Диссертация (1150552), страница 27
Текст из файла (страница 27)
E. Water Dispersion InteractionsStrongly Influence Simulated Structural Properties of Disordered Protein States // Journal of PhysicalChemistry B. ‒ 2015. ‒ T. 119, № 16. ‒ C. 5113-5123.135. Schwarzinger S., Wright P. E., Dyson H. J. Molecular hinges in protein folding: The ureadenatured state of apomyoglobin // Biochemistry. ‒ 2002. ‒ T.
41, № 42. ‒ C. 12681-12686.136. Farrow N. A., Zhang O. W., FormanKay J. D., Kay L. E. Characterization of the backbonedynamics of folded and denatured states of an SH3 domain // Biochemistry. ‒ 1997. ‒ T. 36, № 9. ‒ C.2390-2402.137. Lindorff-Larsen K., Best R. B., DePristo M. A., Dobson C. M., Vendruscolo M.Simultaneous determination of protein structure and dynamics // Nature. ‒ 2005. ‒ T. 433, № 7022. ‒C. 128-132.138.
Allison J. R., Varnai P., Dobson C. M., Vendruscolo M. Determination of the Free EnergyLandscape of alpha-Synuclein Using Spin Label Nuclear Magnetic Resonance Measurements //Journal of the American Chemical Society. ‒ 2009. ‒ T. 131, № 51. ‒ C. 18314-18326.139. Robustelli P., Kohlhoff K., Cavalli A., Vendruscolo M. Using NMR Chemical Shifts asStructural Restraints in Molecular Dynamics Simulations of Proteins // Structure.
‒ 2010. ‒ T. 18, № 8.‒ C. 923-933.140. Huang J. R., Grzesiek S. Ensemble Calculations of Unstructured Proteins Constrained byRDC and PRE Data: A Case Study of Urea-Denatured Ubiquitin // Journal of the American ChemicalSociety. ‒ 2010. ‒ T. 132, № 2. ‒ C.
694-705.141. Salvi N., Abyzov A., Blackledge M. Multi-Timescale Dynamics in IntrinsicallyDisordered Proteins from NMR Relaxation and Molecular Simulation // Journal of Physical ChemistryLetters. ‒ 2016. ‒ T. 7, № 13. ‒ C. 2483-2489.142. Xue Y., Skrynnikov N. R. Motion of a Disordered Polypeptide Chain as Studied byParamagnetic Relaxation Enhancements, N-15 Relaxation, and Molecular Dynamics Simulations:How Fast Is Segmental Diffusion in Denatured Ubiquitin? // Journal of the American ChemicalSociety.
‒ 2011. ‒ T. 133, № 37. ‒ C. 14614-14628.132143. Xue Y., Podkorytov I. S., Rao D. K., Benjamin N., Sun H. L., Skrynnikov N. R.Paramagnetic relaxation enhancements in unfolded proteins: Theory and application to drkN SH3domain // Protein Science. ‒ 2009. ‒ T. 18, № 7.
‒ C. 1401-1424.144. Best R. B., Zheng W. W., Mittal J. Balanced Protein-Water Interactions ImproveProperties of Disordered Proteins and Non-Specific Protein Association // Journal of Chemical Theoryand Computation. ‒ 2014. ‒ T. 10, № 11. ‒ C. 5113-5124.145. Henriques J., Cragnell C., Skepo M. Molecular Dynamics Simulations of IntrinsicallyDisordered Proteins: Force Field Evaluation and Comparison with Experiment // Journal of ChemicalTheory and Computation.
‒ 2015. ‒ T. 11, № 7. ‒ C. 3420-3431.146. Nerenberg P. S., Jo B., So C., Tripathy A., Head-Gordon T. Optimizing Solute-Water vander Waals Interactions To Reproduce Solvation Free Energies // Journal of Physical Chemistry B. ‒2012. ‒ T. 116, № 15. ‒ C. 4524-4534.147. Henriques J., Skepo M. Molecular Dynamics Simulations of Intrinsically DisorderedProteins: On the Accuracy of the TIP4P-D Water Model and the Representativeness of ProteinDisorder Models // Journal of Chemical Theory and Computation.
‒ 2016. ‒ T. 12, № 7. ‒ C. 34073415.148. Palmer A. G., Case D. A. MOLECULAR-DYNAMICS ANALYSIS OF NMRRELAXATION IN A ZINC-FINGER PEPTIDE // Journal of the American Chemical Society. ‒ 1992.‒ T. 114, № 23. ‒ C. 9059-9067.149. Nicholas M. P., Eryilmaz E., Ferrage F., Cowburn D., Ghose R. Nuclear spin relaxation inisotropic and anisotropic media // Progress in Nuclear Magnetic Resonance Spectroscopy. ‒ 2010. ‒ T.57, № 2. ‒ C. 111-158.150. Case D. A.
Molecular dynamics and NMR spin relaxation in proteins // Accounts ofChemical Research. ‒ 2002. ‒ T. 35, № 6. ‒ C. 325-331.151. Maier J. A., Martinez C., Kasavajhala K., Wickstrom L., Hauser K. E., Simmerling C.ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB //Journal of Chemical Theory and Computation. ‒ 2015. ‒ T. 11, № 8. ‒ C. 3696-3713.152.
Zhou B. R., Feng H. Q., Ghirlando R., Kato H., Gruschus J., Bai Y. W. Histone H4 K16QMutation, an Acetylation Mimic, Causes Structural Disorder of Its N-Terminal Basic Patch in theNucleosome // Journal of Molecular Biology. ‒ 2012. ‒ T. 421, № 1. ‒ C. 30-37.153. Luger K., Richmond T. J. The histone tails of the nucleosome // Current Opinion inGenetics & Development. ‒ 1998. ‒ T. 8, № 2. ‒ C. 140-146.154. Marley J., Lu M., Bracken C. A method for efficient isotopic labeling of recombinantproteins // Journal of Biomolecular NMR. ‒ 2001. ‒ T. 20, № 1.
‒ C. 71-75.155. Cordier F., Dingley A. J., Grzesiek S. A doublet-separated sensitivity-enhanced HSQC forthe determination of scalar and dipolar one-bond J-couplings // Journal of Biomolecular NMR. ‒ 1999.‒ T. 13, № 2. ‒ C. 175-180.156. Hall J. B., Fushman D. Direct measurement of the transverse and longitudinal N-15chemical shift anisotropy-dipolar cross-correlation rate constants using H-1-coupled HSQC spectra //Magnetic Resonance in Chemistry. ‒ 2003. ‒ T.
41, № 10. ‒ C. 837-842.133157. Jorgensen W. L., Chandrasekhar J., Madura J. D., Impey R. W., Klein M. L.COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR SIMULATING LIQUID WATER //Journal of Chemical Physics. ‒ 1983. ‒ T. 79, № 2. ‒ C. 926-935.158. Berendsen H. J. C., Grigera J. R., Straatsma T. P. THE MISSING TERM IN EFFECTIVEPAIR POTENTIALS // Journal of Physical Chemistry. ‒ 1987. ‒ T.
91, № 24. ‒ C. 6269-6271.159. Horn H. W., Swope W. C., Pitera J. W., Madura J. D., Dick T. J., Hura G. L., HeadGordon T. Development of an improved four-site water model for biomolecular simulations: TIP4PEw // Journal of Chemical Physics. ‒ 2004. ‒ T. 120, № 20. ‒ C. 9665-9678.160. Jha A. K., Colubri A., Freed K. F., Sosnick T. R. Statistical coil model of the unfoldedstate: Resolving the reconciliation problem // Proceedings of the National Academy of Sciences of theUnited States of America. ‒ 2005.
‒ T. 102, № 37. ‒ C. 13099-13104.161. Krivov G. G., Shapovalov M. V., Dunbrack R. L. Improved prediction of protein sidechain conformations with SCWRL4 // Proteins-Structure Function and Bioinformatics. ‒ 2009. ‒ T.77, № 4. ‒ C. 778-795.162. Joung I. S., Cheatham T. E. Determination of alkali and halide monovalent ion parametersfor use in explicitly solvated biomolecular simulations // Journal of Physical Chemistry B. ‒ 2008.
‒ T.112, № 30. ‒ C. 9020-9041.163. Ryckaert J.-P., Ciccotti G., Berendsen H. J. C. Numerical integration of the cartesianequations of motion of a system with constraints: molecular dynamics of n-alkanes // Journal ofComputational Physics. ‒ 1977. ‒ T. 23, № 3.
‒ C. 327-341.164. Piana S., Lindorff-Larsen K., Dirks R. M., Salmon J. K., Dror R. O., Shaw D. E.Evaluating the Effects of Cutoffs and Treatment of Long-range Electrostatics in Protein FoldingSimulations // Plos One. ‒ 2012. ‒ T. 7, № 6.165. Berendsen H. J.
C., Postma J. P. M., Vangunsteren W. F., Dinola A., Haak J. R.MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH // Journal of ChemicalPhysics. ‒ 1984. ‒ T. 81, № 8. ‒ C. 3684-3690.166. Abyzov A., Salvi N., Schneider R., Maurin D., Ruigrok R. W. H., Jensen M. R.,Blackledge M. Identification of Dynamic Modes in an Intrinsically Disordered Protein UsingTemperature-Dependent NMR Relaxation // Journal of the American Chemical Society. ‒ 2016. ‒ T.138, № 19. ‒ C. 6240-6251.167. Palmer A. G.
NMR probes of molecular dynamics: Overview and comparison with othertechniques // Annual Review of Biophysics and Biomolecular Structure. ‒ 2001. ‒ T. 30. ‒ C. 129-155.168. Dyson H. J., Wright P. E. Unfolded proteins and protein folding studied by NMR //Chemical Reviews. ‒ 2004. ‒ T. 104, № 8. ‒ C. 3607-3622.169. Gao M., Nadaud P.
S., Bernier M. W., North J. A., Hammel P. C., Poirier M. G., JaroniecC. P. Histone H3 and H4 N-Terminal Tails in Nucleosome Arrays at Cellular Concentrations Probedby Magic Angle Spinning NMR Spectroscopy // Journal of the American Chemical Society. ‒ 2013. ‒T. 135, № 41. ‒ C. 15278-15281.170. Wishart D. S., Sykes B. D., Richards F. M. THE CHEMICAL-SHIFT INDEX - A FASTAND SIMPLE METHOD FOR THE ASSIGNMENT OF PROTEIN SECONDARY STRUCTURETHROUGH NMR-SPECTROSCOPY // Biochemistry. ‒ 1992. ‒ T. 31, № 6.
‒ C. 1647-1651.134171. Lawrence C. W., Showalter S. A. Carbon-Detected N-15 NMR Spin Relaxation of anIntrinsically Disordered Protein: FCP1 Dynamics Unbound and in Complex with RAP74 // Journal ofPhysical Chemistry Letters. ‒ 2012. ‒ T. 3, № 10. ‒ C. 1409-1413.172. Wirmer J., Peti W., Schwalbe H. Motional properties of unfolded ubiquitin: a model for arandom coil protein // Journal of Biomolecular Nmr. ‒ 2006. ‒ T. 35, № 3. ‒ C. 175-186.173. Gonzalez M. A., Abascal J.
L. F. The shear viscosity of rigid water models // Journal ofChemical Physics. ‒ 2010. ‒ T. 132, № 9.174. Oldfield C. J., Dunker A. K. Intrinsically Disordered Proteins and Intrinsically DisorderedProtein Regions // Annual Review of Biochemistry, Vol 83 / Kornberg R. D., 2014. ‒ C. 553-584.175. The theory of polymer dynamics. / Doi M., Edwards S. F.: Clarendon Press, 1986..
![](https://s.studizba.com/z.php?f=/templates/si/i/noavatar.png&w=100&h=100&t=1"){kind=avatar}
