G protein-coupled receptors (GPCRs) are medically important membrane proteins that sample inactive, intermediate, and active conformational states characterized by relatively slow interconversions (~?s–ms). On a faster timescale (~ps–ns), the conformational landscape of GPCRs is governed by the rapid dynamics of amino acid side chains. Such dynamics are essential for protein functions such as ligand recognition and allostery. Unfortunately, technical challenges have almost entirely precluded the study of side-chain dynamics for GPCRs. Here, we investigate the rapid side-chain dynamics of a thermostabilized ?1B-adrenergic receptor (?1B-AR) as probed by methyl relaxation. We determined order parameters for Ile, Leu, and Val methyl groups in the presence of inverse agonists that bind orthosterically (prazosin, tamsulosin) or allosterically (conopeptide ?-TIA). Despite the differences in the ligands, the receptor's overall side-chain dynamics are very similar, including those of the apo form. However, ?-TIA increases the flexibility of Ile1764x56 and possibly of Ile2145x49, adjacent to Pro2155x50 of the highly conserved P5x50I3x40F6x44 motif crucial for receptor activation, suggesting differences in the mechanisms for orthosteric and allosteric receptor inactivation. Overall, increased Ile side-chain rigidity was found for residues closer to the center of the membrane bilayer, correlating with denser packing and lower protein surface exposure. In contrast to two microbial membrane proteins, in ?1B-AR Leu exhibited higher flexibility than Ile side chains on average, correlating with the presence of Leu in less densely packed areas and with higher protein-surface exposure than Ile. Our findings demonstrate the feasibility of studying receptor-wide side-chain dynamics in GPCRs to gain functional insights.
This article is protected by copyright. All rights reserved.
[ASAP] Observation of Sub-Microsecond Protein Methyl-Side Chain Dynamics by Nanoparticle-Assisted NMR Spin Relaxation
Observation of Sub-Microsecond Protein Methyl-Side Chain Dynamics by Nanoparticle-Assisted NMR Spin Relaxation
Xinyao Xiang, Alexandar L. Hansen, Lei Yu, Gregory Jameson, Lei Bruschweiler-Li, Chunhua Yuan, and Rafael Bru?schweiler
https://pubs.acs.org/na101/home/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/jacs.1c04687/20210824/images/medium/ja1c04687_0005.gif
Journal of the American Chemical Society
DOI: 10.1021/jacs.1c04687
http://feeds.feedburner.com/~r/acs/jacsat/~4/8joQZH1-cyY
nmrlearner
Journal club
0
08-26-2021 06:47 AM
[NMR paper] Observation of Sub-Microsecond Protein Methyl-Side Chain Dynamics by Nanoparticle-Assisted NMR Spin Relaxation
Observation of Sub-Microsecond Protein Methyl-Side Chain Dynamics by Nanoparticle-Assisted NMR Spin Relaxation
Amino-acid side-chain properties in proteins are key determinants of protein function. NMR spin relaxation of side chains is an important source of information about local protein dynamics and flexibility. However, traditional solution NMR relaxation methods are most sensitive to sub-nanosecond dynamics lacking information on slower ns-?s time-scale motions. Nanoparticle-assisted NMR spin relaxation (NASR) of methyl-side chains is introduced here as a window into these ns-?s...
nmrlearner
Journal club
0
08-26-2021 06:47 AM
[NMR paper] Probing Side-Chain Dynamics in Proteins by NMR Relaxation of Isolated (13)C Magnetization Modes in (13)CH(3) Methyl Groups
Probing Side-Chain Dynamics in Proteins by NMR Relaxation of Isolated (13)C Magnetization Modes in (13)CH(3) Methyl Groups
The dynamics of methyl-bearing side chains in proteins were probed by ^(13)C relaxation measurements of a number of ^(13)C magnetization modes in selectively ^(13)CH(3)-labeled methyl groups of proteins. We first show how ^(13)C magnetization modes in a ^(13)CH(3) spin-system can be isolated using acute-angle ¹H radio-frequency pulses. The parameters of methyl-axis dynamics, a measure of methyl-axis ordering (S(axis)²) and the correlation time of fast local methyl-axis...
nmrlearner
Journal club
0
03-27-2021 02:09 AM
[NMR paper] Side Chain Dynamics of the Trifluoroacetone Cysteine Derivative Characterized by 19F NMR Relaxation and Molecular Dynamics Simulations.
Side Chain Dynamics of the Trifluoroacetone Cysteine Derivative Characterized by 19F NMR Relaxation and Molecular Dynamics Simulations.
Related Articles Side Chain Dynamics of the Trifluoroacetone Cysteine Derivative Characterized by 19F NMR Relaxation and Molecular Dynamics Simulations.
J Phys Chem B. 2019 Apr 11;:
Authors: Rashid S, Lee BL, Wajda B, Spyracopoulos L
Abstract
19F NMR spectroscopy is a powerful tool for the study of the structures, dynamics, and interactions of proteins bearing cysteine residues chemically...
nmrlearner
Journal club
0
04-12-2019 05:25 PM
[NMR paper] Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes as Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations.
Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes as Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations.
Related Articles Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes as Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations.
Biochemistry. 2018 Apr 17;:
Authors: Baird-Titus JM, Thapa M, Doerdelmann T, Combs KA, Rance M
Abstract
An important but poorly characterized contribution to the thermodynamics of protein-DNA interactions is...
nmrlearner
Journal club
0
04-18-2018 01:41 PM
NMR Relaxation and Molecular Dynamics Simulations of Side Chain Dynamics in Proteins
NMR Relaxation and Molecular Dynamics Simulations of Side Chain Dynamics in Proteins
Publication date: 2 February 2018
Source:Biophysical Journal, Volume 114, Issue 3, Supplement 1</br>
Author(s): Falk Hoffmann, Mengjun Xue, Frans Mulder, Lars Schäfer</br>
</br></br>
</br></br>
More...
nmrlearner
Journal club
0
02-07-2018 03:41 PM
Estimating side-chain order in methyl-protonated, perdeuterated proteins via multiple-quantum relaxation violated coherence transfer NMR spectroscopy
Estimating side-chain order in methyl-protonated, perdeuterated proteins via multiple-quantum relaxation violated coherence transfer NMR spectroscopy
Abstract Relaxation violated coherence transfer NMR spectroscopy (Tugarinov et al. in J Am Chem Soc 129:1743â??1750, 2007) is an established experimental tool for quantitative estimation of the amplitudes of side-chain motions in methyl-protonated, highly deuterated proteins. Relaxation violated coherence transfer experiments monitor the build-up of methyl proton multiple-quantum coherences that can be created in magnetically equivalent...
nmrlearner
Journal club
0
02-11-2012 10:31 AM
[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...
Side-Chain Dynamics of the ?1B-Adrenergic Receptor determined by NMR via Methyl Relaxation
Linear Mode
