1
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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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2
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Muhammednazaar S, Yao J, Guo R, Rhee MS, Kim KH, Kang SG, Hong H. Lipid Bilayer Strengthens the Cooperative Network of a Membrane-Integral Enzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542905. [PMID: 37398072 PMCID: PMC10312574 DOI: 10.1101/2023.05.30.542905] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Lipid bilayer provides a two-dimensional hydrophobic solvent milieu for membrane proteins in cells. Although the native bilayer is widely recognized as an optimal environment for folding and function of membrane proteins, the underlying physical basis remains elusive. Here, employing the intramembrane protease GlpG of Escherichia coli as a model, we elucidate how the bilayer stabilizes a membrane protein and engages the protein's residue interaction network compared to the nonnative hydrophobic medium, micelles. We find that the bilayer enhances GlpG stability by promoting residue burial in the protein interior compared to micelles. Strikingly, while the cooperative residue interactions cluster into multiple distinct regions in micelles, the whole packed regions of the protein act as a single cooperative unit in the bilayer. Molecular dynamics (MD) simulation indicates that lipids less efficiently solvate GlpG than detergents. Thus, the bilayerinduced enhancement of stability and cooperativity likely stems from the dominant intraprotein interactions outcompeting the weak lipid solvation. Our findings reveal a foundational mechanism in the folding, function, and quality control of membrane proteins. The enhanced cooperativity benefits function facilitating propagation of local structural perturbation across the membrane. However, the same phenomenon can render the proteins' conformational integrity vulnerable to missense mutations causing conformational diseases1,2.
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Affiliation(s)
| | - Jiaqi Yao
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Ruiqiong Guo
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - May S Rhee
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Kelly H Kim
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Seung-Gu Kang
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, 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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Ernst M, Robertson JL. The Role of the Membrane in Transporter Folding and Activity. J Mol Biol 2021; 433:167103. [PMID: 34139219 PMCID: PMC8756397 DOI: 10.1016/j.jmb.2021.167103] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/23/2022]
Abstract
The synthesis, folding, and function of membrane transport proteins are critical factors for defining cellular physiology. Since the stability of these proteins evolved amidst the lipid bilayer, it is no surprise that we are finding that many of these membrane proteins demonstrate coupling of their structure or activity in some way to the membrane. More and more transporter structures are being determined with some information about the surrounding membrane, and computational modeling is providing further molecular details about these solvation structures. Thus, the field is moving towards identifying which molecular mechanisms - lipid interactions, membrane perturbations, differential solvation, and bulk membrane effects - are involved in linking membrane energetics to transporter stability and function. In this review, we present an overview of these mechanisms and the growing evidence that the lipid bilayer is a major determinant of the fold, form, and function of membrane transport proteins in membranes.
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Affiliation(s)
- Melanie Ernst
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Janice L Robertson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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4
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Marx DC, Fleming KG. Membrane proteins enter the fold. Curr Opin Struct Biol 2021; 69:124-130. [PMID: 33975156 DOI: 10.1016/j.sbi.2021.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/15/2021] [Accepted: 03/21/2021] [Indexed: 11/19/2022]
Abstract
Membrane proteins have historically been recalcitrant to biophysical folding studies. However, recent adaptations of methods from the soluble protein folding field have found success in their applications to transmembrane proteins composed of both α-helical and β-barrel conformations. Avoiding aggregation is critical for the success of these experiments. Altogether these studies are leading to discoveries of folding trajectories, foundational stabilizing forces and better-defined endpoints that enable more accurate interpretation of thermodynamic data. Increased information on membrane protein folding in the cell shows that the emerging biophysical principles are largely recapitulated even in the complex biological environment.
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Affiliation(s)
- Dagan C Marx
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, United States
| | - Karen G Fleming
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, United States.
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5
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Domański J, Sansom MSP, Stansfeld PJ, Best RB. Atomistic mechanism of transmembrane helix association. PLoS Comput Biol 2020; 16:e1007919. [PMID: 32497094 PMCID: PMC7272003 DOI: 10.1371/journal.pcbi.1007919] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/30/2020] [Indexed: 01/21/2023] Open
Abstract
Transmembrane helix association is a fundamental step in the folding of helical membrane proteins. The prototypical example of this association is formation of the glycophorin dimer. While its structure and stability have been well-characterized experimentally, the detailed assembly mechanism is harder to obtain. Here, we use all-atom simulations within phospholipid membrane to study glycophorin association. We find that initial association results in the formation of a non-native intermediate, separated by a significant free energy barrier from the dimer with a native binding interface. We have used transition-path sampling to determine the association mechanism. We find that the mechanism of the initial bimolecular association to form the intermediate state can be mediated by many possible contacts, but seems to be particularly favoured by formation of non-native contacts between the C-termini of the two helices. On the other hand, the contacts which are key to determining progression from the intermediate to the native state are those which define the native binding interface, reminiscent of the role played by native contacts in determining folding of globular proteins. As a check on the simulations, we have computed association and dissociation rates from the transition-path sampling. We obtain results in reasonable accord with available experimental data, after correcting for differences in native state stability. Our results yield an atomistic description of the mechanism for a simple prototype of helical membrane protein folding. Many important cellular functions are performed by membrane proteins, and in particular by association of proteins via transmembrane helices. However, the mechanism of how the helices associate has been challenging to study, by either experiment or simulation. Here, we use advanced molecular simulation methods to overcome the slow time scales involved in helix association and dissociation and obtain a view of the association mechanism in atomic detail. We show that association occurs via an initially non-native dimer, before proceeding to the native state, and we validate our results by comparison to available experimental kinetic data. Our methods will also aid in the study of the assembly mechanism of larger transmembrane proteins via molecular simulation.
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Affiliation(s)
- Jan Domański
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Phillip J. Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, United Kingdom
- School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Campus, Coventry, United Kingdom
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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6
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Lu C, Liu Z, Zhang E, He F, Ma Z, Wang H. MPLs-Pred: Predicting Membrane Protein-Ligand Binding Sites Using Hybrid Sequence-Based Features and Ligand-Specific Models. Int J Mol Sci 2019; 20:ijms20133120. [PMID: 31247932 PMCID: PMC6651575 DOI: 10.3390/ijms20133120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/23/2019] [Accepted: 06/23/2019] [Indexed: 02/07/2023] Open
Abstract
Membrane proteins (MPs) are involved in many essential biomolecule mechanisms as a pivotal factor in enabling the small molecule and signal transport between the two sides of the biological membrane; this is the reason that a large portion of modern medicinal drugs target MPs. Therefore, accurately identifying the membrane protein-ligand binding sites (MPLs) will significantly improve drug discovery. In this paper, we propose a sequence-based MPLs predictor called MPLs-Pred, where evolutionary profiles, topology structure, physicochemical properties, and primary sequence segment descriptors are combined as features applied to a random forest classifier, and an under-sampling scheme is used to enhance the classification capability with imbalanced samples. Additional ligand-specific models were taken into consideration in refining the prediction. The corresponding experimental results based on our method achieved an appreciable performance, with 0.63 MCC (Matthews correlation coefficient) as the overall prediction precision, and those values were 0.604, 0.7, and 0.692, respectively, for the three main types of ligands: drugs, metal ions, and biomacromolecules. MPLs-Pred is freely accessible at http://icdtools.nenu.edu.cn/.
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Affiliation(s)
- Chang Lu
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China
- Institute of Computational Biology, Northeast Normal University, Changchun 130117, China
| | - Zhe Liu
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China
- Institute of Computational Biology, Northeast Normal University, Changchun 130117, China
| | - Enju Zhang
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China
- Institute of Computational Biology, Northeast Normal University, Changchun 130117, China
| | - Fei He
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China.
- Institute of Computational Biology, Northeast Normal University, Changchun 130117, China.
| | - Zhiqiang Ma
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China.
- Institute of Computational Biology, Northeast Normal University, Changchun 130117, China.
| | - Han Wang
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China.
- Institute of Computational Biology, Northeast Normal University, Changchun 130117, China.
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7
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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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8
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Gaines JC, Acebes S, Virrueta A, Butler M, Regan L, O'Hern CS. Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins. Proteins 2018; 86:581-591. [PMID: 29427530 PMCID: PMC5912992 DOI: 10.1002/prot.25479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/23/2018] [Accepted: 02/06/2018] [Indexed: 12/26/2022]
Abstract
We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins.
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Affiliation(s)
- J C Gaines
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, 06520
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
| | - S Acebes
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520
| | - A Virrueta
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520
| | - M Butler
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, 90007
| | - L Regan
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, 06520
- Department of Chemistry, Yale University, New Haven, Connecticut, 06520
| | - C S O'Hern
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, 06520
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520
- Department of Physics, Yale University, New Haven, Connecticut, 06520
- Department of Applied Physics, Yale University, New Haven, Connecticut, 06520
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9
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Domański J, Sansom MSP, Stansfeld PJ, Best RB. Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association. J Chem Theory Comput 2018; 14:1706-1715. [PMID: 29424543 PMCID: PMC5852462 DOI: 10.1021/acs.jctc.7b00983] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Indexed: 01/21/2023]
Abstract
Atomistic simulations have recently been shown to be sufficiently accurate to reversibly fold globular proteins and have provided insights into folding mechanisms. Gaining similar understanding from simulations of membrane protein folding and association would be of great medical interest. All-atom simulations of the folding and assembly of transmembrane protein domains are much more challenging, not least due to very slow diffusion within the lipid bilayer membrane. Here, we focus on a simple and well-characterized prototype of membrane protein folding and assembly, namely the dimerization of glycophorin A, a homodimer of single transmembrane helices. We have determined the free energy landscape for association of the dimer using the CHARMM36 force field. We find that the native structure is a metastable state, but not stable as expected from experimental estimates of the dissociation constant and numerous experimental structures obtained under a variety of conditions. We explore two straightforward approaches to address this problem and demonstrate that they result in stable dimers with dissociation constants consistent with experimental data.
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Affiliation(s)
- Jan Domański
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892-0520, United States
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Phillip J. Stansfeld
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Robert B. Best
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892-0520, United States
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10
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Anderson SM, Mueller BK, Lange EJ, Senes A. Combination of Cα-H Hydrogen Bonds and van der Waals Packing Modulates the Stability of GxxxG-Mediated Dimers in Membranes. J Am Chem Soc 2017; 139:15774-15783. [PMID: 29028318 PMCID: PMC5927632 DOI: 10.1021/jacs.7b07505] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The GxxxG motif is frequently found at the dimerization interface of a transmembrane structural motif called GASright, which is characterized by a short interhelical distance and a right-handed crossing angle between the helices. In GASright dimers, such as glycophorin A (GpA), BNIP3, and members of the ErbB family, the backbones of the helices are in contact, and they invariably display networks of 4 to 8 weak hydrogen bonds between Cα-H carbon donors and carbonyl acceptors on opposing helices (Cα-H···O═C hydrogen bonds). These networks of weak hydrogen bonds at the helix-helix interface are presumably stabilizing, but their energetic contribution to dimerization has yet to be determined experimentally. Here, we present a computational and experimental structure-based analysis of GASright dimers of different predicted stabilities, which show that a combination of van der Waals packing and Cα-H hydrogen bonding predicts the experimental trend of dimerization propensities. This finding provides experimental support for the hypothesis that the networks of Cα-H hydrogen bonds are major contributors to the free energy of association of GxxxG-mediated dimers. The structural comparison between groups of GASright dimers of different stabilities reveals distinct sequence as well as conformational preferences. Stability correlates with shorter interhelical distances, narrower crossing angles, better packing, and the formation of larger networks of Cα-H hydrogen bonds. The identification of these structural rules provides insight on how nature could modulate stability in GASright and finely tune dimerization to support biological function.
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Affiliation(s)
- Samantha M Anderson
- Department of Biochemistry, University of Wisconsin-Madison , 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Benjamin K Mueller
- Department of Biochemistry, University of Wisconsin-Madison , 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Evan J Lange
- Department of Biochemistry, University of Wisconsin-Madison , 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Alessandro Senes
- Department of Biochemistry, University of Wisconsin-Madison , 433 Babcock Drive, Madison, Wisconsin 53706, United States
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11
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Membrane proteins structures: A review on computational modeling tools. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2021-2039. [DOI: 10.1016/j.bbamem.2017.07.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/04/2017] [Accepted: 07/13/2017] [Indexed: 01/02/2023]
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12
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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: 27] [Impact Index Per Article: 3.9] [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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13
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Khadria AS, Senes A. Fluorophores, environments, and quantification techniques in the analysis of transmembrane helix interaction using FRET. Biopolymers 2016; 104:247-64. [PMID: 25968159 DOI: 10.1002/bip.22667] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/15/2015] [Accepted: 05/04/2015] [Indexed: 12/31/2022]
Abstract
Förster resonance energy transfer (FRET) has been widely used as a spectroscopic tool in vitro to study the interactions between transmembrane (TM) helices in detergent and lipid environments. This technique has been instrumental to many studies that have greatly contributed to quantitative understanding of the physical principles that govern helix-helix interactions in the membrane. These studies have also improved our understanding of the biological role of oligomerization in membrane proteins. In this review, we focus on the combinations of fluorophores used, the membrane mimetic environments, and measurement techniques that have been applied to study model systems as well as biological oligomeric complexes in vitro. We highlight the different formalisms used to calculate FRET efficiency and the challenges associated with accurate quantification. The goal is to provide the reader with a comparative summary of the relevant literature for planning and designing FRET experiments aimed at measuring TM helix-helix associations.
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Affiliation(s)
- Ambalika S Khadria
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | - Alessandro Senes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706
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14
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Screening for transmembrane association in divisome proteins using TOXGREEN, a high-throughput variant of the TOXCAT assay. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2573-2583. [PMID: 27453198 DOI: 10.1016/j.bbamem.2016.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 07/15/2016] [Accepted: 07/19/2016] [Indexed: 11/21/2022]
Abstract
TOXCAT is a widely used genetic assay to study interactions of transmembrane helices within the inner membrane of the bacterium Escherichia coli. TOXCAT is based on a fusion construct that links a transmembrane domain of interest with a cytoplasmic DNA-binding domain from the Vibrio cholerae ToxR protein. Interaction driven by the transmembrane domain results in dimerization of the ToxR domain, which, in turn, activates the expression of the reporter gene chloramphenicol acetyl transferase (CAT). Quantification of CAT is used as a measure of the ability of the transmembrane domain to self-associate. Because the quantification of CAT is relatively laborious, we developed a high-throughput variant of the assay, TOXGREEN, based on the expression of super-folded GFP and detection of fluorescence directly in unprocessed cell cultures. Careful side-by-side comparison of TOXCAT and TOXGREEN demonstrates that the methods have comparable response, dynamic range, sensitivity and intrinsic variability both in LB and minimal media. The greatly enhanced workflow makes TOXGREEN much more scalable and ideal for screening, since hundreds of constructs can be rapidly assessed in 96 well plates. Even for small scale investigations, TOXGREEN significantly reduces time, labor and cost associated with the procedure. We demonstrate applicability with a large screening for self-association among the transmembrane domains of bitopic proteins of the divisome (FtsL, FtsB, FtsQ, FtsI, FtsN, ZipA and EzrA) belonging to 11 bacterial species. The analysis confirms a previously reported tendency for FtsB to self-associate, and suggests that the transmembrane domains of ZipA, EzrA and FtsN may also possibly oligomerize.
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15
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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: 37] [Impact Index Per Article: 4.6] [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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Hong H. Role of Lipids in Folding, Misfolding and Function of Integral Membrane Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 855:1-31. [DOI: 10.1007/978-3-319-17344-3_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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17
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Toward understanding driving forces in membrane protein folding. Arch Biochem Biophys 2014; 564:297-313. [DOI: 10.1016/j.abb.2014.07.031] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 12/13/2022]
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Khadria AS, Mueller BK, Stefely JA, Tan CH, Pagliarini DJ, Senes A. A Gly-zipper motif mediates homodimerization of the transmembrane domain of the mitochondrial kinase ADCK3. J Am Chem Soc 2014; 136:14068-77. [PMID: 25216398 PMCID: PMC4195374 DOI: 10.1021/ja505017f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Interactions between α-helices within the hydrophobic environment of lipid bilayers are integral to the folding and function of transmembrane proteins; however, the major forces that mediate these interactions remain debated, and our ability to predict these interactions is still largely untested. We recently demonstrated that the frequent transmembrane association motif GASright, the GxxxG-containing fold of the glycophorin A dimer, is optimal for the formation of extended networks of Cα-H hydrogen bonds, supporting the hypothesis that these bonds are major contributors to association. We also found that optimization of Cα-H hydrogen bonding and interhelical packing is sufficient to computationally predict the structure of known GASright dimers at near atomic level. Here, we demonstrate that this computational method can be used to characterize the structure of a protein not previously known to dimerize, by predicting and validating the transmembrane dimer of ADCK3, a mitochondrial kinase. ADCK3 is involved in the biosynthesis of the redox active lipid, ubiquinone, and human ADCK3 mutations cause a cerebellar ataxia associated with ubiquinone deficiency, but the biochemical functions of ADCK3 remain largely undefined. Our experimental analyses show that the transmembrane helix of ADCK3 oligomerizes, with an interface based on an extended Gly-zipper motif, as predicted by our models. The data provide strong evidence for the hypothesis that optimization of Cα-H hydrogen bonding is an important factor in the association of transmembrane helices. This work also provides a structural foundation for investigating the role of transmembrane association in regulating the biological activity of ADCK3.
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Affiliation(s)
- Ambalika S Khadria
- Department of Biochemistry, University of Wisconsin-Madison , 433 Babcock Drive, Madison, Wisconsin 53706, United States
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Song Y, Kenworthy AK, Sanders CR. Cholesterol as a co-solvent and a ligand for membrane proteins. Protein Sci 2013; 23:1-22. [PMID: 24155031 DOI: 10.1002/pro.2385] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 09/27/2013] [Accepted: 10/01/2013] [Indexed: 01/23/2023]
Abstract
As of mid 2013 a Medline search on "cholesterol" yielded over 200,000 hits, reflecting the prominence of this lipid in numerous aspects of animal cell biology and physiology under conditions of health and disease. Aberrations in cholesterol homeostasis underlie both a number of rare genetic disorders and contribute to common sporadic and complex disorders including heart disease, stroke, type II diabetes, and Alzheimer's disease. The corresponding author of this review and his lab stumbled only recently into the sprawling area of cholesterol research when they discovered that the amyloid precursor protein (APP) binds cholesterol, a topic covered by the Hans Neurath Award lecture at the 2013 Protein Society Meeting. Here, we first provide a brief overview of cholesterol-protein interactions and then offer our perspective on how and why binding of cholesterol to APP and its C99 domain (β-CTF) promotes the amyloidogenic pathway, which is closely related to the etiology of Alzheimer's disease.
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Affiliation(s)
- Yuanli Song
- Department of Biochemistry, Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
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