1
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Ghanam RH, Eastep GN, Saad JS. Structural Insights into the Mechanism of HIV-1 Tat Secretion from the Plasma Membrane. J Mol Biol 2023; 435:167880. [PMID: 36370804 PMCID: PMC9822876 DOI: 10.1016/j.jmb.2022.167880] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) trans-activator of transcription (Tat) is a small, intrinsically disordered basic protein that plays diverse roles in the HIV-1 replication cycle, including promotion of efficient viral RNA transcription. Tat is released by infected cells and subsequently absorbed by healthy cells, thereby contributing to HIV-1 pathogenesis including HIV-associated neurocognitive disorder. It has been shown that, in HIV-1-infected primary CD4 T-cells, Tat accumulates at the plasma membrane (PM) for secretion, a mechanism mediated by phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). However, the structural basis for Tat interaction with the PM and thereby secretion is lacking. Herein, we employed NMR and biophysical methods to characterize Tat86 (86 amino acids) interactions with PI(4,5)P2 and lipid nanodiscs (NDs). Our data revealed that Arg49, Lys50 and Lys51 (RKK motif) constitute the PI(4,5)P2 binding site, that Tat86 interaction with lipid NDs is dependent on PI(4,5)P2 and phosphatidylserine (PS), and that the arginine-rich motif (RRQRRR) preferentially interacts with PS. Furthermore, we show that Trp11, previously implicated in Tat secretion, penetrates deeply in the membrane; substitution of Trp11 severely reduced Tat86 interaction with membranes. Deletion of the entire highly basic region and Trp11 completely abolished Tat86 binding to lipid NDs. Our data support a mechanism by which HIV-1 Tat secretion from the PM is mediated by a tripartite signal consisting of binding of the RKK motif to PI(4,5)P2, arginine-rich motif to PS, and penetration of Trp11 in the membrane. Altogether, these findings provide new insights into the molecular requirements for Tat binding to membranes during secretion.
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Affiliation(s)
- Ruba H Ghanam
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Gunnar N Eastep
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
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2
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Sugiki T, Lee YH, Alsanousi N, Murata K, Kawamura I, Fujiwara T, Hanada K, Kojima C. A hybrid strategy combining solution NMR spectroscopy and isothermal titration calorimetry to characterize protein-nanodisc interaction. Anal Biochem 2021; 639:114521. [PMID: 34906540 DOI: 10.1016/j.ab.2021.114521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/03/2021] [Accepted: 12/04/2021] [Indexed: 11/19/2022]
Abstract
NMR is a powerful tool for characterizing intermolecular interactions at atomic resolution. However, the nature of the complex interactions of membrane-binding proteins makes it difficult to elucidate the interaction mechanisms. Here, we demonstrated that structural and thermodynamic analyses using solution NMR spectroscopy and isothermal titration calorimetry (ITC) can clearly detect a specific interaction between the pleckstrin homology (PH) domain of ceramide transport protein (CERT) and phosphatidylinositol 4-monophosphate (PI4P) embedded in the lipid nanodisc, and distinguish the specific interaction from nonspecific interactions with the bulk surface of the lipid nanodisc. This NMR-ITC hybrid strategy provides detailed characterization of protein-lipid membrane interactions.
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Affiliation(s)
- Toshihiko Sugiki
- Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Young-Ho Lee
- Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan; Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Chungcheongbuk-do, 28119, South Korea; Bio-Analytical Science, University of Science and Technology, Daejeon, 34113, South Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, South Korea
| | - Nesreen Alsanousi
- Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kaito Murata
- Graduate School of Engineering Science, Yokohama National University, Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan
| | - Izuru Kawamura
- Graduate School of Engineering Science, Yokohama National University, Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kentaro Hanada
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Chojiro Kojima
- Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan; Graduate School of Engineering Science, Yokohama National University, Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan.
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3
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Zhang XX, Young JW, Foster LJ, Duong F. Nanodisc-Based Proteomics Identify Caj1 as an Hsp40 with Affinity for Phosphatidic Acid Lipids. J Proteome Res 2021; 20:4831-4839. [PMID: 34519218 DOI: 10.1021/acs.jproteome.1c00503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many soluble proteins interact with membranes to perform important biological functions, including signal transduction, regulation, transport, trafficking, and biogenesis. Despite their importance, these protein-membrane interactions are difficult to characterize due to their often-transient nature as well as phospholipids' poor solubility in aqueous solution. Here, we employ nanodiscs-small, water-soluble patches of a lipid bilayer encircled with amphipathic scaffold proteins-along with quantitative proteomics to identify lipid-binding proteins in Saccharomyces cerevisiae. Using nanodiscs reconstituted with yeast total lipid extracts or only phosphatidylethanolamine (PE-nanodiscs), we capture several known membrane-interacting proteins, including the Rab GTPases Sec4 and Ypt1, which play key roles in vesicle trafficking. Utilizing PE-nanodiscs enriched with phosphatidic acid (PEPA-nanodiscs), we specifically capture a member of the Hsp40/J-protein family, Caj1, whose function has recently been linked to membrane protein quality control. We show that the Caj1 interaction with liposomes containing PA is modulated by pH and PE lipids and depends on two patches of positively charged residues near the C-terminus of the protein. The protein Caj1 is the first example of an Hsp40/J-domain protein with affinity for membranes and phosphatidic acid lipid specificity. These findings highlight the utility of combining proteomics with lipid nanodiscs to identify and characterize protein-lipid interactions that may not be evident using other methods. Data are available via ProteomeXchange with the identifier PXD027992.
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Affiliation(s)
- Xiao X Zhang
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - John William Young
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Michael Smith Laboratory, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
| | - Franck Duong
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Rathod J, Yen HC, Liang B, Tseng YY, Chen CS, Wu WS. YPIBP: A repository for phosphoinositide-binding proteins in yeast. Comput Struct Biotechnol J 2021; 19:3692-3707. [PMID: 34285772 PMCID: PMC8261538 DOI: 10.1016/j.csbj.2021.06.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/08/2021] [Accepted: 06/22/2021] [Indexed: 11/25/2022] Open
Abstract
Phosphoinositides (PIs) are a family of eight lipids consisting of phosphatidylinositol (PtdIns) and its seven phosphorylated forms. PIs have important regulatory functions in the cell including lipid signaling, protein transport, and membrane trafficking. Yeast has been recognized as a eukaryotic model system to study lipid-protein interactions. Hundreds of yeast PI-binding proteins have been identified, but this research knowledge remains scattered. Besides, the complete PI-binding spectrum and potential PI-binding domains have not been interlinked. No comprehensive databases are available to support the lipid-protein interaction research on phosphoinositides. Here we constructed the first knowledgebase of Yeast Phosphoinositide-Binding Proteins (YPIBP), a repository consisting of 679 PI-binding proteins collected from high-throughput proteome-array and lipid-array studies, QuickGO, and a rigorous literature mining. The YPIBP also contains protein domain information in categories of lipid-binding domains, lipid-related domains and other domains. The YPIBP provides search and browse modes along with two enrichment analyses (PI-binding enrichment analysis and domain enrichment analysis). An interactive visualization is given to summarize the PI-domain-protein interactome. Finally, three case studies were given to demonstrate the utility of YPIBP. The YPIBP knowledgebase consolidates the present knowledge and provides new insights of the PI-binding proteins by bringing comprehensive and in-depth interaction network of the PI-binding proteins. YPIBP is available at http://cosbi7.ee.ncku.edu.tw/YPIBP/.
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Key Words
- ANTH, AP180 N-terminal Homology
- BAR, Bin-Amphiphysin-Rvs
- CAFA, Critical Assessment of Functional Annotation
- CRAL-TRIO, cellular retinaldehyde-binding protein (CRALBP) and TRIO guanine exchange factor
- Cvt, Cytoplasm-to-vacuole targeting
- ENTH, Epsin N-terminal Homology
- FDR, False Discovery Rate
- FYVE, Fab 1 (yeast orthologue of PIKfyve), YOTB, Vac 1 (vesicle transport protein), and EEA1
- GO, Gene Ontology
- ITC, Isothermal Titration Calorimetry
- LBD, Lipid-Binding Domain
- LMPD, LIPID MAPS Proteome Database
- LMSD, LIPID MAPS Structure Database
- LRD, Lipid-Related Domain
- Lipid-binding domain
- OMIM, Online Mendelian Inheritance in Man
- OSBP, Oxysterol-Binding Protein
- PH, Pleckstrin Homology
- PI(3,4)P2, phosphatidylinositol-3,4-bisphosphate
- PI(3,4,5)P3, phosphatidylinositol-3,4,5-trisphosphate
- PI(3,5)P2, phosphatidylinositol-3,5-bisphosphate
- PI(4,5)P2, phosphatidylinositol-4,5-bisphosphate
- PI-binding protein
- PI3P, phosphatidylinositol-3-phosphate
- PI4P, phosphatidylinositol-4-phosphate
- PI5P, phosphatidylinositol-5-phosphate
- PIs, Phosphoinositides
- PMID, PubMed ID
- PX, Phox Homology
- Phosphatidylinositol (PtdIns)
- Phosphoinositides (PIs)
- PtdIns, Phosphatidylinositol
- QCM, Quartz Crystal Microbalance
- S. cerevisiae
- SNX, Sorting Nexin
- SPR, Surface Plasmon Resonance
- YPIBP, Yeast Phosphoinositide-Binding Proteins
- Yeast
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Affiliation(s)
- Jagat Rathod
- Department of Earth Sciences, College of Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Han-Chen Yen
- Department of Electrical Engineering, College of Electrical Engineering and Computer Science, National Cheng Kung University, Tainan 701, Taiwan
| | - Biqing Liang
- Department of Earth Sciences, College of Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Yan-Yuan Tseng
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, MI 48201, USA
| | - Chien-Sheng Chen
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Wei-Sheng Wu
- Department of Electrical Engineering, College of Electrical Engineering and Computer Science, National Cheng Kung University, Tainan 701, Taiwan
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5
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Yamamoto A, Tsukamoto T, Suzuki K, Hashimoto E, Kobashigawa Y, Shibasaki K, Uchida T, Inagaki F, Demura M, Ishimori K. Spectroscopic Characterization of Halorhodopsin Reconstituted into Nanodisks Using Native Lipids. Biophys J 2020; 118:2853-2865. [PMID: 32396848 DOI: 10.1016/j.bpj.2020.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/06/2020] [Accepted: 04/22/2020] [Indexed: 10/24/2022] Open
Abstract
We successfully reconstituted single Natronomonas pharaonis halorhodopsin (NpHR) trimers into a nanodisk (ND) using the native archaeal lipid (NL) and an artificial lipid having a zwitterionic headgroup, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). Incorporation of single trimeric NpHR into NDs was confirmed by sodium dodecyl sulfate polyacrylamide gel electrophoresis, size-exclusion chromatography, and visible circular dichroism spectroscopy. The Cl- binding affinity of NpHR in NDs using NL (NL-ND NpHR) or POPC (POPC-ND NpHR) was examined by absorption spectroscopy, showing that the Cl--releasing affinities (Kd,N↔O) of these ND-reconstituted NpHRs are more than 10 times higher than that obtained from native NpHR membrane fragments (MFs) harvested from a NpHR-overexpressing archaeal strain (MF NpHR). The photoreaction kinetics of these ND-reconstituted NpHRs revealed that the Cl- uptake was faster than that of MF NpHR. These differences in the Cl--releasing and uptake properties of ND-reconstituted NpHRs and MF NpHR may arise from suppression of protein conformational changes associated with Cl- release from the trimeric NpHR caused by ND reconstitution, conformational perturbation in the trimeric state, and loss of the trimer-trimer interactions. On the other hand, POPC-ND NpHR demonstrated accelerated Cl- uptake compared to NL-ND NpHR, suggesting that the negative charge on the archaeal membrane surface regulates the photocycle of NpHR. Although NL-ND NpHR and MF NpHR are embedded in the same lipid, the lower Cl--binding affinity at the initial state (Kd,initial) and faster recovering from the NpHR' state to the original state of the photoreaction cycle were observed for NL-ND NpHR, probably because of insufficient interactions with a chromophore in the native membrane, bacterioruberin in reconstituted NDs. Our results indicate that specific interactions of NpHR with surrounding lipids and bacterioruberin, structural flexibility of the membrane, and interactions between trimeric NpHRs may be necessary for efficient Cl- pumping.
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Affiliation(s)
- Ayumi Yamamoto
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Takashi Tsukamoto
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Kenshiro Suzuki
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Eri Hashimoto
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | | | - Kousuke Shibasaki
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Takeshi Uchida
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Fuyuhiko Inagaki
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.
| | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan.
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6
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Murphy RE, Saad JS. The Interplay between HIV-1 Gag Binding to the Plasma Membrane and Env Incorporation. Viruses 2020; 12:E548. [PMID: 32429351 PMCID: PMC7291237 DOI: 10.3390/v12050548] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 12/21/2022] Open
Abstract
Advancement in drug therapies and patient care have drastically improved the mortality rates of HIV-1 infected individuals. Many of these therapies were developed or improved upon by using structure-based techniques, which underscore the importance of understanding essential mechanisms in the replication cycle of HIV-1 at the structural level. One such process which remains poorly understood is the incorporation of the envelope glycoprotein (Env) into budding virus particles. Assembly of HIV particles is initiated by targeting of the Gag polyproteins to the inner leaflet of the plasma membrane (PM), a process mediated by the N-terminally myristoylated matrix (MA) domain and phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). There is strong evidence that formation of the Gag lattice on the PM is a prerequisite for the incorporation of Env into budding particles. It is also suggested that Env incorporation is mediated by an interaction between its cytoplasmic tail (gp41CT) and the MA domain of Gag. In this review, we highlight the latest developments and current efforts to understand the interplay between gp41CT, MA, and the membrane during assembly. Elucidation of the molecular determinants of Gag-Env-membrane interactions may help in the development of new antiviral therapeutic agents that inhibit particle assembly, Env incorporation and ultimately virus production.
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Affiliation(s)
| | - Jamil S. Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
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7
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Grant BMM, Enomoto M, Back SI, Lee KY, Gebregiworgis T, Ishiyama N, Ikura M, Marshall CB. Calmodulin disrupts plasma membrane localization of farnesylated KRAS4b by sequestering its lipid moiety. Sci Signal 2020; 13:13/625/eaaz0344. [PMID: 32234958 DOI: 10.1126/scisignal.aaz0344] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
KRAS4b is a small guanosine triphosphatase (GTPase) protein that regulates several signal transduction pathways that underlie cell proliferation, differentiation, and survival. KRAS4b function requires prenylation of its C terminus and recruitment to the plasma membrane, where KRAS4b activates effector proteins including the RAF family of kinases. The Ca2+-sensing protein calmodulin (CaM) has been suggested to regulate the localization of KRAS4b through direct, Ca2+-dependent interaction, but how CaM and KRAS4b functionally interact is controversial. Here, we determined a crystal structure, which was supported by solution nuclear magnetic resonance (NMR), that revealed the sequestration of the prenyl moiety of KRAS4b in the hydrophobic pocket of the C-terminal lobe of Ca2+-bound CaM. Our engineered fluorescence resonance energy transfer (FRET)-based biosensor probes (CaMeRAS) showed that, upon stimulation of Ca2+ influx by extracellular ligands, KRAS4b reversibly translocated in a Ca2+-CaM-dependent manner from the plasma membrane to the cytoplasm in live HeLa and HEK293 cells. These results reveal a mechanism underlying the inhibition of KRAS4b activity by Ca2+ signaling pathways.
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Affiliation(s)
- Benjamin M M Grant
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Masahiro Enomoto
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Sung-In Back
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Ki-Young Lee
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Noboru Ishiyama
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada.
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8
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Abstract
The interactions between lipids and proteins are one of the most fundamental processes in living organisms, responsible for critical cellular events ranging from replication, cell division, signaling, and movement. Enabling the central coupling responsible for maintaining the functionality of the breadth of proteins, receptors, and enzymes that find their natural home in biological membranes, the fundamental mechanisms of recognition of protein for lipid, and vice versa, have been a focal point of biochemical and biophysical investigations for many decades. Complexes of lipids and proteins, such as the various lipoprotein factions, play central roles in the trafficking of important proteins, small molecules and metabolites and are often implicated in disease states. Recently an engineered lipoprotein particle, termed the nanodisc, a modified form of the human high density lipoprotein fraction, has served as a membrane mimetic for the investigation of membrane proteins and studies of lipid-protein interactions. In this review, we summarize the current knowledge regarding this self-assembling lipid-protein complex and provide examples for its utility in the investigation of a large number of biological systems.
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9
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Murphy RE, Samal AB, Vlach J, Mas V, Prevelige PE, Saad JS. Structural and biophysical characterizations of HIV-1 matrix trimer binding to lipid nanodiscs shed light on virus assembly. J Biol Chem 2019; 294:18600-18612. [PMID: 31640987 PMCID: PMC6901326 DOI: 10.1074/jbc.ra119.010997] [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] [Received: 09/16/2019] [Revised: 10/16/2019] [Indexed: 12/17/2022] Open
Abstract
During the late phase of the HIV-1 replication cycle, the viral Gag polyproteins are targeted to the plasma membrane for assembly. The Gag-membrane interaction is mediated by binding of Gag's N-terminal myristoylated matrix (MA) domain to phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). The viral envelope (Env) glycoprotein is then recruited to the assembly sites and incorporated into budding particles. Evidence suggests that Env incorporation is mediated by interactions between Gag's MA domain and the cytoplasmic tail of the gp41 subunit of Env (gp41CT). MA trimerization appears to be an obligatory step for this interaction. Insufficient production of a recombinant MA trimer and unavailability of a biologically relevant membrane system have been barriers to detailed structural and biophysical characterization of the putative MA-gp41CT-membrane interactions. Here, we engineered a stable recombinant HIV-1 MA trimer construct by fusing a foldon domain (FD) of phage T4 fibritin to the MA C terminus. Results from NMR experiments confirmed that the FD attachment does not adversely alter the MA structure. Employing hydrogen-deuterium exchange MS, we identified an MA-MA interface in the MA trimer that is implicated in Gag assembly and Env incorporation. Utilizing lipid nanodiscs as a membrane mimetic, we show that the MA trimer binds to membranes 30-fold tighter than does the MA monomer and that incorporation of PI(4,5)P2 and phosphatidylserine enhances the binding of MA to nanodiscs. These findings advance our understanding of a fundamental mechanism in HIV-1 assembly and provide a template for investigating the interaction of MA with gp41CT.
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Affiliation(s)
- R Elliot Murphy
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Alexandra B Samal
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Jiri Vlach
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Vicente Mas
- Centro Nacional de Microbiología and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Peter E Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294.
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10
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Shelby ML, He W, Dang AT, Kuhl TL, Coleman MA. Cell-Free Co-Translational Approaches for Producing Mammalian Receptors: Expanding the Cell-Free Expression Toolbox Using Nanolipoproteins. Front Pharmacol 2019; 10:744. [PMID: 31333463 PMCID: PMC6616253 DOI: 10.3389/fphar.2019.00744] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/07/2019] [Indexed: 12/28/2022] Open
Abstract
Membranes proteins make up more than 60% of current drug targets and account for approximately 30% or more of the cellular proteome. Access to this important class of proteins has been difficult due to their inherent insolubility and tendency to aggregate in aqueous solutions. Understanding membrane protein structure and function demands novel means of membrane protein production that preserve both their native conformational state as well as function. Over the last decade, cell-free expression systems have emerged as an important complement to cell-based expression of membrane proteins due to their simple and customizable experimental parameters. One approach to overcome the solubility and stability limitations of purified membrane proteins is to support them in stable, native-like states within nanolipoprotein particles (NLPs), aka nanodiscs. This has become common practice to facilitate biochemical and biophysical characterization of proteins of interest. NLP technology can be easily coupled with cell-free systems to achieve functional membrane protein production for this purpose. Our approach involves utilizing cell-free expression systems in the presence of NLPs or using co-translation techniques to perform one-pot expression and self-assembly of membrane protein/NLP complexes. We describe how cell-free reactions can be modified to render control over nanoparticle size and monodispersity in support of membrane protein production. These modifications have been exploited to facilitate co-expression of full-length functional membrane proteins such as G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). In particular, we summarize the state of the art in NLP-assisted cell-free coexpression of these important classes of membrane proteins as well as evaluate the advances in and prospects for this technology that will drive drug discovery against these targets. We conclude with a prospective on the use of NLPs to produce as well as deliver functional mammalian membrane-bound proteins for a range of applications.
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Affiliation(s)
- Megan L Shelby
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Wei He
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Amanda T Dang
- University of California at Davis, Davis, CA, United States
| | - Tonya L Kuhl
- University of California at Davis, Davis, CA, United States
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, Livermore, CA, United States.,University of California at Davis, Davis, CA, United States
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11
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Yokogawa M, Fukuda M, Osawa M. Nanodiscs for Structural Biology in a Membranous Environment. Chem Pharm Bull (Tokyo) 2019; 67:321-326. [PMID: 30930435 DOI: 10.1248/cpb.c18-00941] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structures of many membrane proteins have been analyzed in detergent micelles. However, the environment of detergent micelles differs somewhat from that of the lipid bilayer, where membrane proteins exhibit physiological functions. Therefore, a more membrane-like environment has been awaited for structural analysis of membrane proteins. Nanodiscs are "hockey-puck"-shaped lipid bilayer particles that distribute in a monodispersed manner in aqueous solution. We review how nanodiscs or protein-reconstituted nanodiscs are prepared and how they are utilized to analyze protein structure, dynamics, and interactions with lipid molecules using solution NMR and cryo-electron microscopy.
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Affiliation(s)
- Mariko Yokogawa
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy
| | - Masahiro Fukuda
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy
| | - Masanori Osawa
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy
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12
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Fang Z, Marshall CB, Nishikawa T, Gossert AD, Jansen JM, Jahnke W, Ikura M. Inhibition of K-RAS4B by a Unique Mechanism of Action: Stabilizing Membrane-Dependent Occlusion of the Effector-Binding Site. Cell Chem Biol 2018; 25:1327-1336.e4. [DOI: 10.1016/j.chembiol.2018.07.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 02/21/2018] [Accepted: 07/24/2018] [Indexed: 12/19/2022]
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13
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Abstract
Membrane proteins play a most important part in metabolism, signaling, cell motility, transport, development, and many other biochemical and biophysical processes which constitute fundamentals of life on the molecular level. Detailed understanding of these processes is necessary for the progress of life sciences and biomedical applications. Nanodiscs provide a new and powerful tool for a broad spectrum of biochemical and biophysical studies of membrane proteins and are commonly acknowledged as an optimal membrane mimetic system that provides control over size, composition, and specific functional modifications on the nanometer scale. In this review we attempted to combine a comprehensive list of various applications of nanodisc technology with systematic analysis of the most attractive features of this system and advantages provided by nanodiscs for structural and mechanistic studies of membrane proteins.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Stephen G Sligar
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
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14
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The power, pitfalls and potential of the nanodisc system for NMR-based studies. Biol Chem 2016; 397:1335-1354. [DOI: 10.1515/hsz-2016-0224] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022]
Abstract
Abstract
The choice of a suitable membrane mimicking environment is of fundamental importance for the characterization of structure and function of membrane proteins. In this respect, usage of the lipid bilayer nanodisc technology provides a unique potential for nuclear magnetic resonance (NMR)-based studies. This review summarizes the recent advances in this field, focusing on (i) the strengths of the system, (ii) the bottlenecks that may be faced, and (iii) promising capabilities that may be explored in future studies.
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15
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Agamasu C, Ghanam RH, Xu F, Sun Y, Chen Y, Saad JS. The Interplay between Calmodulin and Membrane Interactions with the Pleckstrin Homology Domain of Akt. J Biol Chem 2016; 292:251-263. [PMID: 27872186 DOI: 10.1074/jbc.m116.752816] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/19/2016] [Indexed: 11/06/2022] Open
Abstract
The Akt protein, a serine/threonine kinase, plays important roles in cell survival, apoptosis, and oncogenes. Akt is translocated to the plasma membrane for activation. Akt-membrane binding is mediated by direct interactions between its pleckstrin homology domain (PHD) and phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3). It has been shown that Akt activation in breast cancer cells is modulated by calmodulin (CaM). However, the molecular mechanism of the interplay between CaM and membrane binding is not established. Here, we employed nuclear magnetic resonance (NMR) and biochemical and biophysical techniques to characterize how PI(3,4,5)P3, CaM, and membrane mimetics (nanodisc) bind to Akt(PHD). We show that PI(3,4,5)P3 binding to Akt(PHD) displaces the C-terminal lobe of CaM but not the weakly binding N-terminal lobe. However, binding of a PI(3,4,5)P3-embedded membrane nanodisc to Akt(PHD) with a 103-fold tighter affinity than PI(3,4,5)P3 is able to completely displace CaM. We also show that Akt(PHD) binds to both layers of the nanodisc, indicating proper incorporation of PI(3,4,5)P3 on the nanodisc surface. No detectable binding has been observed between Akt(PHD) and PI(3,4,5)P3-free nanodiscs, demonstrating that PI(3,4,5)P3 is required for membrane binding, CaM displacement, and Akt activation. Using pancreatic cancer cells, we demonstrate that inhibition of Akt-CaM binding attenuated Akt activation. Our findings support a model by which CaM binds to Akt to facilitate its translocation to the membrane. Elucidation of the molecular details of the interplay between membrane and CaM binding to Akt may help in the development of potential targets to control the pathophysiological processes of cell survival.
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Affiliation(s)
| | | | - Fei Xu
- Pathology, University of Alabama at Birmingham and
| | - Yong Sun
- Pathology, University of Alabama at Birmingham and.,the Research Department, Birmingham Veterans Affairs Medical Center, Birmingham, Alabama 35294
| | - Yabing Chen
- Pathology, University of Alabama at Birmingham and.,the Research Department, Birmingham Veterans Affairs Medical Center, Birmingham, Alabama 35294
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16
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Wan C, Wu B, Song Z, Zhang J, Chu H, Wang A, Liu Q, Shi Y, Li G, Wang J. Insights into the molecular recognition of the granuphilin C2A domain with PI(4,5)P2. Chem Phys Lipids 2015; 186:61-7. [PMID: 25595293 DOI: 10.1016/j.chemphyslip.2015.01.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/11/2015] [Accepted: 01/12/2015] [Indexed: 01/06/2023]
Abstract
Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is a key player in regulating the process of excytosis, including insulin secretion. Granuphilin, a tandem C2 domain containing protein, mediates the docking of insulin granules onto plasma membrane. The C2A domain plays key roles in this process through interaction with PI(4,5)P2. In this study, we have investigated the molecular recognition mechanism of granuphilin-C2A domain to PI(4,5)P2 head group, and further to PI(4,5)P2-nanodisc by NMR, ITC, MST and SEC methods. Our results demonstrate that PI(4,5)P2 binds to the concave surface of granuphilin-C2A domain. The key residues involved in the binding were validated by mutation analysis.
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Affiliation(s)
- Chanjuan Wan
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China
| | - Bo Wu
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China.
| | - Zhenwei Song
- Heifei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, PR China
| | - Jiahai Zhang
- Heifei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, PR China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd., Dalian 116023, PR China
| | - Aoli Wang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China
| | - Qingsong Liu
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China
| | - Yunyu Shi
- Heifei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, PR China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd., Dalian 116023, PR China
| | - Junfeng Wang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China.
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17
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TRPV4 channel activity is modulated by direct interaction of the ankyrin domain to PI(4,5)P₂. Nat Commun 2014; 5:4994. [PMID: 25256292 DOI: 10.1038/ncomms5994] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 08/15/2014] [Indexed: 11/09/2022] Open
Abstract
Mutations in the ankyrin repeat domain (ARD) of TRPV4 are responsible for several channelopathies, including Charcot-Marie-Tooth disease type 2C and congenital distal and scapuloperoneal spinal muscular atrophy. However, the molecular pathogenesis mediated by these mutations remains elusive, mainly due to limited understanding of the TRPV4 ARD function. Here we show that phosphoinositide binding to the TRPV4 ARD leads to suppression of the channel activity. Among the phosphoinositides, phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) most potently binds to the TRPV4 ARD. The crystal structure of the TRPV4 ARD in complex with inositol-1,4,5-trisphosphate, the head-group of PI(4,5)P2, and the molecular-dynamics simulations revealed the PI(4,5)P2-binding amino-acid residues. The TRPV4 channel activities were increased by titration or hydrolysis of membrane PI(4,5)P2. Notably, disease-associated TRPV4 mutations that cause a gain-of-function phenotype abolished PI(4,5)P2 binding and PI(4,5)P2 sensitivity. These findings identify TRPV4 ARD as a lipid-binding domain in which interactions with PI(4,5)P2 normalize the channel activity in TRPV4.
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18
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Roos C, Kai L, Haberstock S, Proverbio D, Ghoshdastider U, Ma Y, Filipek S, Wang X, Dötsch V, Bernhard F. High-level cell-free production of membrane proteins with nanodiscs. Methods Mol Biol 2014; 1118:109-130. [PMID: 24395412 DOI: 10.1007/978-1-62703-782-2_7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This chapter addresses two major bottlenecks in cell-free membrane protein production. Firstly, we describe the optimization of expression templates for obtaining membrane proteins in preparative scales. We present details for a newly established tag variation screen providing high success rates in improving expression efficiencies while having only minimal impacts on the target protein structure. Secondly, we present protocols for the efficient co-translational insertion of membrane proteins into defined lipid bilayers. We describe the production of nanodiscs and their implementation into cell-free expression reactions for the co-translational reconstitution of membrane proteins. In addition we give guidelines for the loading of nanodiscs with different lipids in order to systematically analyze effects of lipids on the translocation, functional folding, and stability of cell-free expressed membrane proteins.
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Affiliation(s)
- Christian Roos
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Frankfurt/Main, Germany
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19
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Cho H, Wu M, Bilgin B, Walton SP, Chan C. Latest developments in experimental and computational approaches to characterize protein-lipid interactions. Proteomics 2013; 12:3273-85. [PMID: 22997137 DOI: 10.1002/pmic.201200255] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Revised: 08/30/2012] [Accepted: 09/05/2012] [Indexed: 12/16/2022]
Abstract
Understanding the functional roles of all the molecules in cells is an ultimate goal of modern biology. An important facet is to understand the functional contributions from intermolecular interactions, both within a class of molecules (e.g. protein-protein) or between classes (e.g. protein-DNA). While the technologies for analyzing protein-protein and protein-DNA interactions are well established, the field of protein-lipid interactions is still relatively nascent. Here, we review the current status of the experimental and computational approaches for detecting and analyzing protein-lipid interactions. Experimental technologies fall into two principal categories, namely solution-based and array-based methods. Computational methods include large-scale data-driven analyses and predictions/dynamic simulations based on prior knowledge of experimentally identified interactions. Advances in the experimental technologies have led to improved computational analyses and vice versa, thereby furthering our understanding of protein-lipid interactions and their importance in biological systems.
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Affiliation(s)
- Hyunju Cho
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
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20
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Abstract
Nanodiscs are self-assembled discoidal fragments of lipid bilayers 8-16 nm in diameter, stabilized in solution by two amphipathic helical scaffold proteins. As stable and highly soluble membrane mimetics with controlled lipid composition and ability to add affinity tags to the scaffold protein, nanodiscs represent an attractive model system for solubilization, isolation, purification, and biophysical and biochemical studies of membrane proteins. In this chapter we overview various approaches to structural and functional studies of different classes of integral membrane proteins such as ion channels, transporters, GPCR and other receptors, membrane enzymes, and blood coagulation cascade proteins which have been incorporated into nanodiscs. We outline the advantages provided by homogeneity, ability to control oligomerization state of the target protein and lipid composition of the bilayer. Special attention is paid to the opportunities afforded by nanodisc system for the detailed studies of the role of different lipid properties and protein-lipid interactions in the functional behavior of membrane proteins.
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Affiliation(s)
- Mary A. Schuler
- Department of Biochemistry, University of Illinois, Urbana, IL 61801 USA
- Department of Cell and Developmental Biology, University of Illinois, Urbana, IL 61801 USA
| | - Ilia G. Denisov
- Department of Biochemistry, University of Illinois, Urbana, IL 61801 USA
| | - Stephen G. Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL 61801 USA
- Department of Chemistry, University of Illinois, Urbana, IL 61801 USA
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21
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Yokogawa M, Kobashigawa Y, Yoshida N, Ogura K, Harada K, Inagaki F. NMR analyses of the interaction between the FYVE domain of early endosome antigen 1 (EEA1) and phosphoinositide embedded in a lipid bilayer. J Biol Chem 2012; 287:34936-34945. [PMID: 22915584 DOI: 10.1074/jbc.m112.398255] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphoinositides (PIs) are crucial lipid components of membranes and are involved in a number of cellular processes through interactions with their effector proteins. Recently, we have established a lipid-protein nanoscale bilayer (nanodisc) containing PIs, hereafter referred to as PI-nanodisc and demonstrated that it could be used for both qualitative and quantitative evaluations of protein-membrane interactions. Here, we report further NMR analyses for obtaining structural insights at the residue-specific level between PI-binding effector protein and PI-nanodisc, using the FYVE domain of early endosome antigen 1 (EEA1), denoted as EEA1 FYVE, and PI(3)P-nanodisc as a model system. We performed a combination of the NMR analyses including chemical shift perturbation, transferred cross-saturation, and paramagnetic relaxation enhancement experiments. These enabled an identification of the interaction surface, structural change, and relative orientation of EEA1 FYVE to the PI(3)P-incorporated lipid bilayer, substantiating that NMR analyses of protein-membrane interactions using nanodisc makes it possible to show the residue-specific interactions in the lipid bilayer environment.
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Affiliation(s)
- Mariko Yokogawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | | | - Naoki Yoshida
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kenji Ogura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Kohsuke Harada
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Fuyuhiko Inagaki
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan.
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22
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Autoinhibition and phosphorylation-induced activation mechanisms of human cancer and autoimmune disease-related E3 protein Cbl-b. Proc Natl Acad Sci U S A 2011; 108:20579-84. [PMID: 22158902 DOI: 10.1073/pnas.1110712108] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Cbl-b is a RING-type E3 ubiquitin ligase that functions as a negative regulator of T-cell activation and growth factor receptor and nonreceptor-type tyrosine kinase signaling. Cbl-b dysfunction is related to autoimmune diseases and cancers in humans. However, the molecular mechanism regulating its E3 activity is largely unknown. NMR and small-angle X-ray scattering analyses revealed that the unphosphorylated N-terminal region of Cbl-b forms a compact structure by an intramolecular interaction, which masks the interaction surface of the RING domain with an E2 ubiquitin-conjugating enzyme. Phosphorylation of Y363, located in the helix-linker region between the tyrosine kinase binding and the RING domains, disrupts the interdomain interaction to expose the E2 binding surface of the RING domain. Structural analysis revealed that the phosphorylated helix-RING region forms a compact structure in solution. Moreover, the phosphate group of pY363 is located in the vicinity of the interaction surface with UbcH5B to increase affinity by reducing their electrostatic repulsion. Thus, the phosphorylation of Y363 regulates the E3 activity of Cbl-b by two mechanisms: one is to remove the masking of the RING domain from the tyrosine kinase binding domain and the other is to form a surface to enhance binding affinity to E2.
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23
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Qureshi T, Goto NK. Contemporary methods in structure determination of membrane proteins by solution NMR. Top Curr Chem (Cham) 2011; 326:123-85. [PMID: 22160391 DOI: 10.1007/128_2011_306] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Integral membrane proteins are vital to life, being responsible for information and material exchange between a cell and its environment. Although high-resolution structural information is needed to understand how these functions are achieved, membrane proteins remain an under-represented subset of the protein structure databank. Solution NMR is increasingly demonstrating its ability to help address this knowledge shortfall, with the development of a diverse array of techniques to counter the challenges presented by membrane proteins. Here we document the advances that are helping to define solution NMR as an effective tool for membrane protein structure determination. Developments introduced over the last decade in the production of isotope-labeled samples, reconstitution of these samples into the growing selection of NMR-compatible membrane-mimetic systems, and the approaches used for the acquisition and application of structural restraints from these complexes are reviewed.
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Affiliation(s)
- Tabussom Qureshi
- Department of Chemistry, University of Ottawa, Ottawa, ON, Canada
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