refitting of atoms to ghost templates; f), g) further iterations of d), e); h) until a new conformer is found[12]. 40
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: 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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