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Xiao P, Drewniak P, Dingwell DA, Brown LS, Ladizhansky V. Probing the energy barriers and stages of membrane protein unfolding using solid-state NMR spectroscopy. SCIENCE ADVANCES 2024; 10:eadm7907. [PMID: 38758787 DOI: 10.1126/sciadv.adm7907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/15/2024] [Indexed: 05/19/2024]
Abstract
Understanding how the amino acid sequence dictates protein structure and defines its stability is a fundamental problem in molecular biology. It is especially challenging for membrane proteins that reside in the complex environment of a lipid bilayer. Here, we obtain an atomic-level picture of the thermally induced unfolding of a membrane-embedded α-helical protein, human aquaporin 1, using solid-state nuclear magnetic resonance spectroscopy. Our data reveal the hierarchical two-step pathway that begins with unfolding of a structured extracellular loop and proceeds to an intermediate state with a native-like helical packing. In the second step, the transmembrane domain unravels as a single unit, resulting in a heterogeneous misfolded state with high helical content but with nonnative helical packing. Our results show the importance of loops for the kinetic stabilization of the whole membrane protein structure and support the three-stage membrane protein folding model.
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Affiliation(s)
- Peng Xiao
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Philip Drewniak
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Dylan Archer Dingwell
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Vladimir Ladizhansky
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
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Lazarova T, Mlynarczyk K, Filipek S, Kolinski M, Wassenaar TA, Querol E, Renugopalakrishnan V, Viswanathan S, Padrós E. The effect of triple glutamic mutations E9Q/E194Q/E204Q on the structural stability of bacteriorhodopsin. FEBS J 2013; 281:1181-95. [PMID: 24341610 DOI: 10.1111/febs.12694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 11/21/2013] [Accepted: 12/12/2013] [Indexed: 10/25/2022]
Abstract
In the present study, we report on the structural features of the bacteriorhodopsin triple mutant E9Q/E194Q/E204Q (3Glu) of bacteriorhodopsin by combining experimental and molecular dynamics (MD) approaches. In 3Glu mutant, Glu9, Glu194 and Glu204 residues located at the extracellular side of the protein were mutated altogether to glutamines. UV-visible and differential scanning calorimetry experiments served as diagnostic tools for monitoring the resistance against thermal stress of the active site and the tertiary structures of the 3Glu. The analyses of the UV-visible thermal difference spectra demonstrate that the spectral forms at room temperature and the thermal unfolding path differ in the wild-type bacteriorhodopsin and the 3Glu. Even with these spectral differences, the thermal unfolding of the active site occurs at rather similar melting temperatures in both proteins. A noteworthy consequence of the mutations is the altered two-dimensional packing revealed by the lack of the pre-transition peak in differential scanning calorimetry traces of 3Glu mutant, as previously detected in wild-type and the corresponding single mutants. The infrared spectroscopy data agree with the loss of paracrystalinity, illustrating a substantial conversion of αII to αI helical conformation in the 3Glu mutant. Molecular dynamics simulations show higher dynamics flexibility of most of the extracellular regions of 3Glu, which may account for the somewhat lower tertiary structural stability of the mutated protein. Finally, hydrogen bond analysis reveals that the mutated Glu194 and Glu204 residues create ~ 50% less hydrogen bonds with water molecules compared to wild-type bacteriorhodopsin. These results exemplify the role of the water hydrogen-bonding network for structural integrity and conformational flexibility of bacteriorhodopsin.
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Affiliation(s)
- Tzvetana Lazarova
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, Spain; Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Spain
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Pan Y, Stocks BB, Brown L, Konermann L. Structural Characterization of an Integral Membrane Protein in Its Natural Lipid Environment by Oxidative Methionine Labeling and Mass Spectrometry. Anal Chem 2008; 81:28-35. [DOI: 10.1021/ac8020449] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yan Pan
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, and Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Bradley B. Stocks
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, and Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Leonid Brown
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, and Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Lars Konermann
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, and Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Influence of proline on the thermostability of the active site and membrane arrangement of transmembrane proteins. Biophys J 2008; 95:4384-95. [PMID: 18658225 DOI: 10.1529/biophysj.108.136747] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proline residues play a fundamental and subtle role in the dynamics, structure, and function in many membrane proteins. Temperature derivative spectroscopy and differential scanning calorimetry have been used to determine the effect of proline substitution in the structural stability of the active site and transmembrane arrangement of bacteriorhodopsin. We have analyzed the Pro-to-Ala mutation for the helix-embedded prolines Pro50, Pro91, and Pro186 in the native membrane environment. This information has been complemented with the analysis of the respective crystallographic structures by the FoldX force field. Differential scanning calorimetry allowed us to determine distorted membrane arrangement for P50A and P186A. The protein stability was severely affected for P186A and P91A. In the case of Pro91, a single point mutation is capable of strongly slowing down the conformational diffusion along the denaturation coordinate, becoming a barrier-free downhill process above 371 K. Temperature derivative spectroscopy, applied for first time to study thermal stability of proteins, has been used to monitor the stability of the active site of bacteriorhodopsin. The mutation of Pro91 and Pro186 showed the most striking effects on the retinal binding pocket. These residues are the Pro in closer contact to the active site (activation energies for retinal release of 60.1 and 76.8 kcal/mol, respectively, compared to 115.8 kcal/mol for WT). FoldX analysis of the protein crystal structures indicates that the Pro-to-Ala mutations have both local and long-range effects on the structural stability of residues involved in the architecture of the protein and the active site and in the proton pumping function. Thus, this study provides a complete overview of the substitution effect of helix-embedded prolines in the thermodynamic and dynamic stability of a membrane protein, also related to its structure and function.
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Tuparev N, Petkanchin IB, Taneva SG. Irreversible temperature-induced changes in purple membranes studied by electrooptics. J Colloid Interface Sci 2003; 257:121-6. [PMID: 16256463 DOI: 10.1016/s0021-9797(02)00021-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2001] [Accepted: 09/18/2002] [Indexed: 11/18/2022]
Abstract
The thermal stability of purple membranes is studied by electric light scattering. Information on the polarization mechanisms is obtained. Incomplete recovery of the initial electric state (i.e., of permanent dipole moment, p( perpendicular), and electric polarizability, gamma(fast, ||)) after the membranes are heated at temperatures above 60 degrees C is revealed. Additional slow polarizability components, gamma(slow, perpendicular) and gamma(slow, ||), relaxing at different characteristic frequencies than the fast longitudinal polarizability gamma(fast, ||) appear in the temperature range where the order-disorder transition takes place. The slow polarizability gamma(slow, perpendicular) is probably connected with counterion displacement in the electrical double layer perpendicular to the disk plane. The results are important for understanding the polarization mechanisms and the origin of slow orienting moments.
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Affiliation(s)
- N Tuparev
- Institute of Biophysics, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
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Taneva SG, Goñi FM, Tuparev NP, Petkanchin I, Dér A, Muga A. Effect of Asp85 replacement by Thr on the conformation, surface electric properties and stability of bacteriorhodopsin. Colloids Surf A Physicochem Eng Asp 2002. [DOI: 10.1016/s0927-7757(02)00180-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Wang J, Heyes CD, El-Sayed MA. Refolding of Thermally Denatured Bacteriorhodopsin in Purple Membrane. J Phys Chem B 2001. [DOI: 10.1021/jp013131a] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jianping Wang
- Laser Dynamics Laboratory, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
| | - Colin D. Heyes
- Laser Dynamics Laboratory, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
| | - Mostafa A. El-Sayed
- Laser Dynamics Laboratory, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
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