Protein folding studied by real-time NMR spectroscopy.

Real-time NMR spectroscopy developed to a generally applicable method to follow protein folding reactions. It combines the access to high resolution data with kinetic experiments allowing very detailed insights into the development of the protein structure during different steps of folding. The present review concentrates mainly on the progress of real-time NMR during the last 5 years. Starting from simple 1D experiments, mainly changes of the chemical shifts and line widths of the resonances have been used to analyze the different states populated during the folding reactions. Today, we have a broad spectrum of 1D, 2D, and even 3D NMR methods focusing on different characteristics of the folding polypeptide chains. More than 20 proteins have been investigated so far by these time-resolved experiments and the main results and conclusions are discussed in this report. Real-time NMR provides comprehensive contributions for joining experiment and theory within the 'new view' of protein folding.

[1]  R. L. Baldwin,et al.  Nuclear magnetic resonance evidence for a structural intermediate at an early stage in the refolding of ribonuclease A. , 1978, Journal of molecular biology.

[2]  B. Sykes,et al.  STOPPED FLOW FOURIER TRANSFORM NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY, AN APPLICATION TO THE ALPHA-CHYMOTRYPSIN-CATALYZED HYDROLYSIS OF TERT.-BUTYL-L-PHENYLALANINE , 1975 .

[3]  A. Alexandrescu,et al.  An NMR investigation of solution aggregation reactions preceding the misassembly of acid-denatured cold shock protein A into fibrils. , 1999, Journal of molecular biology.

[4]  R. R. Ernst,et al.  Study of transient chemical reactions by NMR. Fast stopped-flow fourier transform experiments , 1979 .

[5]  K. Kuwajima.  The molten globule state of α‐lactalbumin , 1996, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[6]  H. Schwalbe,et al.  Monitoring the Kinetics of Ion-Dependent Protein Folding by Time-Resolved NMR Spectroscopy at Atomic Resolution , 2000 .

[7]  Charles L Brooks,et al.  Protein and peptide folding explored with molecular simulations. , 2002, Accounts of chemical research.

[8]  A. Fersht,et al.  Real‐time NMR studies on folding of mutants of barnase and chymotrypsin inhibitor 2 , 1998, FEBS letters.

[9]  S. Panchal,et al.  Unfolding kinetics of tryptophan side chains in the dimerization and hinge regions of HIV-I protease tethered dimer by real time NMR spectroscopy. , 2000, Biochemical and biophysical research communications.

[10]  C D Kroenke,et al.  Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. , 2001, Methods in enzymology.

[11]  G. Rose,et al.  Is protein folding hierarchic? II. Folding intermediates and transition states. , 1999, Trends in biochemical sciences.

[12]  C M Dobson,et al.  Slow cooperative folding of a small globular protein HPr. , 1998, Biochemistry.

[13]  Folding of a β-sheet Protein Monitored by Real-time NMR Spectroscopy , 2003 .

[14]  C. Dobson,et al.  Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques. , 1999, Biochemistry.

[15]  J. Baum,et al.  Folding and conformational consequences of glycine to alanine replacements at different positions in a collagen model peptide. , 2002, Biochemistry.

[16]  K. Wüthrich,et al.  Amide protein exchange and surface conformation of the basic pancreatic trypsin inhibitor in solution. Studies with two-dimensional nuclear magnetic resonance. , 1982, Journal of molecular biology.

[17]  R. H. Pain,et al.  Mechanisms of protein folding , 1994 .

[18]  E. Barbar.  NMR characterization of partially folded and unfolded conformational ensembles of proteins. , 1999, Biopolymers.

[19]  H. Dyson,et al.  Characterization of a folding intermediate of apoplastocyanin trapped by proline isomerization. , 1993, Biochemistry.

[20]  D. Laurents,et al.  Characterization of the unfolding pathway of hen egg white lysozyme. , 1997, Biochemistry.

[21]  Robert L. Baldwin,et al.  Direct NMR evidence for an intermediate preceding the rate-limiting step in the unfolding of ribonuclease A , 1995, Nature.

[22]  M. Karplus,et al.  Protein Folding: A Perspective from Theory and Experiment. , 1998, Angewandte Chemie.

[23]  C. Dobson,et al.  The Interaction of the Molecular Chaperone α-Crystallin with Unfolding α-Lactalbumin: A Structural and Kinetic Spectroscopic Study , 2002 .

[24]  J. Carver,et al.  Clusterin is an extracellular chaperone that specifically interacts with slowly aggregating proteins on their off‐folding pathway , 2002, FEBS letters.

[25]  J. Carver,et al.  The Interaction of the Molecular Chaperone, α-Crystallin, with Molten Globule States of Bovine α-Lactalbumin* , 1997, The Journal of Biological Chemistry.

[26]  C M Dobson,et al.  Protein Folding Monitored at Individual Residues During a Two-Dimensional NMR Experiment , 1996, Science.

[27]  P. Wright,et al.  Hydrogen exchange in the carbon monoxide complex of soybean leghemoglobin. , 1996, European journal of biochemistry.

[28]  M. Kirschner,et al.  Sequence-specific and phosphorylation-dependent proline isomerization: a potential mitotic regulatory mechanism. , 1997, Science.

[29]  B. Sykes,et al.  Stopped-flow nuclear magnetic resonance spectroscopy , 1972 .

[30]  H. Senn,et al.  Fast-HMQC using Ernst angle pulses: An efficient tool for screening of ligand binding to target proteins , 1997, Journal of biomolecular NMR.

[31]  T. Schindler,et al.  A protein folding intermediate of ribonuclease T1 characterized at high resolution by 1D and 2D real-time NMR spectroscopy. , 1999, Journal of molecular biology.

[32]  N. S. Bhavesh,et al.  Real time NMR monitoring of local unfolding of HIV‐1 protease tethered dimer driven by autolysis , 2001, FEBS letters.

[33]  K. Kuwajima,et al.  Evidence for identity between the equilibrium unfolding intermediate and a transient folding intermediate: a comparative study of the folding reactions of alpha-lactalbumin and lysozyme. , 1986, Biochemistry.

[34]  C. Dobson.  Protein misfolding, evolution and disease. , 1999, Trends in biochemical sciences.

[35]  A. Fersht,et al.  The refolding of cis- and trans-peptidylprolyl isomers of barstar. , 1993, Biochemistry.

[36]  T. Holak,et al.  Protein folding and stability of human CDK inhibitor p19(INK4d). , 2002, Journal of molecular biology.

[37]  T. Härd,et al.  Simulations of NMR pulse sequences during equilibrium and non-equilibrium chemical exchange , 2000, Journal of biomolecular NMR.

[38]  Jonathan A. Jones,et al.  Characterisation of protein unfolding by NMR diffusion measurements , 1997 .

[39]  H. Dyson,et al.  Insights into protein folding from NMR. , 1996, Annual review of physical chemistry (Print).

[40]  J. E. Tanner,et al.  Spin diffusion measurements : spin echoes in the presence of a time-dependent field gradient , 1965 .

[41]  K. Mayo,et al.  Cell adhesion promoting peptide GVKGDKGNPGWPGAP from the collagen type IV triple helix: cis/trans proline-induced multiple 1H NMR conformations and evidence for a KG/PG multiple turn repeat motif in the all-trans proline state. , 1991, Biochemistry.

[42]  S. Walter Englander,et al.  Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR , 1988, Nature.

[43]  T. Schindler,et al.  15N relaxation study of the cold shock protein CspB at various solvent viscosities , 2003, Journal of biomolecular NMR.

[44]  C. Dobson,et al.  Real-Time NMR Studies of Protein Folding , 1998 .

[45]  J. Baum,et al.  Direct NMR measurement of folding kinetics of a trimeric peptide. , 1996, Biochemistry.

[46]  J. Baum,et al.  Residue-specific real-time NMR diffusion experiments define the association states of proteins during folding. , 2002, Journal of the American Chemical Society.

[47]  G Fischer,et al.  Side-chain effects on peptidyl-prolyl cis/trans isomerisation. , 1998, Journal of molecular biology.

[48]  T. Oas,et al.  Mechanism of fast protein folding. , 2002, Annual review of biochemistry.

[49]  C. Dobson,et al.  The folding of hen lysozyme involves partially structured intermediates and multiple pathways , 1992, Nature.

[50]  T. Szyperski,et al.  GFT NMR, a new approach to rapidly obtain precise high-dimensional NMR spectral information. , 2003, Journal of the American Chemical Society.

[51]  C. Dobson,et al.  Stopped-Flow Photo-CIDNP Observation of Protein Folding , 1997 .

[52]  H. Roder.  Structural characterization of protein folding intermediates by proton magnetic resonance and hydrogen exchange. , 1989, Methods in enzymology.

[53]  C. Dobson,et al.  Protein folding kinetics from magnetization transfer nuclear magnetic resonance , 1984 .

[54]  I D Campbell,et al.  Folding kinetics of the SH3 domain of PI3 kinase by real-time NMR combined with optical spectroscopy. , 1998, Journal of molecular biology.

[55]  L Mayne,et al.  Protein folding studied using hydrogen-exchange labeling and two-dimensional NMR. , 1992, Annual review of biophysics and biomolecular structure.

[56]  C M Dobson,et al.  Slow folding of muscle acylphosphatase in the absence of intermediates. , 1998, Journal of molecular biology.

[57]  G. Rose,et al.  Is protein folding hierarchic? I. Local structure and peptide folding. , 1999, Trends in biochemical sciences.

[58]  Charles S. Johnson,et al.  A PFG NMR experiment for accurate diffusion and flow studies in the presence of eddy currents , 1991 .

[59]  J. Udgaonkar,et al.  Observation of multistate kinetics during the slow folding and unfolding of barstar. , 1999, Biochemistry.

[60]  L. Kay,et al.  Slow dynamics in folded and unfolded states of an SH3 domain. , 2001, Journal of the American Chemical Society.

[61]  C. Roumestand,et al.  Equilibrium and pressure-jump relaxation studies of the conformational transitions of P13MTCP1. , 2002, Journal of molecular biology.

[62]  C. Dobson,et al.  Rapid collapse and slow structural reorganisation during the refolding of bovine alpha-lactalbumin. , 1999, Journal of molecular biology.

[63]  A. Wand,et al.  Two-dimensional 1H NMR studies of cytochrome c: hydrogen exchange in the N-terminal helix. , 1986, Biochemistry.

[64]  D. Raleigh,et al.  15N R(1ρ) measurements allow the determination of ultrafast protein folding rates [1] , 2000 .

[65]  F. Richards,et al.  Improved synthetic methods for the selective deuteration of aromatic amino acids: applications of selective protonation towards the identification of protein folding intermediates through nuclear magnetic resonance. , 1993, Biochimica et biophysica acta.

[66]  Robert L. Baldwin,et al.  NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A , 1988, Nature.