Диссертация (1150552), страница 26
Текст из файла (страница 26)
166, № 2. ‒ C. 368-379.90. Olsson M. H. M., Sondergaard C. R., Rostkowski M., Jensen J. H. PROPKA3: consistenttreatment of internal and surface residues in empirical pKa predictions // Journal of Chemical Theoryand Computation. ‒ 2011. ‒ T. 7, № 2. ‒ C. 525-537.91. Dolinsky T. J., Nielsen J. E., McCammon J. A., Baker N. A. PDB2PQR: an automatedpipeline for the setup of Poisson-Boltzmann electrostatics calculations // Nucleic Acids Research. ‒2004. ‒ T. 32.
‒ C. W665-W667.92. Martí-Renom N. A., Stote R. H., Querol E., Avilés F. X., Karplus M. Refolding of potatocarboxypeptidase inhibitor by molecular dynamics simulations with disulfide bond constraints //Journal of Molecular Biology. ‒ 1998. ‒ T. 284, № 1. ‒ C. 145-172.93. Izmailov S. A., Podkorytov I. S., Skrynnikov N. R. Simple MD-based model for oxidativefolding of peptides and proteins // Scientific Reports. ‒ 2017.
‒ T. in press.94. Best R. B., Vendruscolo M. Structural interpretation of hydrogen exchange protectionfactors in proteins: Characterization of the native state fluctuations of CI2 // Structure. ‒ 2006. ‒ T. 14,№ 1. ‒ C. 97-106.95. Lukavsky P. J., Daujotyte D., Tollervey J. R., Ule J., Stuani C., Buratti E., Baralle F. E.,Damberger F. F., Allain F. H. Molecular basis of UG-rich RNA recognition by the human splicingfactor TDP-43 // Nature Structural & Molecular Biology.
‒ 2013. ‒ T. 20, № 12. ‒ C. 1443-9.96. Mompean M., Romano V., Pantoja-Uceda D., Stuani C., Baralle F. E., Buratti E., LaurentsD. V. The TDP-43 N-terminal domain structure at high resolution // FEBS Journal. ‒ 2016. ‒ T. 283,№ 7. ‒ C. 1242-1260.97. Kuo P. H., Doudeva L. G., Wang Y. T., Shen C. K. J., Yuan H. S. Structural insights intoTDP-43 in nucleic-acid binding and domain interactions // Nucleic Acids Research. ‒ 2009. ‒ T. 37, №6. ‒ C. 1799-1808.98.
Pesiridis G. S., Lee V. M., Trojanowski J. Q. Mutations in TDP-43 link glycine-richdomain functions to amyotrophic lateral sclerosis // Human Molecular Genetics. ‒ 2009. ‒ T. 18, №R2. ‒ C. R156-62.99. Ayala Y. M., Zago P., D'Ambrogio A., Xu Y. F., Petrucelli L., Buratti E., Baralle F. E.Structural determinants of the cellular localization and shuttling of TDP-43 // Journal of Cell Science.‒ 2008.
‒ T. 121, № 22. ‒ C. 3778-3785.100. Griffith I. P. The effect of cross-links on the mobility of proteins in dodecyl sulphate polyacrylamide gels // Biochemical Journal. ‒ 1972. ‒ T. 126, № 3. ‒ C. 553-560.129101. Ferrer-Sueta G., Manta B., Botti H., Radi R., Trujillo M., Denicola A. Factors affectingprotein thiol reactivity and specificity in peroxide reduction // Chemical Research in Toxicology. ‒2011. ‒ T.
24, № 4. ‒ C. 434-450.102. Roos G., Foloppe N., Messens J. Understanding the pKa of redox cysteines: the key roleof hydrogen bonding // Antioxidants & Redox Signaling. ‒ 2013. ‒ T. 18, № 1. ‒ C. 94-127.103. Gupta V., Carroll K. S. Sulfenic acid chemistry, detection and cellular lifetime //Biochimica Et Biophysica Acta-General Subjects. ‒ 2014. ‒ T. 1840, № 2. ‒ C.
847-875.104. Pfuhl M., Chen H. A., Kristensen S. M., Driscoll P. C. NMR exchange broadening arisingfrom specific low affinity protein self-association: analysis of nitrogen-15 nuclear relaxation for ratCD2 domain 1 // Journal of Biomolecular NMR. ‒ 1999.
‒ T. 14, № 4. ‒ C. 307-320.105. Liu Z., Zhang W. P., Xing Q., Ren X. F., Liu M. L., Tang C. Noncovalent dimerization ofubiquitin // Angewandte Chemie-International Edition. ‒ 2012. ‒ T. 51, № 2. ‒ C. 469-472.106. de la Torre J. G., Huertas M. L., Carrasco B. Calculation of hydrodynamic properties ofglobular proteins from their atomic-level structure. // Biophysical Journal. ‒ 2000. ‒ T. 78, № 2. ‒ C.719-730.107. Solyom Z., Schwarten M., Geist L., Konrat R., Willbold D., Brutscher B. BEST-TROSYexperiments for time-efficient sequential resonance assignment of large disordered proteins // Journalof Biomolecular NMR.
‒ 2013. ‒ T. 55, № 4. ‒ C. 311-321.108. Grimsley G. R., Scholtz J. M., Pace C. N. A summary of the measured pK a values of theionizable groups in folded proteins // Protein Science. ‒ 2009. ‒ T. 18, № 1. ‒ C. 247-251.109. Platzer G., Okon M., McIntosh L. P. pH-dependent random coil 1H, 13C, and 15N chemicalshifts of the ionizable amino acids: a guide for protein pKa measurements // Journal of BiomolecularNMR. ‒ 2014. ‒ T.
60, № 2-3. ‒ C. 109-129.110. Christodoulou J., Larsson G., Fucini P., Connell S. R., Pertinhez T. A., Hanson C. L.,Redfield C., Nierhaus K. H., Robinson C. V., Schleucher J., Dobson C. M. Heteronuclear NMRinvestigations of dynamic regions of intact Escherichia coli ribosomes // Proceedings of the NationalAcademy of Sciences of the United States of America. ‒ 2004. ‒ T. 101, № 30. ‒ C. 10949-10954.111. Englander S. W., Mayne L. Protein folding studied using hydrogen-exchange labeling andtwo-dimensional NMR // Annual Review of Biophysics and Biomolecular Structure. ‒ 1992. ‒ T. 21. ‒C.
243-265.112. Karamanos T. K., Kalverda A. P., Thompson G. S., Radford S. E. Mechanisms of amyloidformation revealed by solution NMR // Progress in Nuclear Magnetic Resonance Spectroscopy. ‒2015. ‒ T. 88-89. ‒ C. 86-104.113. de la Torre J. G., Huertas M. L., Carrasco B. HYDRONMR: Prediction of NMRrelaxation of globular proteins from atomic-level structures and hydrodynamic calculations // Journalof Magnetic Resonance B. ‒ 2000.
‒ T. 147, № 1. ‒ C. 138-146.114. Chen C. R., Makhatadze G. I. ProteinVolume: calculating molecular van der Waals andvoid volumes in proteins // BMC Bioinformatics. ‒ 2015. ‒ T. 16, № 1. ‒ C. 101.130115. Halle B., Davidovic M. Biomolecular hydration: from water dynamics to hydrodynamics// Proceedings of the National Academy of Sciences of the United States of America. ‒ 2003. ‒ T. 100,№ 21. ‒ C. 12135-12140.116. Mailer A. G., Clegg P.
S., Pusey P. N. Particle sizing by dynamic light scattering: nonlinear cumulant analysis // Journal of Physics-Condensed Matter. ‒ 2015. ‒ T. 27, № 14. ‒ C. 145102.117. Flory P. J. Molecular size distribution in linear condensation polymers // Journal of theAmerican Chemical Society. ‒ 1936. ‒ T. 58. ‒ C. 1877-1885.118. Kéki S., Zsuga M., Kuki A. Theoretical size distribution in linear step-growthpolymerization for a small number of reacting species // Journal of Physical Chemistry B. ‒ 2013. ‒ T.117, № 15. ‒ C. 4151-4155.119. Meesters A., Ernst M.
H. Numerical evaluation of self-preserving spectra inSmoluchowski coagulation theory. // Journal of Colloid and Interface Science. ‒ 1987. ‒ T. 119, № 2.‒ C. 576-587.120. Karst J. C., Sotomayor-Perez A. C., Ladant D., Chenal A. Estimation of intrinsicallydisordered protein shape and time-averaged apparent // Methods Mol. Biol. ‒ 2012. ‒ T.
896. ‒ C. 163177.121. Hubbard S. J. The structural aspects of limited proteolysis of native proteins // BiochimicaEt Biophysica Acta-Protein Structure and Molecular Enzymology. ‒ 1998. ‒ T. 1382, № 2. ‒ C. 191206.122. Fontana A., deLaureto P. P., DeFilippis V., Scaramella E., Zambonin M.
Probing thepartly folded states of proteins by limited proteolysis // Folding & Design. ‒ 1997. ‒ T. 2, № 2. ‒ C.R17-R26.123. Kurzbach D., Schwarz T. C., Platzer G., Hofler S., Hinderberger D., Konrat R.Compensatory adaptations of structural dynamics in an intrinsically disordered protein complex //Angewandte Chemie-International Edition. ‒ 2014. ‒ T. 53, № 15. ‒ C. 3840-3843.124.
Balguerie A., Dos Reis S., Ritter C., Chaignepain S., Coulary-Salin B., Forge V., BathanyK., Lascu I., Schmitter J. M., Riek R., Saupe S. J. Domain organization and structure-functionrelationship of the HET-s prion protein of Podospora anserina // EMBO Journal. ‒ 2003. ‒ T. 22, № 9.‒ C.
2071-2081.125. Gilbert H. F. Molecular and cellular aspects of thiol-disulfide exchange // Advances inEnzymology and Related Areas of Molecular Biology. ‒ 1990. ‒ T. 63. ‒ C. 69-172.126. Welker E., Wedemeyer W. J., Scheraga H. A. A role for intermolecular disulfide bonds inprion diseases? // Proceedings of the National Academy of Sciences of the United States of America.
‒2001. ‒ T. 98, № 8. ‒ C. 4334-4336.127. Messens J., Collet J. F. Thiol-disulfide exchange in signaling: disulfide bonds as a switch// Antioxidants & Redox Signaling. ‒ 2013. ‒ T. 18, № 13. ‒ C. 1594-1596.128. Harada R., Tochio N., Kigawa T., Sugita Y., Feig M. Reduced native state stability incrowded cellular environment due to protein-protein interactions // Journal of the American ChemicalSociety. ‒ 2013. ‒ T.
135, № 9. ‒ C. 3696-3701.131129. Das M., Kobayashi M., Yamada Y., Sreeramulu S., Ramakrishnan C., Wakatsuki S., KatoR., Varadarajan R. Design of disulfide-linked thioredoxin dimers and multimers through analysis ofcrystal contacts // Journal of Molecular Biology. ‒ 2007. ‒ T. 372, № 5. ‒ C. 1278-1292.130. Murphy K. P., Freire E. Thermodynamics of structural stability and cooperative foldingbehavior in proteins // Advances in Protein Chemistry. ‒ 1992. ‒ T. 43. ‒ C. 313-361.131.
Kim K. S., Woodward C. Protein internal flexibility and global stability: effect of urea onhydrogen exchange rates of bovine pancreatic trypsin inhibitor // Biochemistry. ‒ 1993. ‒ T. 32, № 37.‒ C. 9609-9613.132. Careaga C. L., Falke J. J. Thermal motions of surface -helices in the D-galactosechemosensory receptor: detection by disulfide trapping. // Journal of Molecular Biology. ‒ 1992.
‒ T.226, № 4. ‒ C. 1219-1235.133. Borgia A., Kemplen K. R., Borgia M. B., Soranno A., Shammas S., Wunderlich B.,Nettels D., Best R. B., Clarke J., Schuler B. Transient misfolding dominates multidomain proteinfolding // Nature Communications. ‒ 2015. ‒ T. 6.134. Piana S., Donchev A. G., Robustelli P., Shaw D.