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Lee C, Park M, Wijesinghe WCB, Na S, Lee CG, Hwang E, Yoon G, Lee JK, Roh DH, Kwon YH, Yang J, Hughes SA, Vince JE, Seo JK, Min D, Kwon TH. Oxidative photocatalysis on membranes triggers non-canonical pyroptosis. Nat Commun 2024; 15:4025. [PMID: 38740804 DOI: 10.1038/s41467-024-47634-5] [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: 06/29/2023] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
Intracellular membranes composing organelles of eukaryotes include membrane proteins playing crucial roles in physiological functions. However, a comprehensive understanding of the cellular responses triggered by intracellular membrane-focused oxidative stress remains elusive. Herein, we report an amphiphilic photocatalyst localised in intracellular membranes to damage membrane proteins oxidatively, resulting in non-canonical pyroptosis. Our developed photocatalysis generates hydroxyl radicals and hydrogen peroxides via water oxidation, which is accelerated under hypoxia. Single-molecule magnetic tweezers reveal that photocatalysis-induced oxidation markedly destabilised membrane protein folding. In cell environment, label-free quantification reveals that oxidative damage occurs primarily in membrane proteins related to protein quality control, thereby aggravating mitochondrial and endoplasmic reticulum stress and inducing lytic cell death. Notably, the photocatalysis activates non-canonical inflammasome caspases, resulting in gasdermin D cleavage to its pore-forming fragment and subsequent pyroptosis. These findings suggest that the oxidation of intracellular membrane proteins triggers non-canonical pyroptosis.
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Affiliation(s)
- Chaiheon Lee
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea
- Research Center, O2MEDi inc., Ulsan, Republic of Korea
| | - Mingyu Park
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea
| | - W C Bhashini Wijesinghe
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Seungjin Na
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Chae Gyu Lee
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea
| | - Eunhye Hwang
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea
- Research Center, O2MEDi inc., Ulsan, Republic of Korea
| | - Gwangsu Yoon
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea
| | - Jeong Kyeong Lee
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea
| | - Deok-Ho Roh
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea
| | - Yoon Hee Kwon
- Research Center, O2MEDi inc., Ulsan, Republic of Korea
| | - Jihyeon Yang
- Research Center, O2MEDi inc., Ulsan, Republic of Korea
| | - Sebastian A Hughes
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - James E Vince
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Jeong Kon Seo
- Research Center, O2MEDi inc., Ulsan, Republic of Korea.
- UNIST Central Research Facility, UNIST, Ulsan, Republic of Korea.
| | - Duyoung Min
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea.
| | - Tae-Hyuk Kwon
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
- X-Dynamic Research Center, UNIST, Ulsan, Republic of Korea.
- Research Center, O2MEDi inc., Ulsan, Republic of Korea.
- Graduate School of Carbon Neutrality, UNIST, Ulsan, Republic of Korea.
- Graduate School of Semiconductor Materials and Device Engineering, UNIST, Ulsan, Republic of Korea.
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2
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Yao J, Hong H. Steric trapping strategy for studying the folding of helical membrane proteins. Methods 2024; 225:1-12. [PMID: 38428472 PMCID: PMC11107808 DOI: 10.1016/j.ymeth.2024.02.007] [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: 11/16/2023] [Revised: 02/11/2024] [Accepted: 02/18/2024] [Indexed: 03/03/2024] Open
Abstract
Elucidating the folding energy landscape of membrane proteins is essential to the understanding of the proteins' stabilizing forces, folding mechanisms, biogenesis, and quality control. This is not a trivial task because the reversible control of folding is inherently difficult in a lipid bilayer environment. Recently, novel methods have been developed, each of which has a unique strength in investigating specific aspects of membrane protein folding. Among such methods, steric trapping is a versatile strategy allowing a reversible control of membrane protein folding with minimal perturbation of native protein-water and protein-lipid interactions. In a nutshell, steric trapping exploits the coupling of spontaneous denaturation of a doubly biotinylated protein to the simultaneous binding of bulky monovalent streptavidin molecules. This strategy has been evolved to investigate key elements of membrane protein folding such as thermodynamic stability, spontaneous denaturation rates, conformational features of the denatured states, and cooperativity of stabilizing interactions. In this review, we describe the critical methodological advancement, limitation, and outlook of the steric trapping strategy.
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Affiliation(s)
- Jiaqi Yao
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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3
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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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4
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Min D. Folding speeds of helical membrane proteins. Biochem Soc Trans 2024; 52:491-501. [PMID: 38385525 PMCID: PMC10903471 DOI: 10.1042/bst20231315] [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] [Received: 01/09/2024] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
Membrane proteins play key roles in human health, contributing to cellular signaling, ATP synthesis, immunity, and metabolite transport. Protein folding is the pivotal early step for their proper functioning. Understanding how this class of proteins adopts their native folds could potentially aid in drug design and therapeutic interventions for misfolding diseases. It is an essential piece in the whole puzzle to untangle their kinetic complexities, such as how rapid membrane proteins fold, how their folding speeds are influenced by changing conditions, and what mechanisms are at play. This review explores the folding speed aspect of multipass α-helical membrane proteins, encompassing plausible folding scenarios based on the timing and stability of helix packing interactions, methods for characterizing the folding time scales, relevant folding steps and caveats for interpretation, and potential implications. The review also highlights the recent estimation of the so-called folding speed limit of helical membrane proteins and discusses its consequent impact on the current picture of folding energy landscapes.
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Affiliation(s)
- Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Center for Wave Energy Materials, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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5
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Reddi R, Chatterjee S, Matulef K, Gustafson A, Gao L, Valiyaveetil FI. A facile approach for incorporating tyrosine esters to probe ion-binding sites and backbone hydrogen bonds. J Biol Chem 2024; 300:105517. [PMID: 38042487 PMCID: PMC10790091 DOI: 10.1016/j.jbc.2023.105517] [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: 07/20/2023] [Revised: 11/06/2023] [Accepted: 11/22/2023] [Indexed: 12/04/2023] Open
Abstract
Amide-to-ester substitutions are used to study the role of the amide bonds of the protein backbone in protein structure, function, and folding. An amber suppressor tRNA/synthetase pair has been reported for incorporation of p-hydroxy-phenyl-L-lactic acid (HPLA), thereby introducing ester substitution at tyrosine residues. However, the application of this approach was limited due to the low yields of the modified proteins and the high cost of HPLA. Here we report the in vivo generation of HPLA from the significantly cheaper phenyl-L-lactic acid. We also construct an optimized plasmid with the HPLA suppressor tRNA/synthetase pair that provides higher yields of the modified proteins. The combination of the new plasmid and the in-situ generation of HPLA provides a facile and economical approach for introducing tyrosine ester substitutions. We demonstrate the utility of this approach by introducing tyrosine ester substitutions into the K+ channel KcsA and the integral membrane enzyme GlpG. We introduce the tyrosine ester in the selectivity filter of the M96V mutant of the KcsA to probe the role of the second ion binding site in the conformation of the selectivity filter and the process of inactivation. We use tyrosine ester substitutions in GlpG to perturb backbone H-bonds to investigate the contribution of these H-bonds to membrane protein stability. We anticipate that the approach developed in this study will facilitate further investigations using tyrosine ester substitutions.
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Affiliation(s)
- Ravikumar Reddi
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA
| | - Satyaki Chatterjee
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA
| | - Kimberly Matulef
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA
| | - Andrew Gustafson
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA
| | - Lujia Gao
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA
| | - Francis I Valiyaveetil
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA.
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6
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Recoulat Angelini AA, Incicco JJ, Melian NA, González-Flecha FL. Susceptibility of Cu(I) transport ATPases to sodium dodecyl sulfate. Relevance of the composition of the micellar phase. Arch Biochem Biophys 2023; 745:109704. [PMID: 37527700 DOI: 10.1016/j.abb.2023.109704] [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] [Received: 05/26/2023] [Revised: 07/11/2023] [Accepted: 07/28/2023] [Indexed: 08/03/2023]
Abstract
Sodium dodecyl sulfate (SDS) is a well-known protein denaturing agent. A less known property of this detergent is that it can activate or inactivate some enzymes at sub-denaturing concentrations. In this work we explore the effect of SDS on the ATPase activity of a hyper-thermophilic and a mesophilic Cu(I) ATPases reconstituted in mixed micelles of phospholipids and a non-denaturing detergent. An iterative procedure was used to evaluate the partition of SDS between the aqueous and the micellar phases, allowing to determine the composition of micelles prepared from phospholipid/detergent mixtures. The incubation of enzymes with SDS in the presence of different amounts of phospholipids reveals that higher SDS concentrations are required to obtain the same degree of inactivation when the initial concentration of phospholipids is increased. Remarkably, we found that, if represented as a function of the mole fraction of SDS in the micelle, the degree of inactivation obtained at different amounts of amphiphiles converges to a single inactivation curve. To interpret this result, we propose a simple model involving active and inactive enzyme molecules in equilibrium. This model allowed us to estimate the Gibbs free energy change for the inactivation process and its derivative with respect to the mole fraction of SDS in the micellar phase, the latter being a measure of the susceptibility of the enzyme to SDS. Our results showed that the inactivation free energy changes are similar for both proteins. Conversely, susceptibility to SDS is significantly lower for the hyperthermophilic ATPase, suggesting an inverse relation between thermophilicity and susceptibility to SDS.
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Affiliation(s)
- Alvaro A Recoulat Angelini
- Universidad de Buenos Aires - CONICET, Laboratorio de Biofísica Molecular. Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina
| | - J Jeremías Incicco
- Universidad de Buenos Aires - CONICET, Laboratorio de Biofísica Molecular. Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina
| | - Noelia A Melian
- Universidad de Buenos Aires - CONICET, Laboratorio de Biofísica Molecular. Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina
| | - F Luis González-Flecha
- Universidad de Buenos Aires - CONICET, Laboratorio de Biofísica Molecular. Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina.
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7
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Wijesinghe WCB, Min D. Single-Molecule Force Spectroscopy of Membrane Protein Folding. J Mol Biol 2023; 435:167975. [PMID: 37330286 DOI: 10.1016/j.jmb.2023.167975] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 06/19/2023]
Abstract
Single-molecule force spectroscopy is a unique method that can probe the structural changes of single proteins at a high spatiotemporal resolution while mechanically manipulating them over a wide force range. Here, we review the current understanding of membrane protein folding learned by using the force spectroscopy approach. Membrane protein folding in lipid bilayers is one of the most complex biological processes in which diverse lipid molecules and chaperone proteins are intricately involved. The approach of single protein forced unfolding in lipid bilayers has produced important findings and insights into membrane protein folding. This review provides an overview of the forced unfolding approach, including recent achievements and technical advances. Progress in the methods can reveal more interesting cases of membrane protein folding and clarify general mechanisms and principles.
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Affiliation(s)
- W C Bhashini Wijesinghe
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Center for Wave Energy Materials, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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8
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Factors That Control the Force Needed to Unfold a Membrane Protein in Silico Depend on the Mode of Denaturation. Int J Mol Sci 2023; 24:ijms24032654. [PMID: 36768981 PMCID: PMC9917119 DOI: 10.3390/ijms24032654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/01/2023] Open
Abstract
Single-molecule force spectroscopy methods, such as AFM and magnetic tweezers, have proved extremely beneficial in elucidating folding pathways for soluble and membrane proteins. To identify factors that determine the force rupture levels in force-induced membrane protein unfolding, we applied our near-atomic-level Upside molecular dynamics package to study the vertical and lateral pulling of bacteriorhodopsin (bR) and GlpG, respectively. With our algorithm, we were able to selectively alter the magnitudes of individual interaction terms and identify that, for vertical pulling, hydrogen bond strength had the strongest effect, whereas other non-bonded protein and membrane-protein interactions had only moderate influences, except for the extraction of the last helix where the membrane-protein interactions had a stronger influence. The up-down topology of the transmembrane helices caused helices to be pulled out as pairs. The rate-limiting rupture event often was the loss of H-bonds and the ejection of the first helix, which then propagated tension to the second helix, which rapidly exited the bilayer. The pulling of the charged linkers across the membrane had minimal influence, as did changing the bilayer thickness. For the lateral pulling of GlpG, the rate-limiting rupture corresponded to the separation of the helices within the membrane, with the H-bonds generally being broken only afterward. Beyond providing a detailed picture of the rupture events, our study emphasizes that the pulling mode greatly affects the factors that determine the forces needed to unfold a membrane protein.
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9
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Tiemann JKS, Zschach H, Lindorff-Larsen K, Stein A. Interpreting the molecular mechanisms of disease variants in human transmembrane proteins. Biophys J 2023:S0006-3495(22)03941-8. [PMID: 36600598 DOI: 10.1016/j.bpj.2022.12.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/19/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
Next-generation sequencing of human genomes reveals millions of missense variants, some of which may lead to loss of protein function and ultimately disease. Here, we investigate missense variants in membrane proteins-key drivers in cell signaling and recognition. We find enrichment of pathogenic variants in the transmembrane region across 19,000 functionally classified variants in human membrane proteins. To accurately predict variant consequences, one fundamentally needs to understand the underlying molecular processes. A key mechanism underlying pathogenicity in missense variants of soluble proteins has been shown to be loss of stability. Membrane proteins, however, are widely understudied. Here, we interpret variant effects on a larger scale by performing structure-based estimations of changes in thermodynamic stability using a membrane-specific energy function and analyses of sequence conservation during evolution of 15 transmembrane proteins. We find evidence for loss of stability being the cause of pathogenicity in more than half of the pathogenic variants, indicating that this is a driving factor also in membrane-protein-associated diseases. Our findings show how computational tools aid in gaining mechanistic insights into variant consequences for membrane proteins. To enable broader analyses of disease-related and population variants, we include variant mappings for the entire human proteome.
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Affiliation(s)
- Johanna Katarina Sofie Tiemann
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Henrike Zschach
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Amelie Stein
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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10
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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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11
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Otzen DE, Pedersen JN, Rasmussen HØ, Pedersen JS. How do surfactants unfold and refold proteins? Adv Colloid Interface Sci 2022; 308:102754. [PMID: 36027673 DOI: 10.1016/j.cis.2022.102754] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/25/2022] [Accepted: 08/10/2022] [Indexed: 11/01/2022]
Abstract
Although the anionic surfactant sodium dodecyl sulfate, SDS, has been used for more than half a century as a versatile and efficient protein denaturant for protein separation and size estimation, there is still controversy about its mode of interaction with proteins. The term "rod-like" structures for the complexes that form between SDS and protein, originally introduced by Tanford, is not sufficiently descriptive and does not distinguish between the two current vying models, namely protein-decorated micelles a.k.a. the core-shell model (in which denatured protein covers the surface of micelles) versus beads-on-a-string model (where unfolded proteins are surrounded by surfactant micelles). Thanks to a combination of structural, kinetic and computational work particularly within the last 5-10 years, it is now possible to rule decisively in favor of the core-shell model. This is supported unambiguously by a combination of calorimetric and small-angle X-ray scattering (SAXS) techniques and confirmed by increasingly sophisticated molecular dynamics simulations. Depending on the SDS:protein ratio and the protein molecular mass, the formed structures can range from multiple partly unfolded protein molecules surrounding a single shared micelle to a single polypeptide chain decorating multiple micelles. We also have much new insight into how this species forms. It is preceded by the binding of small numbers of SDS molecules which subsequently grow by accretion. Time-resolved SAXS analysis reveals an asymmetric attack by SDS micelles followed by distribution of the increasingly unfolded protein around the micelle. The compactness of the protein chain continues to evolve at higher SDS concentrations according to single-molecule studies, though the protein remains completely denatured on the tertiary structural level. SDS denaturation can be reversed by addition of nonionic surfactants that absorb SDS forming mixed micelles, leaving the protein free to refold. Refolding can occur in parallel tracks if only a fraction of the protein is initially stripped of SDS. SDS unfolding is nearly always reversible unless carried out at low pH, where charge neutralization can lead to superclusters of protein-surfactant complexes. With the general mechanism of SDS denaturation now firmly established, it largely remains to explore how other ionic surfactants (including biosurfactants) may diverge from this path.
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Affiliation(s)
- Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark.
| | - Jannik Nedergaard Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Helena Østergaard Rasmussen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
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12
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Harris NJ, Pellowe GA, Blackholly LR, Gulaidi-Breen S, Findlay HE, Booth PJ. Methods to study folding of alpha-helical membrane proteins in lipids. Open Biol 2022; 12:220054. [PMID: 35855589 PMCID: PMC9297032 DOI: 10.1098/rsob.220054] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
How alpha-helical membrane proteins fold correctly in the highly hydrophobic membrane interior is not well understood. Their folding is known to be highly influenced by the lipids within the surrounding bilayer, but the majority of folding studies have focused on detergent-solubilized protein rather than protein in a lipid environment. There are different ways to study folding in lipid bilayers, and each method has its own advantages and disadvantages. This review will discuss folding methods which can be used to study alpha-helical membrane proteins in bicelles, liposomes, nanodiscs or native membranes. These folding methods include in vitro folding methods in liposomes such as denaturant unfolding studies, and single-molecule force spectroscopy studies in bicelles, liposomes and native membranes. This review will also discuss recent advances in co-translational folding studies, which use cell-free expression with liposomes or nanodiscs or are performed in vivo with native membranes.
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Affiliation(s)
- Nicola J. Harris
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Grant A. Pellowe
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Laura R. Blackholly
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | | | - Heather E. Findlay
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Paula J. Booth
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
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13
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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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14
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Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein. Proc Natl Acad Sci U S A 2022; 119:2109169119. [PMID: 34969836 PMCID: PMC8740594 DOI: 10.1073/pnas.2109169119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 12/19/2022] Open
Abstract
Defining the denatured state ensemble (DSE) and disordered proteins is essential to understanding folding, chaperone action, degradation, and translocation. As compared with water-soluble proteins, the DSE of membrane proteins is much less characterized. Here, we measure the DSE of the helical membrane protein GlpG of Escherichia coli (E. coli) in native-like lipid bilayers. The DSE was obtained using our steric trapping method, which couples denaturation of doubly biotinylated GlpG to binding of two streptavidin molecules. The helices and loops are probed using limited proteolysis and mass spectrometry, while the dimensions are determined using our paramagnetic biotin derivative and double electron-electron resonance spectroscopy. These data, along with our Upside simulations, identify the DSE as being highly dynamic, involving the topology changes and unfolding of some of the transmembrane (TM) helices. The DSE is expanded relative to the native state but only to 15 to 75% of the fully expanded condition. The degree of expansion depends on the local protein packing and the lipid composition. E. coli's lipid bilayer promotes the association of TM helices in the DSE and, probably in general, facilitates interhelical interactions. This tendency may be the outcome of a general lipophobic effect of proteins within the cell membranes.
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15
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Hong H, Choi HK, Yoon TY. Untangling the complexity of membrane protein folding. Curr Opin Struct Biol 2022; 72:237-247. [PMID: 34995926 DOI: 10.1016/j.sbi.2021.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 11/15/2022]
Abstract
Delineating the folding steps of helical-bundle membrane proteins has been a challenging task. Many questions remain unanswered, including the conformation and stability of the states populated during folding, the shape of the energy barriers between the states, and the role of lipids as a solvent in mediating the folding. Recently, theoretical frames have matured to a point that permits detailed dissection of the folding steps, and advances in experimental techniques at both single-molecule and ensemble levels enable selective modulation of specific steps for quantitative determination of the folding energy landscapes. We also discuss how lipid molecules would play an active role in shaping the folding energy landscape of membrane proteins, and how folding of multi-domain membrane proteins can be understood based on our current knowledge. We conclude this review by offering an outlook for emerging questions in the study of membrane protein folding.
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Affiliation(s)
- Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA.
| | - Hyun-Kyu Choi
- Wallace H. Coulter Department of Biomedical Engineering and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Tae-Young Yoon
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea.
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16
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Harris NJ, Reading E, Booth PJ. Cell-Free Synthesis Strategies to Probe Co-translational Folding of Proteins Within Lipid Membranes. Methods Mol Biol 2022; 2433:273-292. [PMID: 34985751 DOI: 10.1007/978-1-0716-1998-8_17] [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] [Indexed: 06/14/2023]
Abstract
In order to comprehend the molecular basis of transmembrane protein biogenesis, methods are required that are capable of investigating the co-translational folding of these hydrophobic proteins. Equally, in artificial cell studies, controllable methods are desirable for in situ synthesis of membrane proteins that then direct reactions in the synthetic cell membrane. Here we describe a method that exploits cell-free expression systems and tunable membrane mimetics to facilitate co-translational studies. Alteration of the lipid bilayer composition improves the efficiency of the folding system. The approach also enables membrane transport proteins to be made and inserted into artificial cell platforms such as droplet interface bilayers. Importantly, this gives a new facet to the droplet networks by enabling specific transport of molecules across the synthetic bilayer against a concentration gradient. This method also includes a protocol to pause and restart translation of membrane proteins at specified positions during their co-translational folding. This stop-start strategy provides an avenue to investigate whether the proteins fold in sequence order, or if the correct fold of N-terminal regions is reliant on the synthesis of downstream residues.
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Affiliation(s)
| | - Eamonn Reading
- Department of Chemistry, King's College London, London, UK
| | - Paula J Booth
- Department of Chemistry, King's College London, London, UK.
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17
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Hellmann N, Schneider D. A complex unfolding pathway of α-helical membrane proteins in SDS-containing micelles. Biophys J 2021; 120:3857-3859. [PMID: 34416174 DOI: 10.1016/j.bpj.2021.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/20/2021] [Accepted: 08/03/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Nadja Hellmann
- Department of Chemistry, Biochemistry, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg-University Mainz, Mainz, Germany; Institute of Molecular Physiology, Johannes Gutenberg-University Mainz, Mainz, Germany.
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18
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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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19
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Dingfelder F, Macocco I, Benke S, Nettels D, Faccioli P, Schuler B. Slow Escape from a Helical Misfolded State of the Pore-Forming Toxin Cytolysin A. JACS AU 2021; 1:1217-1230. [PMID: 34467360 PMCID: PMC8397351 DOI: 10.1021/jacsau.1c00175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Indexed: 05/12/2023]
Abstract
The pore-forming toxin cytolysin A (ClyA) is expressed as a large α-helical monomer that, upon interaction with membranes, undergoes a major conformational rearrangement into the protomer conformation, which then assembles into a cytolytic pore. Here, we investigate the folding kinetics of the ClyA monomer with single-molecule Förster resonance energy transfer spectroscopy in combination with microfluidic mixing, stopped-flow circular dichroism experiments, and molecular simulations. The complex folding process occurs over a broad range of time scales, from hundreds of nanoseconds to minutes. The very slow formation of the native state occurs from a rapidly formed and highly collapsed intermediate with large helical content and nonnative topology. Molecular dynamics simulations suggest pronounced non-native interactions as the origin of the slow escape from this deep trap in the free-energy surface, and a variational enhanced path-sampling approach enables a glimpse of the folding process that is supported by the experimental data.
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Affiliation(s)
- Fabian Dingfelder
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Iuri Macocco
- Department
of Physics, Trento University, Via Sommarive 14, 38123 Povo (Trento), Italy
- SISSA, Via Bonomea 265, 34136 Trieste, Italy
| | - Stephan Benke
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel Nettels
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Pietro Faccioli
- Department
of Physics, Trento University, Via Sommarive 14, 38123 Povo (Trento), Italy
- INFN-TIFPA, Via Sommarive 14, 38123 Povo (Trento), Italy
| | - Benjamin Schuler
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department
of Physics, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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20
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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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21
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Huysmans GHM, Ciftci D, Wang X, Blanchard SC, Boudker O. The high-energy transition state of the glutamate transporter homologue GltPh. EMBO J 2021; 40:e105415. [PMID: 33185289 PMCID: PMC7780239 DOI: 10.15252/embj.2020105415] [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: 04/24/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 01/03/2023] Open
Abstract
Membrane transporters mediate cellular uptake of nutrients, signaling molecules, and drugs. Their overall mechanisms are often well understood, but the structural features setting their rates are mostly unknown. Earlier single-molecule fluorescence imaging of the archaeal model glutamate transporter homologue GltPh from Pyrococcus horikoshii suggested that the slow conformational transition from the outward- to the inward-facing state, when the bound substrate is translocated from the extracellular to the cytoplasmic side of the membrane, is rate limiting to transport. Here, we provide insight into the structure of the high-energy transition state of GltPh that limits the rate of the substrate translocation process. Using bioinformatics, we identified GltPh gain-of-function mutations in the flexible helical hairpin domain HP2 and applied linear free energy relationship analysis to infer that the transition state structurally resembles the inward-facing conformation. Based on these analyses, we propose an approach to search for allosteric modulators for transporters.
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Affiliation(s)
- Gerard H M Huysmans
- Department of Physiology and BiophysicsWeill Cornell MedicineNew YorkNYUSA
- Mass Spectrometry for Biology Unit, USR 2000CNRSInstitut PasteurParisFrance
| | - Didar Ciftci
- Department of Physiology and BiophysicsWeill Cornell MedicineNew YorkNYUSA
- Tri‐Institutional Training Program in Chemical BiologyNew YorkNYUSA
| | - Xiaoyu Wang
- Department of Physiology and BiophysicsWeill Cornell MedicineNew YorkNYUSA
| | - Scott C Blanchard
- Department of Physiology and BiophysicsWeill Cornell MedicineNew YorkNYUSA
- Tri‐Institutional Training Program in Chemical BiologyNew YorkNYUSA
- St. Jude Children’s Research HospitalMemphisTNUSA
| | - Olga Boudker
- Department of Physiology and BiophysicsWeill Cornell MedicineNew YorkNYUSA
- Tri‐Institutional Training Program in Chemical BiologyNew YorkNYUSA
- Howard Hughes Medical InstituteChevy ChaseMDUSA
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22
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Structural cavities are critical to balancing stability and activity of a membrane-integral enzyme. Proc Natl Acad Sci U S A 2020; 117:22146-22156. [PMID: 32848056 DOI: 10.1073/pnas.1917770117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Packing interaction is a critical driving force in the folding of helical membrane proteins. Despite the importance, packing defects (i.e., cavities including voids, pockets, and pores) are prevalent in membrane-integral enzymes, channels, transporters, and receptors, playing essential roles in function. Then, a question arises regarding how the two competing requirements, packing for stability vs. cavities for function, are reconciled in membrane protein structures. Here, using the intramembrane protease GlpG of Escherichia coli as a model and cavity-filling mutation as a probe, we tested the impacts of native cavities on the thermodynamic stability and function of a membrane protein. We find several stabilizing mutations which induce substantial activity reduction without distorting the active site. Notably, these mutations are all mapped onto the regions of conformational flexibility and functional importance, indicating that the cavities facilitate functional movement of GlpG while compromising the stability. Experiment and molecular dynamics simulation suggest that the stabilization is induced by the coupling between enhanced protein packing and weakly unfavorable lipid desolvation, or solely by favorable lipid solvation on the cavities. Our result suggests that, stabilized by the relatively weak interactions with lipids, cavities are accommodated in membrane proteins without severe energetic cost, which, in turn, serve as a platform to fine-tune the balance between stability and flexibility for optimal activity.
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23
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Mihaljević L, Urban S. Decoding the Functional Evolution of an Intramembrane Protease Superfamily by Statistical Coupling Analysis. Structure 2020; 28:1329-1336.e4. [PMID: 32795403 DOI: 10.1016/j.str.2020.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/12/2020] [Accepted: 07/24/2020] [Indexed: 11/18/2022]
Abstract
How evolution endowed membrane enzymes with specific abilities, and then tuned them to the needs of different cells, is poorly understood. We examined whether statistical coupling analysis (SCA) can be applied to rhomboid proteases, the most widely distributed membrane proteins, to identify amino acid "sectors" that evolved independently to acquire a specific function. SCA revealed three coevolving residue networks that form two sectors. Sector 1 determines substrate specificity, but is paradoxically scattered across the protein, consistent with dynamics driving rhomboid-substrate interactions. Sector 2 is hierarchically composed of a subgroup that maintains the catalytic site, and another that maintains the overall fold, forecasting evolution of rhomboid pseudoproteases. Changing only sector 1 residues of a "recipient" rhomboid converted its substrate specificity and catalytic efficiency to that of the "donor." While used only twice over a decade ago, SCA should be generally applicable to membrane proteins, and our sector grafting approach provides an efficient strategy for designing enzymes.
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Affiliation(s)
- Ljubica Mihaljević
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Siniša Urban
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA.
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24
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Pellowe G, Findlay HE, Lee K, Gemeinhardt TM, Blackholly LR, Reading E, Booth PJ. Capturing Membrane Protein Ribosome Nascent Chain Complexes in a Native-like Environment for Co-translational Studies. Biochemistry 2020; 59:2764-2775. [PMID: 32627541 PMCID: PMC7551657 DOI: 10.1021/acs.biochem.0c00423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/02/2020] [Indexed: 01/02/2023]
Abstract
Co-translational folding studies of membrane proteins lag behind cytosolic protein investigations largely due to the technical difficulty in maintaining membrane lipid environments for correct protein folding. Stalled ribosome-bound nascent chain complexes (RNCs) can give snapshots of a nascent protein chain as it emerges from the ribosome during biosynthesis. Here, we demonstrate how SecM-facilitated nascent chain stalling and native nanodisc technologies can be exploited to capture in vivo-generated membrane protein RNCs within their native lipid compositions. We reveal that a polytopic membrane protein can be successfully stalled at various stages during its synthesis and the resulting RNC extracted within either detergent micelles or diisobutylene-maleic acid co-polymer native nanodiscs. Our approaches offer tractable solutions for the structural and biophysical interrogation of nascent membrane proteins of specified lengths, as the elongating nascent chain emerges from the ribosome and inserts into its native lipid milieu.
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Affiliation(s)
- Grant
A. Pellowe
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Heather E. Findlay
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Karen Lee
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Tim M. Gemeinhardt
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Laura R. Blackholly
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Eamonn Reading
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Paula J. Booth
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
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25
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Harris NJ, Pellowe GA, Booth PJ. Cell-free expression tools to study co-translational folding of alpha helical membrane transporters. Sci Rep 2020; 10:9125. [PMID: 32499529 PMCID: PMC7272624 DOI: 10.1038/s41598-020-66097-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/15/2020] [Indexed: 11/28/2022] Open
Abstract
Most helical membrane proteins fold co-translationally during unidirectional polypeptide elongation by the ribosome. Studies thus far, however, have largely focussed on refolding full-length proteins from artificially induced denatured states that are far removed from the natural co-translational process. Cell-free translation offers opportunities to remedy this deficit in folding studies and has previously been used for membrane proteins. We exploit this cell-free approach to develop tools to probe co-translational folding. We show that two transporters from the ubiquitous Major Facilitator Superfamily can successfully insert into a synthetic bilayer without the need for translocon insertase apparatus that is essential in vivo. We also assess the cooperativity of domain insertion, by expressing the individual transporter domains cell-free. Furthermore, we manipulate the cell-free reaction to pause and re-start protein synthesis at specific points in the protein sequence. We find that full-length protein can still be made when stalling after the first N terminal helix has inserted into the bilayer. However, stalling after the first three helices have exited the ribosome cannot be successfully recovered. These three helices cannot insert stably when ribosome-bound during co-translational folding, as they require insertion of downstream helices.
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Affiliation(s)
- Nicola J Harris
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Grant A Pellowe
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Paula J Booth
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, UK.
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26
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Choi HK, Min D, Kang H, Shon MJ, Rah SH, Kim HC, Jeong H, Choi HJ, Bowie JU, Yoon TY. Watching helical membrane proteins fold reveals a common N-to-C-terminal folding pathway. Science 2020; 366:1150-1156. [PMID: 31780561 DOI: 10.1126/science.aaw8208] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 08/30/2019] [Accepted: 11/05/2019] [Indexed: 02/03/2023]
Abstract
To understand membrane protein biogenesis, we need to explore folding within a bilayer context. Here, we describe a single-molecule force microscopy technique that monitors the folding of helical membrane proteins in vesicle and bicelle environments. After completely unfolding the protein at high force, we lower the force to initiate folding while transmembrane helices are aligned in a zigzag manner within the bilayer, thereby imposing minimal constraints on folding. We used the approach to characterize the folding pathways of the Escherichia coli rhomboid protease GlpG and the human β2-adrenergic receptor. Despite their evolutionary distance, both proteins fold in a strict N-to-C-terminal fashion, accruing structures in units of helical hairpins. These common features suggest that integral helical membrane proteins have evolved to maximize their fitness with cotranslational folding.
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Affiliation(s)
- Hyun-Kyu Choi
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.,Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Duyoung Min
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095, USA.,Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea
| | - Hyunook Kang
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Min Ju Shon
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.,Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Sang-Hyun Rah
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.,Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Hak Chan Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Hawoong Jeong
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Hee-Jung Choi
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.
| | - James U Bowie
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095, USA.
| | - Tae-Young Yoon
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea. .,Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
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27
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Poghosyan AH, Schafer NP, Lyngsø J, Shahinyan AA, Pedersen JS, Otzen DE. Molecular dynamics study of ACBP denaturation in alkyl sulfates demonstrates possible pathways of unfolding through fused surfactant clusters. Protein Eng Des Sel 2019; 32:175-190. [DOI: 10.1093/protein/gzz037] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 08/20/2019] [Accepted: 08/28/2019] [Indexed: 11/15/2022] Open
Abstract
AbstractAnionic surfactants denature proteins at low millimolar concentrations, yet little is known about the underlying molecular mechanisms. Here, we undertake 1-μs-long atomistic molecular dynamics simulations of the denaturation of acyl coenzyme A binding protein (ACBP) and compare our results with previously published and new experimental data. Since increasing surfactant chain length is known to lead to more rapid denaturation, we studied denaturation using both the medium-length alkyl chain surfactant sodium dodecyl sulfate (SDS) and the long alkyl chain surfactant sodium hexadecyl sulfate (SHS). In silico denaturation on the microsecond timescale was not achieved using preformed surfactant micelles but required ACBP to be exposed to monomeric surfactant molecules. Micellar self-assembly occurred together with protein denaturation. To validate our analyses, we calculated small-angle X-ray scattering spectra of snapshots from the simulations. These agreed well with experimental equilibrium spectra recorded on ACBP-SDS mixtures with similar compositions. Protein denaturation occurs through the binding of partial micelles to multiple preferred binding sites followed by the accretion of surfactant monomers until these partial micelles merge to form a mature micelle and the protein chain is left disordered on the surface of the micelle. While the two surfactants attack in a similar fashion, SHS’s longer alkyl chain leads to a more efficient denaturation through the formation of larger clusters that attack ACBP, a more rapid drop in native contacts, a greater expansion in size, as well as a more thorough rearrangement of hydrogen bonds and disruption of helices.
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Affiliation(s)
- Armen H Poghosyan
- International Scientific-Educational Center of National Academy of Sciences of Armenia, 24d Marshal Baghramyan Ave, Yerevan 0019, Armenia
| | - Nicholas P Schafer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
- Center for Theoretical Biological Physics, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Jeppe Lyngsø
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
- Department of Chemistry, Aarhus University, Langelandsgade 120, 8000 Aarhus, Denmark
| | - Aram A Shahinyan
- International Scientific-Educational Center of National Academy of Sciences of Armenia, 24d Marshal Baghramyan Ave, Yerevan 0019, Armenia
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
- Department of Chemistry, Aarhus University, Langelandsgade 120, 8000 Aarhus, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
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28
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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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29
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Gupta A, Mahalakshmi R. Reversible folding energetics of Yersinia Ail barrel reveals a hyperfluorescent intermediate. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183097. [PMID: 31672545 DOI: 10.1016/j.bbamem.2019.183097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 10/01/2019] [Accepted: 10/10/2019] [Indexed: 12/17/2022]
Abstract
Deducing the molecular details of membrane protein folding has lately become an important area of research in biology. Using Ail, an outer membrane protein (OMP) from Yersina pestis as our model, we explore details of β-barrel folding, stability, and unfolding. Ail displays a simple transmembrane β-barrel topology. Here, we find that Ail follows a simple two-state mechanism in its folding and unfolding thermodynamics. Interestingly, Ail displays multi-step folding kinetics. The early kinetic intermediates in the folding pathway populate near the unfolded state (βT ≈ 0.20), and do not display detectable changes in the local environment of the two interface indoles. Interestingly, tryptophans regulate the late events of barrel rearrangement, and Ail thermodynamic stability. We show that W149 → Y/F/A substitution destabilizes Ail by ~0.13-1.7 kcal mol-1, but retains path-independent thermodynamic equilibrium of Ail. In surprising contrast, substituting W42 and retaining W149 shifts the thermodynamic equilibrium to an apparent kinetic retardation of only the unfolding process, which gives rise to an associated increase in scaffold stability by ~0.3-1.1 kcal mol-1. This is accompanied by the formation of an unusual hyperfluorescent state in the unfolding pathway that is more structured, and represents a conformationally dynamic unfolding intermediate with the interface W149 now lipid solvated. The defined role of each tryptophan and poorer folding efficiency of Trp mutants together presents compelling evidence for the importance of interface aromatics in the unique (un)folding pathway of Ail, and offers interesting insight on alternative pathways in generalized OMP assembly and unfolding mechanisms.
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Affiliation(s)
- Ankit Gupta
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066. India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066. India.
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30
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Cho S, Baker RP, Ji M, Urban S. Ten catalytic snapshots of rhomboid intramembrane proteolysis from gate opening to peptide release. Nat Struct Mol Biol 2019; 26:910-918. [PMID: 31570873 PMCID: PMC6858540 DOI: 10.1038/s41594-019-0296-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 08/09/2019] [Indexed: 12/04/2022]
Abstract
Protein cleavage inside the cell membrane triggers various patho-physiological signaling pathways, but the mechanism of catalysis is poorly understood. We solved ten structures of the Escherichia coli rhomboid protease in a bicelle membrane undergoing time-resolved steps that encompass the entire proteolytic reaction on a transmembrane substrate and an aldehyde inhibitor. Extensive gate opening accompanied substrate, but not inhibitor, binding, revealing that substrates and inhibitors take different paths to the active site. Catalysis unexpectedly commenced with, and was guided through subsequent catalytic steps by, motions of an extracellular loop, with local contributions from active site residues. We even captured the elusive tetrahedral intermediate that is uncleaved but covalently attached to the catalytic serine, around which the substrate was forced to bend dramatically. This unexpectedly stable intermediate indicates rhomboid catalysis uses an unprecedented reaction coordinate that may involve mechanically stressing the peptide bond, and could be selectively targeted by inhibitors.
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Affiliation(s)
- Sangwoo Cho
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rosanna P Baker
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ming Ji
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Siniša Urban
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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31
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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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32
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Yang Y, Gunasekara M, Muhammednazaar S, Li Z, Hong H. Proteolysis mediated by the membrane-integrated ATP-dependent protease FtsH has a unique nonlinear dependence on ATP hydrolysis rates. Protein Sci 2019; 28:1262-1275. [PMID: 31008538 DOI: 10.1002/pro.3629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/17/2019] [Indexed: 12/16/2022]
Abstract
ATPases associated with diverse cellular activities (AAA+) proteases utilize ATP hydrolysis to actively unfold native or misfolded proteins and translocate them into a protease chamber for degradation. This basic mechanism yields diverse cellular consequences, including the removal of misfolded proteins, control of regulatory circuits, and remodeling of protein conformation. Among various bacterial AAA+ proteases, FtsH is only membrane-integrated and plays a key role in membrane protein quality control. Previously, we have shown that FtsH has substantial unfoldase activity for degrading membrane proteins overcoming a dual energetic burden of substrate unfolding and membrane dislocation. Here, we asked how efficiently FtsH utilizes ATP hydrolysis to degrade membrane proteins. To answer this question, we measured degradation rates of the model membrane substrate GlpG at various ATP hydrolysis rates in the lipid bilayers. We find that the dependence of degradation rates on ATP hydrolysis rates is highly nonlinear: (i) FtsH cannot degrade GlpG until it reaches a threshold ATP hydrolysis rate; (ii) after exceeding the threshold, the degradation rates steeply increase and saturate at the ATP hydrolysis rates far below the maxima. During the steep increase, FtsH efficiently utilizes ATP hydrolysis for degradation, consuming only 40-60% of the total ATP cost measured at the maximal ATP hydrolysis rates. This behavior does not fundamentally change against water-soluble substrates as well as upon addition of the macromolecular crowding agent Ficoll 70. The Hill analysis shows that the nonlinearity stems from coupling of three to five ATP hydrolysis events to degradation, which represents unique cooperativity compared to other AAA+ proteases including ClpXP, HslUV, Lon, and proteasomes.
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Affiliation(s)
- Yiqing Yang
- Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824
| | - Mihiravi Gunasekara
- Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824
| | | | - Zhen Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824
| | - Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824
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33
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Energy landscape underlying spontaneous insertion and folding of an alpha-helical transmembrane protein into a bilayer. Nat Commun 2018; 9:4949. [PMID: 30470737 PMCID: PMC6251876 DOI: 10.1038/s41467-018-07320-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/18/2018] [Indexed: 11/08/2022] Open
Abstract
Membrane protein folding mechanisms and rates are notoriously hard to determine. A recent force spectroscopy study of the folding of an α-helical membrane protein, GlpG, showed that the folded state has a very high kinetic stability and a relatively low thermodynamic stability. Here, we simulate the spontaneous insertion and folding of GlpG into a bilayer. An energy landscape analysis of the simulations suggests that GlpG folds via sequential insertion of helical hairpins. The rate-limiting step involves simultaneous insertion and folding of the final helical hairpin. The striking features of GlpG's experimentally measured landscape can therefore be explained by a partially inserted metastable state, which leads us to a reinterpretation of the rates measured by force spectroscopy. Our results are consistent with the helical hairpin hypothesis but call into question the two-stage model of membrane protein folding as a general description of folding mechanisms in the presence of bilayers.
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34
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Gaffney KA, Hong H. The rhomboid protease GlpG has weak interaction energies in its active site hydrogen bond network. J Gen Physiol 2018; 151:282-291. [PMID: 30420443 PMCID: PMC6400518 DOI: 10.1085/jgp.201812047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/25/2018] [Indexed: 01/24/2023] Open
Abstract
Rhomboid proteases are membrane-integrated enzymes that hydrolyze peptide bonds in the transmembrane domains of protein substrates. Gaffney and Hong experimentally determine interaction energies between active site residues to reveal weak coupling, which may explain the slow proteolysis mediated by GlpG. Intramembrane rhomboid proteases are of particular interest because of their function to hydrolyze a peptide bond of a substrate buried in the membrane. Crystal structures of the bacterial rhomboid protease GlpG have revealed a catalytic dyad (Ser201-His254) and oxyanion hole (His150/Asn154/the backbone amide of Ser201) surrounded by the protein matrix and contacting a narrow water channel. Although multiple crystal structures have been solved, the catalytic mechanism of GlpG is not completely understood. Because it is a serine protease, hydrogen bonding interactions between the active site residues are thought to play a critical role in the catalytic cycle. Here, we dissect the interaction energies among the active site residues His254, Ser201, and Asn154 of Escherichia coli GlpG, which form a hydrogen bonding network. We combine double mutant cycle analysis with stability measurements using steric trapping. In mild detergent, the active site residues are weakly coupled with interaction energies (ΔΔGInter) of ‒1.4 kcal/mol between His254 and Ser201 and ‒0.2 kcal/mol between Ser201 and Asn154. Further, by analyzing the propagation of single mutations of the active site residues, we find that these residues are important not only for function but also for the folding cooperativity of GlpG. The weak interaction between Ser and His in the catalytic dyad may partly explain the unusually slow proteolysis by GlpG compared with other canonical serine proteases. Our result suggests that the weak hydrogen bonds in the active site are sufficient to carry out the proteolytic function of rhomboid proteases.
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Affiliation(s)
- Kristen A Gaffney
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI
| | - Heedeok Hong
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI .,Department of Chemistry, Michigan State University, East Lansing, MI
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35
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Lipids modulate the insertion and folding of the nascent chains of alpha helical membrane proteins. Biochem Soc Trans 2018; 46:1355-1366. [PMID: 30190329 DOI: 10.1042/bst20170424] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/18/2018] [Accepted: 07/31/2018] [Indexed: 02/08/2023]
Abstract
Membrane proteins must be inserted into a membrane and folded into their correct structure to function correctly. This insertion occurs during translation and synthesis by the ribosome for most α-helical membrane proteins. Precisely how this co-translational insertion and folding occurs, and the role played by the surrounding lipids, is still not understood. Most of the work on the influence of the lipid environment on folding and insertion has focussed on denatured, fully translated proteins, and thus does not replicate folding during unidirectional elongation of nascent chains that occurs in the cell. This review aims to highlight recent advances in elucidating lipid composition and bilayer properties optimal for insertion and folding of nascent chains in the membrane and in the assembly of oligomeric proteins.
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36
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The Rhomboid Superfamily: Structural Mechanisms and Chemical Biology Opportunities. Trends Biochem Sci 2018; 43:726-739. [DOI: 10.1016/j.tibs.2018.06.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/08/2018] [Accepted: 06/30/2018] [Indexed: 12/27/2022]
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37
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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] [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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38
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Membrane properties that shape the evolution of membrane enzymes. Curr Opin Struct Biol 2018; 51:80-91. [PMID: 29597094 DOI: 10.1016/j.sbi.2018.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/14/2018] [Accepted: 03/15/2018] [Indexed: 02/07/2023]
Abstract
Spectacular recent progress in structural biology has led to determination of the structures of many integral membrane enzymes that catalyze reactions in which at least one substrate also is membrane bound. A pattern of results seems to be emerging in which the active site chemistry of these enzymes is usually found to be analogous to what is observed for water soluble enzymes catalyzing the same reaction types. However, in light of the chemical, structural, and physical complexity of cellular membranes plus the presence of transmembrane gradients and potentials, these enzymes may be subject to membrane-specific regulatory mechanisms that are only now beginning to be uncovered. We review the membrane-specific environmental traits that shape the evolution of membrane-embedded biocatalysts.
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39
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Min D, Jefferson RE, Qi Y, Wang JY, Arbing MA, Im W, Bowie JU. Unfolding of a ClC chloride transporter retains memory of its evolutionary history. Nat Chem Biol 2018; 14:489-496. [PMID: 29581582 PMCID: PMC6038805 DOI: 10.1038/s41589-018-0025-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/12/2018] [Indexed: 11/12/2022]
Abstract
ClC chloride channels and transporters are important for chloride homeostasis in species from bacteria to human. Mutations in ClC proteins cause genetically inherited diseases, some of which are likely to have folding defects. The ClC proteins present a challenging and unusual biological folding problem because they are large membrane proteins possessing a complex architecture with many re-entrant helices that go only part way through membrane and loop back out. Here we were able to examine the unfolding of the E. coli ClC transporter, ClC-ec1, using single-molecule forced unfolding methods. We find that the protein can be separated into two stable halves that unfold independently. The independence of the two domains is consistent with an evolutionary model in which the two halves arose from independent folding subunits that later fused together. Maintaining smaller folding domains of lesser complexity within large membrane proteins may be an advantageous strategy to avoid misfolding traps.
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Affiliation(s)
- Duyoung Min
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Robert E Jefferson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yifei Qi
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Jing Yang Wang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mark A Arbing
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, PA, USA
| | - James U Bowie
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA. .,UCLA-DOE and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
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40
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Yang Y, Guo R, Gaffney K, Kim M, Muhammednazaar S, Tian W, Wang B, Liang J, Hong H. Folding-Degradation Relationship of a Membrane Protein Mediated by the Universally Conserved ATP-Dependent Protease FtsH. J Am Chem Soc 2018. [PMID: 29528632 DOI: 10.1021/jacs.8b00832] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
ATP-dependent protein degradation mediated by AAA+ proteases is one of the major cellular pathways for protein quality control and regulation of functional networks. While a majority of studies of protein degradation have focused on water-soluble proteins, it is not well understood how membrane proteins with abnormal conformation are selectively degraded. The knowledge gap stems from the lack of an in vitro system in which detailed molecular mechanisms can be studied as well as difficulties in studying membrane protein folding in lipid bilayers. To quantitatively define the folding-degradation relationship of membrane proteins, we reconstituted the degradation using the conserved membrane-integrated AAA+ protease FtsH as a model degradation machine and the stable helical-bundle membrane protein GlpG as a model substrate in the lipid bilayer environment. We demonstrate that FtsH possesses a substantial ability to actively unfold GlpG, and the degradation significantly depends on the stability and hydrophobicity near the degradation marker. We find that FtsH hydrolyzes 380-550 ATP molecules to degrade one copy of GlpG. Remarkably, FtsH overcomes the dual-energetic burden of substrate unfolding and membrane dislocation with the ATP cost comparable to that for water-soluble substrates by robust ClpAP/XP proteases. The physical principles elucidated in this study provide general insights into membrane protein degradation mediated by ATP-dependent proteolytic systems.
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Affiliation(s)
| | | | | | | | | | - Wei Tian
- Department of Bioengineering , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
| | - Boshen Wang
- Department of Bioengineering , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
| | - Jie Liang
- Department of Bioengineering , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
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41
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Lipid bilayer composition modulates the unfolding free energy of a knotted α-helical membrane protein. Proc Natl Acad Sci U S A 2018; 115:E1799-E1808. [PMID: 29432185 DOI: 10.1073/pnas.1714668115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
α-Helical membrane proteins have eluded investigation of their thermodynamic stability in lipid bilayers. Reversible denaturation curves have enabled some headway in determining unfolding free energies. However, these parameters have been limited to detergent micelles or lipid bicelles, which do not possess the same mechanical properties as lipid bilayers that comprise the basis of natural membranes. We establish reversible unfolding of the membrane transporter LeuT in lipid bilayers, enabling the comparison of apparent unfolding free energies in different lipid compositions. LeuT is a bacterial ortholog of neurotransmitter transporters and contains a knot within its 12-transmembrane helical structure. Urea is used as a denaturant for LeuT in proteoliposomes, resulting in the loss of up to 30% helical structure depending upon the lipid bilayer composition. Urea unfolding of LeuT in liposomes is reversible, with refolding in the bilayer recovering the original helical structure and transport activity. A linear dependence of the unfolding free energy on urea concentration enables the free energy to be extrapolated to zero denaturant. Increasing lipid headgroup charge or chain lateral pressure increases the thermodynamic stability of LeuT. The mechanical and charge properties of the bilayer also affect the ability of urea to denature the protein. Thus, we not only gain insight to the long-sought-after thermodynamic stability of an α-helical protein in a lipid bilayer but also provide a basis for studies of the folding of knotted proteins in a membrane environment.
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42
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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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43
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Seligmann H, Warthi G. Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes. Comput Struct Biotechnol J 2017; 15:412-424. [PMID: 28924459 PMCID: PMC5591391 DOI: 10.1016/j.csbj.2017.08.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/20/2017] [Accepted: 08/05/2017] [Indexed: 12/14/2022] Open
Abstract
A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5'/3' asymmetric (CDA = - 1/1; CDA = - 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (-/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2'/3' hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters. Preliminary results suggest CDA-whole organism associations (body temperature, developmental stability, lifespan). Presumably, CDA impacts spatial kinetics of codon-anticodon interactions, affecting cotranslational protein folding. Some synonymous codons have opposite CDA sign (alanine, leucine, serine, and valine), putatively explaining how synonymous mutations sometimes affect protein function. Correlations between CDA and tRNA synthetase classes are weaker than between CDA and antiparallel betasheet conformation parameters. This effect is stronger for mitochondrial genetic codes, and potentially drives mitochondrial codon-amino acid reassignments. CDA reveals information ruling nucleotide-protein relations embedded in reversed (not reverse-complement) sequences (5'-ZXX-3'/5'-XXZ-3').
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Affiliation(s)
- Hervé Seligmann
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, Postal code 13385, France
- Dept. Ecol Evol Behav, Alexander Silberman Inst Life Sci, The Hebrew University of Jerusalem, IL-91904 Jerusalem, Israel
| | - Ganesh Warthi
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, Postal code 13385, France
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44
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Kaspersen JD, Søndergaard A, Madsen DJ, Otzen DE, Pedersen JS. Refolding of SDS-Unfolded Proteins by Nonionic Surfactants. Biophys J 2017; 112:1609-1620. [PMID: 28445752 PMCID: PMC5406375 DOI: 10.1016/j.bpj.2017.03.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/03/2017] [Accepted: 03/07/2017] [Indexed: 11/30/2022] Open
Abstract
The strong and usually denaturing interaction between anionic surfactants (AS) and proteins/enzymes has both benefits and drawbacks: for example, it is put to good use in electrophoretic mass determinations but limits enzyme efficiency in detergent formulations. Therefore, studies of the interactions between proteins and AS as well as nonionic surfactants (NIS) are of both basic and applied relevance. The AS sodium dodecyl sulfate (SDS) denatures and unfolds globular proteins under most conditions. In contrast, NIS such as octaethylene glycol monododecyl ether (C12E8) and dodecyl maltoside (DDM) protect bovine serum albumin (BSA) from unfolding in SDS. Membrane proteins denatured in SDS can also be refolded by addition of NIS. Here, we investigate whether globular proteins unfolded by SDS can be refolded upon addition of C12E8 and DDM. Four proteins, BSA, α-lactalbumin (αLA), lysozyme, and β-lactoglobulin (βLG), were studied by small-angle x-ray scattering and both near- and far-UV circular dichroism. All proteins and their complexes with SDS were attempted to be refolded by the addition of C12E8, while DDM was additionally added to SDS-denatured αLA and βLG. Except for αLA, the proteins did not interact with NIS alone. For all proteins, the addition of NIS to the protein-SDS samples resulted in extraction of the SDS from the protein-SDS complexes and refolding of βLG, BSA, and lysozyme, while αLA changed to its NIS-bound state instead of the native state. We conclude that NIS competes with globular proteins for association with SDS, making it possible to release and refold SDS-denatured proteins by adding sufficient amounts of NIS, unless the protein also interacts with NIS alone.
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Affiliation(s)
| | | | - Daniel Jhaf Madsen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark.
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark; Department of Chemistry, Aarhus University, Aarhus, Denmark.
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45
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Jefferson RE, Min D, Corin K, Wang JY, Bowie JU. Applications of Single-Molecule Methods to Membrane Protein Folding Studies. J Mol Biol 2017; 430:424-437. [PMID: 28549924 DOI: 10.1016/j.jmb.2017.05.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 02/07/2023]
Abstract
Protein folding is a fundamental life process with many implications throughout biology and medicine. Consequently, there have been enormous efforts to understand how proteins fold. Almost all of this effort has focused on water-soluble proteins, however, leaving membrane proteins largely wandering in the wilderness. The neglect has occurred not because membrane proteins are unimportant but rather because they present many theoretical and technical complications. Indeed, quantitative membrane protein folding studies are generally restricted to a handful of well-behaved proteins. Single-molecule methods may greatly alter this picture, however, because the ability to work at or near infinite dilution removes aggregation problems, one of the main technical challenges of membrane protein folding studies.
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Affiliation(s)
- Robert E Jefferson
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles, 90095, CA, USA
| | - Duyoung Min
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles, 90095, CA, USA
| | - Karolina Corin
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles, 90095, CA, USA
| | - Jing Yang Wang
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles, 90095, CA, USA
| | - James U Bowie
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles, 90095, CA, USA.
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46
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Cordier B, Lemberg M. Probing the Activity of Eukaryotic Rhomboid Proteases In Vitro. Methods Enzymol 2017; 584:99-126. [DOI: 10.1016/bs.mie.2016.09.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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47
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Panigrahi R, Arutyunova E, Panwar P, Gimpl K, Keller S, Lemieux MJ. Reversible Unfolding of Rhomboid Intramembrane Proteases. Biophys J 2016; 110:1379-90. [PMID: 27028647 DOI: 10.1016/j.bpj.2016.01.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/18/2016] [Accepted: 01/22/2016] [Indexed: 12/20/2022] Open
Abstract
Denaturant-induced unfolding of helical membrane proteins provides insights into their mechanism of folding and domain organization, which take place in the chemically heterogeneous, anisotropic environment of a lipid membrane. Rhomboid proteases are intramembrane proteases that play key roles in various diseases. Crystal structures have revealed a compact helical bundle with a buried active site, which requires conformational changes for the cleavage of transmembrane substrates. A dimeric form of the rhomboid protease has been shown to be important for activity. In this study, we examine the mechanism of refolding for two distinct rhomboids to gain insight into their secondary structure-activity relationships. Although helicity is largely abolished in the unfolded states of both proteins, unfolding is completely reversible for HiGlpG but only partially reversible for PsAarA. Refolding of both proteins results in reassociation of the dimer, with a 90% regain of catalytic activity for HiGlpG but only a 70% regain for PsAarA. For both proteins, a broad, gradual transition from the native, folded state to the denatured, partly unfolded state was revealed with the aid of circular dichroism spectroscopy as a function of denaturant concentration, thus arguing against a classical two-state model as found for many globular soluble proteins. Thermal denaturation has irreversible destabilizing effects on both proteins, yet reveals important functional details regarding substrate accessibility to the buried active site. This concerted biophysical and functional analysis demonstrates that HiGlpG, with a simple six-transmembrane-segment organization, is more robust than PsAarA, which has seven predicted transmembrane segments, thus rendering HiGlpG amenable to in vitro studies of membrane-protein folding.
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Affiliation(s)
- Rashmi Panigrahi
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Elena Arutyunova
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Pankaj Panwar
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Katharina Gimpl
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - M Joanne Lemieux
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.
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48
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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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49
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Guo R, Gaffney K, Yang Z, Kim M, Sungsuwan S, Huang X, Hubbell WL, Hong H. Steric trapping reveals a cooperativity network in the intramembrane protease GlpG. Nat Chem Biol 2016; 12:353-360. [PMID: 26999782 PMCID: PMC4837050 DOI: 10.1038/nchembio.2048] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 01/22/2016] [Indexed: 12/21/2022]
Abstract
Membrane proteins are assembled through balanced interactions among protein, lipids and water. Studying their folding while maintaining the native lipid environment is necessary but challenging. Here we present methods for analyzing key elements in membrane protein folding including thermodynamic stability, compactness of the unfolded state and folding cooperativity under native conditions. The methods are based on steric trapping which couples unfolding of a doubly-biotinylated protein to binding of monovalent streptavidin (mSA). We further advanced this technology for general application by developing versatile biotin probes possessing spectroscopic reporters that are sensitized by mSA binding or protein unfolding. By applying these methods to an intramembrane protease GlpG of Escherichia coli, we elucidated a widely unraveled unfolded state, subglobal unfolding of the region encompassing the active site, and a network of cooperative and localized interactions to maintain the stability. These findings provide crucial insights into the folding energy landscape of membrane proteins.
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Affiliation(s)
- Ruiqiong Guo
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Kristen Gaffney
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Zhongyu Yang
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Miyeon Kim
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Suttipun Sungsuwan
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Xuefei Huang
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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50
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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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