51
|
Eichmann C, Orts J, Tzitzilonis C, Vögeli B, Smrt S, Lorieau J, Riek R. Intermolecular detergent-membrane protein noes for the characterization of the dynamics of membrane protein-detergent complexes. J Phys Chem B 2014; 118:14288-301. [PMID: 25419869 DOI: 10.1021/jp509137q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The interaction between membrane proteins and lipids or lipid mimetics such as detergents is key for the three-dimensional structure and dynamics of membrane proteins. In NMR-based structural studies of membrane proteins, qualitative analysis of intermolecular nuclear Overhauser enhancements (NOEs) or paramagnetic resonance enhancement are used in general to identify the transmembrane segments of a membrane protein. Here, we employed a quantitative characterization of intermolecular NOEs between (1)H of the detergent and (1)H(N) of (2)H-perdeuterated, (15)N-labeled α-helical membrane protein-detergent complexes following the exact NOE (eNOE) approach. Structural considerations suggest that these intermolecular NOEs should show a helical-wheel-type behavior along a transmembrane helix or a membrane-attached helix within a membrane protein as experimentally demonstrated for the complete influenza hemagglutinin fusion domain HAfp23. The partial absence of such a NOE pattern along the amino acid sequence as shown for a truncated variant of HAfp23 and for the Escherichia coli inner membrane protein YidH indicates the presence of large tertiary structure fluctuations such as an opening between helices or the presence of large rotational dynamics of the helices. Detergent-protein NOEs thus appear to be a straightforward probe for a qualitative characterization of structural and dynamical properties of membrane proteins embedded in detergent micelles.
Collapse
Affiliation(s)
- Cédric Eichmann
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg , CH-8093 Zürich, Switzerland
| | | | | | | | | | | | | |
Collapse
|
52
|
Folding energetics and oligomerization of polytopic α-helical transmembrane proteins. Arch Biochem Biophys 2014; 564:281-96. [DOI: 10.1016/j.abb.2014.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/26/2014] [Accepted: 07/14/2014] [Indexed: 01/06/2023]
|
53
|
Dutta A, Altenbach C, Mangahas S, Yanamala N, Gardner E, Hubbell WL, Klein-Seetharaman J. Differential dynamics of extracellular and cytoplasmic domains in denatured States of rhodopsin. Biochemistry 2014; 53:7160-9. [PMID: 25268658 PMCID: PMC4245987 DOI: 10.1021/bi401557e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
Rhodopsin
is a model system for understanding membrane protein
folding. Recently, conditions that allow maximally denaturing rhodopsin
without causing aggregation have been determined, opening the door
to the first structural characterization of denatured states of rhodopsin
by nuclear magnetic resonance (NMR) and electron paramagnetic resonance
(EPR) spectroscopy. One-dimensional 1H NMR spectra confirm
a progressive increase in flexibility of resonances in rhodopsin with
increasing denaturant concentrations. Two-dimensional 1H–15N HSQC spectra of [15N]-α-lysine-labeled
rhodopsin in which signals arise primarily from residues in the cytoplasmic
(CP) domain and of [15N]-α,ε-tryptophan-labeled
rhodopsin in which signals arise only from transmembrane (TM) and
extracellular (EC) residues indicate qualitatively that EC and CP
domains may be differentially affected by denaturation. To obtain
residue-specific information, particular residues in EC and CP domains
were investigated by site-directed spin labeling. EPR spectra of the
spin-labeled samples indicate that the EC residues retain more rigidity
in the denatured states than the CP residues. These results support
the notion of residual structure in denatured states of rhodopsin.
Collapse
Affiliation(s)
- Arpana Dutta
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | | | | | | | | | | | | |
Collapse
|
54
|
Wang S, Ladizhansky V. Recent advances in magic angle spinning solid state NMR of membrane proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 82:1-26. [PMID: 25444696 DOI: 10.1016/j.pnmrs.2014.07.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 07/16/2014] [Accepted: 07/20/2014] [Indexed: 05/14/2023]
Abstract
Membrane proteins mediate many critical functions in cells. Determining their three-dimensional structures in the native lipid environment has been one of the main objectives in structural biology. There are two major NMR methodologies that allow this objective to be accomplished. Oriented sample NMR, which can be applied to membrane proteins that are uniformly aligned in the magnetic field, has been successful in determining the backbone structures of a handful of membrane proteins. Owing to methodological and technological developments, Magic Angle Spinning (MAS) solid-state NMR (ssNMR) spectroscopy has emerged as another major technique for the complete characterization of the structure and dynamics of membrane proteins. First developed on peptides and small microcrystalline proteins, MAS ssNMR has recently been successfully applied to large membrane proteins. In this review we describe recent progress in MAS ssNMR methodologies, which are now available for studies of membrane protein structure determination, and outline a few examples, which highlight the broad capability of ssNMR spectroscopy.
Collapse
Affiliation(s)
- Shenlin Wang
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Vladimir Ladizhansky
- Department of Physics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada; Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.
| |
Collapse
|
55
|
Abstract
Membrane proteins have always presented technical challenges for structural studies because of their requirement for a lipid environment. Multiple approaches exist including X-ray crystallography and electron microscopy that can give significant insights into their structure and function. However, nuclear magnetic resonance (NMR) is unique in that it offers the possibility of determining the structures of unmodified membrane proteins in their native environment of phospholipid bilayers under physiological conditions. Furthermore, NMR enables the characterization of the structure and dynamics of backbone and side chain sites of the proteins alone and in complexes with both small molecules and other biopolymers. The learning curve has been steep for the field as most initial studies were performed under non-native environments using modified proteins until ultimately progress in both techniques and instrumentation led to the possibility of examining unmodified membrane proteins in phospholipid bilayers under physiological conditions. This review aims to provide an overview of the development and application of NMR to membrane proteins. It highlights some of the most significant structural milestones that have been reached by NMR spectroscopy of membrane proteins, especially those accomplished with the proteins in phospholipid bilayer environments where they function.
Collapse
|
56
|
Ireland PM, McMahon RM, Marshall LE, Halili M, Furlong E, Tay S, Martin JL, Sarkar-Tyson M. Disarming Burkholderia pseudomallei: structural and functional characterization of a disulfide oxidoreductase (DsbA) required for virulence in vivo. Antioxid Redox Signal 2014; 20:606-17. [PMID: 23901809 PMCID: PMC3901323 DOI: 10.1089/ars.2013.5375] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
AIMS The intracellular pathogen Burkholderia pseudomallei causes the disease melioidosis, a major source of morbidity and mortality in southeast Asia and northern Australia. The need to develop novel antimicrobials is compounded by the absence of a licensed vaccine and the bacterium's resistance to multiple antibiotics. In a number of clinically relevant Gram-negative pathogens, DsbA is the primary disulfide oxidoreductase responsible for catalyzing the formation of disulfide bonds in secreted and membrane-associated proteins. In this study, a putative B. pseudomallei dsbA gene was evaluated functionally and structurally and its contribution to infection assessed. RESULTS Biochemical studies confirmed the dsbA gene encodes a protein disulfide oxidoreductase. A dsbA deletion strain of B. pseudomallei was attenuated in both macrophages and a BALB/c mouse model of infection and displayed pleiotropic phenotypes that included defects in both secretion and motility. The 1.9 Å resolution crystal structure of BpsDsbA revealed differences from the classic member of this family Escherichia coli DsbA, in particular within the region surrounding the active site disulfide where EcDsbA engages with its partner protein E. coli DsbB, indicating that the interaction of BpsDsbA with its proposed partner BpsDsbB may be distinct from that of EcDsbA-EcDsbB. INNOVATION This study has characterized BpsDsbA biochemically and structurally and determined that it is required for virulence of B. pseudomallei. CONCLUSION These data establish a critical role for BpsDsbA in B. pseudomallei infection, which in combination with our structural characterization of BpsDsbA will facilitate the future development of rationally designed inhibitors against this drug-resistant organism.
Collapse
Affiliation(s)
- Philip M Ireland
- 1 Defence Science and Technology Laboratory , Porton Down, Salisbury, Wiltshire, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
57
|
Walden PM, McMahon RM, Archbold JK. Membrane Protein Structures for Rational Antimicrobial Drug Design. Aust J Chem 2014. [DOI: 10.1071/ch14333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Antibiotic resistance is a major global health threat. Bacteria have developed novel resistance mechanisms to many of the latest generations of antibiotics and there is an urgent need to develop new therapies to combat these infections. Infections that are caused by multi-drug resistant Gram-negative bacteria result in poor prognosis, prolonged illness, and greater costs for health care. Recent research has pointed to several key bacterial membrane proteins as potential targets for drug and vaccine development. However, determination of the structures of these membrane proteins is not a trivial task. Here we review recent breakthroughs of the structural determination of bacterial membrane proteins and their potential for the future rational design of novel antimicrobial therapies.
Collapse
|
58
|
Maltsev S, Lorigan GA. Membrane proteins structure and dynamics by nuclear magnetic resonance. Compr Physiol 2013; 1:2175-87. [PMID: 23733702 DOI: 10.1002/cphy.c110022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Membrane proteins represent a challenging class of biological systems to study. They are extremely difficult to crystallize and in most cases they retain their structure and functions only in membrane environments. Therefore, commonly used diffraction methods fail to give detailed molecular structure and other approaches have to be utilized to obtain biologically relevant information. Nuclear magnetic resonance (NMR) spectroscopy, however, can provide powerful structural and dynamical constraints on these complicated systems. Solution- and solid-state NMR are powerful methods for investigating membrane proteins studies. In this work, we briefly review both solution and solid-state NMR techniques for membrane protein studies and illustrate the applications of these methods to elucidate proteins structure, conformation, topology, dynamics, and function. Recent advances in electronics, biological sample preparation, and spectral processing provided opportunities for complex biological systems, such as membrane proteins inside lipid vesicles, to be studied faster and with outstanding quality. New analysis methods therefore have emerged, that benefit from the combination of sample preparation and corresponding specific high-end NMR techniques, which give access to more structural and dynamic information.
Collapse
Affiliation(s)
- Sergey Maltsev
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | | |
Collapse
|
59
|
Yazawa K, Furusawa H, Okahata Y. Real-time monitoring of intermediates reveals the reaction pathway in the thiol-disulfide exchange between disulfide bond formation protein A (DsbA) and B (DsbB) on a membrane-immobilized quartz crystal microbalance (QCM) system. J Biol Chem 2013; 288:35969-81. [PMID: 24145032 PMCID: PMC3861646 DOI: 10.1074/jbc.m113.519876] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/18/2013] [Indexed: 11/06/2022] Open
Abstract
Disulfide bond formation protein B (DsbBS-S,S-S) is an inner membrane protein in Escherichia coli that has two disulfide bonds (S-S, S-S) that play a role in oxidization of a pair of cysteine residues (SH, SH) in disulfide bond formation protein A (DsbASH,SH). The oxidized DsbAS-S, with one disulfide bond (S-S), can oxidize proteins with SH groups for maturation of a folding preprotein. Here, we have described the transient kinetics of the oxidation reaction between DsbASH,SH and DsbBS-S,S-S. We immobilized DsbBS-S,S-S embedded in lipid bilayers on the surface of a 27-MHz quartz crystal microbalance (QCM) device to detect both formation and degradation of the reaction intermediate (DsbA-DsbB), formed via intermolecular disulfide bonds, as a mass change in real time. The obtained kinetic parameters (intermediate formation, reverse, and oxidation rate constants (kf, kr, and kcat, respectively) indicated that the two pairs of cysteine residues in DsbBS-S,S-S were more important for the stability of the DsbA-DsbB intermediate than ubiquinone, an electron acceptor for DsbBS-S,S-S. Our data suggested that the reaction pathway of almost all DsbASH,SH oxidation processes would proceed through this stable intermediate, avoiding the requirement for ubiquinone.
Collapse
Affiliation(s)
- Kenjiro Yazawa
- From the Innovative Flex Course for Frontier Organic Material Systems (iFront), Yamagata University, Yamagata 992-8510, Japan and Department of Biomolecular Engineering, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Hiroyuki Furusawa
- From the Innovative Flex Course for Frontier Organic Material Systems (iFront), Yamagata University, Yamagata 992-8510, Japan and Department of Biomolecular Engineering, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Yoshio Okahata
- From the Innovative Flex Course for Frontier Organic Material Systems (iFront), Yamagata University, Yamagata 992-8510, Japan and Department of Biomolecular Engineering, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| |
Collapse
|
60
|
The α-proteobacteria Wolbachia pipientis protein disulfide machinery has a regulatory mechanism absent in γ-proteobacteria. PLoS One 2013; 8:e81440. [PMID: 24282596 PMCID: PMC3839904 DOI: 10.1371/journal.pone.0081440] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 10/21/2013] [Indexed: 11/19/2022] Open
Abstract
The α-proteobacterium Wolbachia pipientis infects more than 65% of insect species worldwide and manipulates the host reproductive machinery to enable its own survival. It can live in mutualistic relationships with hosts that cause human disease, including mosquitoes that carry the Dengue virus. Like many other bacteria, Wolbachia contains disulfide bond forming (Dsb) proteins that introduce disulfide bonds into secreted effector proteins. The genome of the Wolbachia strain wMel encodes two DsbA-like proteins sharing just 21% sequence identity to each other, α-DsbA1 and α-DsbA2, and an integral membrane protein, α-DsbB. α-DsbA1 and α-DsbA2 both have a Cys-X-X-Cys active site that, by analogy with Escherichia coli DsbA, would need to be oxidized to the disulfide form to serve as a disulfide bond donor toward substrate proteins. Here we show that the integral membrane protein α-DsbB oxidizes α-DsbA1, but not α-DsbA2. The interaction between α-DsbA1 and α-DsbB is very specific, involving four essential cysteines located in the two periplasmic loops of α-DsbB. In the electron flow cascade, oxidation of α-DsbA1 by α-DsbB is initiated by an oxidizing quinone cofactor that interacts with the cysteine pair in the first periplasmic loop. Oxidizing power is transferred to the second cysteine pair, which directly interacts with α-DsbA1. This reaction is inhibited by a non-catalytic disulfide present in α-DsbA1, conserved in other α-proteobacterial DsbAs but not in γ-proteobacterial DsbAs. This is the first characterization of the integral membrane protein α-DsbB from Wolbachia and reveals that the non-catalytic cysteines of α-DsbA1 regulate the redox relay system in cooperation with α-DsbB.
Collapse
|
61
|
Rösner HI, Kragelund BB. Structure and dynamic properties of membrane proteins using NMR. Compr Physiol 2013; 2:1491-539. [PMID: 23798308 DOI: 10.1002/cphy.c110036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Integral membrane proteins are one of the most challenging groups of macromolecules despite their apparent conformational simplicity. They manage and drive transport, circulate information, and participate in cellular movements via interactions with other proteins and through intricate conformational changes. Their structural and functional decoding is challenging and has imposed demanding experimental development. Solution nuclear magnetic resonance (NMR) spectroscopy is one of the techniques providing the capacity to make a significant difference in the deciphering of the membrane protein structure-function paradigm. The method has evolved dramatically during the last decade resulting in a plethora of new experiments leading to a significant increase in the scientific repertoire for studying membrane proteins. Besides solving the three-dimensional structures using state-of-the-art approaches, a large variety of developments of well-established techniques are available providing insight into membrane protein flexibility, dynamics, and interactions. Inspired by the speed of development in the application of new strategies, by invention of methods to measure solvent accessibility and describe low-populated states, this review seeks to introduce the vast possibilities solution NMR can offer to the study of membrane protein structure-function analyses with special focus on applicability.
Collapse
Affiliation(s)
- Heike I Rösner
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | |
Collapse
|
62
|
Cross TA, Murray DT, Watts A. Helical membrane protein conformations and their environment. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2013; 42:731-55. [PMID: 23996195 PMCID: PMC3818118 DOI: 10.1007/s00249-013-0925-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/25/2013] [Accepted: 08/12/2013] [Indexed: 02/02/2023]
Abstract
Evidence that membrane proteins respond conformationally and functionally to their environment is growing. Structural models, by necessity, have been characterized in preparations where the protein has been removed from its native environment. Different structural methods have used various membrane mimetics that have recently included lipid bilayers as a more native-like environment. Structural tools applied to lipid bilayer-embedded integral proteins are informing us about important generic characteristics of how membrane proteins respond to the lipid environment as compared with their response to other nonlipid environments. Here, we review the current status of the field, with specific reference to observations of some well-studied α-helical membrane proteins, as a starting point to aid the development of possible generic principles for model refinement.
Collapse
Affiliation(s)
- Timothy A. Cross
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Dylan T. Murray
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Anthony Watts
- Biomembrane structure Unit, Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| |
Collapse
|
63
|
Tumulka F, Roos C, Löhr F, Bock C, Bernhard F, Dötsch V, Abele R. Conformational stabilization of the membrane embedded targeting domain of the lysosomal peptide transporter TAPL for solution NMR. JOURNAL OF BIOMOLECULAR NMR 2013; 57:141-154. [PMID: 24013930 DOI: 10.1007/s10858-013-9774-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 08/21/2013] [Indexed: 06/02/2023]
Abstract
The ATP binding cassette transporter TAPL translocates cytosolic peptides into the lumen of lysosomes driven by the hydrolysis of ATP. Functionally, this transporter can be divided into coreTAPL, comprising the transport function, and an additional N-terminal transmembrane domain called TMD0, which is essential for lysosomal targeting and mediates the interaction with the lysosomal associated membrane proteins LAMP-1 and LAMP-2. To elucidate the structure of this unique domain, we developed protocols for the production of high quantities of cell-free expressed TMD0 by screening different N-terminal expression tags. Independently of the amino acid sequence, high expression was detected for AU-rich sequences in the first seven codons, decreasing the free energy of RNA secondary structure formation at translation initiation. Furthermore, avoiding NGG codons in the region of translation initiation demonstrated a positive effect on expression. For NMR studies, conditions were optimized for high solubilization efficiency, long-term stability, and high quality spectra. A most critical step was the careful exchange of the detergent used for solubilization by the detergent dihexanoylphosphatidylcholine. Several constructs of different size were tested in order to stabilize the fold of TMD0 as well as to reduce the conformation exchange. NMR spectra with sufficient resolution and homogeneity were finally obtained with a TMD0 derivative only modified by a C-terminal His10-tag and containing a codon optimized AT-rich sequence.
Collapse
Affiliation(s)
- Franz Tumulka
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | | | | | | | | | | | | |
Collapse
|
64
|
Araki K, Iemura SI, Kamiya Y, Ron D, Kato K, Natsume T, Nagata K. Ero1-α and PDIs constitute a hierarchical electron transfer network of endoplasmic reticulum oxidoreductases. J Cell Biol 2013; 202:861-74. [PMID: 24043701 PMCID: PMC3776355 DOI: 10.1083/jcb.201303027] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 08/08/2013] [Indexed: 01/20/2023] Open
Abstract
Ero1-α and endoplasmic reticulum (ER) oxidoreductases of the protein disulfide isomerase (PDI) family promote the efficient introduction of disulfide bonds into nascent polypeptides in the ER. However, the hierarchy of electron transfer among these oxidoreductases is poorly understood. In this paper, Ero1-α-associated oxidoreductases were identified by proteomic analysis and further confirmed by surface plasmon resonance. Ero1-α and PDI were found to constitute a regulatory hub, whereby PDI induced conformational flexibility in an Ero1-α shuttle cysteine (Cys99) facilitated intramolecular electron transfer to the active site. In isolation, Ero1-α also oxidized ERp46, ERp57, and P5; however, kinetic measurements and redox equilibrium analysis revealed that PDI preferentially oxidized other oxidoreductases. PDI accepted electrons from the other oxidoreductases via its a' domain, bypassing the a domain, which serves as the electron acceptor from reduced glutathione. These observations provide an integrated picture of the hierarchy of cooperative redox interactions among ER oxidoreductases in mammalian cells.
Collapse
Affiliation(s)
- Kazutaka Araki
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
- Laboratory of Molecular and Cellular Biology, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8047, Japan
| | - Shun-ichiro Iemura
- Innovative drug development translational research section, Fukushima Medical University, Fukushima 960-1295, Japan
| | - Yukiko Kamiya
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagaya City University, Nagoya 467-8603, Japan
| | - David Ron
- Metabolic Research Laboratories; and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke’s Hospital; University of Cambridge, Cambridge CB2 0QQ, England, UK
| | - Koichi Kato
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagaya City University, Nagoya 467-8603, Japan
- The Glycoscience Institute, Ochanomizu University, Tokyo 112-8610, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
| | - Kazuhiro Nagata
- Laboratory of Molecular and Cellular Biology, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8047, Japan
| |
Collapse
|
65
|
De Simone A, Gustavsson M, Montalvao RW, Shi L, Veglia G, Vendruscolo M. Structures of the excited states of phospholamban and shifts in their populations upon phosphorylation. Biochemistry 2013; 52:6684-94. [PMID: 23968132 DOI: 10.1021/bi400517b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phospholamban is an integral membrane protein that controls the calcium balance in cardiac muscle cells. As the function and regulation of this protein require the active involvement of low populated states in equilibrium with the native state, it is of great interest to acquire structural information about them. In this work, we calculate the conformations and populations of the ground state and the three main excited states of phospholamban by incorporating nuclear magnetic resonance residual dipolar couplings as replica-averaged structural restraints in molecular dynamics simulations. We then provide a description of the manner in which phosphorylation at Ser16 modulates the activity of the protein by increasing the sizes of the populations of its excited states. These results demonstrate that the approach that we describe provides a detailed characterization of the different states of phospholamban that determine the function and regulation of this membrane protein. We anticipate that the knowledge of conformational ensembles enable the design of new dominant negative mutants of phospholamban by modulating the relative populations of its conformational substates.
Collapse
Affiliation(s)
- Alfonso De Simone
- Division of Molecular Biosciences, Imperial College London , London SW7 2AZ, U.K
| | | | | | | | | | | |
Collapse
|
66
|
Solid-state NMR spectroscopy structure determination of a lipid-embedded heptahelical membrane protein. Nat Methods 2013; 10:1007-12. [DOI: 10.1038/nmeth.2635] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 07/22/2013] [Indexed: 12/25/2022]
|
67
|
Goldbourt A. Biomolecular magic-angle spinning solid-state NMR: recent methods and applications. Curr Opin Biotechnol 2013; 24:705-15. [DOI: 10.1016/j.copbio.2013.02.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 02/06/2013] [Accepted: 02/08/2013] [Indexed: 12/28/2022]
|
68
|
Ortega-Roldan JL, Ossa F, Schnell JR. Characterization of the human sigma-1 receptor chaperone domain structure and binding immunoglobulin protein (BiP) interactions. J Biol Chem 2013; 288:21448-21457. [PMID: 23760505 PMCID: PMC3774411 DOI: 10.1074/jbc.m113.450379] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 05/31/2013] [Indexed: 01/09/2023] Open
Abstract
The sigma-1 receptor (S1R) is a ligand-regulated membrane protein chaperone involved in the ER stress response. S1R activity is implicated in diseases of the central nervous system including amnesia, schizophrenia, depression, Alzheimer disease, and addiction. S1R has been shown previously to regulate the Hsp70 binding immunoglobulin protein (BiP) and the inositol triphosphate receptor calcium channel through a C-terminal domain. We have developed methods for bacterial expression and reconstitution of the chaperone domain of human S1R into detergent micelles that enable its study by solution NMR spectroscopy. The chaperone domain is found to contain a helix at the N terminus followed by a largely dynamic region and a structured, helical C-terminal region that encompasses a membrane associated domain containing four helices. The helical region at residues ∼198-206 is strongly amphipathic and proposed to anchor the chaperone domain to micelles and membranes. Three of the helices in the C-terminal region closely correspond to previously identified cholesterol and drug recognition sites. In addition, it is shown that the chaperone domain interacts with full-length BiP or the isolated nucleotide binding domain of BiP, but not the substrate binding domain, suggesting that the nucleotide binding domain is sufficient for S1R interactions.
Collapse
Affiliation(s)
| | - Felipe Ossa
- From the Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Jason R Schnell
- From the Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.
| |
Collapse
|
69
|
Structure determination of α-helical membrane proteins by solution-state NMR: emphasis on retinal proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:578-88. [PMID: 23831435 DOI: 10.1016/j.bbabio.2013.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 06/24/2013] [Indexed: 11/27/2022]
Abstract
The biochemical processes of living cells involve a numerous series of reactions that work with exceptional specificity and efficiency. The tight control of this intricate reaction network stems from the architecture of the proteins that drive the chemical reactions and mediate protein-protein interactions. Indeed, the structure of these proteins will determine both their function and interaction partners. A detailed understanding of the proximity and orientation of pivotal functional groups can reveal the molecular mechanistic basis for the activity of a protein. Together with X-ray crystallography and electron microscopy, NMR spectroscopy plays an important role in solving three-dimensional structures of proteins at atomic resolution. In the challenging field of membrane proteins, retinal-binding proteins are often employed as model systems and prototypes to develop biophysical techniques for the study of structural and functional mechanistic aspects. The recent determination of two 3D structures of seven-helical trans-membrane retinal proteins by solution-state NMR spectroscopy highlights the potential of solution NMR techniques in contributing to our understanding of membrane proteins. This review summarizes the multiple strategies available for expression of isotopically labeled membrane proteins. Different environments for mimicking lipid bilayers will be presented, along with the most important NMR methods and labeling schemes used to generate high-quality NMR spectra. The article concludes with an overview of types of conformational restraints used for generation of high-resolution structures of membrane proteins. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
Collapse
|
70
|
Hemmis CW, Schildbach JF. Thioredoxin-like proteins in F and other plasmid systems. Plasmid 2013; 70:168-89. [PMID: 23721857 DOI: 10.1016/j.plasmid.2013.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 05/12/2013] [Accepted: 05/13/2013] [Indexed: 11/29/2022]
Abstract
Bacterial conjugation is the process by which a conjugative plasmid transfers from donor to recipient bacterium. During this process, single-stranded plasmid DNA is actively and specifically transported from the cytoplasm of the donor, through a large membrane-spanning assembly known as the pore complex, and into the cytoplasm of the recipient. In Gram negative bacteria, construction of the pore requires localization of a subset of structural and catalytically active proteins to the bacterial periplasm. Unlike the cytoplasm, the periplasm contains proteins that promote disulfide bond formation within or between cysteine-containing proteins. To ensure proper protein folding and assembly, bacteria employ periplasmic redox systems for thiol oxidation, disulfide bond/sulfenic acid reduction, and disulfide bond isomerization. Recent data suggest that plasmid-based proteins belonging to the disulfide bond formation family play an integral role in the conjugative process by serving as mediators in folding and/or assembly of pore complex proteins. Here we report the identification of 165 thioredoxin-like family members across 89 different plasmid systems. Using phylogenetic analysis, all but nine family members were categorized into thioredoxin-like subfamilies. In addition, we discuss the diversity, conservation, and putative roles of thioredoxin-like proteins in plasmid systems, which include homologs of DsbA, DsbB, DsbC, DsbD, DsbG, and CcmG from Escherichia coli, TlpA from Bradyrhizobium japonicum, Com1 from Coxiella burnetii, as well as TrbB and TraF from plasmid F, and the absolute conservation of a disulfide isomerase in plasmids containing homologs of the transfer proteins TraH, TraN, and TraU.
Collapse
Affiliation(s)
- Casey W Hemmis
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | | |
Collapse
|
71
|
Tang M, Nesbitt AE, Sperling LJ, Berthold DA, Schwieters CD, Gennis RB, Rienstra CM. Structure of the disulfide bond generating membrane protein DsbB in the lipid bilayer. J Mol Biol 2013; 425:1670-82. [PMID: 23416557 PMCID: PMC3670690 DOI: 10.1016/j.jmb.2013.02.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/11/2013] [Accepted: 02/08/2013] [Indexed: 12/16/2022]
Abstract
The integral membrane protein DsbB in Escherichia coli is responsible for oxidizing the periplasmic protein DsbA, which forms disulfide bonds in substrate proteins. We have developed a high-resolution structural model by combining experimental X-ray and solid-state NMR with molecular dynamics (MD) simulations. We embedded the high-resolution DsbB structure, derived from the joint calculation with X-ray reflections and solid-state NMR restraints, into the lipid bilayer and performed MD simulations to provide a mechanistic view of DsbB function in the membrane. Further, we revealed the membrane topology of DsbB by selective proton spin diffusion experiments, which directly probe the correlations of DsbB with water and lipid acyl chains. NMR data also support the model of a flexible periplasmic loop and an interhelical hydrogen bond between Glu26 and Tyr153.
Collapse
Affiliation(s)
- Ming Tang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Anna E. Nesbitt
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Lindsay J. Sperling
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Deborah A. Berthold
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Charles D. Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert B. Gennis
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| |
Collapse
|
72
|
Maslennikov I, Choe S. Advances in NMR structures of integral membrane proteins. Curr Opin Struct Biol 2013; 23:555-62. [PMID: 23721747 DOI: 10.1016/j.sbi.2013.05.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/26/2013] [Accepted: 05/01/2013] [Indexed: 01/26/2023]
Abstract
Integral membrane proteins (IMPs) play a central role in cell communication with the environment. Their structures are essential for our understanding of the molecular mechanisms of signaling and for drug design, yet they remain badly underrepresented in the protein structure databank. Solution NMR is, aside from X-ray crystallography, the major tool in structural biology. Here we review recently reported solution NMR structures of polytopic IMPs and discuss the new approaches, which were developed in the course of these studies to overcome barriers in the field. Advances in cell-free protein expression, combinatorial isotope labeling, resonance assignment, and collection of structural data greatly accelerated IMP structure determination by solution NMR. In addition, novel membrane-mimicking media made possible determination of solution NMR structures of IMPs in a native-like lipid environment.
Collapse
|
73
|
Sperling LJ, Tang M, Berthold DA, Nesbitt AE, Gennis RB, Rienstra CM. Solid-state NMR study of a 41 kDa membrane protein complex DsbA/DsbB. J Phys Chem B 2013; 117:6052-60. [PMID: 23527473 DOI: 10.1021/jp400795d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The disulfide bond generation system in E. coli is led by a periplasmic protein, DsbA, and an integral membrane protein, DsbB. Here we present a solid-state NMR (SSNMR) study of a 41 kDa membrane protein complex DsbA/DsbB precipitated in the presence of native lipids to investigate conformational changes and dynamics that occur upon transient complex formation within the electron transfer pathway. Chemical shift changes in the periplasmic enzyme DsbA in three states (wild type, C33S mutant, and in complex with DsbB) reveal structural and/or dynamic information. We report a 4.9 ppm (15)N chemical shift change observed for Pro31 in the active site between the wild type and C33S mutant of DsbA. Additionally, the Pro31 residue remains elusive in the DsbA/DsbB complex, indicating that the dynamics change drastically in the active site between the three states of DsbA. Using three-dimensional SSNMR spectra, partial (13)C and (15)N de novo chemical shift assignments throughout DsbA in the DsbA/DsbB complex were compared with the shifts from DsbA alone to map site-specific chemical shift perturbations. These results demonstrate that there are further structural and dynamic changes of DsbA in the native membrane observed by SSNMR, beyond the differences between the crystal structures of DsbA and the DsbA/DsbB complex.
Collapse
Affiliation(s)
- Lindsay J Sperling
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | | | | | | | | | | |
Collapse
|
74
|
Oxenoid K, Chou JJ. The present and future of solution NMR in investigating the structure and dynamics of channels and transporters. Curr Opin Struct Biol 2013; 23:547-54. [PMID: 23628285 PMCID: PMC3740178 DOI: 10.1016/j.sbi.2013.03.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Revised: 02/23/2013] [Accepted: 03/22/2013] [Indexed: 01/13/2023]
Abstract
Overview of successful applications of solution NMR in structural characterization of integral membrane proteins. Comprehensive review of the advancements in the use of NMR in investigating the structure and dynamics of ion channels. The latest NMR technology used to investigate membrane transporters. Discussion of the future prospects of NMR in providing more dynamic views of membrane channels and transporters. Discussion of the technical challenges to overcome.
Membrane channels, transporters and receptors constitute essential means for cells to maintain homeostasis and communicate with the surroundings. Investigation of their molecular architecture and the dynamic process of transporting substrate or transmitting signals across the membrane barrier has been one of the frontiers in biomedical research. The past decade has seen numerous successes in the use of X-ray or electron crystallography in determining atomic-resolution structures of membrane proteins, and in some cases, even snapshots of different physiological states of the same protein have been obtained. But there are also many cases in which long-standing efforts to crystallize proteins have yet to succeed. Therefore we have practical needs for developing complementary biophysical tools such as NMR spectroscopy and electron microscopy for tackling these systems. This paper provides a number of key examples where the utility of solution NMR was pivotal in providing structural and functional information on ion channels and transporters.
Collapse
Affiliation(s)
- Kirill Oxenoid
- Jack and Eileen Connors Structural Biology Laboratory, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | | |
Collapse
|
75
|
Madeo J, Zubair A, Marianne F. A review on the role of quinones in renal disorders. SPRINGERPLUS 2013; 2:139. [PMID: 23577302 PMCID: PMC3618882 DOI: 10.1186/2193-1801-2-139] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 03/10/2013] [Indexed: 12/12/2022]
Abstract
Quinones are electron and proton carriers that play a primary role in the aerobic metabolism of virtually every cell in nature. Most physiological quinones are benzoquinones. They undergo highly regulated redox reactions in the mitochondria, Golgi apparatus, plasma membrane and endoplasmic reticulum. Important consequences of these electron transfer reactions are the production of and protection against reactive oxygen species (ROS). Quinones have been extensively studied for both their cytotoxic as well as cellular protective properties and they have been particularly useful in rational drug design. The role of quinones in medicine is explored in this literature review with a particular focus on renal diseases. Due to their high basal metabolism and detoxification role, the kidneys are particularly sensitive to oxidative stress. Regardless of the underlying etiology, ROS plays an important role in both acute kidney injury (AKI) and chronic kidney diseases (CKD). Depending on the oxidative state of the kidney, quinones can be nephrotoxoic or nephro-protective. Many factors play a role in the interaction between quinones and the kidney and the consequences of this are just beginning to be explored.
Collapse
Affiliation(s)
- Jennifer Madeo
- Department of Medicine, Nassau University Medical Center, 2201 Hempstead Turnpike, East Meadow, NY 11554 USA
| | | | | |
Collapse
|
76
|
Reckel S, Hiller S. Perspectives of solution NMR spectroscopy for structural and functional studies of integral membrane proteins. Mol Phys 2013. [DOI: 10.1080/00268976.2013.783639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
77
|
Neale C, Ghanei H, Holyoake J, Bishop RE, Privé GG, Pomès R. Detergent-mediated protein aggregation. Chem Phys Lipids 2013; 169:72-84. [PMID: 23466535 PMCID: PMC5007131 DOI: 10.1016/j.chemphyslip.2013.02.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 02/14/2013] [Accepted: 02/18/2013] [Indexed: 10/27/2022]
Abstract
Because detergents are commonly used to solvate membrane proteins for structural evaluation, much attention has been devoted to assessing the conformational bias imparted by detergent micelles in comparison to the native environment of the lipid bilayer. Here, we conduct six 500-ns simulations of a system with >600,000 atoms to investigate the spontaneous self assembly of dodecylphosphocholine detergent around multiple molecules of the integral membrane protein PagP. This detergent formed equatorial micelles in which acyl chains surround the protein's hydrophobic belt, confirming existing models of the detergent solvation of membrane proteins. In addition, unexpectedly, the extracellular and periplasmic apical surfaces of PagP interacted with the headgroups of detergents in other micelles 85 and 60% of the time, respectively, forming complexes that were stable for hundreds of nanoseconds. In some cases, an apical surface of one molecule of PagP interacted with an equatorial micelle surrounding another molecule of PagP. In other cases, the apical surfaces of two molecules of PagP simultaneously bound a neat detergent micelle. In these ways, detergents mediated the non-specific aggregation of folded PagP. These simulation results are consistent with dynamic light scattering experiments, which show that, at detergent concentrations ≥600 mM, PagP induces the formation of large scattering species that are likely to contain many copies of the PagP protein. Together, these simulation and experimental results point to a potentially generic mechanism of detergent-mediated protein aggregation.
Collapse
Affiliation(s)
- Chris Neale
- Molecular Structure and Function, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Hamed Ghanei
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - John Holyoake
- Molecular Structure and Function, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
- Ontario Cancer Institute and Campbell Family Cancer Research Institute, UHN, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Russell E. Bishop
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Gilbert G. Privé
- Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Ontario Cancer Institute and Campbell Family Cancer Research Institute, UHN, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Régis Pomès
- Molecular Structure and Function, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| |
Collapse
|
78
|
Banigan JR, Gayen A, Traaseth NJ. Combination of ¹⁵N reverse labeling and afterglow spectroscopy for assigning membrane protein spectra by magic-angle-spinning solid-state NMR: application to the multidrug resistance protein EmrE. JOURNAL OF BIOMOLECULAR NMR 2013; 55:391-9. [PMID: 23539118 PMCID: PMC3747971 DOI: 10.1007/s10858-013-9724-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 03/15/2013] [Indexed: 05/20/2023]
Abstract
Magic-angle-spinning (MAS) solid-state NMR spectroscopy has emerged as a viable method to characterize membrane protein structure and dynamics. Nevertheless, the spectral resolution for uniformly labeled samples is often compromised by redundancy of the primary sequence and the presence of helical secondary structure that results in substantial resonance overlap. The ability to simplify the spectrum in order to obtain unambiguous site-specific assignments is a major bottleneck for structure determination. To address this problem, we used a combination of (15)N reverse labeling, afterglow spectroscopic techniques, and frequency-selective dephasing experiments that dramatically improved the ability to resolve peaks in crowded spectra. This was demonstrated using the polytopic membrane protein EmrE, an efflux pump involved in multidrug resistance. Residues preceding the (15)N reverse labeled amino acid were imaged using a 3D NCOCX afterglow experiment and those following were recorded using a frequency-selective dephasing experiment. Our approach reduced the spectral congestion and provided a sensitive way to obtain chemical shift assignments for a membrane protein where no high-resolution structure is available. This MAS methodology is widely applicable to the study of other polytopic membrane proteins in functional lipid bilayer environments.
Collapse
Affiliation(s)
| | | | - Nathaniel J. Traaseth
- Author for correspondence: Nathaniel J. Traaseth 100 Washington Square East New York, NY 10003 Phone: (212) 992-9784
| |
Collapse
|
79
|
Abstract
Finding a way to determine the structures of integral membrane proteins using solution nuclear magnetic resonance (NMR) spectroscopy has proved to be challenging. A residual-dipolar-coupling-based refinement approach can be used to resolve the structure of membrane proteins up to 40 kDa in size, but to do this you need a weak-alignment medium that is detergent-resistant and it has thus far been difficult to obtain such a medium suitable for weak alignment of membrane proteins. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400-nm-long six-helix bundles, each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, toward collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes using counter ions and small DNA-binding molecules. This detergent-resistant liquid-crystal medium offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility and structural programmability. Production of sufficient nanotubes for four or five NMR experiments can be completed in 1 week by a single individual.
Collapse
|
80
|
Barrett PJ, Chen J, Cho MK, Kim JH, Lu Z, Mathew S, Peng D, Song Y, Van Horn WD, Zhuang T, Sönnichsen FD, Sanders CR. The quiet renaissance of protein nuclear magnetic resonance. Biochemistry 2013; 52:1303-20. [PMID: 23368985 DOI: 10.1021/bi4000436] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
From roughly 1985 through the start of the new millennium, the cutting edge of solution protein nuclear magnetic resonance (NMR) spectroscopy was to a significant extent driven by the aspiration to determine structures. Here we survey recent advances in protein NMR that herald a renaissance in which a number of its most important applications reflect the broad problem-solving capability displayed by this method during its classical era during the 1970s and early 1980s.
Collapse
Affiliation(s)
- Paul J Barrett
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232-8725, United States
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
81
|
Arora A. Solution NMR spectroscopy for the determination of structures of membrane proteins in a lipid environment. Methods Mol Biol 2013; 974:389-413. [PMID: 23404285 DOI: 10.1007/978-1-62703-275-9_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Several recent advancements have transformed solution NMR spectroscopy into a competitive, elegant, and eminently viable technique for determining the solution structures of membrane proteins at the level of atomic resolution. Once a good level of cell-based or cell-free expression and purification of a suitably sized membrane protein has been achieved, then NMR offers a combination of several versatile strategies, for example, choice of appropriate deuterated or non-deuterated detergents, temperature, and ionic strength; isotope labelling with (2)H, (13)C, (15)N, with or without protonation of Ile (δ1), Leu, and Val methyl protons; combinatorial labelling of specific amino acids; transverse relaxation-optimized NMR spectroscopy-based, Nonuniform sampling-based, and other NMR experiments; measurement of residual dipolar couplings using stretched polyacrylamide gels or DNA nanotubes; and spin-labelling and paramagnetic relaxation enhancements. Strategic combinations of these advancements together with availability of highly sensitive cryogenically cooled probes equipped high-field NMR spectrometers (up to 1 GHz (1)H frequency) have allowed the perseverant investigator to successfully overcome several of the conventional pitfalls associated with the NMR technique and membrane proteins, viz., low sensitivity, poor sample stability, spectral crowding, and a limited number of NOEs and other constraints for structure calculations. This has resulted in an unprecedented growth in the number of successfully determined NMR structures of large and complex membrane proteins, and this technique now holds great promise for the structure determination of an ever larger body of membrane proteins.
Collapse
Affiliation(s)
- Ashish Arora
- Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, UP, India.
| |
Collapse
|
82
|
Piek S, Kahler CM. A comparison of the endotoxin biosynthesis and protein oxidation pathways in the biogenesis of the outer membrane of Escherichia coli and Neisseria meningitidis. Front Cell Infect Microbiol 2012; 2:162. [PMID: 23267440 PMCID: PMC3526765 DOI: 10.3389/fcimb.2012.00162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 12/01/2012] [Indexed: 01/13/2023] Open
Abstract
The Gram-negative bacterial cell envelope consists of an inner membrane (IM) that surrounds the cytoplasm and an asymmetrical outer-membrane (OM) that forms a protective barrier to the external environment. The OM consists of lipopolysaccahride (LPS), phospholipids, outer membrane proteins (OMPs), and lipoproteins. Oxidative protein folding mediated by periplasmic oxidoreductases is required for the biogenesis of the protein components, mainly constituents of virulence determinants such as pili, flagella, and toxins, of the Gram-negative OM. Recently, periplasmic oxidoreductases have been implicated in LPS biogenesis of Escherichia coli and Neisseria meningitidis. Differences in OM biogenesis, in particular the transport pathways for endotoxin to the OM, the composition and role of the protein oxidation, and isomerization pathways and the regulatory networks that control them have been found in these two Gram-negative species suggesting that although form and function of the OM is conserved, the pathways required for the biosynthesis of the OM and the regulatory circuits that control them have evolved to suit the lifestyle of each organism.
Collapse
Affiliation(s)
- Susannah Piek
- Department of Pathology and Laboratory Medicine, The University of Western Australia Perth, WA, Australia
| | | |
Collapse
|
83
|
Zhou DH, Nieuwkoop AJ, Berthold DA, Comellas G, Sperling LJ, Tang M, Shah GJ, Brea EJ, Lemkau LR, Rienstra CM. Solid-state NMR analysis of membrane proteins and protein aggregates by proton detected spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2012; 54:291-305. [PMID: 22986689 PMCID: PMC3484199 DOI: 10.1007/s10858-012-9672-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Accepted: 09/05/2012] [Indexed: 05/04/2023]
Abstract
Solid-state NMR has emerged as an important tool for structural biology and chemistry, capable of solving atomic-resolution structures for proteins in membrane-bound and aggregated states. Proton detection methods have been recently realized under fast magic-angle spinning conditions, providing large sensitivity enhancements for efficient examination of uniformly labeled proteins. The first and often most challenging step of protein structure determination by NMR is the site-specific resonance assignment. Here we demonstrate resonance assignments based on high-sensitivity proton-detected three-dimensional experiments for samples of different physical states, including a fully-protonated small protein (GB1, 6 kDa), a deuterated microcrystalline protein (DsbA, 21 kDa), a membrane protein (DsbB, 20 kDa) prepared in a lipid environment, and the extended core of a fibrillar protein (α-synuclein, 14 kDa). In our implementation of these experiments, including CONH, CO(CA)NH, CANH, CA(CO)NH, CBCANH, and CBCA(CO)NH, dipolar-based polarization transfer methods have been chosen for optimal efficiency for relatively high protonation levels (full protonation or 100 % amide proton), fast magic-angle spinning conditions (40 kHz) and moderate proton decoupling power levels. Each H-N pair correlates exclusively to either intra- or inter-residue carbons, but not both, to maximize spectral resolution. Experiment time can be reduced by at least a factor of 10 by using proton detection in comparison to carbon detection. These high-sensitivity experiments are especially important for membrane proteins, which often have rather low expression yield. Proton-detection based experiments are expected to play an important role in accelerating protein structure elucidation by solid-state NMR with the improved sensitivity and resolution.
Collapse
Affiliation(s)
- Donghua H. Zhou
- Department of Physics, Oklahoma State University, Stillwater, OK 74074, USA,
| | - Andrew J. Nieuwkoop
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
- Leibniz-Institut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Deborah A. Berthold
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Gemma Comellas
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Lindsay J. Sperling
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ming Tang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Gautam J. Shah
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Elliott J. Brea
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Luisel R. Lemkau
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| |
Collapse
|
84
|
Chung KY, Kim TH, Manglik A, Alvares R, Kobilka BK, Prosser RS. Role of detergents in conformational exchange of a G protein-coupled receptor. J Biol Chem 2012; 287:36305-11. [PMID: 22893704 PMCID: PMC3476297 DOI: 10.1074/jbc.m112.406371] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 08/09/2012] [Indexed: 11/06/2022] Open
Abstract
The G protein-coupled β(2)-adrenoreceptor (β(2)AR) signals through the heterotrimeric G proteins G(s) and G(i) and β-arrestin. As such, the energy landscape of β(2)AR-excited state conformers is expected to be complex. Upon tagging Cys-265 of β(2)AR with a trifluoromethyl probe, (19)F NMR was used to assess conformations and possible equilibria between states. Here, we report key differences in β(2)AR conformational dynamics associated with the detergents used to stabilize the receptor. In dodecyl maltoside (DDM) micelles, the spectra are well represented by a single Lorentzian line that shifts progressively downfield with activation by appropriate ligand. The results are consistent with interconversion between two or more states on a time scale faster than the greatest difference in ligand-dependent chemical shift (i.e. >100 Hz). Given that high detergent off-rates of DDM monomers may facilitate conformational exchange between functional states of β(2)AR, we utilized the recently developed maltose-neopentyl glycol (MNG-3) diacyl detergent. In MNG-3 micelles, spectra indicated at least three distinct states, the relative populations of which depended on ligand, whereas no ligand-dependent shifts were observed, consistent with the slow exchange limit. Thus, detergent has a profound effect on the equilibrium kinetics between functional states. MNG-3, which has a critical micelle concentration in the nanomolar regime, exhibits an off-rate that is 4 orders of magnitude lower than that of DDM. High detergent off-rates are more likely to facilitate conformational exchange between distinct functional states associated with the G protein-coupled receptor.
Collapse
Affiliation(s)
- Ka Young Chung
- From the Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305
- the School of Pharmacy, Sungkyunkwan University, Suwon 440-746, South Korea, and
| | - Tae Hun Kim
- the Department of Chemistry, University of Toronto, Mississauga, Ontario L5L 1C6, Canada
| | - Aashish Manglik
- From the Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305
| | - Rohan Alvares
- the Department of Chemistry, University of Toronto, Mississauga, Ontario L5L 1C6, Canada
| | - Brian K. Kobilka
- From the Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305
| | - R. Scott Prosser
- the Department of Chemistry, University of Toronto, Mississauga, Ontario L5L 1C6, Canada
| |
Collapse
|
85
|
Huang C, Bhaskaran R, Mohanty S. Eukaryotic N-glycosylation occurs via the membrane-anchored C-terminal domain of the Stt3p subunit of oligosaccharyltransferase. J Biol Chem 2012; 287:32450-8. [PMID: 22865878 DOI: 10.1074/jbc.m112.342253] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
N-glycosylation is an essential and highly conserved protein modification. In eukaryotes, it is catalyzed by a multisubunit membrane-associated enzyme, oligosaccharyltransferase (OT). We report the high resolution structure of the C-terminal domain of eukaryotic Stt3p. Unlike its soluble β-sheet-rich prokaryotic counterparts, our model reveals that the C-terminal domain of yeast Stt3p is highly helical and has an overall oblate spheroid-shaped structure containing a membrane-embedded region. Anchoring of this protein segment to the endoplasmic reticulum membrane is likely to bring the membrane-embedded donor substrate closer, thus facilitating glycosylation efficiency. Structural comparison of the region near the WWDYG signature motif revealed that the acceptor substrate-binding site of yeast OT strikingly resembles its prokaryotic counterparts, suggesting a conserved mechanism of N-glycosylation from prokaryotes to eukaryotes. Furthermore, comparison of the NMR and cryo-EM structures of yeast OT revealed that the molecular architecture of this acceptor substrate-recognizing domain has interesting spatial specificity for interactions with other essential OT subunits.
Collapse
Affiliation(s)
- Chengdong Huang
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
| | | | | |
Collapse
|
86
|
Requirements on Paramagnetic Relaxation Enhancement Data for Membrane Protein Structure Determination by NMR. Structure 2012; 20:1019-27. [DOI: 10.1016/j.str.2012.03.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 03/19/2012] [Accepted: 03/26/2012] [Indexed: 02/07/2023]
|
87
|
Facile backbone structure determination of human membrane proteins by NMR spectroscopy. Nat Methods 2012; 9:834-9. [PMID: 22609626 DOI: 10.1038/nmeth.2033] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 04/25/2012] [Indexed: 12/31/2022]
Abstract
Although nearly half of today's major pharmaceutical drugs target human integral membrane proteins (hIMPs), only 30 hIMP structures are currently available in the Protein Data Bank, largely owing to inefficiencies in protein production. Here we describe a strategy for the rapid structure determination of hIMPs, using solution NMR spectroscopy with systematically labeled proteins produced via cell-free expression. We report new backbone structures of six hIMPs, solved in only 18 months from 15 initial targets. Application of our protocols to an additional 135 hIMPs with molecular weight <30 kDa yielded 38 hIMPs suitable for structural characterization by solution NMR spectroscopy without additional optimization.
Collapse
|
88
|
Abstract
SIGNIFICANCE Disulfide bond formation is an essential reaction involved in the folding and maturation of many secreted and membrane proteins. Both prokaryotic and eukaryotic cells utilize various disulfide oxidoreductases and redox-active cofactors to accelerate this oxidative reaction, and higher eukaryotes have diversified and refined these disulfide-introducing cascades over the course of evolution. RECENT ADVANCES In the past decade, atomic resolution structures have been solved for an increasing number of disulfide oxidoreductases, thereby revealing the structural and mechanistic basis of cellular disulfide bond formation systems. CRITICAL ISSUES In this review, we focus on the evolution, structure, and regulatory mechanisms of endoplasmic reticulum oxidoreductin 1 (Ero1) family enzymes, the primary disulfide bond-generating catalysts in the endoplasmic reticulum (ER). Detailed comparison of Ero1 with other oxidoreductases, such as Prx4, QSOX, Erv1/2, and disulfide bond protein B (DsbB), provides important insight into how this ER-resident flavoenzyme acts in a regulated and specific manner to maintain redox and protein homeostasis in eukaryotic cells. FUTURE DIRECTIONS Currently, it is presumed that multiple pathways in addition to that mediated by Ero1 cooperate to achieve oxidative folding of many secretory and membrane proteins in mammalian cells. The important open question is how each oxidative pathway works distinctly or redundantly in response to various cellular conditions.
Collapse
Affiliation(s)
- Kazutaka Araki
- Laboratory of Molecular and Cellular Biology, Kyoto Sangyo University, Kyoto, Japan
| | | |
Collapse
|
89
|
Kroncke BM, Columbus L. Identification and removal of nitroxide spin label contaminant: impact on PRE studies of α-helical membrane proteins in detergent. Protein Sci 2012; 21:589-95. [PMID: 22389096 DOI: 10.1002/pro.2038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 01/23/2012] [Accepted: 01/24/2012] [Indexed: 11/06/2022]
Abstract
NMR paramagnetic relaxation enhancement (PRE) provides long-range distance constraints (~15-25 Å) that can be critical to determining overall protein topology, especially where long-range NOE information is unavailable such as in the case of larger proteins that require deuteration. However, several challenges currently limit the use of NMR PRE for α-helical membrane proteins. One challenge is the nonspecific association of the nitroxide spin label to the protein-detergent complex that can result in spurious PRE derived distance restraints. The effect of the nitroxide spin label contaminant is evaluated and quantified and a robust method for the removal of the contaminant is provided to advance the application of PRE restraints to membrane protein NMR structure determination.
Collapse
Affiliation(s)
- Brett M Kroncke
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | | |
Collapse
|
90
|
Tie JK, Jin DY, Stafford DW. Mycobacterium tuberculosis vitamin K epoxide reductase homologue supports vitamin K-dependent carboxylation in mammalian cells. Antioxid Redox Signal 2012; 16:329-38. [PMID: 21939388 PMCID: PMC3246416 DOI: 10.1089/ars.2011.4043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AIMS Vitamin K epoxide reductase complex, subunit 1 (VKORC1) is a critical participant in the production of active forms of reduced vitamin K and is required for modification of vitamin K-dependent proteins. Homologues of VKORC1 (VKORH) exist throughout evolution, but in bacteria they appear to function in oxidative protein folding as well as quinone reduction. In the current study we explore two questions: Do VKORHs function in the mammalian vitamin K cycle? Is the pair of loop cysteines-C43 and C51 in human VKORC1-conserved in all VKORC1s, essential for the activity of vitamin K epoxide reduction? RESULTS We used our recently developed cell-based assay to compare the function of VKORHs to that of human VKORC1 in mammalian cells. We identified for the first time a VKORH (from Mycobacterium tuberculosis [Mt-VKORH]) that can function in the mammalian vitamin K cycle with vitamin K epoxide or vitamin K as substrate. Consistent with our previous in vitro results, the loop cysteines of human VKORC1 are not essential for its activity in vivo. Moreover, the corresponding loop cysteines of Mt-VKORH (C57 and C65), which are essential for its activity in disulfide bond formation during protein folding in Escherichia coli, are not required in the mammalian vitamin K cycle. INNOVATION AND CONCLUSIONS Our results indicate that VKORC1 in eukaryotes and Mt-VKORH in bacteria, that is, in their respective native environments, employ apparently different mechanisms for electron transfer. However, when Mt-VKORH is in the mammalian cell system, it employs a mechanism similar to that of VKORC1.
Collapse
Affiliation(s)
- Jian-Ke Tie
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | | |
Collapse
|
91
|
Scott JL, Musselman CA, Adu-Gyamfi E, Kutateladze TG, Stahelin RV. Emerging methodologies to investigate lipid-protein interactions. Integr Biol (Camb) 2012; 4:247-58. [PMID: 22327461 DOI: 10.1039/c2ib00143h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cellular membranes are composed of hundreds of different lipids, ion channels, receptors and scaffolding complexes that act as signalling and trafficking platforms for processes fundamental to life. Cellular signalling and membrane trafficking are often regulated by peripheral proteins, which reversibly interact with lipid molecules in highly regulated spatial and temporal fashions. In most cases, one or more modular lipid-binding domain(s) mediate recruitment of peripheral proteins to specific cellular membranes. These domains, of which more than 10 have been identified since 1989, harbour structurally selective lipid-binding sites. Traditional in vitro and in vivo studies have elucidated how these domains coordinate their cognate lipids and thus how the parent proteins associate with membranes. Cellular activities of peripheral proteins and subsequent physiological processes depend upon lipid binding affinities and selectivity. Thus, the development of novel sensitive and quantitative tools is essential in furthering our understanding of the function and regulation of these proteins. As this field expands into new areas such as computational biology, cellular lipid mapping, single molecule imaging, and lipidomics, there is an urgent need to integrate technologies to detail the molecular architecture and mechanisms of lipid signalling. This review surveys emerging cellular and in vitro approaches for studying protein-lipid interactions and provides perspective on how integration of methodologies directs the future development of the field.
Collapse
Affiliation(s)
- Jordan L Scott
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | | | | | | |
Collapse
|
92
|
Verardi R, Traaseth NJ, Masterson LR, Vostrikov VV, Veglia G. Isotope labeling for solution and solid-state NMR spectroscopy of membrane proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 992:35-62. [PMID: 23076578 PMCID: PMC3555569 DOI: 10.1007/978-94-007-4954-2_3] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this chapter, we summarize the isotopic labeling strategies used to obtain high-quality solution and solid-state NMR spectra of biological samples, with emphasis on integral membrane proteins (IMPs). While solution NMR is used to study IMPs under fast tumbling conditions, such as in the presence of detergent micelles or isotropic bicelles, solid-state NMR is used to study the structure and orientation of IMPs in lipid vesicles and bilayers. In spite of the tremendous progress in biomolecular NMR spectroscopy, the homogeneity and overall quality of the sample is still a substantial obstacle to overcome. Isotopic labeling is a major avenue to simplify overlapped spectra by either diluting the NMR active nuclei or allowing the resonances to be separated in multiple dimensions. In the following we will discuss isotopic labeling approaches that have been successfully used in the study of IMPs by solution and solid-state NMR spectroscopy.
Collapse
Affiliation(s)
- Raffaello Verardi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
| | | | | | | | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455
| |
Collapse
|
93
|
Gautier A, Nietlispach D. Solution NMR studies of integral polytopic α-helical membrane proteins: the structure determination of the seven-helix transmembrane receptor sensory rhodopsin II, pSRII. Methods Mol Biol 2012; 914:25-45. [PMID: 22976021 DOI: 10.1007/978-1-62703-023-6_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
About 30% of the proteins encoded in the genome are expressed as membrane proteins but these represent <1% of all the structures solved today. In view of the physiological and pharmaceutical significance of membrane proteins it is clear that a better and more comprehensive understanding of their three-dimensional (3D) structures at atomic resolution is required. α-Helical integral membrane proteins are generally more difficult to work with than β-barrel-type proteins and this has particularly been true for the polytopic members such as the large family of seven-helical proteins. In this chapter we describe the practical aspects of the solution-state NMR spectroscopy structure determination of the seven-helical transmembrane (7-TM) protein receptor sensory rhodopsin pSRII from the haloalkaliphilic archaeon Natronomonas pharaonis reconstituted in detergent micelles. This is the first time that a three-dimensional structure of a 7-TM protein has been determined by NMR.
Collapse
Affiliation(s)
- Antoine Gautier
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | |
Collapse
|
94
|
Abstract
Prokaryotic diacylglycerol kinase (DAGK) and undecaprenol kinase (UDPK) are the lone members of a family of multispan membrane enzymes that are very small, lack relationships to any other family of proteins-including water soluble kinases-and exhibit an unusual structure and active site architecture. Escherichia coli DAGK plays an important role in recycling diacylglycerol produced as a by-product of biosynthesis of molecules located in the periplasmic space. UDPK seems to play an analogous role in gram-positive bacteria, where its importance is evident because UDPK is essential for biofilm formation by the oral pathogen Streptococcus mutans. DAGK has also long served as a model system for studies of membrane protein biocatalysis, folding, stability, and structure. This review explores our current understanding of the microbial physiology, enzymology, structural biology, and folding of the prokaryotic DAGK family, which is based on over 40 years of studies.
Collapse
Affiliation(s)
- Wade D Van Horn
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | | |
Collapse
|
95
|
Yu TY, Raschle T, Hiller S, Wagner G. Solution NMR spectroscopic characterization of human VDAC-2 in detergent micelles and lipid bilayer nanodiscs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1562-9. [PMID: 22119777 DOI: 10.1016/j.bbamem.2011.11.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 10/27/2011] [Accepted: 11/07/2011] [Indexed: 10/24/2022]
Abstract
Three isoforms of the human voltage-dependent anion channel (VDAC), located in the outer mitochondrial membrane, are crucial regulators of mitochondrial function. Numerous studies have been carried out to elucidate biochemical properties, as well as the three-dimensional structure of VDAC-1. However, functional and structural studies of VDAC-2 and VDAC-3 at atomic resolution are still scarce. VDAC-2 is highly similar to VDAC-1 in amino acid sequence, but has substantially different biochemical functions and expression profiles. Here, we report the reconstitution of functional VDAC-2 in lauryldimethylamine-oxide (LDAO) detergent micelles and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayer nanodiscs. We find that VDAC-2 is properly folded in both membrane-mimicking systems and that structural and functional characterization by solution NMR spectroscopy is feasible. This article is part of a Special Issue entitled: VDAC structure, function, and regulation of mitochondrial metabolism.
Collapse
Affiliation(s)
- Tsyr-Yan Yu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | |
Collapse
|
96
|
Tang M, Sperling LJ, Berthold DA, Schwieters CD, Nesbitt AE, Nieuwkoop AJ, Gennis RB, Rienstra CM. High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. JOURNAL OF BIOMOLECULAR NMR 2011; 51:227-33. [PMID: 21938394 PMCID: PMC3204959 DOI: 10.1007/s10858-011-9565-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 08/29/2011] [Indexed: 05/12/2023]
Abstract
X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 Å crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yielded a significantly improved backbone precision of 0.92 Å in the transmembrane region, a 58% enhancement from using X-ray reflections alone. Furthermore, addition of solid-state NMR restraints greatly improved the overall quality of the structure by promoting 22% of DsbB transmembrane residues into the most favored regions of Ramachandran space in comparison to the crystal structure. This method is widely applicable to any protein system where X-ray data are available, and is particularly useful for the study of weakly diffracting crystals.
Collapse
Affiliation(s)
- Ming Tang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Lindsay J. Sperling
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Deborah A. Berthold
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Charles D. Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna E. Nesbitt
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Andrew J. Nieuwkoop
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Robert B. Gennis
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
- CORRESPONDING AUTHOR:
| |
Collapse
|
97
|
Feng WK, Wang L, Lu Y, Wang XY. A protein oxidase catalysing disulfide bond formation is localized to the chloroplast thylakoids. FEBS J 2011; 278:3419-30. [PMID: 21781282 DOI: 10.1111/j.1742-4658.2011.08265.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In chloroplasts, thiol/disulfide-redox-regulated proteins have been linked to numerous metabolic pathways. However, the biochemical system for disulfide bond formation in chloroplasts remains undetermined. In the present study, we characterized an oxidoreductase, AtVKOR-DsbA, encoded by the gene At4g35760 as a potential disulfide bond oxidant in Arabidopsis. The gene product contains two distinct domains: an integral membrane domain homologous to the catalytic subunit of mammalian vitamin K epoxide reductase (VKOR) and a soluble DsbA-like domain. Transient expression of green fluorescent protein fusion in Arabidopsis protoplasts indicated that AtVKOR-DsbA is located in the chloroplast. The first 45 amino acids from the N-terminus were found to act as a transit peptide targeting the protein to the chloroplast. An immunoblot assay of chloroplast fractions revealed that AtVKOR-DsbA was localized in the thylakoid. A motility complementation assay showed that the full-length of AtVKOR-DsbA, if lacking its transit peptide, could catalyze the formation of disulfide bonds. Among the 10 cysteine residues present in the mature protein, eight cysteines (four in the AtVKOR domain and four in the AtDsbA domain) were found to be essential for promoting disulfide bond formation. The topological arrangement of AtVKOR-DsbA was assayed using alkaline phosphatase sandwich fusions. From these results, we developed a possible topology model of AtVKOR-DsbA in chloroplasts. We propose that the integral membrane domain of AtVKOR-DsbA contains four transmembrane helices, and that both termini and the cysteines involved in catalyzing the formation of disulfide bonds face the oxidative thylakoid lumen. These studies may help to resolve some of the issues surrounding the structure and function of AtVKOR-DsbA in Arabidopsis chloroplasts.
Collapse
Affiliation(s)
- Wei-Ke Feng
- College of Life Science, Shandong Agricultural University, Shandong Taian, China
| | | | | | | |
Collapse
|
98
|
Optimal mutation sites for PRE data collection and membrane protein structure prediction. Structure 2011; 19:484-95. [PMID: 21481772 DOI: 10.1016/j.str.2011.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Revised: 02/11/2011] [Accepted: 02/11/2011] [Indexed: 01/16/2023]
Abstract
Nuclear magnetic resonance paramagnetic relaxation enhancement (PRE) measures long-range distances to isotopically labeled residues, providing useful constraints for protein structure prediction. The method usually requires labor-intensive conjugation of nitroxide labels to multiple locations on the protein, one at a time. Here a computational procedure, based on protein sequence and simple secondary structure models, is presented to facilitate optimal placement of a minimum number of labels needed to determine the correct topology of a helical transmembrane protein. Tests on DsbB (four helices) using just one label lead to correct topology predictions in four of five cases, with the predicted structures <6 Å to the native structure. Benchmark results using simulated PRE data show that we can generally predict the correct topology for five and six to seven helices using two and three labels, respectively, with an average success rate of 76% and structures of similar precision. The results show promise in facilitating experimentally constrained structure prediction of membrane proteins.
Collapse
|
99
|
Ganguly S, Weiner BE, Meiler J. Membrane protein structure determination using paramagnetic tags. Structure 2011; 19:441-3. [PMID: 21481766 DOI: 10.1016/j.str.2011.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The combination of paramagnetic tagging strategies with NMR or EPR spectroscopic techniques can revolutionize de novo structure determination of helical membrane proteins. Leveraging the full potential of this approach requires optimal labeling strategies and prediction of membrane protein topology from sparse and low-resolution distance restraints, as addressed by Chen et al. (2011).
Collapse
Affiliation(s)
- Soumya Ganguly
- Departments of Chemistry, Pharmacology, and Biomedical Informatics, Center for Structural Biology, Institute for Chemical Biology, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
| | | | | |
Collapse
|
100
|
Affiliation(s)
- Simon G Patching
- Astbury Centre for Structural Molecular Biology and Institute of Membrane and Systems Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
| |
Collapse
|