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107. Sun Y-J, Rose J, Wang B-C, Hsiao C-D: The structure of glutamine-binding protein complexed with glutamine at 1.94 A resolutoin: comparisons with other amino acid binding proteins. J Mol Biol 1998, 278:219-229. 108. Skarzynski T, Kim DH, Lees WJ, Walsh CT, Duncan K: Stereochemical course of enzymatic enolpyruvyl transfer and catalytic conformation of the active site revealed by the crystal structure of the fluorinated analogue of the reaction tetrahedral intermediate bound to the active site of the C115A mutant of MurA. Biochemistry 1998, 37(8):2572-2577. 109. Krebs WG, Gerstein M: The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Nucleic Acids Res 2000, 28(8):1665-1675. 110. van der Spoel D, de Groot BL, Hayward S, Berendsen HJ, Vogel HJ. Bending of the calmodulin central helix: a theoretical study. Protein Sci 1996;5(10):2044-2053 111. Taylor TJ, Vaisman II: Protein Structural Domain Assignment with a Delaunay Tessellation Derived Lattice. Proceedings of the 3 rd Intl. Symp. On Voronoi Diagrams in Science and Engineering 2006 112. Wetlaufer DB Nucleation, Rapid Folding, and Globular Intrachain Regions in Proteins. Proc. Nat. Acad. Sci. 1973:70(3):697-701 113. Hariharan PC, Pople JA: The Influence of Polarization Functions on Molecular Orbital Hydrogenation Energies. Theoret. Chim Acta 1973:28:213-222 114. Karplus S, Lifson S: Consistent Force Field Calculations on 2,5- Diketopiperazine and Its 3.6-Dimethyl Derivatives. Biopolymers heoret. Chim Acta 1971:10:1973-1982 292
115. Miyazawa T: Normal Vibrations of Monosubstituted Amides in the cis Configuration and Infrared Spectra of Diketopiperazine. J Mol. Spec. 1960:4:155- 167 116. W. Damm, J. Tirado-Rives, and W. L. Jorgensen J. Am. Chem. Soc. 1996:118,11225 117. Smith J, Cusack S, Tidor B, Karplus M: Inelastic neutron scattering analysis of low-frequency motions in proteins: Harmonic and damped harmonic models of bovine pancreatic tryspin inhibitor. J. Chem. Phys. 1990:93(5),2974 118. Svensson M, Humbel S, Froese RDJ, Matsubara T, Sieber S, Morokuma K: ONIOM: A Multilayered Integrated MO + MM Method for Geometry Optimizations and Single Point Energy Predictions. A Test for Diels-Alder Reactions and Pt(P(t-Bu)3)2 + H2 Oxidative. J. Phys. Chem. 1996:100,19357 119. Newcomer M, Lewis BA, Quiocho FA: The Radius of Gyration of L-Arabinose- binding Protein Decreases upon Binding of Ligand. J. Biol. Chem. 1981:254(24),13218 120. Abele R, Svergun D, Keinanen K, Koch M, Madden DR: A Molecular Envelope of the Ligand-Binding Domain of a Glutamate Receptor in the Presence and Absence of Agonist. Biochemistry 1999:38,10949 121. Schlauderer GJ, Schulz GE: The structure of bovine mitochondrial adenylate kinase: Comparison with isoenzymes in other compartments. Protein Science 1996:5,434 122. Guerois R, Nielsen JE, Serrano L: Predicting Changes in the Stability of 293
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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
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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
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Figure 2.3: Secondary structure Res
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Figure 2.5: Conservation: full set
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Figure 2.7: Solvent accessible surf
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completely random predictor, with a
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samples 1800 1600 1400 1200 1000 80
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m = distance from nearest residues
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Hinge All Hinge Residues residues R
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in hinge residues HI p-value 1 277
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Total resid. in Hinge Atlas 54839 H
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Chi- Computer annotated set Hinge A
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BMC: Bioinformatics, we present the
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hinges. Kundu et al. use the lowest
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Domains can move relative to each o
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The quantity ! E(i) represents the
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Identification of local minima As w
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compute FoldX_energy (stability of
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energy element of each cluster was
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At least two sets of atomic coordin
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! FN (false negatives): Number of r
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We observed qualitatively (figures
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pairs of structures used to generat
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coordinate set does not significant
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The LIR family is composed of eight
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CaM is a major calcium-binding prot
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The results of running FlexOracle a
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Figure 3.2: Results for individual
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a. 139
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Figure 3.3: Folylpolyglutamate Synt
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. c. 143
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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
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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
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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
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Chapter 5: The Conformation Explore
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ending, which involves a rigid regi
Page 241 and 242: lengths and angles)[89]. The equili
Page 243 and 244: for holo as well as apo forms, but
Page 245 and 246: queried using the “?” button. O
Page 247 and 248: coordinate. This phenomenon is know
Page 249 and 250: ! At the end of each equilibration
Page 251 and 252: aborted. This marked the correspond
Page 253 and 254: sRMSD has a major limitation that m
Page 255 and 256: with respect to the starting struct
Page 257 and 258: generated structure with respect to
Page 259 and 260: Ribose Binding Protein (RBP) As des
Page 261 and 262: strikingly similar both to the holo
Page 263 and 264: 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
Page 269 and 270: Figure 5.4: Results for biotin carb
Page 271 and 272: Figure 5.6: Results for Adenylate K
Page 273 and 274: close to the holo. The structure wi
Page 275 and 276: Table 5.1: MolMovDB ID, PDB ID, fre
Page 277 and 278: with sRMSD; however its main utilit
Page 279 and 280: morph server, and left confident th
Page 281 and 282: 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
Page 291: 98. Morris GM, Goodsell DS, Hallida
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