Sekhar, A. & Kay, L. E. NMR paves the way in which for atomic degree descriptions of sparsely populated, transiently fashioned biomolecular conformers. Proc. Natl Acad. Sci. USA 110, 12867–12874 (2013).
ADS
CAS
PubMed
PubMed Central
Google Scholar
Orellana, L. Giant-scale conformational adjustments and protein perform: breaking the in silico barrier. Entrance. Mol. Biosci. 6, 117 (2019).
CAS
PubMed
PubMed Central
Google Scholar
Nussinov, R. Introduction to protein ensembles and allostery. Chem. Rev. 116, 6263–6266 (2016).
PubMed
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).
CAS
PubMed
PubMed Central
Google Scholar
Bertini, I., Luchinat, C. & Parigi, G. Magnetic susceptibility in paramagnetic NMR. Prog. Nucl. Magn. Reson. Spectrosc. 40, 249–273 (2002).
CAS
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).
CAS
PubMed
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).
ADS
CAS
PubMed
Google Scholar
Cianfrocco, M. A. et al. Human TFIID binds to core promoter DNA in a reorganized structural state. Cell 152, 120–131 (2013).
CAS
PubMed
PubMed Central
Google Scholar
Zhao, J., Benlekbir, S. & Rubinstein, J. L. Electron cryomicroscopy remark of rotational states in a eukaryotic V-ATPase. Nature 521, 241–245 (2015).
ADS
CAS
PubMed
Google Scholar
Neudecker, P. et al. Construction of an intermediate state in protein folding and aggregation. Science 336, 362–366 (2012).
ADS
CAS
PubMed
Google Scholar
Dethoff, E. A., Petzold, Okay., Chugh, J., Casiano-Negroni, A. & Al-Hashimi, H. M. Visualizing transient low-populated buildings of RNA. Nature 491, 724–728 (2012).
ADS
CAS
PubMed
PubMed Central
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).
CAS
PubMed
PubMed Central
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).
ADS
CAS
PubMed
PubMed Central
Google Scholar
Bonomi, M. & Vendruscolo, M. Willpower of protein structural ensembles utilizing cryo-electron microscopy. Curr. Opin. Struct. Biol. 56, 37–45 (2019).
CAS
PubMed
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).
ADS
CAS
PubMed
PubMed Central
Google Scholar
Leung, H. T. et al. A rigorous and environment friendly technique to reweight very massive conformational ensembles utilizing common experimental information and to find out their relative info content material. J. Chem. Concept Comput. 12, 383–394 (2016).
CAS
PubMed
Google Scholar
Clore, G. M. & Iwahara, J. Concept, follow, and purposes of paramagnetic rest enhancement for the characterization of transient low-population states of organic macromolecules and their complexes. Chem. Rev. 109, 4108–4139 (2009).
CAS
PubMed
PubMed Central
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 section. J. Am. Chem. Soc. 136, 3752–3755 (2014).
CAS
PubMed
PubMed Central
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).
ADS
CAS
PubMed
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).
CAS
PubMed
PubMed Central
Google Scholar
Bertini, I. et al. Experimentally exploring the conformational area sampled by area reorientation in calmodulin. Proc. Natl Acad. Sci. USA 101, 6841–6846 (2004).
ADS
CAS
PubMed
PubMed Central
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).
CAS
PubMed
Google Scholar
Xu, D. et al. Ligand proton pseudocontact shifts decided from paramagnetic rest dispersion within the restrict of NMR intermediate trade. J. Phys. Chem. Lett. 9, 3361–3367 (2018).
CAS
PubMed
Google Scholar
Eichmuller, C. & Skrynnikov, N. R. Statement of microsecond time-scale protein dynamics within the presence of Ln3+ ions: software to the N-terminal area of cardiac troponin C. J. Biomol. NMR 37, 79–95 (2007).
PubMed
Google Scholar
Kerns, S. J. et al. The power panorama of adenylate kinase throughout catalysis. Nat. Struct. Mol. Biol. 22, 124–131 (2015).
CAS
PubMed
PubMed Central
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).
CAS
PubMed
Google Scholar
Hanson, J. A. et al. Illuminating the mechanistic roles of enzyme conformational dynamics. Proc. Natl Acad. Sci. USA 104, 18055–18060 (2007).
ADS
CAS
PubMed
PubMed Central
Google Scholar
Aden, J. & Wolf-Watz, M. NMR identification of transient complexes vital to adenylate kinase catalysis. J. Am. Chem. Soc. 129, 14003–14012 (2007).
PubMed
Google Scholar
Pelz, B., Zoldak, G., Zeller, F., Zacharias, M. & Rief, M. Subnanometre enzyme mechanics probed by single-molecule pressure spectroscopy. Nat. Commun. 7, 10848 (2016).
ADS
CAS
PubMed
PubMed Central
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).
CAS
PubMed
Google Scholar
Carver, J. P. & Richards, R. E. Common 2-site resolution for chemical trade produced dependence of T2 upon Carr–Purcell pulse separation. J. Magazine. Res. 6, 89–105 (1972).
ADS
CAS
Google Scholar
Aviram, H. Y. et al. Direct remark of ultrafast large-scale dynamics of an enzyme below turnover circumstances. Proc. Natl Acad. Sci. USA 115, 3243–3248 (2018).
CAS
PubMed
PubMed Central
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).
CAS
PubMed
Google Scholar
Schwieters, C. D., Kuszewski, J. J., Tjandra, N. & Clore, G. M. The Xplor-NIH NMR molecular construction willpower bundle. J. Magazine. Res. 160, 65–73 (2003).
ADS
CAS
Google Scholar
Fallon, J. L. & Quiocho, F. A. A closed compact construction of native Ca2+-calmodulin. Construction 11, 1303–1307 (2003).
CAS
PubMed
Google Scholar
Cowan-Jacob, S. W. et al. The crystal construction of a c-Src advanced in an lively conformation suggests potential steps in c-Src activation. Construction 13, 861–871 (2005).
CAS
PubMed
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).
Google Scholar
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).
CAS
PubMed
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).
CAS
PubMed
PubMed Central
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).
PubMed
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).
ADS
PubMed
PubMed Central
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).
CAS
PubMed
PubMed Central
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).
ADS
CAS
PubMed
PubMed Central
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).
CAS
PubMed
PubMed Central
Google Scholar
Saio, T. & Ishimori, Okay. Accelerating structural life science by paramagnetic lanthanide probe strategies. Biochim. Biophys. Acta 1864, 129332 (2019).
Google Scholar
Nitsche, C. & Otting, G. Pseudocontact shifts in biomolecular NMR utilizing paramagnetic metallic tags. Prog. Nucl. Magn. Reson. Spectrosc. 98-99, 20–49 (2017).
CAS
PubMed
Google Scholar
Ma, R. S. et al. Willpower of pseudocontact shifts of low-populated excited states by NMR chemical trade saturation switch. Phys. Chem. Chem. Phys. 18, 13794–13798 (2016).
CAS
PubMed
Google Scholar
Gerstein, M., Lesk, A. M. & Chothia, C. Structural mechanisms for area actions in proteins. Biochemistry 33, 6739–6749 (1994).
CAS
PubMed
Google Scholar
Jumper, J. et al. Extremely correct protein construction prediction with AlphaFold. Nature 596, 583–589 (2021).
ADS
CAS
PubMed
PubMed Central
Google Scholar
Schmitz, C., Stanton-Cook dinner, M. J., Su, X. C., Otting, G. & Huber, T. Numbat: an interactive software program device for becoming Delta chi-tensors to molecular coordinates utilizing pseudocontact shifts. J. Biomol. NMR 41, 179–189 (2008).
CAS
PubMed
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).
CAS
PubMed
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).
CAS
PubMed
Google Scholar
Joss, D., Walliser, R. M., Zimmermann, Okay. & Häussinger, D. Conformationally locked lanthanide chelating tags for handy pseudocontact shift protein nuclear magnetic resonance spectroscopy. J. Biomol. NMR 72, 29–38 (2018).
CAS
PubMed
Google Scholar
Romero, P. R. et al. BioMagResBank (BMRB) as a useful resource for structural biology. Strategies Mol. Biol. 2112, 187–218 (2020).
CAS
PubMed
PubMed Central
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).
Google Scholar
Ishima, R. & Torchia, D. A. Extending the vary of amide proton rest dispersion experiments in proteins utilizing a constant-time relaxation-compensated CPMG method. J. Biomol. NMR 25, 243–248 (2003).
CAS
PubMed
Google Scholar
Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system primarily based on UNIX pipes. J. Biomol. NMR 6, 277–293 (1995).
CAS
PubMed
Google Scholar
Vranken, W. F. et al. The CCPN information mannequin for NMR spectroscopy: growth of a software program pipeline. Proteins 59, 687–696 (2005).
CAS
PubMed
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).
CAS
PubMed Central
Google Scholar
Niklasson, M. et al. Complete evaluation of NMR information utilizing superior line form becoming. J. Biomol. NMR 69, 93–99 (2017).
CAS
PubMed
PubMed Central
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).
CAS
PubMed
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).
CAS
PubMed
PubMed Central
Google Scholar
Berry, M. B. & Phillips, G. N. Jr. Crystal buildings of Bacillus stearothermophilus adenylate kinase with certain Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid place and 6 coordinate octahedral geometry for certain Mg2+ and Mn2+. Proteins 32, 276–288 (1998).
CAS
PubMed
Google Scholar
Diederichs, Okay. & Schulz, G. E. The refined construction of the advanced 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).
CAS
PubMed
Google Scholar
Schlauderer, G. J., Proba, Okay. & 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).
CAS
PubMed
Google Scholar
Henzler-Wildman, Okay. A. et al. Intrinsic motions alongside an enzymatic response trajectory. Nature 450, 838–844 (2007).
ADS
CAS
PubMed
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).
CAS
PubMed
Google Scholar
Arnold, Okay., Bordoli, L., Kopp, J. & Schwede, T. The SWISS-MODEL workspace: a web-based surroundings for protein construction homology modelling. Bioinformatics 22, 195–201 (2006).
CAS
PubMed
PubMed Central
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).
CAS
PubMed
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).
CAS
PubMed
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).
CAS
PubMed
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).
CAS
PubMed
Google Scholar
Ulrich, E. L. et al. BioMagResBank. Nucleic Acids Res. 36, D402–D408 (2007).
PubMed
PubMed Central
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).
CAS
PubMed
Google Scholar