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Wang DTW, Tang TYC, Kuo CT, Yu YT, Chen EHL, Lee MT, Tsai RF, Chen HY, Chiang YW, Chen RPY. Cholesterol twists the transmembrane Di-Gly region of amyloid-precursor protein. PNAS NEXUS 2023; 2:pgad162. [PMID: 37265546 PMCID: PMC10230161 DOI: 10.1093/pnasnexus/pgad162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/08/2023] [Indexed: 06/03/2023]
Abstract
Nearly 95% of Alzheimer's disease (AD) occurs sporadically without genetic linkage. Aging, hypertension, high cholesterol content, and diabetes are known nongenomic risk factors of AD. Aggregation of Aβ peptides is an initial event of AD pathogenesis. Aβ peptides are catabolic products of a type I membrane protein called amyloid precursor protein (APP). Aβ40 is the major product, whereas the 2-residue-longer version, Aβ42, induces amyloid plaque formation in the AD brain. Since cholesterol content is one risk factor for sporadic AD, we aimed to explore whether cholesterol in the membrane affects the structure of the APP transmembrane region, thereby modulating the γ-secretase cutting behavior. Here, we synthesized several peptides containing the APP transmembrane region (sequence 693-726, corresponding to the Aβ22-55 sequence) with one or two Cys mutations for spin labeling. We performed three electron spin resonance experiments to examine the structural changes of the peptides in liposomes composed of dioleoyl phosphatidylcholine and different cholesterol content. Our results show that cholesterol increases membrane thickness by 10% and peptide length accordingly. We identified that the di-glycine region of Aβ36-40 (sequence VGGVV) exhibits the most profound change in response to cholesterol compared with other segments, explaining how the presence of cholesterol affects the γ-secretase cutting site. This study provides spectroscopic evidence showing how cholesterol modulates the structure of the APP transmembrane region in a lipid bilayer.
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Affiliation(s)
- David Tzu-Wei Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Tiffany Y C Tang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chun-Ting Kuo
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Yun-Ting Yu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Eric H L Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Tao Lee
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
- Department of Physics, National Central University, Zhongli 320317, Taiwan
| | - Ruei-Fong Tsai
- Department of Chemistry, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Hung-Ying Chen
- Department of Chemistry, National Tsing Hua University, Hsinchu 300044, Taiwan
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2
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Chu BK, Tsai R, Hung C, Kuo Y, Chen EH, Chiang Y, Chan SI, Chen RP. Location of the cross-β structure in prion fibrils: A search by seeding and electron spin resonance spectroscopy. Protein Sci 2022; 31:e4326. [PMID: 35634767 PMCID: PMC9112485 DOI: 10.1002/pro.4326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 12/19/2022]
Abstract
Prion diseases are transmissible fatal neurodegenerative disorders spreading between humans and other mammals. The pathogenic agent, prion, is a protease-resistant, β-sheet-rich protein aggregate, converted from a membrane protein called PrPC . PrPSc is the misfolded form of PrPC and undergoes self-propagation to form the infectious amyloids. Since the key hallmark of prion disease is amyloid formation, identifying and studying which segments are involved in the amyloid core can provide molecular details about prion diseases. It has been known that the prion protein could also form non-infectious fibrils in the presence of denaturants. In this study, we employed a combination of site-directed nitroxide spin-labeling, fibril seeding, and electron spin resonance (ESR) spectroscopy to identify the structure of the in vitro-prepared full-length mouse prion fibrils. It is shown that in the in vitro amyloidogenesis, the formation of the amyloid core is linked to an α-to-β structural transformation involving the segment 160-224, which contains strand 2, helix 2, and helix 3. This method is particularly suitable for examining the hetero-seeded amyloid fibril structure, as the unlabeled seeds are invisible by ESR spectroscopy. It can be applied to study the structures of different strains of infectious prions or other amyloid fibrils in the future.
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Affiliation(s)
- Brett K.‐Y. Chu
- Institute of Biological ChemistryAcademia SinicaTaipeiTaiwan
- Department of ChemistryNational Taiwan UniversityTaipeiTaiwan
| | - Ruei‐Fong Tsai
- Department of ChemistryNational Tsing Hua UniversityHsinchuTaiwan
| | - Chien‐Lun Hung
- Department of ChemistryNational Tsing Hua UniversityHsinchuTaiwan
| | - Yun‐Hsuan Kuo
- Department of ChemistryNational Tsing Hua UniversityHsinchuTaiwan
| | - Eric H.‐L. Chen
- Institute of Biological ChemistryAcademia SinicaTaipeiTaiwan
| | - Yun‐Wei Chiang
- Department of ChemistryNational Tsing Hua UniversityHsinchuTaiwan
| | - Sunney I. Chan
- Department of ChemistryNational Taiwan UniversityTaipeiTaiwan
- Institute of ChemistryAcademia SinicaTaipeiTaiwan
| | - Rita P.‐Y. Chen
- Institute of Biological ChemistryAcademia SinicaTaipeiTaiwan
- Institute of Biochemical SciencesNational Taiwan UniversityTaipeiTaiwan
- Neuroscience Program of Academia SinicaAcademia SinicaTaipeiTaiwan
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3
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Puthenveetil R, Christenson ET, Vinogradova O. New Horizons in Structural Biology of Membrane Proteins: Experimental Evaluation of the Role of Conformational Dynamics and Intrinsic Flexibility. MEMBRANES 2022; 12:227. [PMID: 35207148 PMCID: PMC8877495 DOI: 10.3390/membranes12020227] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
A plethora of membrane proteins are found along the cell surface and on the convoluted labyrinth of membranes surrounding organelles. Since the advent of various structural biology techniques, a sub-population of these proteins has become accessible to investigation at near-atomic resolutions. The predominant bona fide methods for structure solution, X-ray crystallography and cryo-EM, provide high resolution in three-dimensional space at the cost of neglecting protein motions through time. Though structures provide various rigid snapshots, only an amorphous mechanistic understanding can be inferred from interpolations between these different static states. In this review, we discuss various techniques that have been utilized in observing dynamic conformational intermediaries that remain elusive from rigid structures. More specifically we discuss the application of structural techniques such as NMR, cryo-EM and X-ray crystallography in studying protein dynamics along with complementation by conformational trapping by specific binders such as antibodies. We finally showcase the strength of various biophysical techniques including FRET, EPR and computational approaches using a multitude of succinct examples from GPCRs, transporters and ion channels.
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Affiliation(s)
- Robbins Puthenveetil
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 35A Convent Dr., Bethesda, MD 20892, USA
| | | | - Olga Vinogradova
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
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4
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Probing Structural Dynamics of Membrane Proteins Using Electron Paramagnetic Resonance Spectroscopic Techniques. BIOPHYSICA 2021. [DOI: 10.3390/biophysica1020009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Membrane proteins are essential for the survival of living organisms. They are involved in important biological functions including transportation of ions and molecules across the cell membrane and triggering the signaling pathways. They are targets of more than half of the modern medical drugs. Despite their biological significance, information about the structural dynamics of membrane proteins is lagging when compared to that of globular proteins. The major challenges with these systems are low expression yields and lack of appropriate solubilizing medium required for biophysical techniques. Electron paramagnetic resonance (EPR) spectroscopy coupled with site directed spin labeling (SDSL) is a rapidly growing powerful biophysical technique that can be used to obtain pertinent structural and dynamic information on membrane proteins. In this brief review, we will focus on the overview of the widely used EPR approaches and their emerging applications to answer structural and conformational dynamics related questions on important membrane protein systems.
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5
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Sahu ID, Lorigan GA. Site-Directed Spin Labeling EPR for Studying Membrane Proteins. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3248289. [PMID: 29607317 PMCID: PMC5828257 DOI: 10.1155/2018/3248289] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 12/21/2017] [Indexed: 01/13/2023]
Abstract
Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy is a rapidly expanding powerful biophysical technique to study the structural and dynamic properties of membrane proteins in a native environment. Membrane proteins are responsible for performing important functions in a wide variety of complicated biological systems that are responsible for the survival of living organisms. In this review, a brief introduction of the most popular SDSL EPR techniques and illustrations of recent applications for studying pertinent structural and dynamic properties on membrane proteins will be discussed.
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Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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6
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Le Breton N, Adrianaivomananjaona T, Gerbaud G, Etienne E, Bisetto E, Dautant A, Guigliarelli B, Haraux F, Martinho M, Belle V. Dimerization interface and dynamic properties of yeast IF1 revealed by Site-Directed Spin Labeling EPR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:89-97. [PMID: 26518384 DOI: 10.1016/j.bbabio.2015.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/21/2015] [Accepted: 10/25/2015] [Indexed: 11/21/2022]
Abstract
The mitochondrial ATPase inhibitor, IF1, regulates the activity of the mitochondrial ATP synthase. The oligomeric state of IF1 related to pH is crucial for its inhibitory activity. Although extensive structural studies have been performed to characterize the oligomeric states of bovine IF1, only little is known concerning those of yeast IF1. While bovine IF1 can be found as an inhibitory dimer at low pH and a non-inhibitory tetramer at high pH, a monomer/dimer equilibrium has been described for yeast IF1, high pH values favoring the monomeric state. Combining different strategies involving the grafting of nitroxide spin labels combined with Electron Paramagnetic Resonance (EPR) spectroscopy, the present study brings the first structural characterization, at the residue level, of yeast IF1 in its dimeric form. The results show that the dimerization interface involves the central region of the peptide revealing that the dimer corresponds to a non-inhibitory state. Moreover, we demonstrate that the C-terminal region of the peptide is highly dynamic and that this segment is probably folded back onto the central region. Finally, the pH-dependence of the inter-label distance distribution has been observed indicating a conformational change between two structural states in the dimer.
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Affiliation(s)
- Nolwenn Le Breton
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille, France
| | - Tiona Adrianaivomananjaona
- Lifesearch, 72 rue du Fauboug St Honoré, F-75008 Paris, France; CEA, Institut de Biologie et de Technologies de Saclay IBITECS, SB2SM, F-91191 Gif sur Yvette, France; CEA, CNRS, Université Paris Sud, Institut de Biologie Intégrative de la Cellule I2BC, UMR 9198, F-91191 Gif sur Yvette, France
| | - Guillaume Gerbaud
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille, France
| | - Emilien Etienne
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille, France
| | - Elena Bisetto
- CEA, Institut de Biologie et de Technologies de Saclay IBITECS, SB2SM, F-91191 Gif sur Yvette, France; Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, I-33100 Udine, Italy
| | - Alain Dautant
- University Bordeaux-CNRS, IBGC, UMR 5095, 1 rue Camille Saint-Saëns, F-33000 Bordeaux, France
| | - Bruno Guigliarelli
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille, France
| | - Francis Haraux
- CEA, Institut de Biologie et de Technologies de Saclay IBITECS, SB2SM, F-91191 Gif sur Yvette, France; CEA, CNRS, Université Paris Sud, Institut de Biologie Intégrative de la Cellule I2BC, UMR 9198, F-91191 Gif sur Yvette, France.
| | - Marlène Martinho
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille, France
| | - Valérie Belle
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille, France.
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7
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Abstract
Membrane proteins are very important in controlling bioenergetics, functional activity, and initializing signal pathways in a wide variety of complicated biological systems. They also represent approximately 50% of the potential drug targets. EPR spectroscopy is a very popular and powerful biophysical tool that is used to study the structural and dynamic properties of membrane proteins. In this article, a basic overview of the most commonly used EPR techniques and examples of recent applications to answer pertinent structural and dynamic related questions on membrane protein systems will be presented.
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Affiliation(s)
- Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States of America
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States of America
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8
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Sung TC, Li CY, Lai YC, Hung CL, Shih O, Yeh YQ, Jeng US, Chiang YW. Solution Structure of Apoptotic BAX Oligomer: Oligomerization Likely Precedes Membrane Insertion. Structure 2015; 23:1878-1888. [PMID: 26299946 DOI: 10.1016/j.str.2015.07.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/06/2015] [Accepted: 07/28/2015] [Indexed: 12/23/2022]
Abstract
Proapoptotic BAX protein is largely cytosolic in healthy cells, but it oligomerizes and translocates to mitochondria upon receiving apoptotic stimuli. A long-standing challenge has been the inability to capture any structural information beyond the onset of activation. Here, we present solution structures of an activated BAX oligomer by means of spectroscopic and scattering methods, providing details about the monomer-monomer interfaces in the oligomer and how the oligomer is assembled from homodimers. We show that this soluble oligomer undergoes a direct conversion into membrane-inserted oligomer, which has the ability of inducing apoptosis and structurally resembles a membrane-embedded oligomer formed from BAX monomers in lipid environment. Structural differences between the soluble and the membrane-inserted oligomers are manifested in the C-terminal helices. Our data suggest an alternative pathway of apoptosis in which BAX oligomer formation occurs prior to membrane insertion.
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Affiliation(s)
- Tai-Ching Sung
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Ching-Yu Li
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yei-Chen Lai
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chien-Lun Hung
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.
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9
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Hacker SM, Hintze C, Marx A, Drescher M. Monitoring enzymatic ATP hydrolysis by EPR spectroscopy. Chem Commun (Camb) 2015; 50:7262-4. [PMID: 24872080 DOI: 10.1039/c4cc02422b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An adenosine triphosphate (ATP) analogue modified with two nitroxide radicals is developed and employed to study its enzymatic hydrolysis by electron paramagnetic resonance spectroscopy. For this application, we demonstrate that EPR holds the potential to complement fluorogenic substrate analogues in monitoring enzymatic activity.
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Affiliation(s)
- Stephan M Hacker
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
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10
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Yang C, Lo WL, Kuo YH, Sang JC, Lee CY, Chiang YW, Chen RPY. Revealing structural changes of prion protein during conversion from α-helical monomer to β-oligomers by means of ESR and nanochannel encapsulation. ACS Chem Biol 2015; 10:493-501. [PMID: 25375095 DOI: 10.1021/cb500765e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Under nondenaturing neutral pH conditions, full-length mouse recombinant prion protein lacking the only disulfide bridge can spontaneously convert from an α-helical-dominant conformer (α-state) to a β-sheet-rich conformer (β-state), which then associates into β-oligomers, and the kinetics of this spontaneous conversion depends on the properties of the buffer used. The molecular details of this structural conversion have not been reported due to the difficulty of exploring big protein aggregates. We introduced spin probes into different structural segments (three helices and the loop between strand 1 and helix 1), and employed a combined approach of ESR spectroscopy and protein encapsulation in nanochannels to reveal local structural changes during the α-to-β transition. Nanochannels provide an environment in which prion protein molecules are isolated from each other, but the α-to-β transition can still occur. By measuring dipolar interactions between spin probes during the transition, we showed that helix 1 and helix 3 retained their helicity, while helix 2 unfolded to form an extended structure. Moreover, our pulsed ESR results allowed clear discrimination between the intra- and intermolecular distances between spin labeled residues in helix 2 in the β-oligomers, making it possible to demonstrate that the unfolded helix 2 segment lies at the association interface of the β-oligomers to form cross-β structure.
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Affiliation(s)
- Che Yang
- Institute
of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan, R.O.C
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan, R.O.C
| | - Wei-Lin Lo
- Institute
of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan, R.O.C
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan, R.O.C
| | - Yun-Hsuan Kuo
- Department
of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan, R.O.C
| | - Jason C. Sang
- Institute
of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan, R.O.C
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan, R.O.C
| | - Chung-Yu Lee
- Institute
of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan, R.O.C
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan, R.O.C
| | - Yun-Wei Chiang
- Department
of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan, R.O.C
| | - Rita P.-Y. Chen
- Institute
of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan, R.O.C
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan, R.O.C
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11
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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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12
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Abé C, Dietrich F, Gajula P, Benz M, Vogel KP, van Gastel M, Illenberger S, Ziegler WH, Steinhoff HJ. Monomeric and dimeric conformation of the vinculin tail five-helix bundle in solution studied by EPR spectroscopy. Biophys J 2012; 101:1772-80. [PMID: 21961604 DOI: 10.1016/j.bpj.2011.08.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 08/03/2011] [Accepted: 08/31/2011] [Indexed: 11/28/2022] Open
Abstract
The cytoskeletal adaptor protein vinculin plays an important role in the control of cell adhesion and migration, linking the actin cytoskeleton to adhesion receptor complexes in cell adhesion sites. The conformation of the vinculin tail dimer, which is crucial for protein function, was analyzed using site-directed spin labeling in electron paramagnetic resonance spectroscopy. Interspin distances for a set of six singly and four doubly spin-labeled mutants of the tail domain of vinculin were determined and used as constraints for modeling of the vinculin tail dimer. A comparison of the results obtained by molecular dynamic simulations and a rotamer library approach reveals that the crystal structure of the vinculin tail monomer is essentially preserved in aqueous solution. The orientation of monomers within the dimer observed previously by x-ray crystallography agrees with the solution electron paramagnetic resonance data. Furthermore, the distance between positions 1033 is shown to increase by >3 nm upon interaction of the vinculin tail domain with F-actin.
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Affiliation(s)
- Christoph Abé
- Department of Physics, University of Osnabrück, Osnabrück, Germany
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13
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Huang YW, Chiang YW. Spin-label ESR with nanochannels to improve the study of backbone dynamics and structural conformations of polypeptides. Phys Chem Chem Phys 2011; 13:17521-31. [PMID: 21892486 DOI: 10.1039/c1cp20986h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nanochannels of mesoporous silica materials were previously found useful for reducing the tumbling motion of encapsulated biomolecules while leaving the biomolecular structure undisturbed. Here we show that experiments of cw-ESR distance measurement in nano-confinement can benefit immediately from the above mentioned features of sufficiently slow molecular tumbling, enabling more accurate determination of interspin distances throughout the temperature range, from 200 to 300 K. A 26-residue prion protein peptide, which can fold into either a helical or hairpin structure, as well as its variants, are studied by using ESR. By comparing the spectra obtained in vitrified bulk solutions vs. mesopores, the spectra from the latter display typical slow-motional lineshapes, thereby enabling dipolar anisotropy to be unambiguously revealed throughout the temperature range, whereas the spectra from the former are dominated by the disordering of the side chain and the rotational tumbling of the peptide. The spectral changes regarding the two secondary structures in nano-confinement are found to show a strong correlation with the dynamic properties of the backbones. The effect of viscosity agent perturbation on the motion of an R1 nitroxide side chain, a commonly employed probe, could be substantial in a bulk solution condition, though it is absolutely absent in nanochannels. Under nano-confinement, the probe is proven sufficiently sensitive to the backbone motions. Overall, the distance distributions determined from the mesopore studies not only describe the conformational structures (by average distances), but also the backbone dynamics (by distribution widths) of the spin-labeled peptides.
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Affiliation(s)
- Ya-Wen Huang
- Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan
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14
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Sung TC, Chiang YW. Identification of complex dynamic modes on prion protein peptides using multifrequency ESR with mesoporous materials. Phys Chem Chem Phys 2010; 12:13117-25. [DOI: 10.1039/c0cp00685h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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