1
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Tessmer MH, Stoll S. A novel approach to modeling side chain ensembles of the bifunctional spin label RX. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542139. [PMID: 37292623 PMCID: PMC10245940 DOI: 10.1101/2023.05.24.542139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We introduce a novel approach to modeling side chain ensembles of bifunctional spin labels. This approach utilizes rotamer libraries to generate side chain conformational ensembles. Because the bifunctional label is constrained by two attachment sites, the label is split into two monofunctional rotamers which are first attached to their respective sites, then rejoined by a local optimization in dihedral space. We validate this method against a set of previously published experimental data using the bifunctional spin label, RX. This method is relatively fast and can readily be used for both experimental analysis and protein modeling, providing significant advantages over modeling bifunctional labels with molecular dynamics simulations. Use of bifunctional labels for site directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy dramatically reduces label mobility, which can significantly improve resolution of small changes in protein backbone structure and dynamics. Coupling the use of bifunctional labels with side chain modeling methods allows for improved quantitative application of experimental SDSL EPR data to protein modeling.
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Affiliation(s)
- Maxx H. Tessmer
- Department of Chemistry, University of Washington, Seattle, WA 98103, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, WA 98103, United States
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2
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Tessmer MH, Canarie ER, Stoll S. Comparative evaluation of spin-label modeling methods for protein structural studies. Biophys J 2022; 121:3508-3519. [PMID: 35957530 PMCID: PMC9515001 DOI: 10.1016/j.bpj.2022.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/01/2022] [Accepted: 08/04/2022] [Indexed: 11/18/2022] Open
Abstract
Site-directed spin-labeling electron paramagnetic resonance spectroscopy is a powerful technique for the investigation of protein structure and dynamics. Accurate spin-label modeling methods are essential to make full quantitative use of site-directed spin-labeling electron paramagnetic resonance data for protein modeling and model validation. Using a set of double electron-electron resonance data from seven different site pairs on maltodextrin/maltose-binding protein under two different conditions using five different spin labels, we compare the ability of two widely used spin-label modeling methods, based on accessible volume sampling and rotamer libraries, to predict experimental distance distributions. We present a spin-label modeling approach inspired by canonical side-chain modeling methods and compare modeling accuracy with the established methods.
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Affiliation(s)
- Maxx H Tessmer
- Department of Chemistry, University of Washington, Seattle, Washington
| | | | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington.
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3
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Vallese F, Kim K, Yen LY, Johnston JD, Noble AJ, Calì T, Clarke OB. Architecture of the human erythrocyte ankyrin-1 complex. Nat Struct Mol Biol 2022; 29:706-718. [PMID: 35835865 PMCID: PMC10373098 DOI: 10.1038/s41594-022-00792-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/24/2022] [Indexed: 12/28/2022]
Abstract
The stability and shape of the erythrocyte membrane is provided by the ankyrin-1 complex, but how it tethers the spectrin-actin cytoskeleton to the lipid bilayer and the nature of its association with the band 3 anion exchanger and the Rhesus glycoproteins remains unknown. Here we present structures of ankyrin-1 complexes purified from human erythrocytes. We reveal the architecture of a core complex of ankyrin-1, the Rhesus proteins RhAG and RhCE, the band 3 anion exchanger, protein 4.2, glycophorin A and glycophorin B. The distinct T-shaped conformation of membrane-bound ankyrin-1 facilitates recognition of RhCE and, unexpectedly, the water channel aquaporin-1. Together, our results uncover the molecular details of ankyrin-1 association with the erythrocyte membrane, and illustrate the mechanism of ankyrin-mediated membrane protein clustering.
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Affiliation(s)
- Francesca Vallese
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA.,Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA.,Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA
| | - Kookjoo Kim
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA.,Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA.,Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA
| | - Laura Y Yen
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Jake D Johnston
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA.,Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Alex J Noble
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Tito Calì
- Department of Biomedical Sciences, University of Padua, Padua, Italy.,Padua Neuroscience Center (PNC), University of Padua, Padua, Italy.,Study Center for Neurodegeneration (CESNE), University of Padua, Padua, Italy
| | - Oliver Biggs Clarke
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA. .,Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA. .,Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA.
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4
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Structure, dynamics and assembly of the ankyrin complex on human red blood cell membrane. Nat Struct Mol Biol 2022; 29:698-705. [PMID: 35655099 DOI: 10.1038/s41594-022-00779-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/14/2022] [Indexed: 12/20/2022]
Abstract
The cytoskeleton of a red blood cell (RBC) is anchored to the cell membrane by the ankyrin complex. This complex is assembled during RBC genesis and comprises primarily band 3, protein 4.2 and ankyrin, whose mutations contribute to numerous human inherited diseases. High-resolution structures of the ankyrin complex have been long sought-after to understand its assembly and disease-causing mutations. Here, we analyzed native complexes on the human RBC membrane by stepwise fractionation. Cryo-electron microscopy structures of nine band-3-associated complexes reveal that protein 4.2 stabilizes the cytoplasmic domain of band 3 dimer. In turn, the superhelix-shaped ankyrin binds to this protein 4.2 via ankyrin repeats (ARs) 6-13 and to another band 3 dimer via ARs 17-20, bridging two band 3 dimers in the ankyrin complex. Integration of these structures with both prior data and our biochemical data supports a model of ankyrin complex assembly during erythropoiesis and identifies interactions essential for the mechanical stability of RBC.
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5
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Hustedt EJ, Stein RA, Mchaourab HS. Protein functional dynamics from the rigorous global analysis of DEER data: Conditions, components, and conformations. J Gen Physiol 2021; 153:212643. [PMID: 34529007 PMCID: PMC8449309 DOI: 10.1085/jgp.201711954] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 08/30/2021] [Indexed: 01/03/2023] Open
Abstract
The potential of spin labeling to reveal the dynamic dimension of macromolecules has been recognized since the dawn of the methodology in the 1960s. However, it was the development of pulsed electron paramagnetic resonance spectroscopy to detect dipolar coupling between spin labels and the availability of turnkey instrumentation in the 21st century that realized the full promise of spin labeling. Double electron-electron resonance (DEER) spectroscopy has seen widespread applications to channels, transporters, and receptors. In these studies, distance distributions between pairs of spin labels obtained under different biochemical conditions report the conformational states of macromolecules, illuminating the key movements underlying biological function. These experimental studies have spurred the development of methods for the rigorous analysis of DEER spectroscopic data along with methods for integrating these distributions into structural models. In this tutorial, we describe a model-based approach to obtaining a minimum set of components of the distance distribution that correspond to functionally relevant protein conformations with a set of fractional amplitudes that define the equilibrium between these conformations. Importantly, we review and elaborate on the error analysis reflecting the uncertainty in the various parameters, a critical step in rigorous structural interpretation of the spectroscopic data.
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Affiliation(s)
- Eric J Hustedt
- Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Richard A Stein
- Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Hassane S Mchaourab
- Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
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6
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del Alamo D, Jagessar KL, Meiler J, Mchaourab HS. Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints. PLoS Comput Biol 2021; 17:e1009107. [PMID: 34133419 PMCID: PMC8238229 DOI: 10.1371/journal.pcbi.1009107] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/28/2021] [Accepted: 05/24/2021] [Indexed: 12/20/2022] Open
Abstract
We describe an approach for integrating distance restraints from Double Electron-Electron Resonance (DEER) spectroscopy into Rosetta with the purpose of modeling alternative protein conformations from an initial experimental structure. Fundamental to this approach is a multilateration algorithm that harnesses sets of interconnected spin label pairs to identify optimal rotamer ensembles at each residue that fit the DEER decay in the time domain. Benchmarked relative to data analysis packages, the algorithm yields comparable distance distributions with the advantage that fitting the DEER decay and rotamer ensemble optimization are coupled. We demonstrate this approach by modeling the protonation-dependent transition of the multidrug transporter PfMATE to an inward facing conformation with a deviation to the experimental structure of less than 2Å Cα RMSD. By decreasing spin label rotamer entropy, this approach engenders more accurate Rosetta models that are also more closely clustered, thus setting the stage for more robust modeling of protein conformational changes.
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Affiliation(s)
- Diego del Alamo
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kevin L. Jagessar
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jens Meiler
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
| | - Hassane S. Mchaourab
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
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7
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Anatomy of the red cell membrane skeleton: unanswered questions. Blood 2015; 127:187-99. [PMID: 26537302 DOI: 10.1182/blood-2014-12-512772] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/30/2015] [Indexed: 11/20/2022] Open
Abstract
The red cell membrane skeleton is a pseudohexagonal meshwork of spectrin, actin, protein 4.1R, ankyrin, and actin-associated proteins that laminates the inner membrane surface and attaches to the overlying lipid bilayer via band 3-containing multiprotein complexes at the ankyrin- and actin-binding ends of spectrin. The membrane skeleton strengthens the lipid bilayer and endows the membrane with the durability and flexibility to survive in the circulation. In the 36 years since the first primitive model of the red cell skeleton was proposed, many additional proteins have been discovered, and their structures and interactions have been defined. However, almost nothing is known of the skeleton's physiology, and myriad questions about its structure remain, including questions concerning the structure of spectrin in situ, the way spectrin and other proteins bind to actin, how the membrane is assembled, the dynamics of the skeleton when the membrane is deformed or perturbed by parasites, the role lipids play, and variations in membrane structure in unique regions like lipid rafts. This knowledge is important because the red cell membrane skeleton is the model for spectrin-based membrane skeletons in all cells, and because defects in the red cell membrane skeleton underlie multiple hemolytic anemias.
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8
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Tsytlonok M, Ibrahim SM, Rowling PJE, Xu W, Ruedas-Rama MJ, Orte A, Klenerman D, Itzhaki LS. Single-molecule FRET reveals hidden complexity in a protein energy landscape. Structure 2015; 23:190-198. [PMID: 25565106 PMCID: PMC4291146 DOI: 10.1016/j.str.2014.10.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 10/01/2014] [Accepted: 10/06/2014] [Indexed: 10/27/2022]
Abstract
Here, using single-molecule FRET, we reveal previously hidden conformations of the ankyrin-repeat domain of AnkyrinR, a giant adaptor molecule that anchors integral membrane proteins to the spectrin-actin cytoskeleton through simultaneous binding of multiple partner proteins. We show that the ankyrin repeats switch between high-FRET and low-FRET states, controlled by an unstructured "safety pin" or "staple" from the adjacent domain of AnkyrinR. Opening of the safety pin leads to unravelling of the ankyrin repeat stack, a process that will dramatically affect the relative orientations of AnkyrinR binding partners and, hence, the anchoring of the spectrin-actin cytoskeleton to the membrane. Ankyrin repeats are one of the most ubiquitous molecular recognition platforms in nature, and it is therefore important to understand how their structures are adapted for function. Our results point to a striking mechanism by which the order-disorder transition and, thereby, the activity of repeat proteins can be regulated.
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Affiliation(s)
- Maksym Tsytlonok
- MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Shehu M Ibrahim
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Pamela J E Rowling
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Wenshu Xu
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Maria J Ruedas-Rama
- Department of Physical Chemistry, Faculty of Pharmacy, Campus Cartuja, University of Granada, 18071 Granada, Spain
| | - Angel Orte
- Department of Physical Chemistry, Faculty of Pharmacy, Campus Cartuja, University of Granada, 18071 Granada, Spain
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Laura S Itzhaki
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK.
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9
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Saito M, Watanabe-Nakayama T, Machida S, Osada T, Afrin R, Ikai A. Spectrin-ankyrin interaction mechanics: A key force balance factor in the red blood cell membrane skeleton. Biophys Chem 2015; 200-201:1-8. [PMID: 25866912 DOI: 10.1016/j.bpc.2015.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/19/2015] [Accepted: 03/22/2015] [Indexed: 12/31/2022]
Abstract
As major components of red blood cell (RBC) cytoskeleton, spectrin and F-actin form a network that covers the entire cytoplasmic surface of the plasma membrane. The cross-linked two layered structure, called the membrane skeleton, keeps the structural integrity of RBC under drastically changing mechanical environment during circulation. We performed force spectroscopy experiments on the atomic force microscope (AFM) as a means to clarify the mechanical characteristics of spectrin-ankyrin interaction, a key factor in the force balance of the RBC cytoskeletal structure. An AFM tip was functionalized with ANK1-62k and used to probe spectrin crosslinked to mica surface. A force spectroscopy study gave a mean unbinding force of ~30 pN under our experimental conditions. Two energy barriers were identified in the unbinding process. The result was related to the well-known flexibility of spectrin tetramer and participation of ankyrin 1-spectrin interaction in the overall balance of membrane skeleton dynamics.
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Affiliation(s)
- Masakazu Saito
- Innovation Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
| | - Takahiro Watanabe-Nakayama
- Innovation Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Shinichi Machida
- Innovation Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Toshiya Osada
- Depertment of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B-2 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Rehana Afrin
- Innovation Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan; Biofrontier Center, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Atsushi Ikai
- Innovation Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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10
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Genetet S, Ripoche P, Le Van Kim C, Colin Y, Lopez C. Evidence of a structural and functional ammonium transporter RhBG·anion exchanger 1·ankyrin-G complex in kidney epithelial cells. J Biol Chem 2015; 290:6925-36. [PMID: 25616663 DOI: 10.1074/jbc.m114.610048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The renal ammonium transporter RhBG and anion exchanger 1 kAE1 colocalize in the basolateral domain of α-intercalated cells in the distal nephron. Although we have previously shown that RhBG is linked to the spectrin-based skeleton through ankyrin-G and that its NH3 transport activity is dependent on this association, there is no evidence for an interaction of kAE1 with this adaptor protein. We report here that the kAE1 cytoplasmic N terminus actually binds to ankyrin-G, both in yeast two-hybrid analysis and by coimmunoprecipitation in situ in HEK293 cells expressing recombinant kAE1. A site-directed mutagenesis study allowed the identification of three dispersed regions on kAE1 molecule linking the third and fourth repeat domains of ankyrin-G. One secondary docking site corresponds to a major interacting loop of the erythroid anion exchanger 1 (eAE1) with ankyrin-R, whereas the main binding region of kAE1 does not encompass any eAE1 determinant. Stopped flow spectrofluorometry analysis of recombinant HEK293 cells revealed that the Cl(-)/HCO3 (-) exchange activity of a kAE1 protein mutated on the ankyrin-G binding site was abolished. This disruption impaired plasma membrane expression of kAE1 leading to total retention on cytoplasmic structures in polarized epithelial Madin-Darby canine kidney cell transfectants. kAE1 also directly interacts with RhBG without affecting its surface expression and NH3 transport function. This is the first description of a structural and functional RhBG·kAE1·ankyrin-G complex at the plasma membrane of kidney epithelial cells, comparable with the well known Rh·eAE1·ankyrin-R complex in the red blood cell membrane. This renal complex could participate in the regulation of acid-base homeostasis.
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Affiliation(s)
- Sandrine Genetet
- From INSERM U1134, 75739 Paris, France, the Université Paris Diderot, Sorbonne Paris Cité, UMR_S1134, 75739 Paris, France, the Institut National de la Transfusion Sanguine, 75739 Paris, France, and the Laboratoire d'Excellence GR-Ex, 75238 Paris, France
| | - Pierre Ripoche
- From INSERM U1134, 75739 Paris, France, the Université Paris Diderot, Sorbonne Paris Cité, UMR_S1134, 75739 Paris, France, the Institut National de la Transfusion Sanguine, 75739 Paris, France, and the Laboratoire d'Excellence GR-Ex, 75238 Paris, France
| | - Caroline Le Van Kim
- From INSERM U1134, 75739 Paris, France, the Université Paris Diderot, Sorbonne Paris Cité, UMR_S1134, 75739 Paris, France, the Institut National de la Transfusion Sanguine, 75739 Paris, France, and the Laboratoire d'Excellence GR-Ex, 75238 Paris, France
| | - Yves Colin
- From INSERM U1134, 75739 Paris, France, the Université Paris Diderot, Sorbonne Paris Cité, UMR_S1134, 75739 Paris, France, the Institut National de la Transfusion Sanguine, 75739 Paris, France, and the Laboratoire d'Excellence GR-Ex, 75238 Paris, France
| | - Claude Lopez
- From INSERM U1134, 75739 Paris, France, the Université Paris Diderot, Sorbonne Paris Cité, UMR_S1134, 75739 Paris, France, the Institut National de la Transfusion Sanguine, 75739 Paris, France, and the Laboratoire d'Excellence GR-Ex, 75238 Paris, France
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12
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Edwards SJ, Moth CW, Kim S, Brandon S, Zhou Z, Cobb CE, Hustedt EJ, Beth AH, Smith JA, Lybrand TP. Automated structure refinement for a protein heterodimer complex using limited EPR spectroscopic data and a rigid-body docking algorithm: a three-dimensional model for an ankyrin-CDB3 complex. J Phys Chem B 2014; 118:4717-26. [PMID: 24758720 PMCID: PMC4018176 DOI: 10.1021/jp4099705] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
We report here specialized functions
incorporated recently in the
rigid-body docking software toolkit TagDock to utilize electron paramagnetic
resonance derived (EPR-derived) interresidue distance measurements
and spin-label accessibility data. The TagDock package extensions
include a custom methanethiosulfonate spin label rotamer library to
enable explicit, all-atom spin-label side-chain modeling and scripts
to evaluate spin-label surface accessibility. These software enhancements
enable us to better utilize the biophysical data routinely available
from various spin-labeling experiments. To illustrate the power and
utility of these tools, we report the refinement of an ankyrin:CDB3
complex model that exhibits much improved agreement with the EPR distance
measurements, compared to model structures published previously.
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Affiliation(s)
- Sarah J Edwards
- Department of Chemistry, ‡Department of Molecular Physiology & Biophysics, §Department of Biochemistry, ∥Department of Pharmacology, ⊥Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37235, United States
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13
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Spectrin and phospholipids - the current picture of their fascinating interplay. Cell Mol Biol Lett 2014; 19:158-79. [PMID: 24569979 PMCID: PMC6276000 DOI: 10.2478/s11658-014-0185-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 02/19/2014] [Indexed: 12/02/2022] Open
Abstract
The spectrin-based membrane skeleton is crucial for the mechanical stability and resilience of erythrocytes. It mainly contributes to membrane integrity, protein organization and trafficking. Two transmembrane protein macro-complexes that are linked together by spectrin tetramers play a crucial role in attaching the membrane skeleton to the cell membrane, but they are not exclusive. Considerable experimental data have shown that direct interactions between spectrin and membrane lipids are important for cell membrane cohesion. Spectrin is a multidomain, multifunctional protein with several distinctive structural regions, including lipid-binding sites within CH tandem domains, a PH domain, and triple helical segments, which are excellent examples of ligand specificity hidden in a regular repetitive structure, as recently shown for the ankyrin-sensitive lipid-binding domain of beta spectrin. In this review, we summarize the state of knowledge about interactions between spectrin and membrane lipids.
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14
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Sahu ID, McCarrick RM, Lorigan GA. Use of electron paramagnetic resonance to solve biochemical problems. Biochemistry 2013; 52:5967-84. [PMID: 23961941 PMCID: PMC3839053 DOI: 10.1021/bi400834a] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a very powerful biophysical tool that can provide valuable structural and dynamic information about a wide variety of biological systems. The intent of this review is to provide a general overview for biochemists and biological researchers of the most commonly used EPR methods and how these techniques can be used to answer important biological questions. The topics discussed could easily fill one or more textbooks; thus, we present a brief background on several important biological EPR techniques and an overview of several interesting studies that have successfully used EPR to solve pertinent biological problems. The review consists of the following sections: an introduction to EPR techniques, spin-labeling methods, and studies of naturally occurring organic radicals and EPR active transition metal systems that are presented as a series of case studies in which EPR spectroscopy has been used to greatly further our understanding of several important biological systems.
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Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH
| | | | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH
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15
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Hagelueken G, Abdullin D, Ward R, Schiemann O. mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL. Mol Phys 2013; 111:2757-2766. [PMID: 24954955 PMCID: PMC4056886 DOI: 10.1080/00268976.2013.809804] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/18/2013] [Indexed: 01/07/2023]
Abstract
Nanometer distance measurements based on electron paramagnetic resonance methods in combination with site-directed spin labelling are powerful tools for the structural analysis of macromolecules. The software package mtsslSuite provides scientists with a set of tools for the translation of experimental distance distributions into structural information. The package is based on the previously published mtsslWizard software for in silico spin labelling. The mtsslSuite includes a new version of MtsslWizard that has improved performance and now includes additional types of spin labels. Moreover, it contains applications for the trilateration of paramagnetic centres in biomolecules and for rigid-body docking of subdomains of macromolecular complexes. The mtsslSuite is tested on a number of challenging test cases and its strengths and weaknesses are evaluated.
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Affiliation(s)
- Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Richard Ward
- Biomedical Sciences Research Complex, The University of St. Andrews, Fife, UK
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany ; Biomedical Sciences Research Complex, The University of St. Andrews, Fife, UK
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16
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Abstract
The concept of the cytosol as a space that contains discrete zones of metabolites is discussed relative to the contribution of GAPDH. GAPDH is directed to very specific cell compartments. This chapter describes the utilization of GAPDH's enzymatic function for focal demands (i.e. ATP/ADP and NAD(+)/NADH), and offers a speculative role for GAPDH as perhaps moderating local concentrations of inorganic phosphate and hydrogen ions (i.e. co-substrate and co-product of the glycolytic reaction, respectively). Where known, the structural features of the binding between GAPDH and the compartment components are discussed. The nuances, which are associated with the intracellular distribution of GAPDH, appear to be specific to the cell-type, particularly with regards to the various plasma membrane proteins to which GAPDH binds. The chapter includes discussion on the curious observation of GAPDH being localized to the external surface of the plasma membrane in a human cell type. The default perspective has been that GAPDH localization is synonymous with compartmentation of glycolytic energy. The chapter discusses GAPDH translocation to the nucleus and to non-nuclear cellular structures, emphasizing its glycolytic function. Nevertheless, it is becoming clear that alternate functions of GAPDH play a role in compartmentation, particularly in the translocation to the nucleus.
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Affiliation(s)
- Norbert W Seidler
- Department of Biochemistry, Kansas City University of Medicine and Biosciences, Kansas City, MO, USA
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17
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Borbat PP, Freed JH. Pulse Dipolar Electron Spin Resonance: Distance Measurements. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2013. [DOI: 10.1007/430_2012_82] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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Dixit M, Kim S, Matthews GF, Erreger K, Galli A, Cobb CE, Hustedt EJ, Beth AH. Structural arrangement of the intracellular Ca2+ binding domains of the cardiac Na+/Ca2+ exchanger (NCX1.1): effects of Ca2+ binding. J Biol Chem 2012; 288:4194-207. [PMID: 23233681 DOI: 10.1074/jbc.m112.423293] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cardiac Na(+)/Ca(2+) exchanger (NCX1.1) serves as the primary means of Ca(2+) extrusion across the plasma membrane of cardiomyocytes after the rise in intracellular Ca(2+) during contraction. The exchanger is regulated by binding of Ca(2+) to its intracellular domain, which contains two structurally homologous Ca(2+) binding domains denoted as CBD1 and CBD2. NMR and x-ray crystallographic studies have provided structures for the isolated CBD1 and CBD2 domains and have shown how Ca(2+) binding affects their structures and motional dynamics. However, structural information on the entire Ca(2+) binding domain, denoted CBD12, and how binding of Ca(2+) alters its structure and dynamics is more limited. Site-directed spin labeling has been employed in this work to address these questions. Electron paramagnetic resonance measurements on singly labeled constructs of CBD12 have identified the regions that undergo changes in dynamics as a result of Ca(2+) binding. Double electron-electron resonance (DEER) measurements on doubly labeled constructs of CBD12 have shown that the β-sandwich regions of the CBD1 and CBD2 domains are largely insensitive to Ca(2+) binding and that these two domains are widely separated at their N and C termini. Interdomain distances measured by DEER have been employed to construct structural models for CBD12 in the presence and absence of Ca(2+). These models show that there is not a major change in the relative orientation of the two Ca(2+) binding domains as a result of Ca(2+) binding in the NCX1.1 isoform. Additional measurements have shown that there are significant changes in the dynamics of the F-G loop region of CBD2 that merit further characterization with regard to their possible involvement in regulation of NCX1.1 activity.
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Affiliation(s)
- Mrinalini Dixit
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA
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19
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Gaffney BJ, Bradshaw MD, Frausto SD, Wu F, Freed JH, Borbat P. Locating a lipid at the portal to the lipoxygenase active site. Biophys J 2012; 103:2134-44. [PMID: 23200047 PMCID: PMC3512035 DOI: 10.1016/j.bpj.2012.10.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 11/28/2022] Open
Abstract
Lipoxygenase enzymes initiate diverse signaling pathways by specifically directing oxygen to different carbons of arachidonate and other polyunsaturated acyl chains, but structural origins of this specificity have remained unclear. We therefore determined the nature of the lipoxygenase interaction with the polar-end of a paramagnetic lipid by electron paramagnetic resonance spectroscopy. Distances between selected grid points on soybean seed lipoxygenase-1 (SBL1) and a lysolecithin spin-labeled on choline were measured by pulsed (electron) dipolar spectroscopy. The protein grid was designed by structure-based modeling so that five natural side chains were replaced with spin labels. Pairwise distances in 10 doubly spin-labeled mutants were examined by pulsed dipolar spectroscopy, and a fit to the model was optimized. Finally, experimental distances between the lysolecithin spin and each single spin site on SBL1 were also obtained. With these 15 distances, distance geometry localized the polar-end and the spin of the lysolecithin to the region between the two domains in the SBL1 structure, nearest to E236, K260, Q264, and Q544. Mutation of a nearby residue, E256A, relieved the high pH requirement for enzyme activity of SBL1 and allowed lipid binding at pH 7.2. This general approach could be used to locate other flexible molecules in macromolecular complexes.
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Affiliation(s)
- Betty J Gaffney
- Department of Biological Science Department, Florida State University, Tallahassee, FL, USA.
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20
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Puchulu-Campanella E, Chu H, Anstee DJ, Galan JA, Tao WA, Low PS. Identification of the components of a glycolytic enzyme metabolon on the human red blood cell membrane. J Biol Chem 2012; 288:848-58. [PMID: 23150667 DOI: 10.1074/jbc.m112.428573] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Glycolytic enzymes (GEs) have been shown to exist in multienzyme complexes on the inner surface of the human erythrocyte membrane. Because no protein other than band 3 has been found to interact with GEs, and because several GEs do not bind band 3, we decided to identify the additional membrane proteins that serve as docking sites for GE on the membrane. For this purpose, a method known as "label transfer" that employs a photoactivatable trifunctional cross-linking reagent to deliver a biotin from a derivatized GE to its binding partner on the membrane was used. Mass spectrometry analysis of membrane proteins that were biotinylated following rebinding and photoactivation of labeled GAPDH, aldolase, lactate dehydrogenase, and pyruvate kinase revealed not only the anticipated binding partner, band 3, but also the association of GEs with specific peptides in α- and β-spectrin, ankyrin, actin, p55, and protein 4.2. More importantly, the labeled GEs were also found to transfer biotin to other GEs in the complex, demonstrating for the first time that GEs also associate with each other in their membrane complexes. Surprisingly, a new GE binding site was repeatedly identified near the junction of the membrane-spanning and cytoplasmic domains of band 3, and this binding site was confirmed by direct binding studies. These results not only identify new components of the membrane-associated GE complexes but also provide molecular details on the specific peptides that form the interfacial contacts within each interaction.
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21
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Grey JL, Kodippili GC, Simon K, Low PS. Identification of contact sites between ankyrin and band 3 in the human erythrocyte membrane. Biochemistry 2012; 51:6838-46. [PMID: 22861190 DOI: 10.1021/bi300693k] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The red cell membrane is stabilized by a spectrin/actin-based cortical cytoskeleton connected to the phospholipid bilayer via multiple protein bridges. By virtue of its interaction with ankyrin and adducin, the anion transporter, band 3 (AE1), contributes prominently to these bridges. In a previous study, we demonstrated that an exposed loop comprising residues 175-185 of the cytoplasmic domain of band 3 (cdB3) constitutes a critical docking site for ankyrin on band 3. In this paper, we demonstrate that an adjacent loop, comprising residues 63-73 of cdB3, is also essential for ankyrin binding. Data that support this hypothesis include the following. (1) Deletion or mutation of residues within the latter loop abrogates ankyrin binding without affecting cdB3 structure or its other functions. (2) Association of cdB3 with ankyrin is inhibited by competition with the loop peptide. (3) Resealing of the loop peptide into erythrocyte ghosts alters membrane morphology and stability. To characterize cdB3-ankyrin interaction further, we identified their interfacial contact sites using molecular docking software and the crystal structures of D(3)D(4)-ankyrin and cdB3. The best fit for the interaction reveals multiple salt bridges and hydrophobic contacts between the two proteins. The most important ion pair interactions are (i) cdB3 K69-ankyrin E645, (ii) cdB3 E72-ankyrin K611, and (iii) cdB3 D183-ankyrin N601 and Q634. Mutation of these four residues on ankyrin yielded an ankyrin with a native CD spectrum but little or no affinity for cdB3. These data define the docking interface between cdB3 and ankyrin in greater detail.
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Affiliation(s)
- Jesse L Grey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
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22
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Mankelow TJ, Satchwell TJ, Burton NM. Refined views of multi-protein complexes in the erythrocyte membrane. Blood Cells Mol Dis 2012; 49:1-10. [PMID: 22465511 PMCID: PMC4443426 DOI: 10.1016/j.bcmd.2012.03.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 02/27/2012] [Indexed: 12/20/2022]
Abstract
The erythrocyte membrane has been extensively studied, both as a model membrane system and to investigate its role in gas exchange and transport. Much is now known about the protein components of the membrane, how they are organised into large multi-protein complexes and how they interact with each other within these complexes. Many links between the membrane and the cytoskeleton have also been delineated and have been demonstrated to be crucial for maintaining the deformability and integrity of the erythrocyte. In this study we have refined previous, highly speculative molecular models of these complexes by including the available data pertaining to known protein-protein interactions. While the refined models remain highly speculative, they provide an evolving framework for visualisation of these important cellular structures at the atomic level.
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Affiliation(s)
- T J Mankelow
- Bristol Institute for Transfusion Sciences, N.H.S. Blood & Transplant, UK
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23
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Brandon S, Beth AH, Hustedt EJ. The global analysis of DEER data. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 218:93-104. [PMID: 22578560 PMCID: PMC3608411 DOI: 10.1016/j.jmr.2012.03.006] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 03/10/2012] [Accepted: 03/12/2012] [Indexed: 05/11/2023]
Abstract
Double Electron-Electron Resonance (DEER) has emerged as a powerful technique for measuring long range distances and distance distributions between paramagnetic centers in biomolecules. This information can then be used to characterize functionally relevant structural and dynamic properties of biological molecules and their macromolecular assemblies. Approaches have been developed for analyzing experimental data from standard four-pulse DEER experiments to extract distance distributions. However, these methods typically use an a priori baseline correction to account for background signals. In the current work an approach is described for direct fitting of the DEER signal using a model for the distance distribution which permits a rigorous error analysis of the fitting parameters. Moreover, this approach does not require a priori background correction of the experimental data and can take into account excluded volume effects on the background signal when necessary. The global analysis of multiple DEER data sets is also demonstrated. Global analysis has the potential to provide new capabilities for extracting distance distributions and additional structural parameters in a wide range of studies.
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Affiliation(s)
| | | | - Eric J. Hustedt
- Corresponding author. Address: 735B Light Hall, Vanderbilt University, Nashville, TN 37232, United States. (E.J. Hustedt)
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24
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Hagelueken G, Ward R, Naismith JH, Schiemann O. MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL. APPLIED MAGNETIC RESONANCE 2012; 42:377-391. [PMID: 22448103 PMCID: PMC3296949 DOI: 10.1007/s00723-012-0314-0] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Indexed: 05/09/2023]
Abstract
MtsslWizard is a computer program, which operates as a plugin for the PyMOL molecular graphics system. MtsslWizard estimates distances between spin labels on proteins quickly with user-configurable options through a simple graphical interface. In default mode, the program searches for ensembles of possible MTSSL conformations that do not clash with a static model of the protein. Once conformations are assigned, distance distributions between two or more ensembles are calculated, displayed, and can be exported to other software. The program's use is evaluated in a number of challenging test cases and its strengths and weaknesses evaluated. The benefits of the program are its accuracy and simplicity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00723-012-0314-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gregor Hagelueken
- Biomedical Sciences Research Complex, The University of St. Andrews, Fife, KY16 9ST UK
| | - Richard Ward
- Biomedical Sciences Research Complex, The University of St. Andrews, Fife, KY16 9ST UK
| | - James H. Naismith
- Biomedical Sciences Research Complex, The University of St. Andrews, Fife, KY16 9ST UK
| | - Olav Schiemann
- Biomedical Sciences Research Complex, The University of St. Andrews, Fife, KY16 9ST UK
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25
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Zhang X, Tung CS, Sowa GZ, Hatmal MM, Haworth IS, Qin PZ. Global structure of a three-way junction in a phi29 packaging RNA dimer determined using site-directed spin labeling. J Am Chem Soc 2012; 134:2644-52. [PMID: 22229766 DOI: 10.1021/ja2093647] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The condensation of bacteriophage phi29 genomic DNA into its preformed procapsid requires the DNA packaging motor, which is the strongest known biological motor. The packaging motor is an intricate ring-shaped protein/RNA complex, and its function requires an RNA component called packaging RNA (pRNA). Current structural information on pRNA is limited, which hinders studies of motor function. Here, we used site-directed spin labeling to map the conformation of a pRNA three-way junction that bridges binding sites for the motor ATPase and the procapsid. The studies were carried out on a pRNA dimer, which is the simplest ring-shaped pRNA complex and serves as a functional intermediate during motor assembly. Using a nucleotide-independent labeling scheme, stable nitroxide radicals were attached to eight specific pRNA sites without perturbing RNA folding and dimer formation, and a total of 17 internitroxide distances spanning the three-way junction were measured using Double Electron-Electron Resonance spectroscopy. The measured distances, together with steric chemical constraints, were used to select 3662 viable three-way junction models from a pool of 65 billion. The results reveal a similar conformation among the viable models, with two of the helices (H(T) and H(L)) adopting an acute bend. This is in contrast to a recently reported pRNA tetramer crystal structure, in which H(T) and H(L) stack onto each other linearly. The studies establish a new method for mapping global structures of complex RNA molecules, and provide information on pRNA conformation that aids investigations of phi29 packaging motor and developments of pRNA-based nanomedicine and nanomaterial.
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Affiliation(s)
- Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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26
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Kodippili GC, Spector J, Hale J, Giger K, Hughes MR, McNagny KM, Birkenmeier C, Peters L, Ritchie K, Low PS. Analysis of the mobilities of band 3 populations associated with ankyrin protein and junctional complexes in intact murine erythrocytes. J Biol Chem 2011; 287:4129-38. [PMID: 22147703 DOI: 10.1074/jbc.m111.294439] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Current models of the erythrocyte membrane depict three populations of band 3: (i) a population tethered to spectrin via ankyrin, (ii) a fraction attached to the spectrin-actin junctional complex via adducin, and (iii) a freely diffusing population. Because many studies of band 3 diffusion also distinguish three populations of the polypeptide, it has been speculated that the three populations envisioned in membrane models correspond to the three fractions observed in diffusion analyses. To test this hypothesis, we characterized band 3 diffusion by single-particle tracking in wild-type and ankyrin- and adducin-deficient erythrocytes. We report that ∼40% of total band 3 in wild-type murine erythrocytes is attached to ankyrin, whereas ∼33% is immobilized by adducin, and ∼27% is not attached to any cytoskeletal anchor. More detailed analyses reveal that mobilities of individual ankyrin- and adducin-tethered band 3 molecules are heterogeneous, varying by nearly 2 orders of magnitude and that there is considerable overlap in diffusion coefficients for adducin and ankyrin-tethered populations. Taken together, the data suggest that although the ankyrin- and adducin-immobilized band 3 can be monitored separately, significant heterogeneity still exists within each population, suggesting that structural and compositional properties likely vary considerably within each band 3 complex.
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Affiliation(s)
- Gayani C Kodippili
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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