1
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Fersht AR. From covalent transition states in chemistry to noncovalent in biology: from β- to Φ-value analysis of protein folding. Q Rev Biophys 2024; 57:e4. [PMID: 38597675 DOI: 10.1017/s0033583523000045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Solving the mechanism of a chemical reaction requires determining the structures of all the ground states on the pathway and the elusive transition states linking them. 2024 is the centenary of Brønsted's landmark paper that introduced the β-value and structure-activity studies as the only experimental means to infer the structures of transition states. It involves making systematic small changes in the covalent structure of the reactants and analysing changes in activation and equilibrium-free energies. Protein engineering was introduced for an analogous procedure, Φ-value analysis, to analyse the noncovalent interactions in proteins central to biological chemistry. The methodology was developed first by analysing noncovalent interactions in transition states in enzyme catalysis. The mature procedure was then applied to study transition states in the pathway of protein folding - 'part (b) of the protein folding problem'. This review describes the development of Φ-value analysis of transition states and compares and contrasts the interpretation of β- and Φ-values and their limitations. Φ-analysis afforded the first description of transition states in protein folding at the level of individual residues. It revealed the nucleation-condensation folding mechanism of protein domains with the transition state as an expanded, distorted native structure, containing little fully formed secondary structure but many weak tertiary interactions. A spectrum of transition states with various degrees of structural polarisation was then uncovered that spanned from nucleation-condensation to the framework mechanism of fully formed secondary structure. Φ-analysis revealed how movement of the expanded transition state on an energy landscape accommodates the transition from framework to nucleation-condensation mechanisms with a malleability of structure as a unifying feature of folding mechanisms. Such movement follows the rubric of analysis of classical covalent chemical mechanisms that began with Brønsted. Φ-values are used to benchmark computer simulation, and Φ and simulation combine to describe folding pathways at atomic resolution.
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Affiliation(s)
- Alan R Fersht
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Gonville and Caius College, University of Cambridge, Cambridge, UK
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2
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Selvasingh JA, McDonald EF, Neufer PD, McKinney JR, Meiler J, Ledwitch KV. Dark nanodiscs for evaluating membrane protein thermostability by differential scanning fluorimetry. Biophys J 2024; 123:68-79. [PMID: 37978799 PMCID: PMC10808023 DOI: 10.1016/j.bpj.2023.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/27/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023] Open
Abstract
Measuring protein thermostability provides valuable information on the biophysical rules that govern the structure-energy relationships of proteins. However, such measurements remain a challenge for membrane proteins. Here, we introduce a new experimental system to evaluate membrane protein thermostability. This system leverages a recently developed nonfluorescent membrane scaffold protein to reconstitute proteins into nanodiscs and is coupled with a nano-format of differential scanning fluorimetry (nanoDSF). This approach offers a label-free and direct measurement of the intrinsic tryptophan fluorescence of the membrane protein as it unfolds in solution without signal interference from the "dark" nanodisc. In this work, we demonstrate the application of this method using the disulfide bond formation protein B (DsbB) as a test membrane protein. NanoDSF measurements of DsbB reconstituted in dark nanodiscs loaded with 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dimyristoyl-sn-glycero-3-phosphorylglycerol (DMPG) lipids show a complex biphasic thermal unfolding pattern with a minor unfolding transition followed by a major transition. The inflection points of the thermal denaturation curve reveal two distinct unfolding midpoint melting temperatures (Tm) of 70.5°C and 77.5°C, consistent with a three-state unfolding model. Further, we show that the catalytically conserved disulfide bond between residues C41 and C130 drives the intermediate state of the unfolding pathway for DsbB in a DMPC and DMPG nanodisc. To extend the utility of this method, we evaluate and compare the thermostability of DsbB in different lipid environments. We introduce this method as a new tool that can be used to understand how compositionally and biophysically complex lipid environments drive membrane protein stability.
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Affiliation(s)
- Jazlyn A Selvasingh
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Eli F McDonald
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Preston D Neufer
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Jacob R McKinney
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee; Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, Leipzig, Germany.
| | - Kaitlyn V Ledwitch
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee.
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3
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Selvasingh JA, McDonald EF, Mckinney JR, Meiler J, Ledwitch KV. Dark nanodiscs as a model membrane for evaluating membrane protein thermostability by differential scanning fluorimetry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539917. [PMID: 37214798 PMCID: PMC10197605 DOI: 10.1101/2023.05.08.539917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Measuring protein thermostability provides valuable information on the biophysical rules that govern structure-energy relationships of proteins. However, such measurements remain a challenge for membrane proteins. Here, we introduce a new experimental system to evaluate membrane protein thermostability. This system leverages a recently-developed non-fluorescent membrane scaffold protein (MSP) to reconstitute proteins into nanodiscs and is coupled with a nano-format of differential scanning fluorimetry (nanoDSF). This approach offers a label-free and direct measurement of the intrinsic tryptophan fluorescence of the membrane protein as it unfolds in solution without signal interference from the "dark" nanodisc. In this work, we demonstrate the application of this method using the disulfide bond formation protein B (DsbB) as a test membrane protein. NanoDSF measurements of DsbB reconstituted in dark nanodiscs show a complex biphasic thermal unfolding pattern in the presence of lipids with a minor unfolding transition followed by a major transition. The inflection points of the thermal denaturation curve reveal two distinct unfolding midpoint melting temperatures (Tm) of 70.5 °C and 77.5 °C, consistent with a three-state unfolding model. Further, we show that the catalytically conserved disulfide bond between residues C41 and C130 drives the intermediate state of the unfolding pathway for DsbB in a nanodisc. We introduce this method as a new tool that can be used to understand how compositionally, and biophysically complex lipid environments drive membrane protein stability.
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Affiliation(s)
- Jazlyn A. Selvasingh
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Eli Fritz McDonald
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Jacob R. Mckinney
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Kaitlyn V. Ledwitch
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Lead contact
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4
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Sengupta S, Gera R, Egan C, Morzan UN, Versluis J, Hassanali A, Bakker HJ. Observation of Strong Synergy in the Interfacial Water Response of Binary Ionic and Nonionic Surfactant Mixtures. J Phys Chem Lett 2022; 13:11391-11397. [PMID: 36455883 PMCID: PMC9761666 DOI: 10.1021/acs.jpclett.2c02750] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Interfacial vibrational footprints of the binary mixture of sodium dodecyl sulfate (SDS) and hexaethylene glycol monododecyl ether (C12E6) were probed using heterodyne detected vibrational sum frequency generation (HDVSFG). Our results show that in the presence of C12E6 at CMC (70 μM) the effect of SDS on the orientation of interfacial water molecules is enhanced 10 times compared to just pure surfactants. The experimental results contest the traditional Langmuir adsorption model predictions. This is also evidenced by our molecular dynamics simulations that show a remarkable restructuring and enhanced orientation of the interfacial water molecules upon DS- adsorption to the C12E6 surface. The simulations show that the adsorption free energy of DS- ions to a water surface covered with C12E6 is an enthalpy-driven process and more attractive by ∼10 kBT compared to the adsorption energy of DS- to the surface of pure water.
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Affiliation(s)
| | - Rahul Gera
- AMOLF, Science Park 104, 1098 XGAmsterdam, The Netherlands
| | - Colin Egan
- Condensed
Matter and Statistical Physics Centre, International
Centre for Theoretical Physics, Strada Costiera 11, 34151Trieste, Italy
| | - Uriel N. Morzan
- Condensed
Matter and Statistical Physics Centre, International
Centre for Theoretical Physics, Strada Costiera 11, 34151Trieste, Italy
| | - Jan Versluis
- AMOLF, Science Park 104, 1098 XGAmsterdam, The Netherlands
| | - Ali Hassanali
- Condensed
Matter and Statistical Physics Centre, International
Centre for Theoretical Physics, Strada Costiera 11, 34151Trieste, Italy
| | - Huib J. Bakker
- AMOLF, Science Park 104, 1098 XGAmsterdam, The Netherlands
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5
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Corin K, Bowie JU. How physical forces drive the process of helical membrane protein folding. EMBO Rep 2022; 23:e53025. [PMID: 35133709 PMCID: PMC8892262 DOI: 10.15252/embr.202153025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/17/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022] Open
Abstract
Protein folding is a fundamental process of life with important implications throughout biology. Indeed, tens of thousands of mutations have been associated with diseases, and most of these mutations are believed to affect protein folding rather than function. Correct folding is also a key element of design. These factors have motivated decades of research on protein folding. Unfortunately, knowledge of membrane protein folding lags that of soluble proteins. This gap is partly caused by the greater technical challenges associated with membrane protein studies, but also because of additional complexities. While soluble proteins fold in a homogenous water environment, membrane proteins fold in a setting that ranges from bulk water to highly charged to apolar. Thus, the forces that drive folding vary in different regions of the protein, and this complexity needs to be incorporated into our understanding of the folding process. Here, we review our understanding of membrane protein folding biophysics. Despite the greater challenge, better model systems and new experimental techniques are starting to unravel the forces and pathways in membrane protein folding.
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Affiliation(s)
- Karolina Corin
- Department of Chemistry and BiochemistryMolecular Biology InstituteUCLA‐DOE InstituteUniversity of CaliforniaLos AngelesCAUSA
| | - James U Bowie
- Department of Chemistry and BiochemistryMolecular Biology InstituteUCLA‐DOE InstituteUniversity of CaliforniaLos AngelesCAUSA
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6
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Folding and misfolding of potassium channel monomers during assembly and tetramerization. Proc Natl Acad Sci U S A 2021; 118:2103674118. [PMID: 34413192 DOI: 10.1073/pnas.2103674118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The dynamics and folding of potassium channel pore domain monomers are connected to the kinetics of tetramer assembly. In all-atom molecular dynamics simulations of Kv1.2 and KcsA channels, monomers adopt multiple nonnative conformations while the three helices remain folded. Consistent with this picture, NMR studies also find the monomers to be dynamic and structurally heterogeneous. However, a KcsA construct with a disulfide bridge engineered between the two transmembrane helices has an NMR spectrum with well-dispersed peaks, suggesting that the monomer can be locked into a native-like conformation that is similar to that observed in the folded tetramer. During tetramerization, fluoresence resonance energy transfer (FRET) data indicate that monomers rapidly oligomerize upon insertion into liposomes, likely forming a protein-dense region. Folding within this region occurs along separate fast and slow routes, with τfold ∼40 and 1,500 s, respectively. In contrast, constructs bearing the disulfide bond mainly fold via the faster pathway, suggesting that maintaining the transmembrane helices in their native orientation reduces misfolding. Interestingly, folding is concentration independent despite the tetrameric nature of the channel, indicating that the rate-limiting step is unimolecular and occurs after monomer association in the protein-dense region. We propose that the rapid formation of protein-dense regions may help with the assembly of multimeric membrane proteins by bringing together the nascent components prior to assembly. Finally, despite its name, the addition of KcsA's C-terminal "tetramerization" domain does not hasten the kinetics of tetramerization.
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7
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Otzen DE, Pedersen JN, Somavarapu AK, Clement A, Ji M, Petersen EH, Pedersen JS, Urban S, Schafer NP. Cys-labeling kinetics of membrane protein GlpG: a role for specific SDS binding and micelle changes? Biophys J 2021; 120:4115-4128. [PMID: 34370995 DOI: 10.1016/j.bpj.2021.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/20/2021] [Accepted: 08/03/2021] [Indexed: 01/01/2023] Open
Abstract
Empirically, α-helical membrane protein folding stability in surfactant micelles can be tuned by varying the mole fraction MFSDS of anionic (sodium dodecyl sulfate (SDS)) relative to nonionic (e.g., dodecyl maltoside (DDM)) surfactant, but we lack a satisfying physical explanation of this phenomenon. Cysteine labeling (CL) has thus far only been used to study the topology of membrane proteins, not their stability or folding behavior. Here, we use CL to investigate membrane protein folding in mixed DDM-SDS micelles. Labeling kinetics of the intramembrane protease GlpG are consistent with simple two-state unfolding-and-exchange rates for seven single-Cys GlpG variants over most of the explored MFSDS range, along with exchange from the native state at low MFSDS (which inconveniently precludes measurement of unfolding kinetics under native conditions). However, for two mutants, labeling rates decline with MFSDS at 0-0.2 MFSDS (i.e., native conditions). Thus, an increase in MFSDS seems to be a protective factor for these two positions, but not for the five others. We propose different scenarios to explain this and find the most plausible ones to involve preferential binding of SDS monomers to the site of CL (based on computational simulations) along with changes in size and shape of the mixed micelle with changing MFSDS (based on SAXS studies). These nonlinear impacts on protein stability highlights a multifaceted role for SDS in membrane protein denaturation, involving both direct interactions of monomeric SDS and changes in micelle size and shape along with the general effects on protein stability of changes in micelle composition.
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Affiliation(s)
- Daniel E Otzen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark.
| | - Jannik Nedergaard Pedersen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Arun Kumar Somavarapu
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Anders Clement
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Ming Ji
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Emil Hartvig Petersen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark; Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Sinisa Urban
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nicholas P Schafer
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
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8
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Pedersen JN, Lyngsø J, Zinn T, Otzen DE, Pedersen JS. A complete picture of protein unfolding and refolding in surfactants. Chem Sci 2019; 11:699-712. [PMID: 34123043 PMCID: PMC8145811 DOI: 10.1039/c9sc04831f] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Interactions between proteins and surfactants are of relevance in many applications including food, washing powder formulations, and drug formulation. The anionic surfactant sodium dodecyl sulfate (SDS) is known to unfold globular proteins, while the non-ionic surfactant octaethyleneglycol monododecyl ether (C12E8) can be used to refold proteins from their SDS-denatured state. While unfolding have been studied in detail at the protein level, a complete picture of the interplay between protein and surfactant in these processes is lacking. This gap in our knowledge is addressed in the current work, using the β-sheet-rich globular protein β-lactoglobulin (bLG). We combined stopped-flow time-resolved SAXS, fluorescence, and circular dichroism, respectively, to provide an unprecedented in-depth picture of the different steps involved in both protein unfolding and refolding in the presence of SDS and C12E8. During unfolding, core-shell bLG-SDS complexes were formed within ∼10 ms. This involved an initial rapid process where protein and SDS formed aggregates, followed by two slower processes, where the complexes first disaggregated into single protein structures situated asymmetrically on the SDS micelles, followed by isotropic redistribution of the protein. Refolding kinetics (>100 s) were slower than unfolding (<30 s), and involved rearrangements within the mixing deadtime (∼5 ms) and transient accumulation of unfolded monomeric protein, differing in structure from the original bLG-SDS structure. Refolding of bLG involved two steps: extraction of most of the SDS from the complexes followed by protein refolding. These results reveal that surfactant-mediated unfolding and refolding of proteins are complex processes with rearrangements occurring on time scales from sub-milliseconds to minutes.
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Affiliation(s)
- Jannik Nedergaard Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University Gustav Wieds Vej 14 DK - 8000 Aarhus C Denmark
| | - Jeppe Lyngsø
- Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University Gustav Wieds Vej 14 DK - 8000 Aarhus C Denmark
| | - Thomas Zinn
- ESRF - The European Synchrotron 38043 Grenoble France
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University Gustav Wieds Vej 14 DK - 8000 Aarhus C Denmark
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University Gustav Wieds Vej 14 DK - 8000 Aarhus C Denmark
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9
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Marinko J, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR. Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis. Chem Rev 2019; 119:5537-5606. [PMID: 30608666 PMCID: PMC6506414 DOI: 10.1021/acs.chemrev.8b00532] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Indexed: 12/13/2022]
Abstract
Advances over the past 25 years have revealed much about how the structural properties of membranes and associated proteins are linked to the thermodynamics and kinetics of membrane protein (MP) folding. At the same time biochemical progress has outlined how cellular proteostasis networks mediate MP folding and manage misfolding in the cell. When combined with results from genomic sequencing, these studies have established paradigms for how MP folding and misfolding are linked to the molecular etiologies of a variety of diseases. This emerging framework has paved the way for the development of a new class of small molecule "pharmacological chaperones" that bind to and stabilize misfolded MP variants, some of which are now in clinical use. In this review, we comprehensively outline current perspectives on the folding and misfolding of integral MPs as well as the mechanisms of cellular MP quality control. Based on these perspectives, we highlight new opportunities for innovations that bridge our molecular understanding of the energetics of MP folding with the nuanced complexity of biological systems. Given the many linkages between MP misfolding and human disease, we also examine some of the exciting opportunities to leverage these advances to address emerging challenges in the development of therapeutics and precision medicine.
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Affiliation(s)
- Justin
T. Marinko
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Hui Huang
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Wesley D. Penn
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - John A. Capra
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37245, United States
| | - Jonathan P. Schlebach
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Charles R. Sanders
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
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10
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Sun Y, Zhang J, Wang H, Wang T, Cheng H, Yu B, Oliveira CL. Sulfate dodecyl sodium-induced stability of a model intrinsically disordered protein, bovine casein. Food Hydrocoll 2018. [DOI: 10.1016/j.foodhyd.2018.03.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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11
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Harris NJ, Reading E, Ataka K, Grzegorzewski L, Charalambous K, Liu X, Schlesinger R, Heberle J, Booth PJ. Structure formation during translocon-unassisted co-translational membrane protein folding. Sci Rep 2017; 7:8021. [PMID: 28808343 PMCID: PMC5556060 DOI: 10.1038/s41598-017-08522-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/10/2017] [Indexed: 01/16/2023] Open
Abstract
Correctly folded membrane proteins underlie a plethora of cellular processes, but little is known about how they fold. Knowledge of folding mechanisms centres on reversible folding of chemically denatured membrane proteins. However, this cannot replicate the unidirectional elongation of the protein chain during co-translational folding in the cell, where insertion is assisted by translocase apparatus. We show that a lipid membrane (devoid of translocase components) is sufficient for successful co-translational folding of two bacterial α-helical membrane proteins, DsbB and GlpG. Folding is spontaneous, thermodynamically driven, and the yield depends on lipid composition. Time-resolving structure formation during co-translational folding revealed different secondary and tertiary structure folding pathways for GlpG and DsbB that correlated with membrane interfacial and biological transmembrane amino acid hydrophobicity scales. Attempts to refold DsbB and GlpG from chemically denatured states into lipid membranes resulted in extensive aggregation. Co-translational insertion and folding is thus spontaneous and minimises aggregation whilst maximising correct folding.
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Affiliation(s)
- Nicola J Harris
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London, UK
| | - Eamonn Reading
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London, UK
| | - Kenichi Ataka
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Dahlem, Germany
| | - Lucjan Grzegorzewski
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Dahlem, Germany
| | - Kalypso Charalambous
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London, UK
| | - Xia Liu
- School of Biochemistry, Medical Sciences, University Walk, University of Bristol, Bristol, UK
| | - Ramona Schlesinger
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Dahlem, Germany
| | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Dahlem, Germany
| | - Paula J Booth
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London, UK.
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12
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Kroncke BM, Duran AM, Mendenhall JL, Meiler J, Blume JD, Sanders CR. Documentation of an Imperative To Improve Methods for Predicting Membrane Protein Stability. Biochemistry 2016; 55:5002-9. [PMID: 27564391 PMCID: PMC5024705 DOI: 10.1021/acs.biochem.6b00537] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
There
is a compelling and growing need to accurately predict the
impact of amino acid mutations on protein stability for problems in
personalized medicine and other applications. Here the ability of
10 computational tools to accurately predict mutation-induced perturbation
of folding stability (ΔΔG) for membrane
proteins of known structure was assessed. All methods for predicting
ΔΔG values performed significantly worse
when applied to membrane proteins than when applied to soluble proteins,
yielding estimated concordance, Pearson, and Spearman correlation
coefficients of <0.4 for membrane proteins. Rosetta and PROVEAN
showed a modest ability to classify mutations as destabilizing (ΔΔG < −0.5 kcal/mol), with a 7 in 10 chance of correctly
discriminating a randomly chosen destabilizing variant from a randomly
chosen stabilizing variant. However, even this performance is significantly
worse than for soluble proteins. This study highlights the need for
further development of reliable and reproducible methods for predicting
thermodynamic folding stability in membrane proteins.
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Affiliation(s)
- Brett M Kroncke
- Department of Biochemistry, ‡Center for Structural Biology, §Departments of Chemistry, Pharmacology, and Bioinformatics, and ∥Department of Biostatistics, Vanderbilt University , Nashville, Tennessee 37240, United States
| | - Amanda M Duran
- Department of Biochemistry, ‡Center for Structural Biology, §Departments of Chemistry, Pharmacology, and Bioinformatics, and ∥Department of Biostatistics, Vanderbilt University , Nashville, Tennessee 37240, United States
| | - Jeffrey L Mendenhall
- Department of Biochemistry, ‡Center for Structural Biology, §Departments of Chemistry, Pharmacology, and Bioinformatics, and ∥Department of Biostatistics, Vanderbilt University , Nashville, Tennessee 37240, United States
| | - Jens Meiler
- Department of Biochemistry, ‡Center for Structural Biology, §Departments of Chemistry, Pharmacology, and Bioinformatics, and ∥Department of Biostatistics, Vanderbilt University , Nashville, Tennessee 37240, United States
| | - Jeffrey D Blume
- Department of Biochemistry, ‡Center for Structural Biology, §Departments of Chemistry, Pharmacology, and Bioinformatics, and ∥Department of Biostatistics, Vanderbilt University , Nashville, Tennessee 37240, United States
| | - Charles R Sanders
- Department of Biochemistry, ‡Center for Structural Biology, §Departments of Chemistry, Pharmacology, and Bioinformatics, and ∥Department of Biostatistics, Vanderbilt University , Nashville, Tennessee 37240, United States
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13
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Topological constraints and modular structure in the folding and functional motions of GlpG, an intramembrane protease. Proc Natl Acad Sci U S A 2016; 113:2098-103. [PMID: 26858402 DOI: 10.1073/pnas.1524027113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We investigate the folding of GlpG, an intramembrane protease, using perfectly funneled structure-based models that implicitly account for the absence or presence of the membrane. These two models are used to describe, respectively, folding in detergent micelles and folding within a bilayer, which effectively constrains GlpG's topology in unfolded and partially folded states. Structural free-energy landscape analysis shows that although the presence of multiple folding pathways is an intrinsic property of GlpG's modular functional architecture, the large entropic cost of organizing helical bundles in the absence of the constraining bilayer leads to pathways that backtrack (i.e., local unfolding of previously folded substructures is required when moving from the unfolded to the folded state along the minimum free-energy pathway). This backtracking explains the experimental observation of thermodynamically destabilizing mutations that accelerate GlpG's folding in detergent micelles. In contrast, backtracking is absent from the model when folding is constrained within a bilayer, the environment in which GlpG has evolved to fold. We also characterize a near-native state with a highly mobile transmembrane helix 5 (TM5) that is significantly populated under folding conditions when GlpG is embedded in a bilayer. Unbinding of TM5 from the rest of the structure exposes GlpG's active site, consistent with studies of the catalytic mechanism of GlpG that suggest that TM5 serves as a substrate gate to the active site.
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Min D, Jefferson RE, Bowie JU, Yoon TY. Mapping the energy landscape for second-stage folding of a single membrane protein. Nat Chem Biol 2015; 11:981-7. [PMID: 26479439 DOI: 10.1038/nchembio.1939] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/14/2015] [Indexed: 12/15/2022]
Abstract
Membrane proteins are designed to fold and function in a lipid membrane, yet folding experiments within a native membrane environment are challenging to design. Here we show that single-molecule forced unfolding experiments can be adapted to study helical membrane protein folding under native-like bicelle conditions. Applying force using magnetic tweezers, we find that a transmembrane helix protein, Escherichia coli rhomboid protease GlpG, unfolds in a highly cooperative manner, largely unraveling as one physical unit in response to mechanical tension above 25 pN. Considerable hysteresis is observed, with refolding occurring only at forces below 5 pN. Characterizing the energy landscape reveals only modest thermodynamic stability (ΔG = 6.5 kBT) but a large unfolding barrier (21.3 kBT) that can maintain the protein in a folded state for long periods of time (t1/2 ∼3.5 h). The observed energy landscape may have evolved to limit the existence of troublesome partially unfolded states and impart rigidity to the structure.
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Affiliation(s)
- Duyoung Min
- National Creative Research Initiative Center for Single-Molecule Systems Biology, KAIST, Daejeon, South Korea.,Department of Physics, KAIST, Daejeon, South Korea
| | - Robert E Jefferson
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA
| | - James U Bowie
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA
| | - Tae-Young Yoon
- National Creative Research Initiative Center for Single-Molecule Systems Biology, KAIST, Daejeon, South Korea.,Department of Physics, KAIST, Daejeon, South Korea
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Cooperative folding of a polytopic α-helical membrane protein involves a compact N-terminal nucleus and nonnative loops. Proc Natl Acad Sci U S A 2015; 112:7978-83. [PMID: 26056273 DOI: 10.1073/pnas.1424751112] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Despite the ubiquity of helical membrane proteins in nature and their pharmacological importance, the mechanisms guiding their folding remain unclear. We performed kinetic folding and unfolding experiments on 69 mutants (engineered every 2-3 residues throughout the 178-residue transmembrane domain) of GlpG, a membrane-embedded rhomboid protease from Escherichia coli. The only clustering of significantly positive ϕ-values occurs at the cytosolic termini of transmembrane helices 1 and 2, which we identify as a compact nucleus. The three loops flanking these helices show a preponderance of negative ϕ-values, which are sometimes taken to be indicative of nonnative interactions in the transition state. Mutations in transmembrane helices 3-6 yielded predominantly ϕ-values near zero, indicating that this part of the protein has denatured-state-level structure in the transition state. We propose that loops 1-3 undergo conformational rearrangements to position the folding nucleus correctly, which then drives folding of the rest of the domain. A compact N-terminal nucleus is consistent with the vectorial nature of cotranslational membrane insertion found in vivo. The origin of the interactions in the transition state that lead to a large number of negative ϕ-values remains to be elucidated.
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McMorran LM, Brockwell DJ, Radford SE. Mechanistic studies of the biogenesis and folding of outer membrane proteins in vitro and in vivo: what have we learned to date? Arch Biochem Biophys 2014; 564:265-80. [PMID: 24613287 PMCID: PMC4262575 DOI: 10.1016/j.abb.2014.02.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/16/2014] [Accepted: 02/20/2014] [Indexed: 11/17/2022]
Abstract
Research into the mechanisms by which proteins fold into their native structures has been on-going since the work of Anfinsen in the 1960s. Since that time, the folding mechanisms of small, water-soluble proteins have been well characterised. By contrast, progress in understanding the biogenesis and folding mechanisms of integral membrane proteins has lagged significantly because of the need to create a membrane mimetic environment for folding studies in vitro and the difficulties in finding suitable conditions in which reversible folding can be achieved. Improved knowledge of the factors that promote membrane protein folding and disfavour aggregation now allows studies of folding into lipid bilayers in vitro to be performed. Consequently, mechanistic details and structural information about membrane protein folding are now emerging at an ever increasing pace. Using the panoply of methods developed for studies of the folding of water-soluble proteins. This review summarises current knowledge of the mechanisms of outer membrane protein biogenesis and folding into lipid bilayers in vivo and in vitro and discusses the experimental techniques utilised to gain this information. The emerging knowledge is beginning to allow comparisons to be made between the folding of membrane proteins with current understanding of the mechanisms of folding of water-soluble proteins.
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Affiliation(s)
- Lindsay M McMorran
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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17
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Folding energetics and oligomerization of polytopic α-helical transmembrane proteins. Arch Biochem Biophys 2014; 564:281-96. [DOI: 10.1016/j.abb.2014.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/26/2014] [Accepted: 07/14/2014] [Indexed: 01/06/2023]
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18
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The safety dance: biophysics of membrane protein folding and misfolding in a cellular context. Q Rev Biophys 2014; 48:1-34. [PMID: 25420508 DOI: 10.1017/s0033583514000110] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Most biological processes require the production and degradation of proteins, a task that weighs heavily on the cell. Mutations that compromise the conformational stability of proteins place both specific and general burdens on cellular protein homeostasis (proteostasis) in ways that contribute to numerous diseases. Efforts to elucidate the chain of molecular events responsible for diseases of protein folding address one of the foremost challenges in biomedical science. However, relatively little is known about the processes by which mutations prompt the misfolding of α-helical membrane proteins, which rely on an intricate network of cellular machinery to acquire and maintain their functional structures within cellular membranes. In this review, we summarize the current understanding of the physical principles that guide membrane protein biogenesis and folding in the context of mammalian cells. Additionally, we explore how pathogenic mutations that influence biogenesis may differ from those that disrupt folding and assembly, as well as how this may relate to disease mechanisms and therapeutic intervention. These perspectives indicate an imperative for the use of information from structural, cellular, and biochemical studies of membrane proteins in the design of novel therapeutics and in personalized medicine.
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Predictive energy landscapes for folding α-helical transmembrane proteins. Proc Natl Acad Sci U S A 2014; 111:11031-6. [PMID: 25030446 DOI: 10.1073/pnas.1410529111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We explore the hypothesis that the folding landscapes of membrane proteins are funneled once the proteins' topology within the membrane is established. We extend a protein folding model, the associative memory, water-mediated, structure, and energy model (AWSEM) by adding an implicit membrane potential and reoptimizing the force field to account for the differing nature of the interactions that stabilize proteins within lipid membranes, yielding a model that we call AWSEM-membrane. Once the protein topology is set in the membrane, hydrophobic attractions play a lesser role in finding the native structure, whereas polar-polar attractions are more important than for globular proteins. We examine both the quality of predictions made with AWSEM-membrane when accurate knowledge of the topology and secondary structure is available and the quality of predictions made without such knowledge, instead using bioinformatically inferred topology and secondary structure based on sequence alone. When no major errors are made by the bioinformatic methods used to assign the topology of the transmembrane helices, these two types of structure predictions yield roughly equivalent quality structures. Although the predictive energy landscape is transferable and not structure based, within the correct topological sector we find the landscape is indeed very funneled: Thermodynamic landscape analysis indicates that both the total potential energy and the contact energy decrease as native contacts are formed. Nevertheless the near symmetry of different helical packings with respect to native contact formation can result in multiple packings with nearly equal thermodynamic occupancy, especially at temperatures just below collapse.
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Schlebach JP, Peng D, Kroncke BM, Mittendorf KF, Narayan M, Carter BD, Sanders CR. Reversible folding of human peripheral myelin protein 22, a tetraspan membrane protein. Biochemistry 2013; 52:3229-41. [PMID: 23639031 DOI: 10.1021/bi301635f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Misfolding of the α-helical membrane protein peripheral myelin protein 22 (PMP22) has been implicated in the pathogenesis of the common neurodegenerative disease known as Charcot-Marie-Tooth disease (CMTD) and also several other related peripheral neuropathies. Emerging evidence suggests that the propensity of PMP22 to misfold in the cell may be due to an intrinsic lack of conformational stability. Therefore, quantitative studies of the conformational equilibrium of PMP22 are needed to gain insight into the molecular basis of CMTD. In this work, we have investigated the folding and unfolding of wild type (WT) human PMP22 in mixed micelles. Both kinetic and thermodynamic measurements demonstrate that the denaturation of PMP22 by n-lauroyl sarcosine (LS) in dodecylphosphocholine (DPC) micelles is reversible. Assessment of the conformational equilibrium indicates that a significant fraction of unfolded PMP22 persists even in the absence of the denaturing detergent. However, we find the stability of PMP22 is increased by glycerol, which facilitates quantitation of thermodynamic parameters. To our knowledge, this work represents the first report of reversible unfolding of a eukaryotic multispan membrane protein. The results indicate that WT PMP22 possesses minimal conformational stability in micelles, which parallels its poor folding efficiency in the endoplasmic reticulum. Folding equilibrium measurements for PMP22 in micelles may provide an approach to assess the effects of cellular metabolites or potential therapeutic agents on its stability. Furthermore, these results pave the way for future investigation of the effects of pathogenic mutations on the conformational equilibrium of PMP22.
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Affiliation(s)
- Jonathan P Schlebach
- Department of Biochemistry and ‡Center for Structural Biology, Vanderbilt University School of Medicine , Nashville, Tennessee 37232, United States
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Folding of outer membrane proteins. Arch Biochem Biophys 2013; 531:34-43. [DOI: 10.1016/j.abb.2012.10.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 10/11/2012] [Accepted: 10/19/2012] [Indexed: 11/18/2022]
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22
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The how’s and why’s of protein folding intermediates. Arch Biochem Biophys 2013; 531:14-23. [DOI: 10.1016/j.abb.2012.10.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/05/2012] [Accepted: 10/11/2012] [Indexed: 12/13/2022]
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23
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Andersen KK, Wang H, Otzen DE. A Kinetic Analysis of the Folding and Unfolding of OmpA in Urea and Guanidinium Chloride: Single and Parallel Pathways. Biochemistry 2012; 51:8371-83. [DOI: 10.1021/bi300974y] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kell K. Andersen
- Interdisciplinary Nanoscience Centre (iNANO), Centre
for Insoluble Protein Structures (inSPIN), Department of Molecular
Biology and Genetics, University of Aarhus, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Huabing Wang
- Interdisciplinary Nanoscience Centre (iNANO), Centre
for Insoluble Protein Structures (inSPIN), Department of Molecular
Biology and Genetics, University of Aarhus, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Daniel E. Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Centre
for Insoluble Protein Structures (inSPIN), Department of Molecular
Biology and Genetics, University of Aarhus, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
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Calcutta A, Jessen CM, Behrens MA, Oliveira CL, Renart ML, González-Ros JM, Otzen DE, Pedersen JS, Malmendal A, Nielsen NC. Mapping of unfolding states of integral helical membrane proteins by GPS-NMR and scattering techniques: TFE-induced unfolding of KcsA in DDM surfactant. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2290-301. [DOI: 10.1016/j.bbamem.2012.04.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 03/23/2012] [Accepted: 04/09/2012] [Indexed: 11/25/2022]
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Booth PJ. A successful change of circumstance: a transition state for membrane protein folding. Curr Opin Struct Biol 2012; 22:469-75. [DOI: 10.1016/j.sbi.2012.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 03/09/2012] [Accepted: 03/14/2012] [Indexed: 01/02/2023]
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Harris NJ, Booth PJ. Folding and stability of membrane transport proteins in vitro. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1055-66. [PMID: 22100867 DOI: 10.1016/j.bbamem.2011.11.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 10/26/2011] [Accepted: 11/03/2011] [Indexed: 10/15/2022]
Abstract
Transmembrane transporters are responsible for maintaining a correct internal cellular environment. The inherent flexibility of transporters together with their hydrophobic environment means that they are challenging to study in vitro, but recently significant progress been made. This review will focus on in vitro stability and folding studies of transmembrane alpha helical transporters, including reversible folding systems and thermal denaturation. The successful re-assembly of a small number of ATP binding cassette transporters is also described as this is a significant step forward in terms of understanding the folding and assembly of these more complex, multi-subunit proteins. The studies on transporters discussed here represent substantial advances for membrane protein studies as well as for research into protein folding. The work demonstrates that large flexible hydrophobic proteins are within reach of in vitro folding studies, thus holding promise for furthering knowledge on the structure, function and biogenesis of ubiquitous membrane transporter families. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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Kinetic folding mechanism of an integral membrane protein examined by pulsed oxidative labeling and mass spectrometry. J Mol Biol 2011; 410:146-58. [PMID: 21570983 DOI: 10.1016/j.jmb.2011.04.074] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 04/26/2011] [Accepted: 04/29/2011] [Indexed: 11/21/2022]
Abstract
We report the application of pulsed oxidative labeling for deciphering the folding mechanism of a membrane protein. SDS-denatured bacteriorhodopsin (BR) was refolded by mixing with bicelles in the presence of free retinal. At various time points (20 ms to 1 day), the protein was exposed to a microsecond ·OH pulse that induces oxidative modifications at solvent-accessible methionine side chains. The extent of labeling was determined by mass spectrometry. These measurements were complemented by stopped-flow spectroscopy. Major time-dependent changes in solvent accessibility were detected for M20 (helix A) and M118 (helix D). Our kinetic data indicate a sequential folding mechanism, consistent with models previously suggested by others on the basis of optical data. Yet, ·OH labeling provides additional structural insights. An initial folding intermediate I(1) gets populated within 20 ms, concomitantly with formation of helix A. Subsequent structural consolidation leads to a transient species I(2). Noncovalent retinal binding to I(2) induces folding of helix D, thereby generating an intermediate I(R). In the absence of retinal, the latter transition does not take place. Hence, formation of helix D depends on retinal binding, whereas this is not the case for helix A. As the cofactor settles deeper into its binding pocket, a final transient species I(R) is generated. This intermediate converts into native BR within minutes by formation of the retinal-K216 Schiff base linkage. The combination of pulsed covalent labeling and optical spectroscopy employed here should also be suitable for exploring the folding mechanisms of other membrane proteins.
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Otzen D. Protein–surfactant interactions: A tale of many states. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:562-91. [DOI: 10.1016/j.bbapap.2011.03.003] [Citation(s) in RCA: 362] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/23/2011] [Accepted: 03/04/2011] [Indexed: 10/18/2022]
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