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Botsch JJ, Junker R, Sorgenfrei M, Ogger PP, Stier L, von Gronau S, Murray PJ, Seeger MA, Schulman BA, Bräuning B. Doa10/MARCH6 architecture interconnects E3 ligase activity with lipid-binding transmembrane channel to regulate SQLE. Nat Commun 2024; 15:410. [PMID: 38195637 PMCID: PMC10776854 DOI: 10.1038/s41467-023-44670-5] [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: 06/12/2023] [Accepted: 12/19/2023] [Indexed: 01/11/2024] Open
Abstract
Transmembrane E3 ligases play crucial roles in homeostasis. Much protein and organelle quality control, and metabolic regulation, are determined by ER-resident MARCH6 E3 ligases, including Doa10 in yeast. Here, we present Doa10/MARCH6 structural analysis by cryo-EM and AlphaFold predictions, and a structure-based mutagenesis campaign. The majority of Doa10/MARCH6 adopts a unique circular structure within the membrane. This channel is established by a lipid-binding scaffold, and gated by a flexible helical bundle. The ubiquitylation active site is positioned over the channel by connections between the cytosolic E3 ligase RING domain and the membrane-spanning scaffold and gate. Here, by assaying 95 MARCH6 variants for effects on stability of the well-characterized substrate SQLE, which regulates cholesterol levels, we reveal crucial roles of the gated channel and RING domain consistent with AlphaFold-models of substrate-engaged and ubiquitylation complexes. SQLE degradation further depends on connections between the channel and RING domain, and lipid binding sites, revealing how interconnected Doa10/MARCH6 elements could orchestrate metabolic signals, substrate binding, and E3 ligase activity.
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Affiliation(s)
- J Josephine Botsch
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Technical University of Munich, School of Natural Sciences, Munich, Germany
| | - Roswitha Junker
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Michèle Sorgenfrei
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, 8006, Zurich, Switzerland
| | - Patricia P Ogger
- Research Group of Immunoregulation, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Luca Stier
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Technical University of Munich, School of Natural Sciences, Munich, Germany
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Peter J Murray
- Research Group of Immunoregulation, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, 8006, Zurich, Switzerland
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Bastian Bräuning
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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2
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Barlow AN, Manu MS, Saladi SM, Tarr PT, Yadav Y, Thinn AMM, Zhu Y, Laganowsky AD, Clemons WM, Ramasamy S. Structures of Get3d reveal a distinct architecture associated with the emergence of photosynthesis. J Biol Chem 2023:104752. [PMID: 37100288 DOI: 10.1016/j.jbc.2023.104752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 04/28/2023] Open
Abstract
Homologs of the protein Get3 have been identified in all domains yet remain to be fully characterized. In the eukaryotic cytoplasm, Get3 delivers tail-anchored (TA) integral membrane proteins, defined by a single transmembrane helix at their C-terminus, to the endoplasmic reticulum. While most eukaryotes have a single Get3 gene, plants are notable for having multiple Get3 paralogs. Get3d is conserved across land plants and photosynthetic bacteria and includes a distinctive C-terminal α-crystallin domain. After tracing the evolutionary origin of Get3d, we solve the Arabidopsis thaliana Get3d crystal structure, identify its localization to the chloroplast, and provide evidence for a role in TA protein binding. The structure is identical to that of a cyanobacterial Get3 homolog, which is further refined here. Distinct features of Get3d include an incomplete active site, a 'closed' conformation in the apo-state, and a hydrophobic chamber. Both homologs have ATPase activity and are capable of binding TA proteins, supporting a potential role in TA protein targeting. Get3d is first found with the development of photosynthesis and conserved across 1.2 billion years into the chloroplasts of higher plants across the evolution of photosynthesis suggesting a role in the homeostasis of photosynthetic machinery.
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Affiliation(s)
- Alexandra N Barlow
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, 91125, CA, USA.
| | - M S Manu
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.
| | - Shyam M Saladi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, 91125, CA, USA
| | - Paul T Tarr
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, 91125, CA, USA
| | - Yashpal Yadav
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Aye M M Thinn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, 91125, CA, USA
| | - Yun Zhu
- Department of Chemistry, Texas A&M University, 400 Bizzell St., College Station, 77843, TX, USA
| | - Arthur D Laganowsky
- Department of Chemistry, Texas A&M University, 400 Bizzell St., College Station, 77843, TX, USA
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, 91125, CA, USA.
| | - Sureshkumar Ramasamy
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.
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3
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Fry MY, Saladi SM, Cunha A, Clemons WM. Sequence-based features that are determinant for tail-anchored membrane protein sorting in eukaryotes. Traffic 2021; 22:306-318. [PMID: 34288289 PMCID: PMC8380732 DOI: 10.1111/tra.12809] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/15/2021] [Accepted: 07/18/2021] [Indexed: 11/29/2022]
Abstract
The correct targeting and insertion of tail-anchored (TA) integral membrane proteins is critical for cellular homeostasis. TA proteins are defined by a hydrophobic transmembrane domain (TMD) at their C-terminus and are targeted to either the ER or mitochondria. Derived from experimental measurements of a few TA proteins, there has been little examination of the TMD features that determine localization. As a result, the localization of many TA proteins are misclassified by the simple heuristic of overall hydrophobicity. Because ER-directed TMDs favor arrangement of hydrophobic residues to one side, we sought to explore the role of geometric hydrophobic properties. By curating TA proteins with experimentally determined localizations and assessing hypotheses for recognition, we bioinformatically and experimentally verify that a hydrophobic face is the most accurate singular metric for separating ER and mitochondria-destined yeast TA proteins. A metric focusing on an 11 residue segment of the TMD performs well when classifying human TA proteins. The most inclusive predictor uses both hydrophobicity and C-terminal charge in tandem. This work provides context for previous observations and opens the door for more detailed mechanistic experiments to determine the molecular factors driving this recognition.
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Affiliation(s)
- Michelle Y. Fry
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Shyam M. Saladi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Alexandre Cunha
- Division of Biology and Biological Engineering, Center for Advanced Methods in Biological Image Analysis, Beckman Institute, Pasadena, California, USA
| | - William M. Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
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4
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Curley N, Levy D, Do MA, Brown A, Stickney Z, Marriott G, Lu B. Sequential deletion of CD63 identifies topologically distinct scaffolds for surface engineering of exosomes in living human cells. NANOSCALE 2020; 12:12014-12026. [PMID: 32463402 PMCID: PMC7313400 DOI: 10.1039/d0nr00362j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Exosomes are cell-derived extracellular vesicles that have great potential in the field of nano-medicine. However, a fundamental challenge in the engineering of exosomes is the design of biocompatible molecular scaffolds on their surface to enable cell targeting and therapeutic functions. CD63 is a hallmark protein of natural exosomes that is highly enriched on the external surface of the membrane. We have previously described engineering of CD63 for use as a molecular scaffold in order to introduce cell-targeting features to the exosome surface. Despite this initial success, the restrictive M-shaped topology of full-length CD63 may hinder specific applications that require N- or C-terminal display of cell-targeting moieties on the outer surface of the exosome. In this study, we describe new and topologically distinct CD63 scaffolds that enable robust and flexible surface engineering of exosomes. In particular, we conducted sequential deletions of the transmembrane helix of CD63 to generate a series of CD63 truncates, each genetically-fused to a fluorescent protein. Molecular and cellular characterization studies showed truncates of CD63 harboring the transmembrane helix 3 (TM3) correctly targeted and anchored to the exosome membrane and exhibited distinct n-, N-, Ω-, or I-shaped membrane topologies in the exosomal membrane. We further established that these truncates retained robust membrane-anchoring and exosome-targeting activities when stably expressed in the HEK293 cells. Moreover, HEK293 cells produced engineered exosomes in similar quantities to cells expressing full-length CD63. Based on the results of our systematic sequential deletion studies, we propose a model to understand molecular mechanisms that underlie membrane-anchoring and exosome targeting features of CD63. In summary, we have established new and topologically distinct scaffolds based on engineering of CD63 that enables flexible engineering of the exosome surface for applications in disease-targeted drug delivery and therapy.
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Affiliation(s)
- Natalie Curley
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA.
| | - Daniel Levy
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA.
| | - Mai Anh Do
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA.
| | - Annie Brown
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA.
| | - Zachary Stickney
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA.
| | - Gerard Marriott
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720, USA.
| | - Biao Lu
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA.
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5
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Bai L, You Q, Feng X, Kovach A, Li H. Structure of the ER membrane complex, a transmembrane-domain insertase. Nature 2020; 584:475-478. [PMID: 32494008 PMCID: PMC7442705 DOI: 10.1038/s41586-020-2389-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/07/2020] [Indexed: 11/24/2022]
Abstract
The ER membrane complex (EMC) cooperates with the Sec61 translocon to co-translationally insert a transmembrane helix (TMH) of many multi-pass integral membrane proteins into the ER membrane, and it is also responsible for inserting the TMH of some tail-anchored proteins 1–3. How EMC accomplishes this feat has been unclear. Here we report the first cryo-EM structure of the eukaryotic EMC. We found that the Saccharomyces cerevisiae EMC contains eight subunits (Emc1–6, 7, and 10); has a large lumenal region and a smaller cytosolic region; and has a transmembrane region formed by Emc4, 5, and 6 plus the transmembrane domains (TMDs) of Emc1 and 3. We identified a 5-TMH fold centered around Emc3 that resembles the prokaryotic insertase YidC and that delineates a largely hydrophilic client pocket. The TMD of Emc4 tilts away from the main transmembrane region of EMC and is partially mobile. Mutational studies demonstrated that Emc4 flexibility and the hydrophilicity of the client pocket are required for EMC function. The EMC structure reveals a remarkable evolutionary conservation with the prokaryotic insertases 4,5; suggests a similar mechanism of TMH insertion; and provides a framework for detailed understanding of membrane insertion for numerous eukaryotic integral membrane proteins and tail-anchored proteins.
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Affiliation(s)
- Lin Bai
- Structural Biology Program, Van Andel Institute, Grand Rapids, MI, USA.
| | - Qinglong You
- Structural Biology Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Xiang Feng
- Structural Biology Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Amanda Kovach
- Structural Biology Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Huilin Li
- Structural Biology Program, Van Andel Institute, Grand Rapids, MI, USA.
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6
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Li Y, Fang Q, Miao X, Zhang X, Zhao Y, Yan J, Zhang Y, Wu R, Nie B, Hirtz M, Liu J. Aptamer Conformation-Cooperated Enzyme-Assisted Surface-Enhanced Raman Scattering Enabling Ultrasensitive Detection of Cell Surface Protein Biomarkers in Blood Samples. ACS Sens 2019; 4:2605-2614. [PMID: 31514496 DOI: 10.1021/acssensors.9b00604] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Developing novel strategies for sensitive and specific detection of protein biomarkers is a field of active research. Here, we report an ultrasensitive biosensor to detect protein tyrosine kinase-7 (PTK7), an important protein biomarker on the cell surface, by aptamer conformation-cooperated enzyme-assisted surface-enhanced Raman scattering (SERS) (ACCESS) technology. Our approach features a synergistic combination of the conformational alteration of the anglerfish aptamer triggered by the recognition of the membrane protein (PTK7) and Exo III enzyme-assisted nucleic acid amplification. It transduces the specific binding events between the aptamer and PTK7 protein into dramatically improved SERS signals. Sensitive and specific detection of PTK7 protein has been demonstrated both in the solution and directly on the surface of live CCRF-CEM cells, with a limit of detection better than the commercial enzyme-linked immunosorbent assay method by nearly 5 orders of magnitude. As a flexible, ultrasensitive, and specific approach, ACCESS promises important applications in clinical diagnostics, where only a very limited amount of the biological sample is available.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Baoqing Nie
- School of Electronic and Information Engineering, Soochow University, Suzhou, Jiangsu Province 215006, China
| | - Michael Hirtz
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), Karlsruhe 76131, Germany
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7
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Yokoo H, Kagechika H, Ohsaki A, Hirano T. A Polarity‐Sensitive Fluorescent Amino Acid and its Incorporation into Peptides for the Ratiometric Detection of Biomolecular Interactions. Chempluschem 2019; 84:1716-1719. [DOI: 10.1002/cplu.201900489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/04/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Hidetomo Yokoo
- Institute of Biomaterials and BioengineeringTokyo Medical and Dental University (TMDU) 2-3-10 Kanda-Surugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Hiroyuki Kagechika
- Institute of Biomaterials and BioengineeringTokyo Medical and Dental University (TMDU) 2-3-10 Kanda-Surugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Ayumi Ohsaki
- College of Humanities and SciencesNihon University 3-25-40 Sakurajosui, Setagaya-ku Tokyo 156-8550 Japan
| | - Tomoya Hirano
- Osaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
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8
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Kocman V, Di Mauro GM, Veglia G, Ramamoorthy A. Use of paramagnetic systems to speed-up NMR data acquisition and for structural and dynamic studies. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 102:36-46. [PMID: 31325686 PMCID: PMC6698407 DOI: 10.1016/j.ssnmr.2019.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 05/05/2023]
Abstract
NMR spectroscopy is a powerful experimental technique to study biological systems at the atomic resolution. However, its intrinsic low sensitivity results in long acquisition times that in extreme cases lasts for days (or even weeks) often exceeding the lifetime of the sample under investigation. Different paramagnetic agents have been used in an effort to decrease the spin-lattice (T1) relaxation times of the studied nuclei, which are the main cause for long acquisition times necessary for signal averaging to enhance the signal-to-noise ratio of NMR spectra. Consequently, most of the experimental time is "wasted" in waiting for the magnetization to recover between successive scans. In this review, we discuss how to set up an optimal paramagnetic relaxation enhancement (PRE) system to effectively reduce the T1 relaxation times avoiding significant broadening of NMR signals. Additionally, we describe how PRE-agents can be used to provide structural and dynamic information and can even be used to follow the intermediates of chemical reactions and to speed-up data acquisition. We also describe the unique challenges and benefits associated with the application of PRE to solid-state NMR spectroscopy, explaining how the use of PREs is more complex for membrane mimetic systems as PREs can also be exploited to change the alignment of oriented membrane systems. Functionalization of membrane mimetics, such as bicelles, can provide a controlled region of paramagnetic effect that has the potential, together with the desired alignment, to provide crucial biologically relevant structural information. And finally, we discuss how paramagnetic metals can be utilized to further increase the dynamic nuclear polarization (DNP) effects and how to preserve the enhancements when dissolution DNP is implemented.
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Affiliation(s)
- Vojč Kocman
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA; Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, USA
| | | | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA; Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, USA.
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9
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Ravula T, Hardin NZ, Di Mauro GM, Ramamoorthy A. Styrene maleic acid derivates to enhance the applications of bio-inspired polymer based lipid-nanodiscs. Eur Polym J 2018; 108:597-602. [PMID: 31105326 DOI: 10.1016/j.eurpolymj.2018.09.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Membrane mimetics are essential to study the structure, dynamics and function of membrane-associated proteins by biophysical and biochemical approaches. Among various membrane mimetics that have been developed and demonstrated for studies on membrane proteins, lipid nanodiscs are the latest developments in the field and are increasingly used for various applications. While lipid-nanodiscs can be formed using an amphipathic membrane scaffold protein (MSP), peptide, or synthetic polymer, the synthetic polymer based nanodiscs exhibit unique advantages because of the ability to functionalize them for various applications. In addition to the use of synthetic polymers to extract membrane proteins directly from the cell membranes, recent advances in the development of polymers used for nanodiscs formation are attracting new attention to the field of nanodiscs technology. Here we review the developments of novel polymer modifications that overcome the current limitations and enhance the applications of polymer based nanodiscs to a wider variety of biophysical techniques used to study membrane proteins. A summary of the functionalization of poly(Styrene-co-Maleic Acid), SMA, polymers developed by our research and their advantages are also covered in this review article.
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Affiliation(s)
- Thirupathi Ravula
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, USA
| | - Nathaniel Z Hardin
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, USA
| | - Giacomo M Di Mauro
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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