Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear (1)H-(15)N NMR Spectroscopy.
J Am Chem Soc. 2010 Dec 27;
Authors: Esadze A, Li DW, Wang T, Bru?schweiler R, Iwahara J
Despite their importance in macromolecular interactions and functions, the dynamics of lysine side-chain amino groups in proteins are not well understood. In this study, we have developed the methodology for the investigations of the dynamics of lysine NH(3)(+) groups by NMR spectroscopy and computation. By using (1)H-(15)N heteronuclear correlation experiments optimized for (15)NH(3)(+) moieties, we have analyzed the dynamic behavior of individual lysine NH(3)(+) groups in human ubiquitin at 2 °C and pH 5. We modified the theoretical framework developed previously for CH(3) groups and used it to analyze (15)N relaxation data for the NH(3)(+) groups. For six lysine NH(3)(+) groups out of seven in ubiquitin, we have determined model-free order parameters, correlation times for bond rotation, and reorientation of the symmetry axis occurring on a pico- to nanosecond time scale. From CPMG relaxation dispersion experiment for lysine NH(3)(+) groups, slower dynamics occurring on a millisecond time scale have also been detected for Lys27. The NH(3)(+) groups of Lys48, which plays a key role as the linkage site in ubiquitination for proteasomal degradation, was found to be highly mobile with the lowest order parameter among the six NH(3)(+) groups analyzed by NMR. We compared the experimental order parameters for the lysine NH(3)(+) groups with those from a 1 ?s molecular dynamics simulation in explicit solvent and found good agreement between the two. Furthermore, both the computer simulation and the experimental correlation times for the bond rotations of NH(3)(+) groups suggest that their hydrogen bonding is highly dynamic with a subnanosecond lifetime. This study demonstrates the utility of combining NMR experiment and simulation for an in-depth characterization of the dynamics of these functionally most important side-chains of ubiquitin.
PMID: 21186799 [PubMed - as supplied by publisher]
Quantifying millisecond time-scale exchange in proteins by CPMG relaxation dispersion NMR spectroscopy of side-chain carbonyl groups
Quantifying millisecond time-scale exchange in proteins by CPMG relaxation dispersion NMR spectroscopy of side-chain carbonyl groups
Abstract A new pulse sequence is presented for the measurement of relaxation dispersion profiles quantifying millisecond time-scale exchange dynamics of side-chain carbonyl groups in uniformly 13C labeled proteins. The methodology has been tested using the 87-residue colicin E7 immunity protein, Im7, which is known to fold via a partially structured low populated intermediate that interconverts with the folded, ground state on the millisecond time-scale....
nmrlearner
Journal club
0
06-20-2011 03:31 PM
Quantifying millisecond time-scale exchange in proteins by CPMG relaxation dispersion NMR spectroscopy of side-chain carbonyl groups.
Quantifying millisecond time-scale exchange in proteins by CPMG relaxation dispersion NMR spectroscopy of side-chain carbonyl groups.
Quantifying millisecond time-scale exchange in proteins by CPMG relaxation dispersion NMR spectroscopy of side-chain carbonyl groups.
J Biomol NMR. 2011 Jun 18;
Authors: Hansen AL, Kay LE
A new pulse sequence is presented for the measurement of relaxation dispersion profiles quantifying millisecond time-scale exchange dynamics of side-chain carbonyl groups in uniformly (13)C labeled proteins. The methodology has...
nmrlearner
Journal club
0
06-18-2011 01:10 PM
Threonine side chain conformational population distribution of a type I antifreeze protein on interacting with ice surface studied via (13)C-(15)N dynamic REDOR NMR.
Threonine side chain conformational population distribution of a type I antifreeze protein on interacting with ice surface studied via (13)C-(15)N dynamic REDOR NMR.
Threonine side chain conformational population distribution of a type I antifreeze protein on interacting with ice surface studied via (13)C-(15)N dynamic REDOR NMR.
Solid State Nucl Magn Reson. 2011 Mar 23;
Authors: Mao Y, Jeong M, Wang T, Ba Y
Antifreeze proteins (AFPs) provide survival mechanism for species living in subzero environments by lowering the freezing points of their...
nmrlearner
Journal club
0
04-08-2011 10:00 AM
Probing Protein Side Chain Dynamics via (13)C NMR Relaxation.
Probing Protein Side Chain Dynamics via (13)C NMR Relaxation.
Probing Protein Side Chain Dynamics via (13)C NMR Relaxation.
Protein Pept Lett. 2011 Jan 11;
Authors: Yang D
Protein side chain dynamics is associated with protein stability, folding, and intermolecular interactions. Detailed dynamics information is crucial for the understanding of protein function and biochemical and biophysical properties, which can be obtained using NMR relaxation techniques. In this review, (13)C relaxation of methine, methylene and methyl groups with and without...
nmrlearner
Journal club
0
01-13-2011 12:00 PM
Solid-state NMR detection of (14)N--(13)C dipolar couplings between amino acid side groups provides constraints on amyloid fibril architecture.
Solid-state NMR detection of (14)N--(13)C dipolar couplings between amino acid side groups provides constraints on amyloid fibril architecture.
Solid-state NMR detection of (14)N--(13)C dipolar couplings between amino acid side groups provides constraints on amyloid fibril architecture.
Magn Reson Chem. 2011 Jan 3;
Authors: Middleton DA
Solid-state nuclear magnetic resonance (SSNMR) is a powerful technique for the structural analysis of amyloid fibrils. With suitable isotope labelling patterns, SSNMR can provide constraints on the secondary...
nmrlearner
Journal club
0
01-05-2011 09:51 PM
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear 1H-15N NMR Spectroscopy
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear 1H-15N NMR Spectroscopy
Alexandre Esadze, Da-Wei Li, Tianzhi Wang, Rafael Bru?schweiler and Junji Iwahara
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja107847d/aop/images/medium/ja-2010-07847d_0007.gif
Journal of the American Chemical Society
DOI: 10.1021/ja107847d
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/iFwgRBt-zto
nmrlearner
Journal club
0
12-28-2010 05:27 AM
[NMR paper] What contributions to protein side-chain dynamics are probed by NMR experiments? A mo
What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis.
Related Articles What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis.
J Mol Biol. 2005 May 27;349(1):185-203
Authors: Best RB, Clarke J, Karplus M
Molecular dynamics simulations of the structurally homologous proteins TNfn3 and FNfn10 have been used to investigate the contributions to side-chain dynamics measured by NMR relaxation experiments. The...
nmrlearner
Journal club
0
11-24-2010 11:14 PM
[NMR paper] Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studi
Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studies of R. capsulatus ferrocytochrome c2.
Related Articles Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studies of R. capsulatus ferrocytochrome c2.
Biochemistry. 2001 Jun 5;40(22):6559-69
Authors: Flynn PF, Bieber Urbauer RJ, Zhang H, Lee AL, Wand AJ
A detailed characterization of the main chain and side chain dynamics in R. capsulatus ferrocytochrome c(2) derived from (2)H NMR relaxation of methyl group resonances is...
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear (1)H-(15)N NMR Spectroscopy.
Linear Mode
