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Baumann C, Chiang W, Valsecchi R, Jurt S, Deluigi M, Schuster M, Rosengren KJ, Plückthun A, Zerbe O. Side-chain dynamics of the α 1B -adrenergic receptor determined by NMR via methyl relaxation. Protein Sci 2023; 32:e4801. [PMID: 37805830 PMCID: PMC10593183 DOI: 10.1002/pro.4801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/17/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
G protein-coupled receptors (GPCRs) are medically important membrane proteins that sample inactive, intermediate, and active conformational states characterized by relatively slow interconversions (~μs-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 α1B -adrenergic receptor (α1B -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 ρ-TIA). Despite the differences in the ligands, the receptor's overall side-chain dynamics are very similar, including those of the apo form. However, ρ-TIA increases the flexibility of Ile1764×56 and possibly of Ile2145×49 , adjacent to Pro2155×50 of the highly conserved P5×50 I3×40 F6×44 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 α1B -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.
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Affiliation(s)
| | - Wan‐Chin Chiang
- Department of ChemistryUniversity of ZurichZurichSwitzerland
| | | | - Simon Jurt
- Department of ChemistryUniversity of ZurichZurichSwitzerland
| | - Mattia Deluigi
- Department of BiochemistryUniversity of ZurichZurichSwitzerland
| | | | | | | | - Oliver Zerbe
- Department of ChemistryUniversity of ZurichZurichSwitzerland
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Wand AJ. Deep mining of the protein energy landscape. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:020901. [PMID: 37124940 PMCID: PMC10147411 DOI: 10.1063/4.0000180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
Abstract
For over half a century, it has been known that protein molecules naturally undergo extensive structural fluctuations, and that these internal motions are intimately related to their functional properties. The energy landscape view has provided a powerful framework for describing the various physical states that proteins visit during their lifetimes. This Perspective focuses on the commonly neglected and often disparaged axis of the protein energy landscape: entropy. Initially seen largely as a barrier to functionally relevant states of protein molecules, it has recently become clear that proteins retain considerable conformational entropy in the "native" state, and that this entropy can and often does contribute significantly to the free energy of fundamental protein properties, processes, and functions. NMR spectroscopy, molecular dynamics simulations, and emerging crystallographic views have matured in parallel to illuminate dynamic disorder of the "ground state" of proteins and their importance in not only transiting between biologically interesting structures but also greatly influencing their stability, cooperativity, and contribution to critical properties such as allostery.
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Function-Related Dynamics in Multi-Spanning Helical Membrane Proteins Revealed by Solution NMR. MEMBRANES 2021; 11:membranes11080604. [PMID: 34436367 PMCID: PMC8398610 DOI: 10.3390/membranes11080604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 01/02/2023]
Abstract
A primary biological function of multi-spanning membrane proteins is to transfer information and/or materials through a membrane by changing their conformations. Therefore, particular dynamics of the membrane proteins are tightly associated with their function. The semi-atomic resolution dynamics information revealed by NMR is able to discriminate function-related dynamics from random fluctuations. This review will discuss several studies in which quantitative dynamics information by solution NMR has contributed to revealing the structural basis of the function of multi-spanning membrane proteins, such as ion channels, GPCRs, and transporters.
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Bada Juarez JF, Judge PJ, Adam S, Axford D, Vinals J, Birch J, Kwan TOC, Hoi KK, Yen HY, Vial A, Milhiet PE, Robinson CV, Schapiro I, Moraes I, Watts A. Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization. Nat Commun 2021; 12:629. [PMID: 33504778 PMCID: PMC7840839 DOI: 10.1038/s41467-020-20596-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022] Open
Abstract
Many transmembrane receptors have a desensitized state, in which they are unable to respond to external stimuli. The family of microbial rhodopsin proteins includes one such group of receptors, whose inactive or dark-adapted (DA) state is established in the prolonged absence of light. Here, we present high-resolution crystal structures of the ground (light-adapted) and DA states of Archaerhodopsin-3 (AR3), solved to 1.1 Å and 1.3 Å resolution respectively. We observe significant differences between the two states in the dynamics of water molecules that are coupled via H-bonds to the retinal Schiff Base. Supporting QM/MM calculations reveal how the DA state permits a thermodynamic equilibrium between retinal isomers to be established, and how this same change is prevented in the ground state in the absence of light. We suggest that the different arrangement of internal water networks in AR3 is responsible for the faster photocycle kinetics compared to homologs.
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Affiliation(s)
- Juan F Bada Juarez
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK
| | - Peter J Judge
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK
| | - Suliman Adam
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Javier Vinals
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK
| | - James Birch
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Tristan O C Kwan
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
- National Physical Laboratory, Hampton Road, Teddington, London, TW11 0LW, UK
| | - Kin Kuan Hoi
- Chemistry Research Laboratory, Oxford University, Mansfield Road, Oxford, OX1 3TA, UK
| | - Hsin-Yung Yen
- OMass Therapeutics, The Schrodinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Anthony Vial
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, University of Montpellier, Montpellier, France
| | - Pierre-Emmanuel Milhiet
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, University of Montpellier, Montpellier, France
| | - Carol V Robinson
- Chemistry Research Laboratory, Oxford University, Mansfield Road, Oxford, OX1 3TA, UK
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Isabel Moraes
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.
- National Physical Laboratory, Hampton Road, Teddington, London, TW11 0LW, UK.
| | - Anthony Watts
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK.
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GPCR Activation States Induced by Nanobodies and Mini-G Proteins Compared by NMR Spectroscopy. MOLECULES (BASEL, SWITZERLAND) 2020; 25:molecules25245984. [PMID: 33348734 PMCID: PMC7767065 DOI: 10.3390/molecules25245984] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/04/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022]
Abstract
In this work, we examine methyl nuclear magnetic resonance (NMR) spectra of the methionine ε-[13CH3] labelled thermostabilized β1 adrenergic receptor from turkey in association with a variety of different effectors, including mini-Gs and nanobody 60 (Nb60), which have not been previously studied in complex with β1 adrenergic receptor (β1AR) by NMR. Complexes with pindolol and Nb60 induce highly similar inactive states of the receptor, closely resembling the resting state conformational ensemble. We show that, upon binding of mini-Gs or nanobody 80 (Nb80), large allosteric changes throughout the receptor take place. The conformation of tβ1AR stabilized by the native-like mini-Gs protein is highly similar to the conformation induced by the currently used surrogate Nb80. Interestingly, in both cases residual dynamics are present, which were not observed in the resting states. Finally, we reproduce a pharmaceutically relevant situation, where an antagonist abolishes the interaction of the receptor with the mini-G protein in a competitive manner, validating the functional integrity of our preparation. The presented system is therefore well suited for reproducing the individual steps of the activation cycle of a G protein-coupled receptor (GPCR) in vitro and serves as a basis for functional and pharmacological characterizations of more native-like systems in the future.
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