1
|
Abstract
Membrane proteins (MPs) play essential roles in numerous cellular processes. Because around 70% of the currently marketed drugs target MPs, a detailed understanding of their structure, binding properties, and functional dynamics in a physiologically relevant environment is crucial for a more detailed understanding of this important protein class. We here summarize the benefits of using lipid nanodiscs for NMR structural investigations and provide a detailed overview of the currently used lipid nanodisc systems as well as their applications in solution-state NMR. Despite the increasing use of other structural methods for the structure determination of MPs in lipid nanodiscs, solution NMR turns out to be a versatile tool to probe a wide range of MP features, ranging from the structure determination of small to medium-sized MPs to probing ligand and partner protein binding as well as functionally relevant dynamical signatures in a lipid nanodisc setting. We will expand on these topics by discussing recent NMR studies with lipid nanodiscs and work out a key workflow for optimizing the nanodisc incorporation of an MP for subsequent NMR investigations. With this, we hope to provide a comprehensive background to enable an informed assessment of the applicability of lipid nanodiscs for NMR studies of a particular MP of interest.
Collapse
Affiliation(s)
- Umut Günsel
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| |
Collapse
|
2
|
Bibow S. Opportunities and Challenges of Backbone, Sidechain, and RDC Experiments to Study Membrane Protein Dynamics in a Detergent-Free Lipid Environment Using Solution State NMR. Front Mol Biosci 2019; 6:103. [PMID: 31709261 PMCID: PMC6823230 DOI: 10.3389/fmolb.2019.00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/19/2019] [Indexed: 12/22/2022] Open
Abstract
Whereas solution state NMR provided a wealth of information on the dynamics landscape of soluble proteins, only few studies have investigated membrane protein dynamics in a detergent-free lipid environment. Recent developments of smaller nanodiscs and other lipid-scaffolding polymers, such as styrene maleic acid (SMA), however, open new and promising avenues to explore the function-dynamics relationship of membrane proteins as well as between membrane proteins and their surrounding lipid environment. Favorably sized lipid-bilayer nanodiscs, established membrane protein reconstitution protocols and sophisticated solution NMR relaxation methods probing dynamics over a wide range of timescales will eventually reveal unprecedented lipid-membrane protein interdependencies that allow us to explain things we have not been able to explain so far. In particular, methyl group dynamics resulting from CEST, CPMG, ZZ exchange, and RDC experiments are expected to provide new and surprising insights due to their proximity to lipids, their applicability in large 100+ kDa assemblies and their simple labeling due to the availability of commercial precursors. This review summarizes the recent developments of membrane protein dynamics with a special focus on membrane protein dynamics in lipid-bilayer nanodiscs. Opportunities and challenges of backbone, side chain and RDC dynamics applied to membrane proteins are discussed. Solution-state NMR and lipid nanodiscs bear great potential to change our molecular understanding of lipid-membrane protein interactions.
Collapse
Affiliation(s)
- Stefan Bibow
- Biozentrum, University of Basel, Basel, Switzerland
| |
Collapse
|
3
|
Bibow S, Hiller S. A guide to quantifying membrane protein dynamics in lipids and other native-like environments by solution-state NMR spectroscopy. FEBS J 2018; 286:1610-1623. [PMID: 30133960 DOI: 10.1111/febs.14639] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/04/2018] [Accepted: 08/20/2018] [Indexed: 02/06/2023]
Abstract
Recent biochemical and technical developments permit residue-specific solution NMR measurements of membrane protein (MP) dynamics in lipidic and chaperone-bound environments. This is possible by combinations of improved sample preparations with suitable NMR relaxation experiments to correlate protein function to backbone dynamics on timescales from picoseconds to seconds, even for large MP-lipid assemblies above 100 kDa in molecular mass. Here, we introduce the basic concepts of different NMR relaxation experiments, individually sensitive to specific timescales. We discuss the general limitations of detergent environments and highlight the importance for native-like environments when studying MPs. We then review three practical studies of fast- and slow-timescale MP dynamics in lipid environments, as well as in a natively unfolded, chaperone-bound state. These examples illustrate the new avenues solution NMR spectroscopy is taking to investigate MP dynamics in native-like environments with atomic resolution.
Collapse
|
4
|
Wang P, Chang AY, Novosad V, Chupin VV, Schaller RD, Rozhkova EA. Cell-Free Synthetic Biology Chassis for Nanocatalytic Photon-to-Hydrogen Conversion. ACS NANO 2017; 11:6739-6745. [PMID: 28602073 DOI: 10.1021/acsnano.7b01142] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report on an entirely man-made nano-bio architecture fabricated through noncovalent assembly of a cell-free expressed transmembrane proton pump and TiO2 semiconductor nanoparticles as an efficient nanophotocatalyst for H2 evolution. The system produces hydrogen at a turnover of about 240 μmol of H2 (μmol protein)-1 h-1 and 17.74 mmol of H2 (μmol protein)-1 h-1 under monochromatic green and white light, respectively, at ambient conditions, in water at neutral pH and room temperature, with methanol as a sacrificial electron donor. Robustness and flexibility of this approach allow for systemic manipulation at the nanoparticle-bio interface toward directed evolution of energy transformation materials and artificial systems.
Collapse
Affiliation(s)
- Peng Wang
- Center for Nanoscale Materials, Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439-4855, United States
- State Key Laboratory of Crystal Materials, Shandong University , Jinan, Shandong 250100, People's Republic of China
| | - Angela Y Chang
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Valentyn Novosad
- Materials Science Division, Argonne National Laboratory , Argonne, Illinois 60439-4855, United States
| | - Vladimir V Chupin
- Laboratory Chemistry and Physics of Lipids, Department of General and Applied Physics, Moscow Institute of Physics and Technology , Dolgoprudny, Moscow Region 141701, Russia
| | - Richard D Schaller
- Center for Nanoscale Materials, Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439-4855, United States
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Elena A Rozhkova
- Center for Nanoscale Materials, Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439-4855, United States
| |
Collapse
|
5
|
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.
Collapse
|
6
|
Frey L, Lakomek NA, Riek R, Bibow S. Micelles, Bicelles, and Nanodiscs: Comparing the Impact of Membrane Mimetics on Membrane Protein Backbone Dynamics. Angew Chem Int Ed Engl 2016; 56:380-383. [PMID: 27882643 PMCID: PMC6680326 DOI: 10.1002/anie.201608246] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 09/29/2016] [Indexed: 11/10/2022]
Abstract
Detergents are often used to investigate the structure and dynamics of membrane proteins. Whereas the structural integrity seems to be preserved in detergents for many membrane proteins, their functional activity is frequently compromised, but can be restored in a lipid environment. Herein we show with per‐residue resolution that while OmpX forms a stable β‐barrel in DPC detergent micelles, DHPC/DMPC bicelles, and DMPC nanodiscs, the pico‐ to nanosecond and micro‐ to millisecond motions differ substantially between the detergent and lipid environment. In particular for the β‐strands, there is pronounced dynamic variability in the lipid environment, which appears to be suppressed in micelles. This unexpected complex and membrane‐mimetic‐dependent dynamic behavior indicates that the frequent loss of membrane protein activity in detergents might be related to reduced internal dynamics and that membrane protein activity correlates with lipid flexibility.
Collapse
Affiliation(s)
- Lukas Frey
- Laboratory for Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Roland Riek
- Laboratory for Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Stefan Bibow
- Laboratory for Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| |
Collapse
|
7
|
Frey L, Lakomek N, Riek R, Bibow S. Mizellen, Bizellen und Nanoscheiben: Einfluss von membranimitierenden Umgebungen auf die Membranproteindynamik. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lukas Frey
- Laboratorium für Physikalische Chemie ETH Zürich 8093 Zürich Schweiz
| | | | - Roland Riek
- Laboratorium für Physikalische Chemie ETH Zürich 8093 Zürich Schweiz
| | - Stefan Bibow
- Laboratorium für Physikalische Chemie ETH Zürich 8093 Zürich Schweiz
| |
Collapse
|
8
|
Bagrov DV, Voskoboynikova N, Armeev GA, Mosslehy W, Gluhov GS, Ismagulova TT, Mulkidjanian AY, Kirpichnikov MP, Steinhoff HJ, Shaitan KV. Characterization of lipodisc nanoparticles containing sensory rhodopsin II and its cognate transducer from Natronomonas pharaonis. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916060063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
9
|
NMR Dynamics of Transmembrane and Intracellular Domains of p75NTR in Lipid-Protein Nanodiscs. Biophys J 2016; 109:772-82. [PMID: 26287629 DOI: 10.1016/j.bpj.2015.07.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/25/2015] [Accepted: 07/09/2015] [Indexed: 11/21/2022] Open
Abstract
P75NTR is a type I integral membrane protein that plays a key role in neurotrophin signaling. However, structural data for the receptor in various functional states are sparse and controversial. In this work, we studied the spatial structure and mobility of the transmembrane and intracellular parts of p75NTR, incorporated into lipid-protein nanodiscs of various sizes and compositions, by solution NMR spectroscopy. Our data reveal a high level of flexibility and disorder in the juxtamembrane chopper domain of p75NTR, which results in the motions of the receptor death domain being uncoupled from the motions of the transmembrane helix. Moreover, none of the intracellular domains of p75NTR demonstrated a propensity to interact with the membrane or to self-associate under the experimental conditions. The obtained data are discussed in the context of the receptor activation mechanism.
Collapse
|
10
|
Bortolus M, Dalzini A, Formaggio F, Toniolo C, Gobbo M, Maniero AL. An EPR study of ampullosporin A, a medium-length peptaibiotic, in bicelles and vesicles. Phys Chem Chem Phys 2016; 18:749-60. [DOI: 10.1039/c5cp04136h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
EPR/CD spectroscopies reveal that the peptaibol ampullosporin A changes the orientation and conformation depending on its concentration and bilayer thickness.
Collapse
Affiliation(s)
- Marco Bortolus
- Dipartimento di Scienze Chimiche
- Università degli Studi di Padova
- 35131 Padova
- Italy
- Dipartimento di Scienza dei Materiali
| | - Annalisa Dalzini
- Dipartimento di Scienze Chimiche
- Università degli Studi di Padova
- 35131 Padova
- Italy
| | - Fernando Formaggio
- Dipartimento di Scienze Chimiche
- Università degli Studi di Padova
- 35131 Padova
- Italy
| | - Claudio Toniolo
- Dipartimento di Scienze Chimiche
- Università degli Studi di Padova
- 35131 Padova
- Italy
| | - Marina Gobbo
- Dipartimento di Scienze Chimiche
- Università degli Studi di Padova
- 35131 Padova
- Italy
| | - Anna Lisa Maniero
- Dipartimento di Scienze Chimiche
- Università degli Studi di Padova
- 35131 Padova
- Italy
| |
Collapse
|
11
|
Tu Y, Peng F, Adawy A, Men Y, Abdelmohsen LKEA, Wilson DA. Mimicking the Cell: Bio-Inspired Functions of Supramolecular Assemblies. Chem Rev 2015; 116:2023-78. [DOI: 10.1021/acs.chemrev.5b00344] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yingfeng Tu
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Fei Peng
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Alaa Adawy
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Yongjun Men
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Loai K. E. A. Abdelmohsen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Daniela A. Wilson
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| |
Collapse
|
12
|
Abstract
Structural analyses of protein-protein interactions are required to reveal their functional mechanisms, and accurate protein-protein complex models, based on experimental results, are the starting points for drug development. In addition, structural information about proteins under physiologically relevant conditions is crucially important for understanding biological events. However, for proteins such as those embedded in lipid bilayers and transiently complexed with their effectors under physiological conditions, structural analyses by conventional methods are generally difficult, due to their large molecular weights and inhomogeneity. We have developed the cross-saturation (CS) method, which is an nuclear magnetic resonance measurement technique for the precise identification of the interfaces of protein-protein complexes. In addition, we have developed an extended version of the CS method, termed transferred cross-saturation (TCS), which enables the identification of the residues of protein ligands in close proximity to huge (>150 kDa) and heterogeneous complexes under fast exchange conditions (>0.1 s(-1)). Here, we discuss the outline, basic theory, and practical considerations of the CS and TCS methods. In addition, we will review the recent progress in the construction of models of protein-protein complexes, based on CS and TCS experiments, and applications of TCS to in situ analyses of biologically and medically important proteins in physiologically relevant states.
Collapse
|
13
|
Mäler L. Solution NMR studies of cell-penetrating peptides in model membrane systems. Adv Drug Deliv Rev 2013; 65:1002-11. [PMID: 23137785 DOI: 10.1016/j.addr.2012.10.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 10/17/2012] [Accepted: 10/22/2012] [Indexed: 12/29/2022]
Abstract
Cell-penetrating peptides (CPPs) are a class of short, often cationic peptides that have the capability to translocate across cellular membranes, and although the translocation most likely involves several pathways, they interact directly with membranes, as well as with model bilayers. Most CPPs attain a three-dimensional structure when interacting with bilayers, while they are more or less unstructured in aqueous solution. To understand the relationship between structure and the effect that CPPs have on membranes it is of great importance to investigate CPPs at atomic resolution in a suitable membrane model. Moreover, the location in bilayers is likely to be correlated with the translocation mechanism. Solution-state NMR offers a unique possibility to investigate structure, dynamics and location of proteins and peptides in bilayers. This review focuses on solution NMR as a tool for investigating CPP-lipid interactions. Structural propensities and cell-penetrating capabilities can be derived from a combination of CPP solution structures and studies of the effect that the peptides have on bilayers and the localization in a bilayer.
Collapse
Affiliation(s)
- Lena Mäler
- Department of Biochemistry and Biophysics, The Arrhenius Laboratory, Stockholm University, Stockholm, Sweden.
| |
Collapse
|
14
|
Shenkarev ZO, Paramonov AS, Lyukmanova EN, Gizatullina AK, Zhuravleva AV, Tagaev AA, Yakimenko ZA, Telezhinskaya IN, Kirpichnikov MP, Ovchinnikova TV, Arseniev AS. Peptaibol Antiamoebin I: Spatial Structure, Backbone Dynamics, Interaction with Bicelles and Lipid-Protein Nanodiscs, and Pore Formation in Context of Barrel-Stave Model. Chem Biodivers 2013; 10:838-63. [DOI: 10.1002/cbdv.201200421] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Indexed: 11/12/2022]
|
15
|
Tzitzilonis C, Eichmann C, Maslennikov I, Choe S, Riek R. Detergent/nanodisc screening for high-resolution NMR studies of an integral membrane protein containing a cytoplasmic domain. PLoS One 2013; 8:e54378. [PMID: 23349867 PMCID: PMC3551814 DOI: 10.1371/journal.pone.0054378] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 12/11/2012] [Indexed: 11/29/2022] Open
Abstract
Because membrane proteins need to be extracted from their natural environment and reconstituted in artificial milieus for the 3D structure determination by X-ray crystallography or NMR, the search for membrane mimetic that conserve the native structure and functional activities remains challenging. We demonstrate here a detergent/nanodisc screening study by NMR of the bacterial α-helical membrane protein YgaP containing a cytoplasmic rhodanese domain. The analysis of 2D [15N,1H]-TROSY spectra shows that only a careful usage of low amounts of mixed detergents did not perturb the cytoplasmic domain while solubilizing in parallel the transmembrane segments with good spectral quality. In contrast, the incorporation of YgaP into nanodiscs appeared to be straightforward and yielded a surprisingly high quality [15N,1H]-TROSY spectrum opening an avenue for the structural studies of a helical membrane protein in a bilayer system by solution state NMR.
Collapse
Affiliation(s)
- Christos Tzitzilonis
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland
- Structural Biology Laboratory, The Salk Institute, La Jolla, California, United States of America
| | - Cédric Eichmann
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland
| | - Innokentiy Maslennikov
- Structural Biology Laboratory, The Salk Institute, La Jolla, California, United States of America
| | - Senyon Choe
- Structural Biology Laboratory, The Salk Institute, La Jolla, California, United States of America
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland
- Structural Biology Laboratory, The Salk Institute, La Jolla, California, United States of America
- * E-mail:
| |
Collapse
|
16
|
Grey JL, Thompson DH. Challenges and opportunities for new protein crystallization strategies in structure-based drug design. Expert Opin Drug Discov 2012; 5:1039-45. [PMID: 21116481 DOI: 10.1517/17460441.2010.515583] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Structure-based drug design (SBDD) has emerged as a valuable pharmaceutical lead discovery tool, showing potential for accelerating the discovery process,while reducing developmental costs and boosting potencies of the drug that is ultimately selected. SBDD is an iterative, rational, lead compound sculpting process that involves both the synthesis of new derivatives and the evaluation of their binding to the target structure either through computational docking or elucidation of the target structure as a complex with the lead compound. This method heavily relies on the production of high resolution(< 2 Å) 3D structures of the drug target, obtained through X-ray crystallographic analysis, in the presence or absence of the drug candidate.The lack of generalized methods for high quality crystal production is still a major bottleneck in the process of macromolecular crystallization. This review provides a brief introduction to SBDD and describes several macromolecular crystallization strategies, with an emphasis on advances and challenges facing researchers in the field today. Recent trends in the development of more universal macromolecular crystallization techniques, particularly nucleation-based techniques that are applicable to both soluble and integral membrane proteins, are also discussed.
Collapse
Affiliation(s)
- Jessica Lynn Grey
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
| | | |
Collapse
|
17
|
Carvalho CA, Olivares-Ortega C, Soto-Arriaza MA, Carmona-Ribeiro AM. Interaction of gramicidin with DPPC/DODAB bilayer fragments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:3064-71. [PMID: 22960286 DOI: 10.1016/j.bbamem.2012.08.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 08/09/2012] [Accepted: 08/10/2012] [Indexed: 10/28/2022]
Abstract
The interaction between the antimicrobial peptide gramicidin (Gr) and dipalmitoylphosphatidylcholine (DPPC)/dioctadecyldimethylammonium bromide (DODAB) 1:1 large unilamellar vesicles (LVs) or bilayer fragments (BFs) was evaluated by means of several techniques. The major methods were: 1) Gr intrinsic fluorescence and circular dichroism (CD) spectroscopy; 2) dynamic light scattering for sizing and zeta-potential analysis; 3) determination of the bilayer phase transition from extrinsic fluorescence of bilayer probes; 4) pictures of the dispersions for evaluation of coloidal stability over a range of time and NaCl concentration. For Gr in LVs, the Gr dimeric channel conformation is suggested from: 1) CD and intrinsic fluorescence spectra similar to those in trifluoroethanol (TFE); 2) KCl or glucose permeation through the LVs/Gr bilayer. For Gr in BFs, the intertwined dimeric, non-channel Gr conformation is evidenced by CD and intrinsic fluorescence spectra similar to those in ethanol. Both LVs and BFs shield Gr tryptophans against quenching by acrylamide but the Stern-Volmer quenching constant was slightly higher for Gr in BFs confirming that the peptide is more exposed to the water phase in BFs than in LVs. The DPPC/DODAB/Gr supramolecular assemblies may predict the behavior of other antimicrobial peptides in assemblies with lipids.
Collapse
Affiliation(s)
- Camilla A Carvalho
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05513-970, São Paulo, SP, Brazil
| | | | | | | |
Collapse
|
18
|
|
19
|
Lyukmanova EN, Shenkarev ZO, Khabibullina NF, Kopeina GS, Shulepko MA, Paramonov AS, Mineev KS, Tikhonov RV, Shingarova LN, Petrovskaya LE, Dolgikh DA, Arseniev AS, Kirpichnikov MP. Lipid-protein nanodiscs for cell-free production of integral membrane proteins in a soluble and folded state: comparison with detergent micelles, bicelles and liposomes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:349-58. [PMID: 22056981 DOI: 10.1016/j.bbamem.2011.10.020] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 10/03/2011] [Accepted: 10/18/2011] [Indexed: 11/26/2022]
Abstract
Production of integral membrane proteins (IMPs) in a folded state is a key prerequisite for their functional and structural studies. In cell-free (CF) expression systems membrane mimicking components could be added to the reaction mixture that promotes IMP production in a soluble form. Here lipid-protein nanodiscs (LPNs) of different lipid compositions (DMPC, DMPG, POPC, POPC/DOPG) have been compared with classical membrane mimicking media such as detergent micelles, lipid/detergent bicelles and liposomes by their ability to support CF synthesis of IMPs in a folded and soluble state. Three model membrane proteins of different topology were used: homodimeric transmembrane (TM) domain of human receptor tyrosine kinase ErbB3 (TM-ErbB3, 1TM); voltage-sensing domain of K(+) channel KvAP (VSD, 4TM); and bacteriorhodopsin from Exiguobacterium sibiricum (ESR, 7TM). Structural and/or functional properties of the synthesized proteins were analyzed. LPNs significantly enhanced synthesis of the IMPs in a soluble form regardless of the lipid composition. A partial disintegration of LPNs composed of unsaturated lipids was observed upon co-translational IMP incorporation. Contrary to detergents the nanodiscs resulted in the synthesis of ~80% active ESR and promoted correct folding of the TM-ErbB3. None of the tested membrane mimetics supported CF synthesis of correctly folded VSD, and the protocol of the domain refolding was developed. The use of LPNs appears to be the most promising approach to CF production of IMPs in a folded state. NMR analysis of (15)N-Ile-TM-ErbB3 co-translationally incorporated into LPNs shows the great prospects of this membrane mimetics for structural studies of IMPs produced by CF systems.
Collapse
Affiliation(s)
- E N Lyukmanova
- Russian Academy of Sciences, Moscow, Russian Federation.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Park SH, Berkamp S, Cook GA, Chan MK, Viadiu H, Opella SJ. Nanodiscs versus macrodiscs for NMR of membrane proteins. Biochemistry 2011; 50:8983-5. [PMID: 21936505 DOI: 10.1021/bi201289c] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is challenging to find membrane mimics that stabilize the native structures, dynamics, and functions of membrane proteins. In a recent advance, nanodiscs have been shown to provide a bilayer environment compatible with solution NMR. We show that increasing the lipid to "belt" peptide ratio expands their diameter, slows their reorientation rate, and allows the protein-containing discs to be aligned in a magnetic field for oriented sample solid-state NMR. The spectroscopic properties of membrane proteins with one to seven transmembrane helices in q = 0.1 isotropic bicelles, ~10 nm diameter isotropic nanodiscs, ~30 nm diameter magnetically aligned macrodiscs, and q = 5 magnetically aligned bicelles are compared.
Collapse
Affiliation(s)
- Sang Ho Park
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0307, United States
| | | | | | | | | | | |
Collapse
|
21
|
Warschawski DE, Arnold AA, Beaugrand M, Gravel A, Chartrand É, Marcotte I. Choosing membrane mimetics for NMR structural studies of transmembrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1957-74. [DOI: 10.1016/j.bbamem.2011.03.016] [Citation(s) in RCA: 239] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 03/28/2011] [Accepted: 03/29/2011] [Indexed: 12/11/2022]
|
22
|
Kang C, Li Q. Solution NMR study of integral membrane proteins. Curr Opin Chem Biol 2011; 15:560-9. [DOI: 10.1016/j.cbpa.2011.05.025] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Revised: 05/12/2011] [Accepted: 05/23/2011] [Indexed: 11/29/2022]
|
23
|
De Zotti M, Biondi B, Crisma M, Hjørringgaard CU, Berg A, Brückner H, Toniolo C. Isovaline in naturally occurring peptides: A nondestructive methodology for configurational assignment. Biopolymers 2011; 98:36-49. [DOI: 10.1002/bip.21679] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2011] [Revised: 05/03/2011] [Accepted: 05/10/2011] [Indexed: 11/08/2022]
|
24
|
Mineev KS, Khabibullina NF, Lyukmanova EN, Dolgikh DA, Kirpichnikov MP, Arseniev AS. Spatial structure and dimer--monomer equilibrium of the ErbB3 transmembrane domain in DPC micelles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2081-8. [PMID: 21575594 DOI: 10.1016/j.bbamem.2011.04.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 04/18/2011] [Accepted: 04/29/2011] [Indexed: 11/26/2022]
Abstract
In present work the interaction of two TM α-helices of the ErbB3 receptor tyrosine kinase from the ErbB or HER family (residues 639-670) was studied by means of NMR spectroscopy in a membrane-mimicking environment provided by the DPC micelles. The ErbB3 TM segment appeared to form a parallel symmetric dimer in a left-handed orientation. The interaction between TM spans is accomplished via the non-standard motif and is supported by apolar contacts of bulky side chains and by stacking of aromatic rings together with π-cation interactions of Phe and Arg side chains. The investigation of the dimer--monomer equilibrium revealed thermodynamic properties of the assembly and the presence of two distinct regimes of the dimerization at low and at high peptide/detergent ratio. It was found that the detergent in case of ErbB3 behaves not as an ideal solvent, thus affecting the dimer--monomer equilibrium. Such behavior may account for the problems occurring with the refolding and stability of multispan helical membrane proteins in detergent solutions. The example of ErbB3 allows us to conclude that the thermodynamic parameters of dimerization, measured in micelles for two different helical pairs, cannot be compared without the investigation of their dependence on detergent concentration.
Collapse
Affiliation(s)
- K S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation.
| | | | | | | | | | | |
Collapse
|
25
|
Bricarello DA, Smilowitz JT, Zivkovic AM, German JB, Parikh AN. Reconstituted lipoprotein: a versatile class of biologically-inspired nanostructures. ACS NANO 2011; 5:42-57. [PMID: 21182259 DOI: 10.1021/nn103098m] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
One of biology's most pervasive nanostructures, the phospholipid membrane, represents an ideal scaffold for a host of nanotechnology applications. Whether engineering biomimetic technologies or designing therapies to interface with the cell, this adaptable membrane can provide the necessary molecular-level control of membrane-anchored proteins, glycopeptides, and glycolipids. If appropriately prepared, these components can replicate in vitro or influence in vivo essential living processes such as signal transduction, mass transport, and chemical or energy conversion. To satisfy these requirements, a lipid-based, synthetic nanoscale architecture with molecular-level tunability is needed. In this regard, discrete lipid particles, including reconstituted high density lipoprotein (HDL), have emerged as a versatile and elegant solution. Structurally diverse, native biological HDLs exist as discoidal lipid bilayers of 5-8 nm diameter and lipid monolayer-coated spheres 10-15 nm in diameter, all belted by a robust scaffolding protein. These supramolecular assemblies can be reconstituted using simple self-assembly methods to incorporate a broad range of amphipathic molecular constituents, natural or artificial, and provide a generic platform for stabilization and transport of amphipathic and hydrophobic elements capable of docking with targets at biological or inorganic surfaces. In conjunction with top-down or bottom-up engineering approaches, synthetic HDL can be designed, arrayed, and manipulated for a host of applications including biochemical analyses and fundamental studies of molecular structure. Also highly biocompatible, these assemblies are suitable for medical diagnostics and therapeutics. The collection of efforts reviewed here focuses on laboratory methods by which synthetic HDLs are produced, the advantages conferred by their nanoscopic dimension, and current and emerging applications.
Collapse
Affiliation(s)
- Daniel A Bricarello
- Department of Applied Science, University of California-Davis, Davis, California 95616, United States
| | | | | | | | | |
Collapse
|
26
|
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.
Collapse
Affiliation(s)
- Tabussom Qureshi
- Department of Chemistry, University of Ottawa, Ottawa, ON, Canada
| | | |
Collapse
|
27
|
Raschle T, Hiller S, Etzkorn M, Wagner G. Nonmicellar systems for solution NMR spectroscopy of membrane proteins. Curr Opin Struct Biol 2010; 20:471-9. [PMID: 20570504 DOI: 10.1016/j.sbi.2010.05.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 05/09/2010] [Indexed: 01/28/2023]
Abstract
Integral membrane proteins play essential roles in many biological processes, such as energy transduction, transport of molecules, and signaling. The correct function of membrane proteins is likely to depend strongly on the chemical and physical properties of the membrane. However, membrane proteins are not accessible to many biophysical methods in their native cellular membrane. A major limitation for their functional and structural characterization is thus the requirement for an artificial environment that mimics the native membrane to preserve the integrity and stability of the membrane protein. Most commonly employed are detergent micelles, which can however be detrimental to membrane protein activity and stability. Here, we review recent developments for alternative, nonmicellar solubilization techniques, with a particular focus on their application to solution NMR studies. We discuss the use of amphipols and lipid bilayer systems, such as bicelles and nanolipoprotein particles (NLPs). The latter show great promise for structural studies in near native membranes.
Collapse
|
28
|
Fischer NO, Infante E, Ishikawa T, Blanchette CD, Bourne N, Hoeprich PD, Mason PW. Conjugation to nickel-chelating nanolipoprotein particles increases the potency and efficacy of subunit vaccines to prevent West Nile encephalitis. Bioconjug Chem 2010; 21:1018-22. [PMID: 20509624 DOI: 10.1021/bc100083d] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Subunit antigens are attractive candidates for vaccine development, as they are safe, cost-effective, and rapidly produced. Nevertheless, subunit antigens often need to be adjuvanted and/or formulated to produce products with acceptable potency and efficacy. Here, we describe a simple method for improving the potency and efficacy of a recombinant subunit antigen by its immobilization on nickel-chelating nanolipoprotein particles (NiNLPs). NiNLPs are membrane mimetic nanoparticles that provide a delivery and presentation platform amenable to binding any recombinant subunit immunogens featuring a polyhistidine tag. A His-tagged, soluble truncated form of the West Nile virus (WNV) envelope protein (trE-His) was immobilized on NiNLPs. Single inoculations of the NiNLP-trE-His produced superior anti-WNV immune responses and provided significantly improved protection against a live WNV challenge compared to mice inoculated with trE-His alone. These results have broad implications in vaccine development and optimization, as NiNLP technology is well-suited to many types of vaccines, providing a universal platform for enhancing the potency and efficacy of recombinant subunit immunogens.
Collapse
Affiliation(s)
- Nicholas O Fischer
- Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | | | | | | | | | | | | |
Collapse
|
29
|
Kijac A, Shih AY, Nieuwkoop AJ, Schulten K, Sligar SG, Rienstra CM. Lipid-protein correlations in nanoscale phospholipid bilayers determined by solid-state nuclear magnetic resonance. Biochemistry 2010; 49:9190-8. [PMID: 20804175 PMCID: PMC3136391 DOI: 10.1021/bi1013722] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nanodiscs are examples of discoidal nanoscale lipid-protein particles that have been extremely useful for the biochemical and biophysical characterization of membrane proteins. They are discoidal lipid bilayer fragments encircled and stabilized by two amphipathic helical proteins named membrane scaffolding protein (MSP), ~10 nm in size. Nanodiscs are homogeneous, easily prepared with reproducible success, amenable to preparations with a variety of lipids, and stable over a range of temperatures. Here we present solid-state nuclear magnetic resonance (SSNMR) studies on lyophilized, rehydrated POPC Nanodiscs prepared with uniformly (13)C-, (15)N-labeled MSP1D1 (Δ1-11 truncated MSP). Under these conditions, by SSNMR we directly determine the gel-to-liquid crystal lipid phase transition to be at 3 ± 2 °C. Above this phase transition, the lipid (1)H signals have slow transverse relaxation, enabling filtering experiments as previously demonstrated for lipid vesicles. We incorporate this approach into two- and three-dimensional heteronuclear SSNMR experiments to examine the MSP1D1 residues interfacing with the lipid bilayer. These (1)H-(13)C and (1)H-(13)C-(13)C correlation spectra are used to identify and quantify the number of lipid-correlated and solvent-exposed residues by amino acid type, which furthermore is compared with molecular dynamics studies of MSP1D1 in Nanodiscs. This study demonstrates the utility of SSNMR experiments with Nanodiscs for examining lipid-protein interfaces and has important applications for future structural studies of membrane proteins in physiologically relevant formulations.
Collapse
Affiliation(s)
- Aleksandra Kijac
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Amy Y. Shih
- Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Andrew J. Nieuwkoop
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Klaus Schulten
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Stephen G. Sligar
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Chad M. Rienstra
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| |
Collapse
|
30
|
Shenkarev ZO, Paramonov AS, Lyukmanova EN, Shingarova LN, Yakimov SA, Dubinnyi MA, Chupin VV, Kirpichnikov MP, Blommers MJJ, Arseniev AS. NMR structural and dynamical investigation of the isolated voltage-sensing domain of the potassium channel KvAP: implications for voltage gating. J Am Chem Soc 2010; 132:5630-7. [PMID: 20356312 DOI: 10.1021/ja909752r] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure and dynamics of the isolated voltage-sensing domain (VSD) of the archaeal potassium channel KvAP was studied by high-resolution NMR. The almost complete backbone resonance assignment and partial side-chain assignment of the (2)H,(13)C,(15)N-labeled VSD were obtained for the protein domain solubilized in DPC/LDAO (2:1) mixed micelles. Secondary and tertiary structures of the VSD were characterized using secondary chemical shifts and NOE contacts. These data indicate that the spatial structure of the VSD solubilized in micelles corresponds to the structure of the domain in an open state of the channel. NOE contacts and secondary chemical shifts of amide protons indicate the presence of tightly bound water molecule as well as hydrogen bond formation involving an interhelical salt bridge (Asp62-R133) that stabilizes the overall structure of the domain. The backbone dynamics of the VSD was studied using (15)N relaxation measurements. The loop regions S1-S2 and S2-S3 were found mobile, while the S3-S4 loop (voltage-sensor paddle) was found stable at the ps-ns time scale. The moieties of S1, S2, S3, and S4 helices sharing interhelical contacts (at the level of the Asp62-R133 salt bridge) were observed in conformational exchange on the micros-ms time scale. Similar exchange-induced broadening of characteristic resonances was observed for the VSD solubilized in the membrane of lipid-protein nanodiscs composed of DMPC, DMPG, and POPC/DOPG lipids. Apparently, the observed interhelical motions represent an inherent property of the VSD of the KvAP channel and can play an important role in the voltage gating.
Collapse
Affiliation(s)
- Zakhar O Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Fischer NO, Blanchette CD, Segelke BW, Corzett M, Chromy BA, Kuhn EA, Bench G, Hoeprich PD. Isolation, characterization, and stability of discretely-sized nanolipoprotein particles assembled with apolipophorin-III. PLoS One 2010; 5:e11643. [PMID: 20657844 PMCID: PMC2906516 DOI: 10.1371/journal.pone.0011643] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 06/16/2010] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Nanolipoprotein particles (NLPs) are discoidal, nanometer-sized particles comprised of self-assembled phospholipid membranes and apolipoproteins. NLPs assembled with human apolipoproteins have been used for myriad biotechnology applications, including membrane protein solubilization, drug delivery, and diagnostic imaging. To expand the repertoire of lipoproteins for these applications, insect apolipophorin-III (apoLp-III) was evaluated for the ability to form discretely-sized, homogeneous, and stable NLPs. METHODOLOGY Four NLP populations distinct with regards to particle diameters (ranging in size from 10 nm to >25 nm) and lipid-to-apoLp-III ratios were readily isolated to high purity by size exclusion chromatography. Remodeling of the purified NLP species over time at 4 degrees C was monitored by native gel electrophoresis, size exclusion chromatography, and atomic force microscopy. Purified 20 nm NLPs displayed no remodeling and remained stable for over 1 year. Purified NLPs with 10 nm and 15 nm diameters ultimately remodeled into 20 nm NLPs over a period of months. Intra-particle chemical cross-linking of apoLp-III stabilized NLPs of all sizes. CONCLUSIONS ApoLp-III-based NLPs can be readily prepared, purified, characterized, and stabilized, suggesting their utility for biotechnological applications.
Collapse
Affiliation(s)
- Nicholas O. Fischer
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Craig D. Blanchette
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Brent W. Segelke
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Michele Corzett
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Brett A. Chromy
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Edward A. Kuhn
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Graham Bench
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Paul D. Hoeprich
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| |
Collapse
|
32
|
Popot JL. Amphipols, Nanodiscs, and Fluorinated Surfactants: Three Nonconventional Approaches to Studying Membrane Proteins in Aqueous Solutions. Annu Rev Biochem 2010; 79:737-75. [DOI: 10.1146/annurev.biochem.052208.114057] [Citation(s) in RCA: 241] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jean-Luc Popot
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires, Unité Mixte de Recherche 7099, Centre National de la Recherche Scientifique and Université Paris-7 Denis Diderot, Institut de Biologie Physico-Chimique, F-75005 Paris, France; e-mail:
| |
Collapse
|
33
|
Fukuda M, Nakano M, Miyazaki M, Handa T. Thermodynamic and Kinetic Stability of Discoidal High-Density Lipoprotein Formation from Phosphatidylcholine/Apolipoprotein A-I Mixture. J Phys Chem B 2010; 114:8228-34. [DOI: 10.1021/jp101071t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Masakazu Fukuda
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501
| | - Minoru Nakano
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501
| | - Masakazu Miyazaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501
| | - Tetsurou Handa
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501
| |
Collapse
|
34
|
Bocharov EV, Volynsky PE, Pavlov KV, Efremov RG, Arseniev AS. Structure elucidation of dimeric transmembrane domains of bitopic proteins. Cell Adh Migr 2010; 4:284-98. [PMID: 20421711 DOI: 10.4161/cam.4.2.11930] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The interaction between transmembrane helices is of great interest because it directly determines biological activity of a membrane protein. Either destroying or enhancing such interactions can result in many diseases related to dysfunction of different tissues in human body. One much studied form of membrane proteins known as bitopic protein is a dimer containing two membrane-spanning helices associating laterally. Establishing structure-function relationship as well as rational design of new types of drugs targeting membrane proteins requires precise structural information about this class of objects. At present time, to investigate spatial structure and internal dynamics of such transmembrane helical dimers, several strategies were developed based mainly on a combination of NMR spectroscopy, optical spectroscopy, protein engineering and molecular modeling. These approaches were successfully applied to homo- and heterodimeric transmembrane fragments of several bitopic proteins, which play important roles in normal and in pathological conditions of human organism.
Collapse
Affiliation(s)
- Eduard V Bocharov
- Division of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.
| | | | | | | | | |
Collapse
|
35
|
Yoshiura C, Kofuku Y, Ueda T, Mase Y, Yokogawa M, Osawa M, Terashima Y, Matsushima K, Shimada I. NMR Analyses of the Interaction between CCR5 and Its Ligand Using Functional Reconstitution of CCR5 in Lipid Bilayers. J Am Chem Soc 2010; 132:6768-77. [DOI: 10.1021/ja100830f] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chie Yoshiura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| | - Yoko Mase
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| | - Mariko Yokogawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| | - Yuya Terashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| | - Kouji Matsushima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan, Effector Cell Institute, Inc., Tokyo 150-0036, Japan, and Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo 135-0064, Japan
| |
Collapse
|
36
|
Carmona-Ribeiro AM. Biomimetic nanoparticles: preparation, characterization and biomedical applications. Int J Nanomedicine 2010; 5:249-59. [PMID: 20463941 PMCID: PMC2865020 DOI: 10.2147/ijn.s9035] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Indexed: 11/23/2022] Open
Abstract
Mimicking nature is a powerful approach for developing novel lipid-based devices for drug and vaccine delivery. In this review, biomimetic assemblies based on natural or synthetic lipids by themselves or associated to silica, latex or drug particles will be discussed. In water, self-assembly of lipid molecules into supramolecular structures is fairly well understood. However, their self-assembly on a solid surface or at an interface remains poorly understood. In certain cases, hydrophobic drug granules can be dispersed in aqueous solution via lipid adsorption surrounding the drug particles as nanocapsules. In other instances, hydrophobic drug molecules attach as monomers to borders of lipid bilayer fragments providing drug formulations that are effective in vivo at low drug-to-lipid-molar ratio. Cationic biomimetic particles offer suitable interfacial environment for adsorption, presentation and targeting of biomolecules in vivo. Thereby antigens can effectively be presented by tailored biomimetic particles for development of vaccines over a range of defined and controllable particle sizes. Biomolecular recognition between receptor and ligand can be reconstituted by means of receptor immobilization into supported lipidic bilayers allowing isolation and characterization of signal transduction steps.
Collapse
Affiliation(s)
- Ana Maria Carmona-Ribeiro
- Biocolloids Lab, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
| |
Collapse
|
37
|
Shenkarev ZO, Lyukmanova EN, Paramonov AS, Shingarova LN, Chupin VV, Kirpichnikov MP, Blommers MJJ, Arseniev AS. Lipid−Protein Nanodiscs as Reference Medium in Detergent Screening for High-Resolution NMR Studies of Integral Membrane Proteins. J Am Chem Soc 2010; 132:5628-9. [DOI: 10.1021/ja9097498] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zakhar O. Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia and Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Ekaterina N. Lyukmanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia and Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Alexander S. Paramonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia and Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Lyudmila N. Shingarova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia and Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Vladimir V. Chupin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia and Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Mikhail P. Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia and Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Marcel J. J. Blommers
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia and Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Alexander S. Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia and Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| |
Collapse
|
38
|
Raschle T, Hiller S, Yu TY, Rice AJ, Walz T, Wagner G. Structural and functional characterization of the integral membrane protein VDAC-1 in lipid bilayer nanodiscs. J Am Chem Soc 2010; 131:17777-9. [PMID: 19916553 DOI: 10.1021/ja907918r] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Biophysical studies of membrane proteins are often impeded by the requirement for a membrane mimicking environment. Detergent micelles are the most common choice, but the denaturing properties make them unsatisfactory for studies of many membrane proteins and their interactions. In the present work, we explore phospholipid bilayer nanodiscs as membrane mimics and employ electron microscopy and solution NMR spectroscopy to characterize the structure and function of the human voltage dependent anion channel (VDAC-1) as an example of a polytopic integral membrane protein. Electron microscopy reveals the formation of VDAC-1 multimers, an observation that is consistent with results obtained in native mitochondrial outer membranes. High-resolution NMR spectroscopy demonstrates a well folded VDAC-1 protein and native NADH binding functionality. The observed chemical shift changes upon addition of the native ligand NADH to nanodisc-embedded VDAC-1 resemble those of micelle-embedded VDAC-1, indicating a similar structure and function in the two membrane-mimicking environments. Overall, the ability to study integral membrane proteins at atomic resolution with solution NMR in phospholipid bilayers, rather than in detergent micelles, offers exciting novel possibilities to approach the biophysical properties of membrane proteins under nondenaturing conditions, which makes this technology particular suitable for protein-protein interactions and other functional studies.
Collapse
Affiliation(s)
- Thomas Raschle
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
| | | | | | | | | | | |
Collapse
|
39
|
Shenkarev ZO, Lyukmanova EN, Solozhenkin OI, Gagnidze IE, Nekrasova OV, Chupin VV, Tagaev AA, Yakimenko ZA, Ovchinnikova TV, Kirpichnikov MP, Arseniev AS. Lipid-protein nanodiscs: possible application in high-resolution NMR investigations of membrane proteins and membrane-active peptides. BIOCHEMISTRY (MOSCOW) 2009; 74:756-65. [PMID: 19747096 DOI: 10.1134/s0006297909070086] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
High-resolution NMR is shown to be applicable for investigation of membrane proteins and membrane-active peptides embedded into lipid-protein nanodiscs (LPNs). (15)N-Labeled K+-channel from Streptomyces lividans (KcsA) and the antibiotic antiamoebin I from Emericellopsis minima (Aam-I) were embedded in LPNs of different lipid composition. Formation of stable complexes undergoing isotropic motion in solution was confirmed by size-exclusion chromatography and (31)P-NMR spectroscopy. The 2D 1H-(15)N-correlation spectra were recorded for KcsA in the complex with LPN containing DMPC and for Aam-I in LPNs based on DOPG, DLPC, DMPC, and POPC. The spectra recorded were compared with those in detergent-containing micelles and small bicelles commonly used in high-resolution NMR spectroscopy of membrane proteins. The spectra recorded in LPN environments demonstrated similar signal dispersion but significantly increased (1)H(N) line width. The spectra of Aam-I embedded in LPNs containing phosphatidylcholine showed significant selective line broadening, thus suggesting exchange process(es) between several membrane-bound states of the peptide. (15)N relaxation rates were measured to obtain the effective rotational correlation time of the Aam-I molecule. The obtained value (approximately 40 nsec at 45 degrees C) is indicative of additional peptide motions within the Aam-I/LPN complex.
Collapse
Affiliation(s)
- Z O Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Bayburt TH, Sligar SG. Membrane protein assembly into Nanodiscs. FEBS Lett 2009; 584:1721-7. [PMID: 19836392 DOI: 10.1016/j.febslet.2009.10.024] [Citation(s) in RCA: 557] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 10/09/2009] [Indexed: 01/25/2023]
Abstract
Nanodiscs are soluble nanoscale phospholipid bilayers which can self-assemble integral membrane proteins for biophysical, enzymatic or structural investigations. This means for rendering membrane proteins soluble at the single molecule level offers advantages over liposomes or detergent micelles in terms of size, stability, ability to add genetically modifiable features to the Nanodisc structure and ready access to both sides of the phospholipid bilayer domain. Thus the Nanodisc system provides a novel platform for understanding membrane protein function. We provide an overview of the Nanodisc approach and document through several examples many of the applications to the study of the structure and function of integral membrane proteins.
Collapse
Affiliation(s)
- Timothy H Bayburt
- Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | | |
Collapse
|
41
|
Glück JM, Wittlich M, Feuerstein S, Hoffmann S, Willbold D, Koenig BW. Integral Membrane Proteins in Nanodiscs Can Be Studied by Solution NMR Spectroscopy. J Am Chem Soc 2009; 131:12060-1. [DOI: 10.1021/ja904897p] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Julian M. Glück
- Institute of Structural Biology and Biophysics (ISB-3), Research Centre Jülich, D-52425 Jülich, Germany, and Institute of Physical Biology and BMFZ, Heinrich-Heine-University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Marc Wittlich
- Institute of Structural Biology and Biophysics (ISB-3), Research Centre Jülich, D-52425 Jülich, Germany, and Institute of Physical Biology and BMFZ, Heinrich-Heine-University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Sophie Feuerstein
- Institute of Structural Biology and Biophysics (ISB-3), Research Centre Jülich, D-52425 Jülich, Germany, and Institute of Physical Biology and BMFZ, Heinrich-Heine-University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Silke Hoffmann
- Institute of Structural Biology and Biophysics (ISB-3), Research Centre Jülich, D-52425 Jülich, Germany, and Institute of Physical Biology and BMFZ, Heinrich-Heine-University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Structural Biology and Biophysics (ISB-3), Research Centre Jülich, D-52425 Jülich, Germany, and Institute of Physical Biology and BMFZ, Heinrich-Heine-University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Bernd W. Koenig
- Institute of Structural Biology and Biophysics (ISB-3), Research Centre Jülich, D-52425 Jülich, Germany, and Institute of Physical Biology and BMFZ, Heinrich-Heine-University Düsseldorf, D-40225 Düsseldorf, Germany
| |
Collapse
|
42
|
Abstract
Abstract
A major challenge in the research on membrane-anchored and integral membrane protein complexes is to obtain these in a functionally active, water-soluble, and monodisperse form. This requires the incorporation of the membrane proteins into a native-like membrane or detergent micelle that mimics the properties of the original biological membrane. However, solubilization in detergents or reconstitution in liposomes or supported monolayers sometimes suffers from loss of activity and problematic analyses due to heterogeneity and aggregation. A developing technology termed nanodiscs exploits discoidal phospholipid bilayers encircled by a stabilizing amphipatic helical membrane scaffold protein to reconstitute membranes with integral proteins. After reconstitution, the membrane nanodisc is soluble, stable, and monodisperse. In the present review, we outline the biological inspiration for nanodiscs as discoidal high-density lipoproteins, the assembly and handling of nanodiscs, and finally their diverse biochemical applications. In our view, major advantages of nanodisc technology for integral membrane proteins is homogeneity, control of oligomerization state, access to both sides of the membrane, and control of lipids in the local membrane environment of the integral protein.
Collapse
|
43
|
Nakano M, Fukuda M, Kudo T, Miyazaki M, Wada Y, Matsuzaki N, Endo H, Handa T. Static and Dynamic Properties of Phospholipid Bilayer Nanodiscs. J Am Chem Soc 2009; 131:8308-12. [DOI: 10.1021/ja9017013] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Minoru Nakano
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan, and Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Masakazu Fukuda
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan, and Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Takayuki Kudo
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan, and Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Masakazu Miyazaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan, and Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Yusuke Wada
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan, and Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Naoya Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan, and Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Hitoshi Endo
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan, and Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Tetsurou Handa
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan, and Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| |
Collapse
|
44
|
Zou C, Naider F, Zerbe O. Biosynthesis and NMR-studies of a double transmembrane domain from the Y4 receptor, a human GPCR. JOURNAL OF BIOMOLECULAR NMR 2008; 42:257-269. [PMID: 18937032 DOI: 10.1007/s10858-008-9281-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 09/24/2008] [Accepted: 09/26/2008] [Indexed: 05/26/2023]
Abstract
The human Y4 receptor, a class A G-protein coupled receptor (GPCR) primarily targeted by the pancreatic polypeptide (PP), is involved in a large number of physiologically important functions. This paper investigates a Y4 receptor fragment (N-TM1-TM2) comprising the N-terminal domain, the first two transmembrane (TM) helices and the first extracellular loop followed by a (His)(6) tag, and addresses synthetic problems encountered when recombinantly producing such fragments from GPCRs in Escherichia coli. Rigorous purification and usage of the optimized detergent mixture 28 mM dodecylphosphocholine (DPC)/118 mM% 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] (LPPG) resulted in high quality TROSY spectra indicating protein conformational homogeneity. Almost complete assignment of the backbone, including all TM residue resonances was obtained. Data on internal backbone dynamics revealed a high secondary structure content for N-TM1-TM2. Secondary chemical shifts and sequential amide proton nuclear Overhauser effects defined the TM helices. Interestingly, the properties of the N-terminal domain of this large fragment are highly similar to those determined on the isolated N-terminal domain in the presence of DPC micelles.
Collapse
Affiliation(s)
- Chao Zou
- Institute of Organic Chemistry, University of Zurich, Switzerland
| | | | | |
Collapse
|
45
|
Aravinda S, Shamala N, Balaram P. Aib Residues in Peptaibiotics and Synthetic Sequences: Analysis of Nonhelical Conformations. Chem Biodivers 2008; 5:1238-62. [PMID: 18649312 DOI: 10.1002/cbdv.200890112] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|