NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model Free Framework and Markov State Simulations.
J Phys Chem B. 2013 May 2;
Authors: Xia J, Deng NJ, Levy RM
Abstract
Calculating NMR relaxation effects for proteins with dynamics on multiple timescales generally requires very long trajectories based on conventional molecular dynamics simulations. In this report, we have built Markov state models from multiple MD trajectories and used the resulting MSM to capture the very fast internal motions of the protein within a free energy basin on a time scale up to hundreds of picoseconds and the more than three orders of magnitude slower conformational exchange between macrostates. To interpret the relaxation data, we derive new equations using the model free framework which includes two slowly exchanging macrostates, each of which also exhibits fast local motions.. Using simulations of HIV-1 Protease as an example, we show how the populations of slowly exchanging conformational states as well as order parameters for the different states can be determined from the NMR relaxation data.
PMID: 23638941 [PubMed - as supplied by publisher]
[NMR paper] Fast hydrogen exchange affects (15)N relaxation measurements in intrinsically disordered proteins.
Fast hydrogen exchange affects (15)N relaxation measurements in intrinsically disordered proteins.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Fast hydrogen exchange affects (15)N relaxation measurements in intrinsically disordered proteins.
J Biomol NMR. 2013 Jan 12;
Authors: Kim S, Wu KP, Baum J
Abstract
Unprotected amide protons can undergo fast hydrogen exchange (HX) with protons from the solvent. Generally, NMR experiments using the out-and-back...
nmrlearner
Journal club
0
02-03-2013 10:22 AM
Mathematical treatment of adiabatic fast passage pulses for the computation of nuclear spin relaxation rates in proteins with conformational exchange
Mathematical treatment of adiabatic fast passage pulses for the computation of nuclear spin relaxation rates in proteins with conformational exchange
Abstract Although originally designed for broadband inversion and decoupling in NMR spectroscopy, recent methodological developments have introduced adiabatic fast passage (AFP) pulses into the field of protein dynamics. AFP pulses employ a frequency sweep, and have not only superior inversion properties with respect to offset effects, but they are also easily implemented into a pulse sequence. As magnetization is dragged from the +z to...
nmrlearner
Journal club
0
09-30-2011 08:01 PM
Measuring Screw-Sense Preference in a Helical Oligomer by Comparison of 13C NMR Signal Separation at Slow and Fast Exchange
Measuring Screw-Sense Preference in a Helical Oligomer by Comparison of 13C NMR Signal Separation at Slow and Fast Exchange
Jordi Sola?, Gareth A. Morris and Jonathan Clayden
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja1097034/aop/images/medium/ja-2010-097034_0001.gif
Journal of the American Chemical Society
DOI: 10.1021/ja1097034
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/NJjFWlcOo9Q
nmrlearner
Journal club
0
02-26-2011 01:07 PM
TROSY-selected ZZ-exchange experiment for characterizing slow chemical exchange in large proteins
TROSY-selected ZZ-exchange experiment for characterizing slow chemical exchange in large proteins
Abstract A TROSY-selected ZZ-exchange experiment is described for measuring slow chemical exchange rates by monitoring the TROSY component of 15N longitudinal magnetization. Application of the proposed pulse sequence to the cadherin 8 N-terminal extracelluar domain demonstrates that enhanced sensitivity is obtained, compared to a previously described TROSY-detected ZZ-exchange sequence (Sahu et al. J Am Chem Soc 129: 13232â??13237, 2007), by preserving the TROSY effect during the mixing...
nmrlearner
Journal club
0
01-09-2011 12:46 PM
[NMR paper] Slow internal dynamics in proteins: application of NMR relaxation dispersion spectros
Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme.
Related Articles Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme.
J Am Chem Soc. 2002 Feb 20;124(7):1443-51
Authors: Mulder FA, Hon B, Mittermaier A, Dahlquist FW, Kay LE
Recently developed carbon transverse relaxation dispersion experiments (Skrynnikov, N. R.; et al. J. Am. Chem. Soc. 2001, 123, 4556-4566) were...
nmrlearner
Journal club
0
11-24-2010 08:49 PM
[NMR paper] NMR 15N relaxation and structural studies reveal slow conformational exchange in bars
NMR 15N relaxation and structural studies reveal slow conformational exchange in barstar C40/82A.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles NMR 15N relaxation and structural studies reveal slow conformational exchange in barstar C40/82A.
J Mol Biol. 1997 May 2;268(2):494-511
Authors: Wong KB, Fersht AR, Freund SM
Barstar an 89-residue protein consisting of four helices and a three-stranded parallel beta-sheet, is the intracellular inhibitor of the...
nmrlearner
Journal club
0
08-22-2010 03:31 PM
[NMR paper] NMR 15N relaxation and structural studies reveal slow conformational exchange in bars
NMR 15N relaxation and structural studies reveal slow conformational exchange in barstar C40/82A.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles NMR 15N relaxation and structural studies reveal slow conformational exchange in barstar C40/82A.
J Mol Biol. 1997 May 2;268(2):494-511
Authors: Wong KB, Fersht AR, Freund SM
Barstar an 89-residue protein consisting of four helices and a three-stranded parallel beta-sheet, is the intracellular inhibitor of the...
nmrlearner
Journal club
0
08-22-2010 03:03 PM
[NMR paper] Internal motions of apo-neocarzinostatin as studied by 13C NMR methine relaxation at
Internal motions of apo-neocarzinostatin as studied by 13C NMR methine relaxation at natural abundance.
Related Articles Internal motions of apo-neocarzinostatin as studied by 13C NMR methine relaxation at natural abundance.
J Biomol NMR. 1995 Apr;5(3):233-44
Authors: Mispelter J, Lefèvre C, Adjadj E, Quiniou E, Favaudon V
Dynamics of the backbone and some side chains of apo-neocarzinostatin, a 10.7 kDa carrier protein, have been studied from 13C relaxation rates R1, R2 and steady-state 13C-(1H) NOEs, measured at natural abundance. Relaxation...