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Lu Y, Zhang H, Niedzwiedzki DM, Jiang J, Blankenship RE, Gross ML. Fast Photochemical Oxidation of Proteins Maps the Topology of Intrinsic Membrane Proteins: Light-Harvesting Complex 2 in a Nanodisc. Anal Chem 2016; 88:8827-34. [PMID: 27500903 PMCID: PMC5201186 DOI: 10.1021/acs.analchem.6b01945] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although membrane proteins are crucial participants in photosynthesis and other biological processes, many lack high-resolution structures. Prior to achieving a high-resolution structure, we are investigating whether MS-based footprinting can provide coarse-grained protein structure by following structural changes that occur upon ligand binding, pH change, and membrane binding. Our platform probes topology and conformation of membrane proteins by combining MS-based footprinting, specifically fast photochemical oxidation of proteins (FPOP), and lipid Nanodiscs, which are more similar to the native membrane environment than are the widely used detergent micelles. We describe here results that show a protein's outer membrane regions are more heavily footprinted by OH radicals whereas the regions spanning the lipid bilayer remain inert to the labeling. Nanodiscs generally exhibit more protection of membrane proteins compared to detergent micelles and less shielding to those protein residues that exist outside the membrane. The combination of immobilizing the protein in Nanodiscs and footprinting with FPOP is a feasible approach to map extra-membrane protein surfaces, even at the amino-acid level, and to illuminate intrinsic membrane protein topology.
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Affiliation(s)
- Yue Lu
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Dariusz M. Niedzwiedzki
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jing Jiang
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Robert E. Blankenship
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Louis JM, Baber JL, Ghirlando R, Aniana A, Bax A, Roche J. Insights into the Conformation of the Membrane Proximal Regions Critical to the Trimerization of the HIV-1 gp41 Ectodomain Bound to Dodecyl Phosphocholine Micelles. PLoS One 2016; 11:e0160597. [PMID: 27513582 PMCID: PMC4981318 DOI: 10.1371/journal.pone.0160597] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/21/2016] [Indexed: 01/06/2023] Open
Abstract
The transitioning of the ectodomain of gp41 from a pre-hairpin to a six-helix bundle conformation is a crucial aspect of virus-cell fusion. To gain insight into the intermediary steps of the fusion process we have studied the pH and dodecyl phosphocholine (DPC) micelle dependent trimer association of gp41 by systematic deletion analysis of an optimized construct termed 17-172 (residues 528 to 683 of Env) that spans the fusion peptide proximal region (FPPR) to the membrane proximal external region (MPER) of gp41, by sedimentation velocity and double electron-electron resonance (DEER) EPR spectroscopy. Trimerization at pH 7 requires the presence of both the FPPR and MPER regions. However, at pH 4, the protein completely dissociates to monomers. DEER measurements reveal a partial fraying of the C-terminal MPER residues in the 17-172 trimer while the other regions, including the FPPR, remain compact. In accordance, truncating nine C-terminal MPER residues (675-683) in the 17-172 construct does not shift the trimer-monomer equilibrium significantly. Thus, in the context of the gp41 ectodomain spanning residues 17-172, trimerization is clearly dependent on FPPR and MPER regions even when the terminal residues of MPER unravel. The antibody Z13e1, which spans both the 2F5 and 4E10 epitopes in MPER, binds to 17-172 with a Kd of 1 ± 0.12 μM. Accordingly, individual antibodies 2F5 and 4E10 also recognize the 17-172 trimer/DPC complex. We propose that binding of the C-terminal residues of MPER to the surface of the DPC micelles models a correct positioning of the trimeric transmembrane domain anchored in the viral membrane.
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Affiliation(s)
- John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (JL)); (JR)
| | - James L. Baber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
- * E-mail: (JL)); (JR)
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53
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Artificial membranes for membrane protein purification, functionality and structure studies. Biochem Soc Trans 2016; 44:877-82. [DOI: 10.1042/bst20160054] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Indexed: 11/17/2022]
Abstract
Membrane proteins represent one of the most important targets for pharmaceutical companies. Unfortunately, technical limitations have long been a major hindrance in our understanding of the function and structure of such proteins. Recent years have seen the refinement of classical approaches and the emergence of new technologies that have resulted in a significant step forward in the field of membrane protein research. This review summarizes some of the current techniques used for studying membrane proteins, with overall advantages and drawbacks for each method.
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54
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Nanoparticle suspensions enclosed in methylcellulose: a new approach for quantifying nanoparticles in transmission electron microscopy. Sci Rep 2016; 6:25275. [PMID: 27141843 PMCID: PMC4855187 DOI: 10.1038/srep25275] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/14/2016] [Indexed: 01/13/2023] Open
Abstract
Nanoparticles are of increasing importance in biomedicine but quantification is problematic because current methods depend on indirect measurements at low resolution. Here we describe a new high-resolution method for measuring and quantifying nanoparticles in suspension. It involves premixing nanoparticles in a hydrophilic support medium (methylcellulose) before introducing heavy metal stains for visualization in small air-dried droplets by transmission electron microscopy (TEM). The use of methylcellulose avoids artifacts of conventional negative stain-TEM by (1) restricting interactions between the nanoparticles, (2) inhibiting binding to the specimen support films and (3) reducing compression after drying. Methylcellulose embedment provides effective electron imaging of liposomes, nanodiscs and viruses as well as comprehensive visualization of nanoparticle populations in droplets of known size. These qualities facilitate unbiased sampling, rapid size measurement and estimation of nanoparticle numbers by means of ratio counting using a colloidal gold calibrant. Specimen preparation and quantification take minutes and require a few microliters of sample using only basic laboratory equipment and a standard TEM.
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Hiruma-Shimizu K, Shimizu H, Thompson GS, Kalverda AP, Patching SG. Deuterated detergents for structural and functional studies of membrane proteins: Properties, chemical synthesis and applications. Mol Membr Biol 2016; 32:139-55. [DOI: 10.3109/09687688.2015.1125536] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
| | - Hiroki Shimizu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido, Japan,
| | - Gary S. Thompson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK,
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK, and
| | - Arnout P. Kalverda
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK,
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK, and
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Schmid J, Heider D, Wendel NJ, Sperl N, Sieber V. Bacterial Glycosyltransferases: Challenges and Opportunities of a Highly Diverse Enzyme Class Toward Tailoring Natural Products. Front Microbiol 2016; 7:182. [PMID: 26925049 PMCID: PMC4757703 DOI: 10.3389/fmicb.2016.00182] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/02/2016] [Indexed: 11/13/2022] Open
Abstract
The enzyme subclass of glycosyltransferases (GTs; EC 2.4) currently comprises 97 families as specified by CAZy classification. One of their important roles is in the biosynthesis of disaccharides, oligosaccharides, and polysaccharides by catalyzing the transfer of sugar moieties from activated donor molecules to other sugar molecules. In addition GTs also catalyze the transfer of sugar moieties onto aglycons, which is of great relevance for the synthesis of many high value natural products. Bacterial GTs show a higher sequence similarity in comparison to mammalian ones. Even when most GTs are poorly explored, state of the art technologies, such as protein engineering, domain swapping or computational analysis strongly enhance our understanding and utilization of these very promising classes of proteins. This perspective article will focus on bacterial GTs, especially on classification, screening and engineering strategies to alter substrate specificity. The future development in these fields as well as obstacles and challenges will be highlighted and discussed.
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Affiliation(s)
- Jochen Schmid
- Chemistry of Biogenic Resources, Technische Universität München Straubing, Germany
| | - Dominik Heider
- Department of Bioinformatics, Straubing Center of Science, University of Applied Sciences Weihenstephan-Triesdorf Straubing, Germany
| | - Norma J Wendel
- Department of Bioinformatics, Straubing Center of Science, University of Applied Sciences Weihenstephan-Triesdorf Straubing, Germany
| | - Nadine Sperl
- Chemistry of Biogenic Resources, Technische Universität München Straubing, Germany
| | - Volker Sieber
- Chemistry of Biogenic Resources, Technische Universität München Straubing, Germany
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Ghirlando R, Mutskova R, Schwartz C. Enrichment and characterization of ferritin for nanomaterial applications. NANOTECHNOLOGY 2016; 27:045102. [PMID: 26656976 PMCID: PMC6284806 DOI: 10.1088/0957-4484/27/4/045102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Ferritin is a ubiquitous iron storage protein utilized as a nanomaterial for labeling biomolecules and nanoparticle construction. Commercially available preparations of horse spleen ferritin, widely used as a starting material, contain a distribution of ferritins with different iron loads. We describe a detailed approach to the enrichment of differentially loaded ferritin molecules by common biophysical techniques such as size exclusion chromatography and preparative ultracentrifugation, and characterize these preparations by dynamic light scattering, and analytical ultracentrifugation. We demonstrate a combination of methods to standardize an approach for determining the chemical load of nearly any particle, including nanoparticles and metal colloids. Purification and characterization of iron content in monodisperse ferritin species is particularly critical for several applications in nanomaterial science.
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Affiliation(s)
- Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda MD 20892
| | - Radina Mutskova
- Honors College, Integrated Life Sciences, University of Maryland, College Park MD 20742
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Characterization of the direct interaction between KcsA-Kv1.3 and its inhibitors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1974-80. [DOI: 10.1016/j.bbamem.2015.06.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 05/28/2015] [Accepted: 06/08/2015] [Indexed: 11/19/2022]
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Inagaki S, Ghirlando R, Vishnivetskiy SA, Homan KT, White JF, Tesmer JJG, Gurevich VV, Grisshammer R. G Protein-Coupled Receptor Kinase 2 (GRK2) and 5 (GRK5) Exhibit Selective Phosphorylation of the Neurotensin Receptor in Vitro. Biochemistry 2015; 54:4320-9. [PMID: 26120872 PMCID: PMC4512254 DOI: 10.1021/acs.biochem.5b00285] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
G protein-coupled
receptor kinases (GRKs) play an important role
in the desensitization of G protein-mediated signaling of G protein-coupled
receptors (GPCRs). The level of interest in mapping their phosphorylation
sites has increased because recent studies suggest that the differential
pattern of receptor phosphorylation has distinct biological consequences. In vitro phosphorylation experiments using well-controlled
systems are useful for deciphering the complexity of these physiological
reactions and understanding the targeted event. Here, we report on
the phosphorylation of the class A GPCR neurotensin receptor 1 (NTSR1)
by GRKs under defined experimental conditions afforded by nanodisc
technology. Phosphorylation of NTSR1 by GRK2 was agonist-dependent,
whereas phosphorylation by GRK5 occurred in an activation-independent
manner. In addition, the negatively charged lipids in the immediate
vicinity of NTSR1 directly affect phosphorylation by GRKs. Identification
of phosphorylation sites in agonist-activated NTSR1 revealed that
GRK2 and GRK5 target different residues located on the intracellular
receptor elements. GRK2 phosphorylates only the C-terminal Ser residues,
whereas GRK5 phosphorylates Ser and Thr residues located in intracellular
loop 3 and the C-terminus. Interestingly, phosphorylation assays using
a series of NTSR1 mutants show that GRK2 does not require acidic residues
upstream of the phospho-acceptors for site-specific phosphorylation,
in contrast to the β2-adrenergic and μ-opioid
receptors. Differential phosphorylation of GPCRs by GRKs is thought
to encode a particular signaling outcome, and our in vitro study revealed NTSR1 differential phosphorylation by GRK2 and GRK5.
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Affiliation(s)
- Sayaka Inagaki
- †Membrane Protein Structure Function Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland 20852, United States
| | - Rodolfo Ghirlando
- ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, United States
| | - Sergey A Vishnivetskiy
- §Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Kristoff T Homan
- ∥Departments of Pharmacology and Biological Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jim F White
- †Membrane Protein Structure Function Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland 20852, United States
| | - John J G Tesmer
- ∥Departments of Pharmacology and Biological Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vsevolod V Gurevich
- §Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Reinhard Grisshammer
- †Membrane Protein Structure Function Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland 20852, United States
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61
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Ding Y, Fujimoto LM, Yao Y, Marassi FM. Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation. JOURNAL OF BIOMOLECULAR NMR 2015; 61:275-86. [PMID: 25578899 PMCID: PMC4398618 DOI: 10.1007/s10858-014-9893-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/20/2014] [Indexed: 05/22/2023]
Abstract
Solid-state NMR studies of sedimented soluble proteins has been developed recently as an attractive approach for overcoming the size limitations of solution NMR spectroscopy while bypassing the need for sample crystallization or precipitation (Bertini et al. Proc Natl Acad Sci USA 108(26):10396-10399, 2011). Inspired by the potential benefits of this method, we have investigated the ability to sediment lipid bilayer nanodiscs reconstituted with a membrane protein. In this study, we show that nanodiscs containing the outer membrane protein Ail from Yersinia pestis can be sedimented for solid-state NMR structural studies, without the need for precipitation or lyophilization. Optimized preparations of Ail in phospholipid nanodiscs support both the structure and the fibronectin binding activity of the protein. The same sample can be used for solution NMR, solid-state NMR and activity assays, facilitating structure-activity correlation experiments across a wide range of timescales.
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Affiliation(s)
- Yi Ding
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla CA 92037, USA
| | - L. Miya Fujimoto
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla CA 92037, USA
| | - Yong Yao
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla CA 92037, USA
| | - Francesca M. Marassi
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla CA 92037, USA
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla CA 92037, USA. [Tel: 858-795-5282; Mail: ]
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62
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Real-time monitoring of binding events on a thermostabilized human A2A receptor embedded in a lipid bilayer by surface plasmon resonance. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1224-33. [PMID: 25725488 DOI: 10.1016/j.bbamem.2015.02.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/19/2015] [Accepted: 02/13/2015] [Indexed: 12/12/2022]
Abstract
Membrane proteins (MPs) are prevalent drug discovery targets involved in many cell processes. Despite their high potential as drug targets, the study of MPs has been hindered by limitations in expression, purification and stabilization in order to acquire thermodynamic and kinetic parameters of small molecules binding. These bottlenecks are grounded on the mandatory use of detergents to isolate and extract MPs from the cell plasma membrane and the coexistence of multiple conformations, which reflects biochemical versatility and intrinsic instability of MPs. In this work ,we set out to define a new strategy to enable surface plasmon resonance (SPR) measurements on a thermostabilized and truncated version of the human adenosine (A2A) G-protein-coupled receptor (GPCR) inserted in a lipid bilayer nanodisc in a label- and detergent-free manner by using a combination of affinity tags and GFP-based fluorescence techniques. We were able to detect and characterize small molecules binding kinetics on a GPCR fully embedded in a lipid environment. By providing a comparison between different binding assays in membranes, nanodiscs and detergent micelles, we show that nanodiscs can be used for small molecule binding studies by SPR to enhance the MP stability and to trigger a more native-like behaviour when compared to kinetics on A2A receptors isolated in detergent. This work provides thus a new methodology in drug discovery to characterize the binding kinetics of small molecule ligands for MPs targets in a lipid environment.
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64
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Zhao H, Schuck P. Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:3-14. [PMID: 25615855 PMCID: PMC4304681 DOI: 10.1107/s1399004714010372] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/07/2014] [Indexed: 12/29/2022]
Abstract
Reversible macromolecular interactions are ubiquitous in signal transduction pathways, often forming dynamic multi-protein complexes with three or more components. Multivalent binding and cooperativity in these complexes are often key motifs of their biological mechanisms. Traditional solution biophysical techniques for characterizing the binding and cooperativity are very limited in the number of states that can be resolved. A global multi-method analysis (GMMA) approach has recently been introduced that can leverage the strengths and the different observables of different techniques to improve the accuracy of the resulting binding parameters and to facilitate the study of multi-component systems and multi-site interactions. Here, GMMA is described in the software SEDPHAT for the analysis of data from isothermal titration calorimetry, surface plasmon resonance or other biosensing, analytical ultracentrifugation, fluorescence anisotropy and various other spectroscopic and thermodynamic techniques. The basic principles of these techniques are reviewed and recent advances in view of their particular strengths in the context of GMMA are described. Furthermore, a new feature in SEDPHAT is introduced for the simulation of multi-method data. In combination with specific statistical tools for GMMA in SEDPHAT, simulations can be a valuable step in the experimental design.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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66
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Das BB, Park SH, Opella SJ. Membrane protein structure from rotational diffusion. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1848:229-45. [PMID: 24747039 PMCID: PMC4201901 DOI: 10.1016/j.bbamem.2014.04.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 04/02/2014] [Indexed: 02/02/2023]
Abstract
The motional averaging of powder pattern line shapes is one of the most fundamental aspects of sold-state NMR. Since membrane proteins in liquid crystalline phospholipid bilayers undergo fast rotational diffusion, all of the signals reflect the angles of the principal axes of their dipole-dipole and chemical shift tensors with respect to the axis defined by the bilayer normal. The frequency span and sign of the axially symmetric powder patterns that result from motional averaging about a common axis provide sufficient structural restraints for the calculation of the three-dimensional structure of a membrane protein in a phospholipid bilayer environment. The method is referred to as rotationally aligned (RA) solid-state NMR and demonstrated with results on full-length, unmodified membrane proteins with one, two, and seven trans-membrane helices. RA solid-state NMR is complementary to other solid-state NMR methods, in particular oriented sample (OS) solid-state NMR of stationary, aligned samples. Structural distortions of membrane proteins from the truncations of terminal residues and other sequence modifications, and the use of detergent micelles instead of phospholipid bilayers have also been demonstrated. Thus, it is highly advantageous to determine the structures of unmodified membrane proteins in liquid crystalline phospholipid bilayers under physiological conditions. RA solid-state NMR provides a general method for obtaining accurate and precise structures of membrane proteins under near-native conditions.
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Affiliation(s)
- Bibhuti B Das
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307 USA
| | - Sang Ho Park
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307 USA
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307 USA.
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Influence of the lipid membrane environment on structure and activity of the outer membrane protein Ail from Yersinia pestis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:712-20. [PMID: 25433311 DOI: 10.1016/j.bbamem.2014.11.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 10/24/2014] [Accepted: 11/19/2014] [Indexed: 11/20/2022]
Abstract
The surrounding environment has significant consequences for the structural and functional properties of membrane proteins. While native structure and function can be reconstituted in lipid bilayer membranes, the detergents used for protein solubilization are not always compatible with biological activity and, hence, not always appropriate for direct detection of ligand binding by NMR spectroscopy. Here we describe how the sample environment affects the activity of the outer membrane protein Ail (attachment invasion locus) from Yersinia pestis. Although Ail adopts the correct β-barrel fold in micelles, the high detergent concentrations required for NMR structural studies are not compatible with the ligand binding functionality of the protein. We also describe preparations of Ail embedded in phospholipid bilayer nanodiscs, optimized for NMR studies and ligand binding activity assays. Ail in nanodiscs is capable of binding its human ligand fibronectin and also yields high quality NMR spectra that reflect the proper fold. Binding activity assays, developed to be performed directly with the NMR samples, show that ligand binding involves the extracellular loops of Ail. The data show that even when detergent micelles support the protein fold, detergents can interfere with activity in subtle ways.
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68
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Postis V, Rawson S, Mitchell JK, Lee SC, Parslow RA, Dafforn TR, Baldwin SA, Muench SP. The use of SMALPs as a novel membrane protein scaffold for structure study by negative stain electron microscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:496-501. [PMID: 25450810 PMCID: PMC4331651 DOI: 10.1016/j.bbamem.2014.10.018] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 10/06/2014] [Accepted: 10/15/2014] [Indexed: 12/17/2022]
Abstract
Despite the great progress recently made in resolving their structures, investigation of the structural biology of membrane proteins still presents major challenges. Even with new technical advances such as lipidic cubic phase crystallisation, obtaining well-ordered crystals remains a significant hurdle in membrane protein X-ray crystallographic studies. As an alternative, electron microscopy has been shown to be capable of resolving > 3.5 Å resolution detail in membrane proteins of modest (~ 300 kDa) size, without the need for crystals. However, the conventional use of detergents for either approach presents several issues, including the possible effects on structure of removing the proteins from their natural membrane environment. As an alternative, it has recently been demonstrated that membrane proteins can be effectively isolated, in the absence of detergents, using a styrene maleic acid co-polymer (SMA). This approach yields SMA lipid particles (SMALPs) in which the membrane proteins are surrounded by a small disk of lipid bilayer encircled by polymer. Here we use the Escherichia coli secondary transporter AcrB as a model membrane protein to demonstrate how a SMALP scaffold can be used to visualise membrane proteins, embedded in a near-native lipid environment, by negative stain electron microscopy, yielding structures at a modest resolution in a short (days) timeframe. Moreover, we show that AcrB within a SMALP scaffold is significantly more active than the equivalent DDM stabilised form. The advantages of SMALP scaffolds within electron microscopy are discussed and we conclude that they may prove to be an important tool in studying membrane protein structure and function. Maintaining membrane proteins in a native-like environment is difficult. SMALP scaffolds efficiently extract AcrB from the membrane. We show SMALP scaffolds to be a robust tool for rapid structural analysis by EM.
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Affiliation(s)
- Vincent Postis
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, LS1 3HE, UK
| | - Shaun Rawson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Jennifer K Mitchell
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Sarah C Lee
- School of Biosciences, University of Birmingham, Birmingham, Edgbaston B15 2TT, UK
| | - Rosemary A Parslow
- School of Biosciences, University of Birmingham, Birmingham, Edgbaston B15 2TT, UK
| | - Tim R Dafforn
- School of Biosciences, University of Birmingham, Birmingham, Edgbaston B15 2TT, UK
| | - Stephen A Baldwin
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
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69
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Lin PC, Lin S, Wang PC, Sridhar R. Techniques for physicochemical characterization of nanomaterials. Biotechnol Adv 2014; 32:711-26. [PMID: 24252561 PMCID: PMC4024087 DOI: 10.1016/j.biotechadv.2013.11.006] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 11/05/2013] [Accepted: 11/12/2013] [Indexed: 12/12/2022]
Abstract
Advances in nanotechnology have opened up a new era of diagnosis, prevention and treatment of diseases and traumatic injuries. Nanomaterials, including those with potential for clinical applications, possess novel physicochemical properties that have an impact on their physiological interactions, from the molecular level to the systemic level. There is a lack of standardized methodologies or regulatory protocols for detection or characterization of nanomaterials. This review summarizes the techniques that are commonly used to study the size, shape, surface properties, composition, purity and stability of nanomaterials, along with their advantages and disadvantages. At present there are no FDA guidelines that have been developed specifically for nanomaterial based formulations for diagnostic or therapeutic use. There is an urgent need for standardized protocols and procedures for the characterization of nanoparticles, especially those that are intended for use as theranostics.
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MESH Headings
- Chemistry, Physical/methods
- Circular Dichroism
- Contrast Media/chemistry
- Humans
- Light
- Magnetic Resonance Spectroscopy
- Mass Spectrometry
- Microscopy, Atomic Force
- Microscopy, Electron, Scanning
- Microscopy, Electron, Transmission
- Microscopy, Scanning Tunneling
- Molecular Imaging/methods
- Nanomedicine/methods
- Nanoparticles/chemistry
- Nanostructures/chemistry
- Nanotechnology/methods
- Nanotechnology/trends
- Scattering, Radiation
- Spectrometry, Fluorescence
- Spectrophotometry, Infrared
- Spectrum Analysis, Raman
- Surface Properties
- Technology, Pharmaceutical/methods
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Affiliation(s)
- Ping-Chang Lin
- Laboratory of Molecular Imaging, Department of Radiology, Howard University, Washington, DC 20060, USA
| | - Stephen Lin
- Laboratory of Molecular Imaging, Department of Radiology, Howard University, Washington, DC 20060, USA
| | - Paul C Wang
- Laboratory of Molecular Imaging, Department of Radiology, Howard University, Washington, DC 20060, USA
| | - Rajagopalan Sridhar
- Department of Radiation Oncology, Howard University, Washington, DC 20060, USA.
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70
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71
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Twenty years of gas phase structural biology. Structure 2014; 21:1541-50. [PMID: 24010713 DOI: 10.1016/j.str.2013.08.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 08/06/2013] [Accepted: 08/06/2013] [Indexed: 01/01/2023]
Abstract
Over the past two decades, mass spectrometry (MS) of protein complexes from their native state has made inroads into structural biology. To coincide with the 20(th) anniversary of Structure, and given that it is now approximately 20 years since the first mass spectra of noncovalent protein complexes were reported, it is timely to consider progress of MS as a structural biology tool. Early reports focused on soluble complexes, contributing to ligand binding studies, subunit interaction maps, and topological models. Recent discoveries have enabled delivery of membrane complexes, encapsulated in detergent micelles, prompting new opportunities. By maintaining interactions between membrane and cytoplasmic subunits in the gas phase, it is now possible to investigate the effects of lipids, nucleotides, and drugs on intact membrane assemblies. These investigations reveal allosteric and synergistic effects of small molecule binding and expose the consequences of posttranslational modifications. In this review, we consider recent progress in the study of protein complexes, focusing particularly on complexes extracted from membranes, and outline future prospects for gas phase structural biology.
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72
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Zhao H, Mayer ML, Schuck P. Analysis of protein interactions with picomolar binding affinity by fluorescence-detected sedimentation velocity. Anal Chem 2014; 86:3181-7. [PMID: 24552356 PMCID: PMC3988680 DOI: 10.1021/ac500093m] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
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The study of high-affinity
protein interactions with equilibrium
dissociation constants (KD) in the picomolar
range is of significant interest in many fields, but the characterization
of stoichiometry and free energy of such high-affinity binding can
be far from trivial. Analytical ultracentrifugation has long been
considered a gold standard in the study of protein interactions but
is typically applied to systems with micromolar KD. Here we present a new approach for the study of high-affinity
interactions using fluorescence detected sedimentation velocity analytical
ultracentrifugation (FDS-SV). Taking full advantage of the large data
sets in FDS-SV by direct boundary modeling with sedimentation coefficient
distributions c(s), we demonstrate detection and
hydrodynamic resolution of protein complexes at low picomolar concentrations.
We show how this permits the characterization of the antibody–antigen
interactions with low picomolar binding constants, 2 orders of magnitude
lower than previously achieved. The strongly size-dependent separation
and quantitation by concentration, size, and shape of free and complex
species in free solution by FDS-SV has significant potential for studying
high-affinity multistep and multicomponent protein assemblies.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health , Bethesda, Maryland 20892, United States
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73
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Yeliseev AA. Methods for recombinant expression and functional characterization of human cannabinoid receptor CB2. Comput Struct Biotechnol J 2013; 6:e201303011. [PMID: 24688719 PMCID: PMC3962128 DOI: 10.5936/csbj.201303011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 08/08/2013] [Accepted: 08/10/2013] [Indexed: 12/22/2022] Open
Abstract
Cannabinoid receptor CB2 is a seven transmembrane-domain integral membrane protein that belongs to a large superfamily of G protein-coupled receptors (GPCR). CB2 is a part of the endocannabinoid system that plays vital role in regulation of immune response, inflammation, pain sensitivity, obesity and other physiological responses. Information about the structure and mechanisms of functioning of this receptor in cell membranes is essential for the rational development of specific pharmaceuticals. Here we review the methodology for recombinant expression, purification, stabilization and biochemical characterization of CB2 suitable for preparation of multi-milligram quantities of functionally active receptor. The biotechnological protocols include expression of the recombinant CB2 in E. coli cells as a fusion with the maltose binding protein, stabilization with a high affinity ligand and a derivative of cholesterol in detergent micelles, efficient purification by tandem affinity chromatography, and reconstitution of the receptor into lipid bilayers. The purified recombinant CB2 receptor is amenable to functional and structural studies including nuclear magnetic resonance spectroscopy and a wide range of biochemical and biophysical techniques.
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Affiliation(s)
- Alexei A Yeliseev
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Bethesda, MD 20892, USA
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74
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Functional properties of cell-free expressed human endothelin A and endothelin B receptors in artificial membrane environments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2182-92. [DOI: 10.1016/j.bbamem.2013.05.031] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 05/27/2013] [Accepted: 05/29/2013] [Indexed: 01/06/2023]
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Abstract
The last two decades have led to significant progress in the field of analytical ultracentrifugation driven by instrumental, theoretical, and computational methods. This review will highlight key developments in sedimentation equilibrium (SE) and sedimentation velocity (SV) analysis. For SE, this includes the analysis of tracer sedimentation equilibrium at high concentrations with strong thermodynamic non-ideality, and for ideally interacting systems the development of strategies for the analysis of heterogeneous interactions towards global multi-signal and multi-speed SE analysis with implicit mass conservation. For SV, this includes the development and applications of numerical solutions of the Lamm equation, noise decomposition techniques enabling direct boundary fitting, diffusion deconvoluted sedimentation coefficient distributions, and multi-signal sedimentation coefficient distributions. Recently, effective particle theory has uncovered simple physical rules for the co-migration of rapidly exchanging systems of interacting components in SV. This has opened new possibilities for the robust interpretation of the boundary patterns of heterogeneous interacting systems. Together, these SE and SV techniques have led to new approaches to study macromolecular interactions across the entire the spectrum of affinities, including both attractive and repulsive interactions, in both dilute and highly concentrated solutions, which can be applied to single-component solutions of self-associating proteins as well as the study of multi-protein complex formation in multi-component solutions.
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Affiliation(s)
- Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, U.S.A
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Zhao H, Brautigam CA, Ghirlando R, Schuck P. Overview of current methods in sedimentation velocity and sedimentation equilibrium analytical ultracentrifugation. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2013; Chapter 20:Unit20.12. [PMID: 23377850 PMCID: PMC3652391 DOI: 10.1002/0471140864.ps2012s71] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Modern computational strategies have allowed for the direct modeling of the sedimentation process of heterogeneous mixtures, resulting in sedimentation velocity (SV) size-distribution analyses with significantly improved detection limits and strongly enhanced resolution. These advances have transformed the practice of SV, rendering it the primary method of choice for most existing applications of analytical ultracentrifugation (AUC), such as the study of protein self- and hetero-association, the study of membrane proteins, and applications in biotechnology. New global multisignal modeling and mass conservation approaches in SV and sedimentation equilibrium (SE), in conjunction with the effective-particle framework for interpreting the sedimentation boundary structure of interacting systems, as well as tools for explicit modeling of the reaction/diffusion/sedimentation equations to experimental data, have led to more robust and more powerful strategies for the study of reversible protein interactions and multiprotein complexes. Furthermore, modern mathematical modeling capabilities have allowed for a detailed description of many experimental aspects of the acquired data, thus enabling novel experimental opportunities, with important implications for both sample preparation and data acquisition. The goal of the current unit is to describe the current tools for the study of soluble proteins, detergent-solubilized membrane proteins and their interactions by SV and SE.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
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