scholarly journals Conformational exchange of aromatic side chains by 1H CPMG relaxation dispersion

2018 ◽  
Vol 72 (1-2) ◽  
pp. 105-114 ◽  
Author(s):  
Heiner N. Raum ◽  
Matthias Dreydoppel ◽  
Ulrich Weininger
Keyword(s):  
Relaxation Dispersion ◽  
Conformational Exchange ◽  
Side Chains ◽  
Cpmg Relaxation Dispersion ◽  
1H Cpmg Relaxation Dispersion ◽  
Aromatic Side Chains

scholarly journals 1H R1ρ relaxation dispersion experiments in aromatic side chains

2021 ◽  
Author(s):  
Matthias Dreydoppel ◽  
Roman J. Lichtenecker ◽  
Mikael Akke ◽  
Ulrich Weininger
Keyword(s):  
Chemical Shift ◽  
Active Sites ◽  
Isotope Labeling ◽  
Relaxation Dispersion ◽  
Conformational Exchange ◽  
Side Chains ◽  
Transverse Relaxation Rate ◽  
Spin Lock ◽  
Spin Pairs ◽  
Aromatic Side Chains

AbstractAromatic side chains are attractive probes of protein dynamic, since they are often key residues in enzyme active sites and protein binding sites. Dynamic processes on microsecond to millisecond timescales can be studied by relaxation dispersion experiments that attenuate conformational exchange contributions to the transverse relaxation rate by varying the refocusing frequency of applied radio-frequency fields implemented as either CPMG pulse trains or continuous spin-lock periods. Here we present an aromatic 1H R1ρ relaxation dispersion experiment enabling studies of two to three times faster exchange processes than achievable by existing experiments for aromatic side chains. We show that site-specific isotope labeling schemes generating isolated 1H–13C spin pairs with vicinal 2H–12C moieties are necessary to avoid anomalous relaxation dispersion profiles caused by Hartmann–Hahn matching due to the 3JHH couplings and limited chemical shift differences among 1H spins in phenylalanine, tyrosine and the six-ring moiety of tryptophan. This labeling pattern is sufficient in that remote protons do not cause additional complications. We validated the approach by measuring ring-flip kinetics in the small protein GB1. The determined rate constants, kflip, agree well with previous results from 13C R1ρ relaxation dispersion experiments, and yield 1H chemical shift differences between the two sides of the ring in good agreement with values measured under slow-exchange conditions. The aromatic1H R1ρ relaxation dispersion experiment in combination with the site-selective 1H–13C/2H–12C labeling scheme enable measurement of exchange rates up to kex = 2kflip = 80,000 s–1, and serve as a useful complement to previously developed 13C-based methods.

scholarly journals Site-selective 1H/2H labeling enables artifact-free 1H CPMG relaxation dispersion experiments in aromatic side chains

2019 ◽  
Vol 73 (10-11) ◽  
pp. 633-639
Author(s):  
Heiner N. Raum ◽  
Julia Schörghuber ◽  
Matthias Dreydoppel ◽  
Roman J. Lichtenecker ◽  
Ulrich Weininger
Keyword(s):  
Active Sites ◽  
Relaxation Dispersion ◽  
Side Chains ◽  
Anomalous Relaxation ◽  
Cpmg Relaxation Dispersion ◽  
Key Residues ◽  
Site Selective ◽  
Unfolding Kinetics ◽  
Kinetics Of ◽  
Aromatic Side Chains

Abstract Aromatic side chains are often key residues in enzyme active sites and protein binding sites, making them attractive probes of protein dynamics on the millisecond timescale. Such dynamic processes can be studied by aromatic 13C or 1H CPMG relaxation dispersion experiments. Aromatic 1H CPMG relaxation dispersion experiments in phenylalanine, tyrosine and the six-ring moiety of tryptophan, however, are affected by 3J 1H–1H couplings which are causing anomalous relaxation dispersion profiles. Here we show that this problem can be addressed by site-selective 1H/2H labeling of the aromatic side chains and that artifact-free relaxation dispersion profiles can be acquired. The method has been further validated by measuring folding–unfolding kinetics of the small protein GB1. The determined rate constants and populations agree well with previous results from 13C CPMG relaxation dispersion experiments. Furthermore, the CPMG-derived chemical shift differences between the folded and unfolded states are in excellent agreement with those obtained directly from the spectra. In summary, site-selective 1H/2H labeling enables artifact-free aromatic 1H CPMG relaxation dispersion experiments in phenylalanine and the six-ring moiety of tryptophan, thereby extending the available methods for studying millisecond dynamics in aromatic protein side chains.

Enhancing the Sensitivity of CPMG Relaxation Dispersion to Conformational Exchange Processes by Multiple-Quantum Spectroscopy

2016 ◽  
Vol 128 (38) ◽  
pp. 11662-11666 ◽  
Author(s):  
Tairan Yuwen ◽  
Pramodh Vallurupalli ◽  
Lewis E. Kay
Keyword(s):  
Relaxation Dispersion ◽  
Conformational Exchange ◽  
Multiple Quantum ◽  
Exchange Processes ◽  
Cpmg Relaxation Dispersion

scholarly journals Off-resonance rotating-frame relaxation dispersion experiment for 13C in aromatic side chains using L-optimized TROSY-selection

2014 ◽  
Vol 59 (1) ◽  
pp. 23-29 ◽  
Author(s):  
Ulrich Weininger ◽  
Ulrika Brath ◽  
Kristofer Modig ◽  
Kaare Teilum ◽  
Mikael Akke
Keyword(s):  
Relaxation Dispersion ◽  
Side Chains ◽  
Rotating Frame ◽  
Rotating Frame Relaxation ◽  
Aromatic Side Chains

scholarly journals UV Raman Markers for Structural Analysis of Aromatic Side Chains in Proteins

2011 ◽  
Vol 27 (11) ◽  
pp. 1077 ◽  
Author(s):  
Hideo TAKEUCHI
Keyword(s):  
Structural Analysis ◽  
Side Chains ◽  
Uv Raman ◽  
Aromatic Side Chains

Privileged hydration sites in aromatic side chains: effect on conformational equilibrium

2017 ◽  
Vol 19 (42) ◽  
pp. 28684-28695 ◽  
Author(s):  
Belén Hernández ◽  
Fernando Pflüger ◽  
Manuel Dauchez ◽  
Mahmoud Ghomi
Keyword(s):  
Conformational Equilibrium ◽  
Theoretical Calculations ◽  
Side Chains ◽  
Aromatic Side Chains

The most energetically favourable hydration sites of aromatic (Phe, Tyr, Trp and His) side chains revealed by DFT-based theoretical calculations.

Langmuir-Blodgett films of linear polysiloxanes incorporating aromatic side-chains: structure-property relationships

1994 ◽  
Vol 242 (1-2) ◽  
pp. 61-66 ◽  
Author(s):  
T. Richardson ◽  
W.H. Abd. Majid ◽  
E.C.A. Cochrane ◽  
S. Holder ◽  
D. Lacey
Keyword(s):  
Side Chains ◽  
Structure Property ◽  
Langmuir Blodgett ◽  
Structure Property Relationships ◽  
Langmuir Blodgett Films ◽  
Aromatic Side Chains

scholarly journals Analysis of Artifacts Caused by Pulse Imperfections in CPMG Pulse Trains in NMR Relaxation Dispersion Experiments

2018 ◽  
Vol 4 (3) ◽  
pp. 33 ◽  
Author(s):  
Tsuyoshi Konuma ◽  
Aritaka Nagadoi ◽  
Jun-ichi Kurita ◽  
Takahisa Ikegami
Keyword(s):  
Dipolar Coupling ◽  
Residual Dipolar Coupling ◽  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Conformational Exchange ◽  
Resonance Effects ◽  
Pulse Trains ◽  
At Resonance ◽  
Selective Inversion ◽  
Resonance Relaxation

Nuclear magnetic resonance relaxation dispersion (rd) experiments provide kinetics and thermodynamics information of molecules undergoing conformational exchange. Rd experiments often use a Carr-Purcell-Meiboom-Gill (CPMG) pulse train equally separated by a spin-state selective inversion element (U-element). Even with measurement parameters carefully set, however, parts of 1H–15N correlations sometimes exhibit large artifacts that may hamper the subsequent analyses. We analyzed such artifacts with a combination of NMR measurements and simulation. We found that particularly the lowest CPMG frequency (νcpmg) can also introduce large artifacts into amide 1H–15N and aromatic 1H–13C correlations whose 15N/13C resonances are very close to the carrier frequencies. The simulation showed that the off-resonance effects and miscalibration of the CPMG π pulses generate artifact maxima at resonance offsets of even and odd multiples of νcpmg, respectively. We demonstrate that a method once introduced into the rd experiments for molecules having residual dipolar coupling significantly reduces artifacts. In the method the 15N/13C π pulse phase in the U-element is chosen between x and y. We show that the correctly adjusted sequence is tolerant to miscalibration of the CPMG π pulse power as large as ±10% for most amide 15N and aromatic 13C resonances of proteins.

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