Sekhar, A. & Kay, L. E. NMR paves the way in which for atomic degree descriptions of sparsely populated, transiently shaped biomolecular conformers. Proc. Natl Acad. Sci. USA 110, 12867–12874 (2013).
Google Scholar
Orellana, L. Massive-scale conformational adjustments and protein operate: breaking the in silico barrier. Entrance. Mol. Biosci. 6, 117 (2019).
Google Scholar
Nussinov, R. Introduction to protein ensembles and allostery. Chem. Rev. 116, 6263–6266 (2016).
Google Scholar
Haliloglu, T. & Bahar, I. Adaptability of protein buildings to allow practical interactions and evolutionary implications. Curr. Opin. Struct. Biol. 35, 17–23 (2015).
Google Scholar
Bertini, I., Luchinat, C. & Parigi, G. Magnetic susceptibility in paramagnetic NMR. Prog. Nucl. Magn. Reson. Spectrosc. 40, 249–273 (2002).
Google Scholar
Kleckner, I. R. & Foster, M. P. An introduction to NMR-based approaches for measuring protein dynamics. Biochim. Biophys. Acta 1814, 942–968 (2011).
Google Scholar
Boehr, D. D., McElheny, D., Dyson, H. J. & Wright, P. E. The dynamic power panorama of dihydrofolate reductase catalysis. Science 313, 1638–1642 (2006).
Google Scholar
Cianfrocco, M. A. et al. Human TFIID binds to core promoter DNA in a reorganized structural state. Cell 152, 120–131 (2013).
Google Scholar
Zhao, J., Benlekbir, S. & Rubinstein, J. L. Electron cryomicroscopy statement of rotational states in a eukaryotic V-ATPase. Nature 521, 241–245 (2015).
Google Scholar
Neudecker, P. et al. Construction of an intermediate state in protein folding and aggregation. Science 336, 362–366 (2012).
Google Scholar
Dethoff, E. A., Petzold, Ok., Chugh, J., Casiano-Negroni, A. & Al-Hashimi, H. M. Visualizing transient low-populated buildings of RNA. Nature 491, 724–728 (2012).
Google Scholar
Zhao, B., Guffy, S. L., Williams, B. & Zhang, Q. An excited state underlies gene regulation of a transcriptional riboswitch. Nat. Chem. Biol. 13, 968–974 (2017).
Google Scholar
Fraser, J. S. et al. Accessing protein conformational ensembles utilizing room-temperature X-ray crystallography. Proc. Natl Acad. Sci. USA 108, 16247–16252 (2011).
Google Scholar
Bonomi, M. & Vendruscolo, M. Dedication of protein structural ensembles utilizing cryo-electron microscopy. Curr. Opin. Struct. Biol. 56, 37–45 (2019).
Google Scholar
Vogeli, B., Olsson, S., Guntert, P. & Riek, R. The precise NOE as a substitute in ensemble construction willpower. Biophys. J. 110, 113–126 (2016).
Google Scholar
Leung, H. T. et al. A rigorous and environment friendly methodology to reweight very massive conformational ensembles utilizing common experimental knowledge and to find out their relative info content material. J. Chem. Idea Comput. 12, 383–394 (2016).
Google Scholar
Clore, G. M. & Iwahara, J. Idea, follow, and functions of paramagnetic rest enhancement for the characterization of transient low-population states of organic macromolecules and their complexes. Chem. Rev. 109, 4108–4139 (2009).
Google Scholar
Maltsev, A. S., Grishaev, A., Roche, J., Zasloff, M. & Bax, A. Improved cross validation of a static ubiquitin construction derived from excessive precision residual dipolar couplings measured in a drug-based liquid crystalline part. J. Am. Chem. Soc. 136, 3752–3755 (2014).
Google Scholar
Korzhnev, D. M., Religa, T. L., Banachewicz, W., Fersht, A. R. & Kay, L. E. A transient and low-populated protein-folding intermediate at atomic decision. Science 329, 1312–1316 (2010).
Google Scholar
Nerli, S., McShan, A. C. & Sgourakis, N. G. Chemical shift-based strategies in NMR construction willpower. Prog. Nucl. Magn. Reson. Spectrosc. 106-107, 1–25 (2018).
Google Scholar
Bertini, I. et al. Experimentally exploring the conformational house sampled by area reorientation in calmodulin. Proc. Natl Acad. Sci. USA 101, 6841–6846 (2004).
Google Scholar
Hass, M. A. S. et al. A minor conformation of a lanthanide tag on adenylate kinase characterised by paramagnetic rest dispersion NMR spectroscopy. J. Biomol. NMR 61, 123–136 (2015).
Google Scholar
Xu, D. et al. Ligand proton pseudocontact shifts decided from paramagnetic rest dispersion within the restrict of NMR intermediate alternate. J. Phys. Chem. Lett. 9, 3361–3367 (2018).
Google Scholar
Eichmuller, C. & Skrynnikov, N. R. Statement of microsecond time-scale protein dynamics within the presence of Ln3+ ions: utility to the N-terminal area of cardiac troponin C. J. Biomol. NMR 37, 79–95 (2007).
Google Scholar
Kerns, S. J. et al. The power panorama of adenylate kinase throughout catalysis. Nat. Struct. Mol. Biol. 22, 124–131 (2015).
Google Scholar
Moon, S., Bannen, R. M., Rutkoski, T. J., Phillips, G. N. Jr & Bae, E. Effectiveness and limitations of native structural entropy optimization within the thermal stabilization of mesophilic and thermophilic adenylate kinases. Proteins 82, 2631–2642 (2014).
Google Scholar
Hanson, J. A. et al. Illuminating the mechanistic roles of enzyme conformational dynamics. Proc. Natl Acad. Sci. USA 104, 18055–18060 (2007).
Google Scholar
Aden, J. & Wolf-Watz, M. NMR identification of transient complexes essential to adenylate kinase catalysis. J. Am. Chem. Soc. 129, 14003–14012 (2007).
Google Scholar
Pelz, B., Zoldak, G., Zeller, F., Zacharias, M. & Rief, M. Subnanometre enzyme mechanics probed by single-molecule power spectroscopy. Nat. Commun. 7, 10848 (2016).
Google Scholar
Mukhopadhyay, A. et al. Crystal construction of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative micro organism. J. Biol. Inorg. Chem. 16, 51–61 (2011).
Google Scholar
Carver, J. P. & Richards, R. E. Common 2-site resolution for chemical alternate produced dependence of T2 upon Carr–Purcell pulse separation. J. Magazine. Res. 6, 89–105 (1972).
Google Scholar
Aviram, H. Y. et al. Direct statement of ultrafast large-scale dynamics of an enzyme below turnover situations. Proc. Natl Acad. Sci. USA 115, 3243–3248 (2018).
Google Scholar
Skrynnikov, N. R., Dahlquist, F. W. & Kay, L. E. Reconstructing NMR spectra of “invisible” excited protein states utilizing HSQC and HMQC experiments. J. Am. Chem. Soc. 124, 12352–12360 (2002).
Google Scholar
Schwieters, C. D., Kuszewski, J. J., Tjandra, N. & Clore, G. M. The Xplor-NIH NMR molecular construction willpower package deal. J. Magazine. Res. 160, 65–73 (2003).
Google Scholar
Fallon, J. L. & Quiocho, F. A. A closed compact construction of native Ca2+-calmodulin. Construction 11, 1303–1307 (2003).
Google Scholar
Cowan-Jacob, S. W. et al. The crystal construction of a c-Src complicated in an energetic conformation suggests doable steps in c-Src activation. Construction 13, 861–871 (2005).
Google Scholar
Müntener, T., Kottelat, J., Huber, A. & Häussinger, D. New lanthanide chelating tags for PCS NMR spectroscopy with discount steady, inflexible linkers for quick and irreversible conjugation to proteins. Bioconjugate Chem. 29, 3344–3351 (2018).
Chou, J. J., Li, S., Klee, C. B. & Bax, A. Resolution construction of Ca2+-calmodulin reveals versatile hand-like properties of its domains. Nat. Struct. Biol. 8, 990–997 (2001).
Google Scholar
Russel, D. et al. Placing the items collectively: integrative modeling platform software program for construction willpower of macromolecular assemblies. PLoS Biol. 10, e1001244 (2012).
Google Scholar
Häussinger, D., Huang, J. R. & Grzesiek, S. DOTA-M8: a particularly inflexible, high-affinity lanthanide chelating tag for PCS NMR spectroscopy. J. Am. Chem. Soc. 131, 14761–14767 (2009).
Google Scholar
Morgado, L., Burmann, B. M., Sharpe, T., Mazur, A. & Hiller, S. The dynamic dimer construction of the chaperone Set off Issue. Nat. Commun. 8, 1992 (2017).
Google Scholar
Kovermann, M., Grundstrom, C., Sauer-Eriksson, A. E., Sauer, U. H. & Wolf-Watz, M. Structural foundation for ligand binding to an enzyme by a conformational choice pathway. Proc. Natl Acad. Sci. USA 114, 6298–6303 (2017).
Google Scholar
Li, D., Liu, M. S. & Ji, B. Mapping the dynamics panorama of conformational transitions in enzyme: the adenylate kinase case. Biophys. J. 109, 647–660 (2015).
Google Scholar
Stiller, J. B. et al. Probing the transition state in enzyme catalysis by high-pressure NMR dynamics. Nat. Catal. 2, 726–734 (2019).
Google Scholar
Saio, T. & Ishimori, Ok. Accelerating structural life science by paramagnetic lanthanide probe strategies. Biochim. Biophys. Acta 1864, 129332 (2019).
Nitsche, C. & Otting, G. Pseudocontact shifts in biomolecular NMR utilizing paramagnetic steel tags. Prog. Nucl. Magn. Reson. Spectrosc. 98-99, 20–49 (2017).
Google Scholar
Ma, R. S. et al. Dedication of pseudocontact shifts of low-populated excited states by NMR chemical alternate saturation switch. Phys. Chem. Chem. Phys. 18, 13794–13798 (2016).
Google Scholar
Gerstein, M., Lesk, A. M. & Chothia, C. Structural mechanisms for area actions in proteins. Biochemistry 33, 6739–6749 (1994).
Google Scholar
Jumper, J. et al. Extremely correct protein construction prediction with AlphaFold. Nature 596, 583–589 (2021).
Google Scholar
Schmitz, C., Stanton-Cook dinner, M. J., Su, X. C., Otting, G. & Huber, T. Numbat: an interactive software program software for becoming Delta chi-tensors to molecular coordinates utilizing pseudocontact shifts. J. Biomol. NMR 41, 179–189 (2008).
Google Scholar
Cai, M., Huang, Y., Craigie, R. & Clore, G. M. A easy protocol for expression of isotope-labeled proteins in Escherichia coli grown in shaker flasks at excessive cell density. J. Biomol. NMR 73, 743–748 (2019).
Google Scholar
Otting, G., Ruckert, M., Levitt, M. H. & Moshref, A. NMR experiments for the signal willpower of homonuclear scalar and residual dipolar couplings. J. Biomol. NMR 16, 343–346 (2000).
Google Scholar
Joss, D., Walliser, R. M., Zimmermann, Ok. & Häussinger, D. Conformationally locked lanthanide chelating tags for handy pseudocontact shift protein nuclear magnetic resonance spectroscopy. J. Biomol. NMR 72, 29–38 (2018).
Google Scholar
Romero, P. R. et al. BioMagResBank (BMRB) as a useful resource for structural biology. Strategies Mol. Biol. 2112, 187–218 (2020).
Google Scholar
Orton, H. W., Huber, T. & Otting, G. Paramagpy: software program for becoming magnetic susceptibility tensors utilizing paramagnetic results measured in NMR spectra. Magn. Reson. 1, 1–12 (2020).
Ishima, R. & Torchia, D. A. Extending the vary of amide proton rest dispersion experiments in proteins utilizing a constant-time relaxation-compensated CPMG strategy. J. Biomol. NMR 25, 243–248 (2003).
Google Scholar
Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based mostly on UNIX pipes. J. Biomol. NMR 6, 277–293 (1995).
Google Scholar
Vranken, W. F. et al. The CCPN knowledge mannequin for NMR spectroscopy: improvement of a software program pipeline. Proteins 59, 687–696 (2005).
Google Scholar
Lee, W., Rahimi, M., Lee, Y. & Chiu, A. POKY: a software program suite for multidimensional NMR and 3D construction calculation of biomolecules. Bioinformatics. 37, 3041–3042 (2021).
Google Scholar
Niklasson, M. et al. Complete evaluation of NMR knowledge utilizing superior line form becoming. J. Biomol. NMR 69, 93–99 (2017).
Google Scholar
Newville, M., Stensitzki, T., Allen, D. B. & Ingargiola, A. LMFIT: Non-Linear Least-Sq. Minimization and Curve-Becoming for Python https://lmfit.github.io/lmfit-py/ (2014).
Counago, R., Chen, S. & Shamoo, Y. In vivo molecular evolution reveals biophysical origins of organismal health. Mol. Cell 22, 441–449 (2006).
Google Scholar
Abele, U. & Schulz, G. E. Excessive-resolution buildings of adenylate kinase from yeast ligated with inhibitor Ap5A, displaying the pathway of phosphoryl switch. Protein Sci. 4, 1262–1271 (1995).
Google Scholar
Berry, M. B. & Phillips, G. N. Jr. Crystal buildings of Bacillus stearothermophilus adenylate kinase with sure Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid place and 6 coordinate octahedral geometry for sure Mg2+ and Mn2+. Proteins 32, 276–288 (1998).
Google Scholar
Diederichs, Ok. & Schulz, G. E. The refined construction of the complicated between adenylate kinase from beef coronary heart mitochondrial matrix and its substrate AMP at 1.85 Å decision. J. Mol. Biol. 217, 541–549 (1991).
Google Scholar
Schlauderer, G. J., Proba, Ok. & Schulz, G. E. Construction of a mutant adenylate kinase ligated with an ATP-analogue displaying area closure over ATP. J. Mol. Biol. 256, 223–227 (1996).
Google Scholar
Henzler-Wildman, Ok. A. et al. Intrinsic motions alongside an enzymatic response trajectory. Nature 450, 838–844 (2007).
Google Scholar
Muller, C. W., Schlauderer, G. J., Reinstein, J. & Schulz, G. E. Adenylate kinase motions throughout catalysis: an brisk counterweight balancing substrate binding. Construction 4, 147–156 (1996).
Google Scholar
Arnold, Ok., Bordoli, L., Kopp, J. & Schwede, T. The SWISS-MODEL workspace: a web-based atmosphere for protein construction homology modelling. Bioinformatics 22, 195–201 (2006).
Google Scholar
Phrase, J. M., Lovell, S. C., Richardson, J. S. & Richardson, D. C. Asparagine and glutamine: utilizing hydrogen atom contacts within the alternative of side-chain amide orientation. J. Mol. Biol. 285, 1735–1747 (1999).
Google Scholar
Chattopadhyaya, R., Meador, W. E., Means, A. R. & Quiocho, F. A. Calmodulin construction refined at 1.7 Å decision. J. Mol. Biol. 228, 1177–1192 (1992).
Google Scholar
Xu, W., Doshi, A., Lei, M., Eck, M. J. & Harrison, S. C. Crystal buildings of c-Src reveal options of its autoinhibitory mechanism. Mol. Cell 3, 629–638 (1999).
Google Scholar
Bertini, I., Janik, M. B., Lee, Y. M., Luchinat, C. & Rosato, A. Magnetic susceptibility tensor anisotropies for a lanthanide ion sequence in a set protein matrix. J. Am. Chem. Soc. 123, 4181–4188 (2001).
Google Scholar
Ulrich, E. L. et al. BioMagResBank. Nucleic Acids Res. 36, D402–D408 (2007).
Google Scholar
Tollinger, M., Skrynnikov, N. R., Mulder, F. A., Forman-Kay, J. D. & Kay, L. E. Sluggish dynamics in folded and unfolded states of an SH3 area. J. Am. Chem. Soc. 123, 11341–11352 (2001).
Google Scholar