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Penn WD, McKee AG, Kuntz CP, Woods H, Nash V, Gruenhagen TC, Roushar FJ, Chandak M, Hemmerich C, Rusch DB, Meiler J, Schlebach JP. Probing biophysical sequence constraints within the transmembrane domains of rhodopsin by deep mutational scanning. Sci Adv 2020; 6:eaay7505. [PMID: 32181350 PMCID: PMC7056298 DOI: 10.1126/sciadv.aay7505] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/11/2019] [Indexed: 05/15/2023]
Abstract
Membrane proteins must balance the sequence constraints associated with folding and function against the hydrophobicity required for solvation within the bilayer. We recently found the expression and maturation of rhodopsin are limited by the hydrophobicity of its seventh transmembrane domain (TM7), which contains polar residues that are essential for function. On the basis of these observations, we hypothesized that rhodopsin's expression should be less tolerant of mutations in TM7 relative to those within hydrophobic TM domains. To test this hypothesis, we used deep mutational scanning to compare the effects of 808 missense mutations on the plasma membrane expression of rhodopsin in HEK293T cells. Our results confirm that a higher proportion of mutations within TM7 (37%) decrease rhodopsin's plasma membrane expression relative to those within a hydrophobic TM domain (TM2, 25%). These results in conjunction with an evolutionary analysis suggest solvation energetics likely restricts the evolutionary sequence space of polar TM domains.
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Affiliation(s)
- Wesley D. Penn
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Andrew G. McKee
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Charles P. Kuntz
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Hope Woods
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN 37235, USA
| | - Veronica Nash
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | | | | | - Mahesh Chandak
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Chris Hemmerich
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Douglas B. Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Jonathan P. Schlebach
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
- Corresponding author.
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Roushar FJ, Gruenhagen TC, Penn WD, Li B, Meiler J, Jastrzebska B, Schlebach JP. Contribution of Cotranslational Folding Defects to Membrane Protein Homeostasis. J Am Chem Soc 2018; 141:204-215. [PMID: 30537820 DOI: 10.1021/jacs.8b08243] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Membrane proteins are prone to misfolding and degradation within the cell, yet the nature of the conformational defects involved in this process remain poorly understood. The earliest stages of membrane protein folding are mediated by the Sec61 translocon, a molecular machine that facilitates the lateral partitioning of the polypeptide into the membrane. Proper membrane integration is an essential prerequisite for folding of the nascent chain. However, the marginal energetic drivers of this reaction suggest the translocon may operate with modest fidelity. In this work, we employed biophysical modeling in conjunction with quantitative biochemical measurements in order to evaluate the extent to which cotranslational folding defects influence membrane protein homeostasis. Protein engineering was employed to selectively perturb the topological energetics of human rhodopsin, and the expression and cellular trafficking of engineered variants were quantitatively compared. Our results reveal clear relationships between topological energetics and the efficiency of rhodopsin biogenesis, which appears to be limited by the propensity of a polar transmembrane domain to achieve its correct topological orientation. Though the polarity of this segment is functionally constrained, we find that its topology can be stabilized in a manner that enhances biogenesis without compromising the functional properties of rhodopsin. Furthermore, sequence alignments reveal this topological instability has been conserved throughout the course of evolution. These results suggest that topological defects significantly contribute to the inefficiency of membrane protein folding in the cell. Additionally, our findings suggest that the marginal stability of rhodopsin may represent an evolved trait.
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Affiliation(s)
- Francis J Roushar
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Timothy C Gruenhagen
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Wesley D Penn
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Bian Li
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Jens Meiler
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Beata Jastrzebska
- Department of Pharmacology , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Jonathan P Schlebach
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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Gruenhagen TC, Ziarek JJ, Schlebach JP. Bicelle size modulates the rate of bacteriorhodopsin folding. Protein Sci 2018; 27:1109-1112. [PMID: 29604129 DOI: 10.1002/pro.3414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 11/09/2022]
Abstract
The conformational equilibria of integral membrane proteins have proven extremely difficult to characterize within native lipid bilayers. To circumvent technical issues, investigations of the structure and stability of α-helical membrane proteins are often carried out in mixed micelle or bicelle solvents that mimic the membrane and facilitate measurements of reversible folding. Under these conditions, the energetics of membrane protein folding are typically proportional to the mole fraction of an anionic detergent in the micelle. However, investigations of the folding and unfolding of bacteriorhodopsin (bR) surprisingly revealed that the folding rate is also highly sensitive to the bulk molar concentration of lipids and detergents. We show here that this rate enhancement coincides with changes in bicelle size and suggest this effect arises through restriction of the conformational search space during folding. In conjunction with previous mutagenic studies, these results provide additional evidence that a topological search limits the rate of bR folding. Furthermore, this finding provides insights into the manner by which micellar and bicellar environments influence the conformational stability of polytopic membrane proteins.
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Affiliation(s)
| | - Joshua J Ziarek
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, 47405-7102
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