Chemical exchange in biomacromolecules: Past, present, and future
Tóm tắt
Từ khóa
Tài liệu tham khảo
Cavanagh, 2007
Forsén, 1963, Study of moderately rapid chemical exchange reactions by means of nuclear magnetic double resonance, J. Chem. Phys., 39, 2892, 10.1063/1.1734121
Gutowsky, 1953, Dissociation, chemical exchange, and the proton magnetic resonance in some aqueous electrolytes, J. Chem. Phys., 21, 1688, 10.1063/1.1698644
Fejzo, 1990, Elimination of cross-relaxation effects from two-dimensional chemical-exchange spectra of macromolecules, J. Am. Chem. Soc., 112, 2574, 10.1021/ja00163a014
Palmer, 1991, Intramolecular motions of a zinc finger DNA-binding domain from xfin characterized by proton-detected natural abundance 13C heteronuclear NMR spectroscopy, J. Am. Chem. Soc., 113, 4371, 10.1021/ja00012a001
Kay, 1989, Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease, Biochemistry, 28, 8972, 10.1021/bi00449a003
Palmer, 2001, Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules, Methods Enzymol., 339, 204, 10.1016/S0076-6879(01)39315-1
Massi, 2006, Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase, Biochemistry, 45, 10787, 10.1021/bi060764c
Hodsdon, 1997, Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange, Biochemistry, 36, 2278, 10.1021/bi962018l
Wang, 2004, Dynamics of ATP-binding cassette contribute to allosteric control, nucleotide binding and energy tranduction in ABC transporters, J. Mol. Biol., 342, 525, 10.1016/j.jmb.2004.07.001
Akke, 1993, Effects of ion binding on the backbone dynamics in calbindin D9k determined by 15N NMR relaxation, Biochemistry, 32, 9832, 10.1021/bi00088a039
Loria, 1999, A relaxation-compensated Carr–Purcell–Meiboom–Gill sequence for characterizing chemical exchange by NMR spectroscopy, J. Am. Chem. Soc., 121, 2331, 10.1021/ja983961a
Szyperski, 1993, Protein dynamics studied by rotating frame 15N spin relaxation times, J. Biomol. NMR, 3, 151, 10.1007/BF00178259
Akke, 1996, Monitoring macromolecular motions on microsecond to millisecond time scales by R1ρ–R1 constant relaxation time NMR spectroscopy, J. Am. Chem. Soc., 118, 911, 10.1021/ja953503r
Otten, 2010, Probing microsecond time scale dynamics in proteins by methyl 1H Carr–Purcell–Meiboom–Gill relaxation dispersion NMR measurements: application to activation of the signaling protein NtrCr, J. Am. Chem. Soc., 132, 17004, 10.1021/ja107410x
Baldwin, 2010, 13CHD2 methyl group probes of millisecond time scale exchange in proteins by 1H relaxation dispersion: an application to proteasome gating residue dynamics, J. Am. Chem. Soc., 132, 10992, 10.1021/ja104578n
Weininger, 2012, Specific 12CβD212CγD2S13CεHD2 isotopomer labeling of methionine to characterize protein dynamics by 1H and 13C NMR relaxation dispersion, J. Am. Chem. Soc., 134, 18562, 10.1021/ja309294u
Hansen, 2012, Quantifying millisecond exchange dynamics in proteins by CPMG relaxation dispersion NMR using side-chain 1H probes, J. Am. Chem. Soc., 134, 3178, 10.1021/ja210711v
Krushelnitsky, 2013, Solid-state NMR approaches to internal dynamics of proteins: from picoseconds to microseconds and seconds, Acc. Chem. Res., 46, 2028, 10.1021/ar300292p
Abergel, 2003, On the use of the stochastic Liouville equation in NMR: application to R1ρ relaxation in the presence of exchange, Concepts Magn. Reson. A, 19, 134, 10.1002/cmr.a.10091
Sugase, 2013, Fast and accurate fitting of relaxation dispersion data using the flexible software package GLOVE, J. Biomol. NMR, 56, 275, 10.1007/s10858-013-9747-5
Bieri, 2011, Automated NMR relaxation dispersion data analysis using NESSY, BMC Bioinformatics, 12, 421, 10.1186/1471-2105-12-421
Trott, 2004, Theoretical study of R1ρ rotating-frame and R2 free-precession relaxation in the presence of n-site chemical exchange, J. Magn. Reson., 170, 104, 10.1016/j.jmr.2004.06.005
Jeener, 1979, Investigation of exchange processes by two-dimensional NMR spectroscopy, J. Chem. Phys., 71, 4546, 10.1063/1.438208
Montelione, 1989, 2D chemical exchange NMR spectroscopy by proton-detected heteronuclear correlation, J. Am. Chem. Soc., 111, 3096, 10.1021/ja00190a072
Wider, 1991, Studies of slow conformational equilibria in macromolecules by exchange of heteronuclear longitudinal 2-spin-order in a 2D difference correlation experiment, J. Biomol. NMR, 1, 93, 10.1007/BF01874572
Farrow, 1994, A heteronuclear correlation experiment for simultaneous determination of 15N longitudinal decay and chemical exchange rates of systems in slow equilibrium, J. Biomol. NMR, 4, 727, 10.1007/BF00404280
Li, 2013, Mechanism of E-cadherin dimerization probed by NMR relaxation dispersion, Proc. Natl. Acad. Sci. U. S. A., 110, 16462, 10.1073/pnas.1314303110
Miloushev, 2008, Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherins, Structure, 16, 1195, 10.1016/j.str.2008.05.009
Hu, 2011, Simultaneous quantification and identification of individual chemicals in metabolite mixtures by two-dimensional extrapolated time-zero 1H–13C HSQC (HSQC(0)), J. Am. Chem. Soc., 133, 1662, 10.1021/ja1095304
Li, 2009, TROSY-selected ZZ-exchange experiment for characterizing slow chemical exchange in large proteins, J. Biomol. NMR, 45, 357, 10.1007/s10858-009-9385-0
Sahu, 2007, TROSY-based z-exchange spectroscopy: application to the determination of the activation energy for intermolecular protein translocation between specific sites on different DNA molecules, J. Am. Chem. Soc., 129, 13232, 10.1021/ja074604f
Palmer, 2005, Solution NMR spin relaxation methods for characterizing chemical exchange in high-molecular-weight systems, Methods Enzymol., 394, 430, 10.1016/S0076-6879(05)94018-4
Morrison, 2012, Antiparallel EmrE exports drugs by exchanging between asymmetric structures, Nature, 481, 45, 10.1038/nature10703
Wang, 2002, Titration and exchange studies of liver fatty acid-binding protein with 13C-labeled long-chain fatty acids, Biochemistry, 41, 5453, 10.1021/bi011914g
Igumenova, 2007, Characterization of chemical exchange using residual dipolar coupling, J. Am. Chem. Soc., 129, 13396, 10.1021/ja0761636
Vallurupalli, 2007, Measurement of bond vector orientations in invisible excited states of proteins, Proc. Natl. Acad. Sci. U. S. A., 104, 18473, 10.1073/pnas.0708296104
Sarkar, 2007, Singlet-state exchange NMR spectroscopy for the study of very slow dynamic processes, J. Am. Chem. Soc., 129, 328, 10.1021/ja0647396
Davis, 1994, Direct measurements of the dissociation-rate constant for inhibitor-enzyme complexes via the T1ρ and T2 (CPMG) methods, J. Magn. Reson., Ser. B, 104, 266, 10.1006/jmrb.1994.1084
Traaseth, 2012, Heteronuclear adiabatic relaxation dispersion (HARD) for quantitative analysis of conformational dynamics in proteins, J. Magn. Reson., 219, 75, 10.1016/j.jmr.2012.03.024
Mangia, 2010, Probing slow protein dynamics by adiabatic R1ρ and R2ρ NMR experiments, J. Am. Chem. Soc., 132, 9979, 10.1021/ja1038787
Carver, 1972, A general two-site solution for the chemical exchange produced dependence of T2 upon the Carr–Purcell pulse separation, J. Magn. Reson., 6, 89
Allerhand, 1966, Analysis of Carr–Purcell spin-echo NMR experiments on multiple-spin systems. II. The effect of chemical exchange, J. Chem. Phys., 45, 902, 10.1063/1.1727703
Jen, 1978, Chemical exchange and NMR T2 relaxation—the multisite case, J. Magn. Reson., 30, 111
Ishima, 1999, Estimating the time scale of chemical exchange of proteins from measurements of transverse relaxation rates in solution, J. Biomol. NMR, 14, 369, 10.1023/A:1008324025406
Trott, 2002, R1ρ relaxation outside of the fast-exchange limit, J. Magn. Reson., 154, 157, 10.1006/jmre.2001.2466
Trott, 2003, An average-magnetization analysis of R1ρ relaxation outside of the fast exchange, Mol. Phys., 101, 753, 10.1080/0026897021000054826
Miloushev, 2005, R1ρ relaxation for two-site chemical exchange: general approximations and some exact solutions, J. Magn. Reson., 177, 221, 10.1016/j.jmr.2005.07.023
Baldwin, 2013, An R1ρ expression for a spin in chemical exchange between two sites with unequal transverse relaxation rates, J. Biomol. NMR, 55, 211, 10.1007/s10858-012-9694-6
Ishima, 2006, Accuracy of optimized chemical-exchange parameters derived by fitting CPMG R2 dispersion profiles when R20a≠R20b, J. Biomol. NMR, 34, 10.1007/s10858-005-6226-7
Fawzi, 2011, Atomic-resolution dynamics on the surface of amyloid-β protofibrils probed by solution NMR, Nature, 480, 268, 10.1038/nature10577
Skrynnikov, 2002, Reconstructing NMR spectra of “invisible” excited protein states using HSQC and HMQC experiments, J. Am. Chem. Soc., 124, 12352, 10.1021/ja0207089
Auer, 2010, Measurement of signs of chemical shift differences between ground and excited protein states: a comparison between H(S/M)QC and R1ρ methods, J. Biomol. NMR, 46, 205, 10.1007/s10858-009-9394-z
Baldwin, 2012, Measurement of the signs of methyl 13C chemical shift differences between interconverting ground and excited protein states by R1ρ: an application to αB-crystallin, J. Biomol. NMR, 53, 1, 10.1007/s10858-012-9617-6
Palmer, 1992, Suppression of the effects of cross-correlation between dipolar and anisotropic chemical shift relaxation mechanisms in the measurement of spin-spin relaxation rates, Mol. Phys., 75, 699, 10.1080/00268979200100511
Mulder, 2001, Measurement of slow (μs-ms) time scale dynamics in protein side chains by 15N relaxation dispersion NMR spectroscopy: application to Asn and Gln residues in a cavity mutant of T4 lysozyme, J. Am. Chem. Soc., 123, 967, 10.1021/ja003447g
Skrynnikov, 2001, Probing slow time scale dynamics at methyl-containing side chains in proteins by relaxation dispersion NMR measurements: application to methionine residues in a cavity mutant of T4 lysozyme, J. Am. Chem. Soc., 123, 4556, 10.1021/ja004179p
Hansen, 2008, An improved 15N relaxation dispersion experiment for the measurement of millisecond time-scale dynamics in proteins, J. Phys. Chem. B, 112, 5898, 10.1021/jp074793o
Esadze, 2011, Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear 1H–15N NMR spectroscopy, J. Am. Chem. Soc., 133, 909, 10.1021/ja107847d
Korzhnev, 2002, An NMR experiment for the accurate measurement of heteronuclear spin-lock relaxation rates, J. Am. Chem. Soc., 124, 10743, 10.1021/ja0204776
Massi, 2004, NMR R1ρ rotating-frame relaxation with weak radio frequency fields, J. Am. Chem. Soc., 126, 2247, 10.1021/ja038721w
Ban, 2012, Exceeding the limit of dynamics studies on biomolecules using high spin-lock field strengths with a cryogenically cooled probehead, J. Magn. Reson., 221, 1, 10.1016/j.jmr.2012.05.005
Kloiber, 2000, Differential multiple-quantum relaxation arising from cross-correlated time-modulation of isotropic chemical shifts, J. Biomol. NMR, 18, 33, 10.1023/A:1008317212558
Dittmer, 2004, Evidence for slow motion in proteins by multiple refocusing of heteronuclear nitrogen/proton multiple quantum coherences in NMR, J. Am. Chem. Soc., 126, 1314, 10.1021/ja0386243
Korzhnev, 2004, Multiple-quantum relaxation dispersion NMR spectroscopy probing millisecond time-scale dynamics in proteins: theory and application, J. Am. Chem. Soc., 126, 7320, 10.1021/ja049968b
Lundström, 2004, Quantitative analysis of conformational exchange contributions to 1H–15N multiple-quantum relaxation using field-dependent measurements. Time scale and structural characterization of exchange in a calmodulin C-terminal domain mutant, J. Am. Chem. Soc., 126, 928, 10.1021/ja037529r
Orekhov, 2004, Double- and zero-quantum NMR relaxation dispersion experiments sampling millisecond time scale dynamics in proteins, J. Am. Chem. Soc., 126, 1886, 10.1021/ja038620y
Del Rio, 2006, Detection of correlated dynamics on multiple timescales by measurement of the differential relaxation of zero- and double-quantum coherences involving sidechain methyl groups in proteins, J. Magn. Reson., 180, 1, 10.1016/j.jmr.2006.01.002
Hansen, 2007, An exchange-free measure of 15N transverse relaxation: an NMR spectroscopy application to the study of a folding intermediate with pervasive chemical exchange, J. Am. Chem. Soc., 129, 11468, 10.1021/ja072717t
Gill, 2011, Multiplet-filtered and gradient-selected zero-quantum TROSY experiments for 13C1H3 methyl groups in proteins, J. Biomol. NMR, 51, 245, 10.1007/s10858-011-9533-1
Salvi, 2012, Time scales of slow motions in ubiquitin explored by heteronuclear double resonance, J. Am. Chem. Soc., 134, 2481, 10.1021/ja210238g
Majumdar, 2004, Probing slow backbone dynamics in proteins using TROSY-based experiments to detect cross-correlated time-modulation of isotropic chemical shifts, J. Biomol. NMR, 28, 213, 10.1023/B:JNMR.0000013705.98136.99
Wang, 2002, Differential multiple quantum relaxation caused by chemical exchange outside the fast exchange limit, J. Biomol. NMR, 24, 263, 10.1023/A:1021687604854
Millet, 2000, The static magnetic field dependence of chemical exchange linebroadening defines the NMR chemical shift time scale, J. Am. Chem. Soc., 122, 2867, 10.1021/ja993511y
Wang, 2001, CPMG sequences with enhanced sensitivity to chemical exchange, J. Biomol. NMR, 21, 361, 10.1023/A:1013328206498
Wang, 2001, Functional dynamics in the active site of the ribonuclease binase, Proc. Natl. Acad. Sci. U. S. A., 98, 7684, 10.1073/pnas.121069998
Wang, 2003, Mapping chemical exchange in proteins with MW>50kD, J. Am. Chem. Soc., 125, 8968, 10.1021/ja035139z
Phan, 1996, Dynamic studies of a fibronectin type I module pair at three frequencies: anisotropic modeling and direct determination of conformational exchange, J. Biomol. NMR, 8, 369, 10.1007/BF00228140
Kroenke, 1998, Longitudinal and transverse 1H–15N dipolar/15N chemical shift anisotropy relaxation interference: unambiguous determination of rotational diffusion tensors and chemical exchange effects in biological macromolecules, J. Am. Chem. Soc., 120, 7905, 10.1021/ja980832l
Mulder, 1999, Microsecond time scale dynamics in the RXR DNA-binding domain from a combination of spin-echo and off-resonance rotating frame relaxation measurements, J. Biomol. NMR, 13, 275, 10.1023/A:1008354232281
Ban, 2013, Enhanced accuracy of kinetic information from CT-CPMG experiments by transverse rotating-frame spectroscopy, J. Biomol. NMR, 57, 73, 10.1007/s10858-013-9769-z
Lakomek, 2012, Measurement of 15N relaxation rates in perdeuterated proteins by TROSY-based methods, J. Biomol. NMR, 53, 209, 10.1007/s10858-012-9626-5
Igumenova, 2006, Off-resonance TROSY-selected R1ρ experiment with improved sensitivity for medium- and high-molecular-weight proteins, J. Am. Chem. Soc., 128, 8110, 10.1021/ja061692f
Vallurupalli, 2008, Probing structure in invisible protein states with anisotropic NMR chemical shifts, J. Am. Chem. Soc., 130, 2734, 10.1021/ja710817g
Ban, 2011, Kinetics of conformational sampling in ubiquitin, Angew. Chem., Int. Ed. Engl., 50, 11437, 10.1002/anie.201105086
Massi, 2005, Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1ρ relaxation experiments, Protein Sci., 14, 735, 10.1110/ps.041139505
Ishima, 2003, Extending the range of amide proton relaxation dispersion experiments in protein using a constant-time relaxation-compensated CPMG approach, J. Biomol. NMR, 25, 243, 10.1023/A:1022851228405
Eichmuller, 2005, A new amide proton R1ρ experiment permits accurate characterization of microsecond time-scale conformational exchange, J. Biomol. NMR, 32, 281, 10.1007/s10858-005-0658-y
Lundström, 2005, Off-resonance rotating-frame amide proton spin relaxation experiments measuring microsecond chemical exchange in proteins, J. Biomol. NMR, 32, 163, 10.1007/s10858-005-5027-3
Auer, 2009, Measuring the signs of 1Hα chemical shift differences between ground and excited protein states by off-resonance spin-lock R1ρ NMR spectroscopy, J. Am. Chem. Soc., 131, 10832, 10.1021/ja904315m
Lundström, 2009, Accurate measurement of α proton chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy, J. Am. Chem. Soc., 131, 1915, 10.1021/ja807796a
Vallurupalli, 2009, CPMG relaxation dispersion NMR experiments measuring glycine 1Hα and 13Cα chemical shifts in the ‘invisible’ excited states of proteins, J. Biomol. NMR, 45, 45, 10.1007/s10858-009-9310-6
Lundström, 2008, Measurement of carbonyl chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy: comparison between uniformly and selectively 13C labeled samples, J. Biomol. NMR, 42, 35, 10.1007/s10858-008-9260-4
Hansen, 2008, Probing chemical shifts of invisible states of proteins with relaxation dispersion NMR spectroscopy: how well can we do?, J. Am. Chem. Soc., 130, 2667, 10.1021/ja078337p
Ishima, 2004, Carbonyl carbon transverse relaxation dispersion measurements and ms-μs timescale motion in a protein hydrogen bond network, J. Biomol. NMR, 29, 187, 10.1023/B:JNMR.0000019249.50306.5d
O’Connell, 2009, Partially folded equilibrium intermediate of the villin headpiece HP67 defined by 13C relaxation dispersion, J. Biomol. NMR, 45, 85, 10.1007/s10858-009-9340-0
Lundström, 2009, Measuring 13Cβ chemical shifts of invisible excited states in proteins by relaxation dispersion NMR spectroscopy, J. Biomol. NMR, 44, 139, 10.1007/s10858-009-9321-3
Weininger, 2012, Conformational exchange of aromatic side chains characterized by L-optimized TROSY-selected 13C CPMG relaxation dispersion, J. Biomol. NMR, 54, 9, 10.1007/s10858-012-9656-z
Ishima, 2001, Optimized labeling of 13CHD2 methyl isotopomers in perdeuterated proteins: potential advantages for 13C relaxation studies of methyl dynamics of larger proteins, J. Biomol. NMR, 21, 167, 10.1023/A:1012482426306
Korzhnev, 2004, Probing slow dynamics in high molecular weight proteins by methyl-TROSY NMR spectroscopy: application to a 723-residue enzyme, J. Am. Chem. Soc., 126, 3964, 10.1021/ja039587i
Grey, 2006, Characterizing a partially folded intermediate of the villin headpiece domain under non-denaturing conditions: contribution of His41 to the pH-dependent stability of the N-terminal subdomain, J. Mol. Biol., 355, 1078, 10.1016/j.jmb.2005.11.001
Bouvignies, 2012, Measurement of proton chemical shifts in invisible states of slowly exchanging protein systems by chemical exchange saturation transfer, J. Phys. Chem. B, 116, 14311, 10.1021/jp311109u
Vallurupalli, 2012, Studying “invisible” excited protein states in slow exchange with a major state conformation, J. Am. Chem. Soc., 134, 8148, 10.1021/ja3001419
Hansen, 2013, Probing slowly exchanging protein systems via 13Cα-CEST: monitoring folding of the Im7 protein, J. Biomol. NMR, 55, 279, 10.1007/s10858-013-9711-4
Fawzi, 2012, Probing exchange kinetics and atomic resolution dynamics in high-molecular-weight complexes using dark-state exchange saturation transfer NMR spectroscopy, Nat. Protoc., 7, 1523, 10.1038/nprot.2012.077
van Zijl, 2011, Chemical exchange saturation transfer (CEST): what is in a name and what isn’t?, Magn. Reson. Med., 65, 927, 10.1002/mrm.22761
Lauzon, 2011, Using the water signal to detect invisible exchanging protons in the catalytic triad of a serine protease, J. Biomol. NMR, 50, 299, 10.1007/s10858-011-9527-z
Al-Hashimi, 2013, NMR studies of nucleic acid dynamics, J. Magn. Reson., 237, 191, 10.1016/j.jmr.2013.08.014
Hoogstraten, 2000, Active site dynamics in the lead-dependent ribozyme, Biochemistry, 39, 9951, 10.1021/bi0007627
Johnson, 2008, Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling, J. Am. Chem. Soc., 130, 16757, 10.1021/ja805759z
Wunderlich, 2012, Synthesis of (6-13C)pyrimidine nucleotides as spin-labels for RNA dynamics, J. Am. Chem. Soc., 134, 7558, 10.1021/ja302148g
Nikolova, 2009, Preparation, resonance assignment, and preliminary dynamics characterization of residue specific 13C/15N-labeled elongated DNA for the study of sequence-directed dynamics by NMR, J. Biomol. NMR, 45, 9, 10.1007/s10858-009-9350-y
Hansen, 2009, Extending the range of microsecond-to-millisecond chemical exchange detected in labeled and unlabeled nucleic acids by selective carbon R1ρ NMR spectroscopy, J. Am. Chem. Soc., 131, 3818, 10.1021/ja8091399
Latham, 2009, NMR chemical exchange as a probe for ligand-binding kinetics in a theophylline-binding RNA aptamer, J. Am. Chem. Soc., 131, 5052, 10.1021/ja900695m
Nikolova, 2011, Transient Hoogsteen base pairs in canonical duplex DNA, Nature, 470, 10.1038/nature09775
Nikolova, 2012, Probing transient Hoogsteen hydrogen bonds in canonical duplex DNA using NMR relaxation dispersion and single-atom substitution, J. Am. Chem. Soc., 134, 3667, 10.1021/ja2117816
Kloiber, 2011, Probing RNA dynamics via longitudinal exchange and CPMG relaxation dispersion NMR spectroscopy using a sensitive 13C-methyl label, Nucleic Acids Res., 39, 4340, 10.1093/nar/gkq1361
Palmer, 1992, Molecular dynamics analysis of NMR relaxation in a zinc-finger peptide, J. Am. Chem. Soc., 114, 9059, 10.1021/ja00049a043
Kordel, 1992, Backbone dynamics of calbindin D9k: comparison of molecular dynamics simulations and 15N NMR relaxation measurements, J. Am. Chem. Soc., 114, 4934, 10.1021/ja00038a086
Lipari, 1982, Protein dynamics and NMR relaxation: comparison of simulations with experiment, Nature, 300, 197, 10.1038/300197a0
Levy, 1983, Trajectory studies of NMR relaxation in flexible molecules, Adv. Chem. Ser., 204, 445, 10.1021/ba-1983-0204.ch018
Grey, 2003, Disulfide bond isomerization in basic pancreatic trypsin inhibitor: multisite chemical exchange quantified by CPMG relaxation dispersion and chemical shift modeling, J. Am. Chem. Soc., 125, 14324, 10.1021/ja0367389
Stafford, 2013, Thermal adaptation of conformational dynamics in ribonuclease H, PLoS Comput. Biol., 9, e1003218, 10.1371/journal.pcbi.1003218
De Simone, 2013, Characterization of the interdomain motions in hen lysozyme using residual dipolar couplings as replica-averaged structural restraints in molecular dynamics simulations, Biochemistry, 52, 6480, 10.1021/bi4007513
Robustelli, 2010, Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins, Structure, 18, 923, 10.1016/j.str.2010.04.016
Korzhnev, 2010, A transient and low-populated protein-folding intermediate at atomic resolution, Science, 329, 1312, 10.1126/science.1191723
Bouvignies, 2011, Solution structure of a minor and transiently formed state of a T4 lysozyme mutant, Nature, 477, 111, 10.1038/nature10349
Neudecker, 2012, Structure of an intermediate state in protein folding and aggregation, Science, 336, 362, 10.1126/science.1214203
Abergel, 2005, A Markov model for relaxation and exchange in NMR spectroscopy, J. Phys. Chem. B, 109, 4837, 10.1021/jp0458304
Xue, 2012, Microsecond time-scale conformational exchange in proteins: using long molecular dynamics trajectory to simulate NMR relaxation dispersion data, J. Am. Chem. Soc., 134, 2555, 10.1021/ja206442c
Shaw, 2010, Atomic-level characterization of the structural dynamics of proteins, Science, 330, 341, 10.1126/science.1187409
Otting, 1993, Disulfide bond isomerization in BPTI and BPTI(G36S): an NMR study of correlated mobility in proteins, Biochemistry, 32, 3571, 10.1021/bi00065a008
Skalicky, 2001, Aromatic ring-flipping in supercooled water: implications for NMR-based structural biology of proteins, J. Am. Chem. Soc., 123, 388, 10.1021/ja003220l
Denisov, 1996, Using buried water molecules to explore the energy landscape of proteins, Nat. Struct. Biol., 3, 505, 10.1038/nsb0696-505
Hernandez, 2012, Experimentally assessing molecular dynamics sampling of the protein native state conformational distribution, Biophys. Chem., 163–164, 21, 10.1016/j.bpc.2012.02.002
Persson, 2013, Transient access to the protein interior: simulation versus NMR, J. Am. Chem. Soc., 135, 8735, 10.1021/ja403405d
Piana, 2013, Atomic-level description of ubiquitin folding, Proc. Natl. Acad. Sci. U. S. A., 110, 5915, 10.1073/pnas.1218321110
Farber, 2011, Concerted dynamics link allosteric sites in the PBX homeodomain, J. Mol. Biol., 405, 819, 10.1016/j.jmb.2010.11.016
Petit, 2009, Hidden dynamic allostery in a PDZ domain, Proc. Natl. Acad. Sci. U. S. A., 106, 18249, 10.1073/pnas.0904492106
Boehr, 2013, A distal mutation perturbs dynamic amino acid networks in dihydrofolate reductase, Biochemistry, 52, 4605, 10.1021/bi400563c
Popovych, 2006, Dynamically driven protein allostery, Nat. Struct. Mol. Biol., 13, 831, 10.1038/nsmb1132
Brüschweiler, 2009, Direct observation of the dynamic process underlying allosteric signal transmission, J. Am. Chem. Soc., 131, 3063, 10.1021/ja809947w
Kleckner, 2012, Mechanisms of allosteric gene regulation by NMR quantification of microsecond-millisecond protein dynamics, J. Mol. Biol., 415, 372, 10.1016/j.jmb.2011.11.019
Vugmeyster, 2000, 15N R1ρ measurements allow the determination of ultrafast protein folding rates, J. Am. Chem. Soc., 122, 5387, 10.1021/ja000225+
Meinhold, 2011, Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion, Proc. Natl. Acad. Sci. U. S. A., 108, 9078, 10.1073/pnas.1105682108
Neudecker, 2007, φ-Value analysis of a three-state protein folding pathway by NMR relaxation dispersion spectroscopy, Proc. Natl. Acad. Sci. U. S. A., 104, 15717, 10.1073/pnas.0705097104
Cho, 2010, φ-Value analysis for ultrafast folding proteins by NMR relaxation dispersion, J. Am. Chem. Soc., 132, 450, 10.1021/ja909052h
Volkman, 2001, Two-state allosteric behavior in a single-domain signaling protein, Science, 291, 2429, 10.1126/science.291.5512.2429
Hammes, 2009, Conformational selection or induced fit: a flux description of reaction mechanism, Proc. Natl. Acad. Sci. U. S. A., 106, 13737, 10.1073/pnas.0907195106
Sugase, 2007, Mechanism of coupled folding and binding of an intrinsically disordered protein, Nature, 447, 1021, 10.1038/nature05858
Cho, 2011, Tuning protein autoinhibition by domain destabilization, Nat. Struct. Mol. Biol., 18, 550, 10.1038/nsmb.2039
Tzeng, 2013, Allosteric inhibition through suppression of transient conformational states, Nat. Chem. Biol., 9, 462, 10.1038/nchembio.1250
Boehr, 2010, Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands, Proc. Natl. Acad. Sci. U. S. A., 107, 1373, 10.1073/pnas.0914163107
Bhabha, 2011, A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis, Science, 332, 234, 10.1126/science.1198542
Eisenmesser, 2005, Intrinsic dynamics of an enzyme underlies catalysis, Nature, 438, 117, 10.1038/nature04105
Labeikovsky, 2007, Structure and dynamics of Pin1 during catalysis by NMR, J. Mol. Biol., 367, 1370, 10.1016/j.jmb.2007.01.049
Kamerlin, 2010, At the dawn of the 21st century: is dynamics the missing link for understanding enzyme catalysis?, Proteins, 78, 1339, 10.1002/prot.22654
Doshi, 2012, Resolving the complex role of enzyme conformational dynamics in catalytic function, Proc. Natl. Acad. Sci. U. S. A., 109, 5699, 10.1073/pnas.1117060109
Adamczyk, 2011, Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions, Proc. Natl. Acad. Sci. U. S. A., 108, 14115, 10.1073/pnas.1111252108
Li, 2011, The feasibility of parameterizing four-state equilibria using relaxation dispersion measurements, J. Biomol. NMR, 51, 57, 10.1007/s10858-011-9541-1
Shaka, 1985, Computer-optimized decoupling scheme for wideband applications and low-level operation, J. Magn. Reson., 64, 547
Marion, 1989, Rapid recording of 2D NMR spectra without phase cycling. Application to the study of hydrogen exchange in proteins, J. Magn. Reson., 85, 393
Mulder, 1998, An off-resonance rotating frame relaxation experiment for the investigation of macromolecular dynamics using adiabatic rotations, J. Magn. Reson., 131, 351, 10.1006/jmre.1998.1380
Kay, 1992, Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity, J. Am. Chem. Soc., 114, 10663, 10.1021/ja00052a088
Shaka, 1983, An improved sequence for broadband decoupling: WALTZ-16, J. Magn. Reson., 52, 334