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Kyrychenko A, Ladokhin AS. Fluorescent Probes and Quenchers in Studies of Protein Folding and Protein-Lipid Interactions. CHEM REC 2024; 24:e202300232. [PMID: 37695081 PMCID: PMC11113672 DOI: 10.1002/tcr.202300232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/20/2023] [Indexed: 09/12/2023]
Abstract
Fluorescence spectroscopy provides numerous methodological tools for structural and functional studies of biological macromolecules and their complexes. All fluorescence-based approaches require either existence of an intrinsic probe or an introduction of an extrinsic one. Moreover, studies of complex systems often require an additional introduction of a specific quencher molecule acting in combination with a fluorophore to provide structural or thermodynamic information. Here, we review the fundamentals and summarize the latest progress in applications of different classes of fluorescent probes and their specific quenchers, aimed at studies of protein folding and protein-membrane interactions. Specifically, we discuss various environment-sensitive dyes, FRET probes, probes for short-distance measurements, and several probe-quencher pairs for studies of membrane penetration of proteins and peptides. The goals of this review are: (a) to familiarize the readership with the general concept that complex biological systems often require both a probe and a quencher to decipher mechanistic details of functioning and (b) to provide example of the immediate applications of the described methods.
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Affiliation(s)
- Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody sq., Kharkiv, 61022, Ukraine
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, United States
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2
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Maity S, Price BD, Wilson CB, Mukherjee A, Starck M, Parker D, Wilson MZ, Lovett JE, Han S, Sherwin MS. Triggered Functional Dynamics of AsLOV2 by Time-Resolved Electron Paramagnetic Resonance at High Magnetic Fields. Angew Chem Int Ed Engl 2023; 62:e202212832. [PMID: 36638360 DOI: 10.1002/anie.202212832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
We present time-resolved Gd-Gd electron paramagnetic resonance (TiGGER) at 240 GHz for tracking inter-residue distances during a protein's mechanical cycle in the solution state. TiGGER makes use of Gd-sTPATCN spin labels, whose favorable qualities include a spin-7/2 EPR-active center, short linker, narrow intrinsic linewidth, and virtually no anisotropy at high fields (8.6 T) when compared to nitroxide spin labels. Using TiGGER, we determined that upon light activation, the C-terminus and N-terminus of AsLOV2 separate in less than 1 s and relax back to equilibrium with a time constant of approximately 60 s. TiGGER revealed that the light-activated long-range mechanical motion is slowed in the Q513A variant of AsLOV2 and is correlated to the similarly slowed relaxation of the optically excited chromophore as described in recent literature. TiGGER has the potential to valuably complement existing methods for the study of triggered functional dynamics in proteins.
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Affiliation(s)
- Shiny Maity
- Dept. of Chemistry and Biochemistry, Univ. of California, Santa Barbara, CA 93106, USA
| | - Brad D Price
- Dept. of Physics, Univ. of California, Santa Barbara, CA 93106, USA
| | - C Blake Wilson
- Dept. of Physics, Univ. of California, Santa Barbara, CA 93106, USA.,Laboratory of Chemical Physics, Nat. Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892-0520, USA
| | - Arnab Mukherjee
- Dept. of Chemical Engineering, Univ. of California, Santa Barbara, CA 93106, USA
| | | | - David Parker
- Dept. of Chemistry, Univ. of Durham, Durham, DH1 3LE, UK
| | - Maxwell Z Wilson
- Dept. of Molecular, Cellular, and Developmental Biology, Univ. of California, Santa Barbara, CA 93106, USA
| | - Janet E Lovett
- School of Physics and Astronomy and the Biomedical Sciences Research Complex, Univ. of St. Andrews, St. Andrews, KY16 9SS, UK
| | - Songi Han
- Dept. of Chemistry and Biochemistry, Univ. of California, Santa Barbara, CA 93106, USA
| | - Mark S Sherwin
- Dept. of Physics, Univ. of California, Santa Barbara, CA 93106, USA
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3
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Ma L, Li X, Petersen RB, Peng A, Huang K. Probing the interactions between amyloidogenic proteins and bio-membranes. Biophys Chem 2023; 296:106984. [PMID: 36889133 DOI: 10.1016/j.bpc.2023.106984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/11/2023] [Accepted: 02/22/2023] [Indexed: 03/01/2023]
Abstract
Protein misfolding diseases (PMDs) in humans are characterized by the deposition of protein aggregates in tissues, including Alzheimer's disease, Parkinson's disease, type 2 diabetes, and amyotrophic lateral sclerosis. Misfolding and aggregation of amyloidogenic proteins play a central role in the onset and progression of PMDs, and these processes are regulated by multiple factors, especially the interaction between proteins and bio-membranes. Bio-membranes induce conformational changes in amyloidogenic proteins and affect their aggregation; on the other hand, the aggregates of amyloidogenic proteins may cause membrane damage or dysfunction leading to cytotoxicity. In this review, we summarize the factors that affect the binding of amyloidogenic proteins and membranes, the effects of bio-membranes on the aggregation of amyloidogenic proteins, mechanisms of membrane disruption by amyloidogenic aggregates, technical approaches for detecting these interactions, and finally therapeutic strategies targeting membrane damage caused by amyloidogenic proteins.
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Affiliation(s)
- Liang Ma
- Department of Pharmacy, Wuhan Mental Health Center, Wuhan, China; Department of Pharmacy, Wuhan Hospital for Psychotherapy, Wuhan, China
| | - Xi Li
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Robert B Petersen
- Foundational Sciences, Central Michigan University College of Medicine, Mount Pleasant, MI, USA
| | - Anlin Peng
- Department of Pharmacy, The Third Hospital of Wuhan, Tongren Hospital of Wuhan University, Wuhan, China.
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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4
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A conformational switch in clathrin light chain regulates lattice structure and endocytosis at the plasma membrane of mammalian cells. Nat Commun 2023; 14:732. [PMID: 36759616 PMCID: PMC9911608 DOI: 10.1038/s41467-023-36304-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Conformational changes in endocytic proteins are regulators of clathrin-mediated endocytosis. Three clathrin heavy chains associated with clathrin light chains (CLC) assemble into triskelia that link into a geometric lattice that curves to drive endocytosis. Structural changes in CLC have been shown to regulate triskelia assembly in solution, yet the nature of these changes, and their effects on lattice growth, curvature, and endocytosis in cells are unknown. Here, we develop a new correlative fluorescence resonance energy transfer (FRET) and platinum replica electron microscopy method, named FRET-CLEM. With FRET-CLEM, we measure conformational changes in clathrin at thousands of individual morphologically distinct clathrin-coated structures. We discover that the N-terminus of CLC repositions away from the plasma membrane and triskelia vertex as coats curve. Preventing this conformational switch with chemical tools increases lattice sizes and inhibits endocytosis. Thus, a specific conformational switch in the light chain regulates lattice curvature and endocytosis in mammalian cells.
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Cui TR, Qiao YC, Gao JW, Wang CH, Zhang Y, Han L, Yang Y, Ren TL. Ultrasensitive Detection of COVID-19 Causative Virus (SARS-CoV-2) Spike Protein Using Laser Induced Graphene Field-Effect Transistor. Molecules 2021; 26:6947. [PMID: 34834039 PMCID: PMC8621829 DOI: 10.3390/molecules26226947] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/08/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022] Open
Abstract
COVID-19 is a highly contagious human infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the war with the virus is still underway. Since no specific drugs have been made available yet and there is an imbalance between supply and demand for vaccines, early diagnosis and isolation are essential to control the outbreak. Current nucleic acid testing methods require high sample quality and laboratory conditions, which cannot meet flexible applications. Here, we report a laser-induced graphene field-effect transistor (LIG-FET) for detecting SARS-CoV-2. The FET was manufactured by different reduction degree LIG, with an oyster reef-like porous graphene channel to enrich the binding point between the virus protein and sensing area. After immobilizing specific antibodies in the channel, the FET can detect the SARS-CoV-2 spike protein in 15 min at a concentration of 1 pg/mL in phosphate-buffered saline (PBS) and 1 ng/mL in human serum. In addition, the sensor shows great specificity to the spike protein of SARS-CoV-2. Our sensors can realize fast production for COVID-19 rapid testing, as each LIG-FET can be fabricated by a laser platform in seconds. It is the first time that LIG has realized a virus sensing FET without any sample pretreatment or labeling, which paves the way for low-cost and rapid detection of COVID-19.
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Affiliation(s)
- Tian-Rui Cui
- School of Integrated Circuit, Tsinghua University, Beijing 100084, China; (T.-R.C.); (Y.-C.Q.)
- Beijing National Research Center for Information Science and Technology (BNRist), Tsinghua University, Beijing 100084, China
| | - Yan-Cong Qiao
- School of Integrated Circuit, Tsinghua University, Beijing 100084, China; (T.-R.C.); (Y.-C.Q.)
- Beijing National Research Center for Information Science and Technology (BNRist), Tsinghua University, Beijing 100084, China
| | - Jian-Wei Gao
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (J.-W.G.); (C.-H.W.); (Y.Z.)
| | - Chun-Hua Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (J.-W.G.); (C.-H.W.); (Y.Z.)
| | - Yu Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (J.-W.G.); (C.-H.W.); (Y.Z.)
| | - Lin Han
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (J.-W.G.); (C.-H.W.); (Y.Z.)
| | - Yi Yang
- School of Integrated Circuit, Tsinghua University, Beijing 100084, China; (T.-R.C.); (Y.-C.Q.)
- Beijing National Research Center for Information Science and Technology (BNRist), Tsinghua University, Beijing 100084, China
| | - Tian-Ling Ren
- School of Integrated Circuit, Tsinghua University, Beijing 100084, China; (T.-R.C.); (Y.-C.Q.)
- Beijing National Research Center for Information Science and Technology (BNRist), Tsinghua University, Beijing 100084, China
- Center for Flexible Electronics Technology, Tsinghua University, Beijing 100084, China
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Deal J, Pleshinger DJ, Johnson SC, Leavesley SJ, Rich TC. Milestones in the development and implementation of FRET-based sensors of intracellular signals: A biological perspective of the history of FRET. Cell Signal 2020; 75:109769. [PMID: 32898611 DOI: 10.1016/j.cellsig.2020.109769] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 01/24/2023]
Abstract
Fӧrster resonance energy transfer (FRET) has been described for more than a century. FRET has become a mainstay for the study of protein localization in living cells and tissues. It has also become widely used in the fields that comprise cellular signaling. FRET-based probes have been developed to monitor second messenger signals, the phosphorylation state of peptides and proteins, and subsequent cellular responses. Here, we discuss the milestones that led to FRET becoming a widely used tool for the study of biological systems: the theoretical description of FRET, the insight to use FRET as a molecular ruler, and the isolation and genetic modification of green fluorescent protein (GFP). Each of these milestones were critical to the development of a myriad of FRET-based probes and reporters in common use today. FRET-probes offer a unique opportunity to interrogate second messenger signals and subsequent protein phosphorylation - and perhaps the most effective approach for study of cAMP/PKA pathways. As such, FRET probes are widely used in the study of intracellular signaling pathways. Yet, somehow, the potential of FRET-based probes to provide windows through which we can visualize complex cellular signaling systems has not been fully reached. Hence we conclude by discussing the technical challenges to be overcome if FRET-based probes are to live up to their potential for the study of complex signaling networks.
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Affiliation(s)
- J Deal
- Basic Medical Sciences Graduate Program, University of South Alabama, Mobile, AL 36688, USA; Center for Lung Biology, Departments of Biomolecular Engineering, University of South Alabama, Mobile, AL 36688, USA
| | - D J Pleshinger
- Center for Lung Biology, Departments of Biomolecular Engineering, University of South Alabama, Mobile, AL 36688, USA; Pharmacology and Biomolecular Engineering, University of South Alabama, Mobile, AL 36688, USA
| | - S C Johnson
- Basic Medical Sciences Graduate Program, University of South Alabama, Mobile, AL 36688, USA; Pharmacology and Biomolecular Engineering, University of South Alabama, Mobile, AL 36688, USA
| | - S J Leavesley
- Basic Medical Sciences Graduate Program, University of South Alabama, Mobile, AL 36688, USA; Center for Lung Biology, Departments of Biomolecular Engineering, University of South Alabama, Mobile, AL 36688, USA; Pharmacology and Biomolecular Engineering, University of South Alabama, Mobile, AL 36688, USA; Chemical and Biomolecular Engineering, University of South Alabama, Mobile, AL 36688, USA
| | - T C Rich
- Basic Medical Sciences Graduate Program, University of South Alabama, Mobile, AL 36688, USA; Center for Lung Biology, Departments of Biomolecular Engineering, University of South Alabama, Mobile, AL 36688, USA; Pharmacology and Biomolecular Engineering, University of South Alabama, Mobile, AL 36688, USA.
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Haffke M, Duckely M, Bergsdorf C, Jaakola VP, Shrestha B. Development of a biochemical and biophysical suite for integral membrane protein targets: A review. Protein Expr Purif 2020; 167:105545. [DOI: 10.1016/j.pep.2019.105545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/18/2019] [Accepted: 11/24/2019] [Indexed: 12/11/2022]
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Gupta K, Toombes GE, Swartz KJ. Exploring structural dynamics of a membrane protein by combining bioorthogonal chemistry and cysteine mutagenesis. eLife 2019; 8:50776. [PMID: 31714877 PMCID: PMC6850778 DOI: 10.7554/elife.50776] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022] Open
Abstract
The functional mechanisms of membrane proteins are extensively investigated with cysteine mutagenesis. To complement cysteine-based approaches, we engineered a membrane protein with thiol-independent crosslinkable groups using azidohomoalanine (AHA), a non-canonical methionine analogue containing an azide group that can selectively react with cycloalkynes through a strain-promoted azide-alkyne cycloaddition (SPAAC) reaction. We demonstrate that AHA can be readily incorporated into the Shaker Kv channel in place of methionine residues and modified with azide-reactive alkyne probes in Xenopus oocytes. Using voltage-clamp fluorometry, we show that AHA incorporation permits site-specific fluorescent labeling to track voltage-dependent conformational changes similar to cysteine-based methods. By combining AHA incorporation and cysteine mutagenesis in an orthogonal manner, we were able to site-specifically label the Shaker Kv channel with two different fluorophores simultaneously. Our results identify a facile and straightforward approach for chemical modification of membrane proteins with bioorthogonal chemistry to explore their structure-function relationships in live cells. Living cells can sense cues from their environment via molecules located at the interface between the inside and the outside of the cell. These molecules are mostly proteins and are made up of building blocks known as amino acids. To understand how these proteins work, fluorescent probes can be attached to amino acids within them – which can then tell when different parts of proteins move in response to a signal. Scientists often target fluorescent probes at the amino acid cysteine, because it has a chemically reactive side group and is rare enough so that unique positions can be labeled in the protein of interest. However, being able to target other amino acids would allow scientists to ask, and potentially solve, more precise questions about these proteins. Methionine is another amino acid that has a low abundance in most proteins. Previous research has shown that the cell’s normal protein-building machinery can incorporate synthetic versions of methionine into proteins. This suggested that the introduction of chemically reactive alternatives to methionine could offer a way to label membrane proteins with fluorescent probes and free up the cysteines to be targeted with other approaches. Gupta et al. set out to develop a straightforward method to achieve this and started with a well-studied membrane protein, called Shaker, and cells from female African clawed frogs, which are widely used to study membrane proteins. Gupta et al. found that the cells could readily take up a chemically reactive methionine alternative called azidohomoalanine (AHA) from their surrounding solution and incorporate it within the Shaker protein. The AHA took the place of the methionines that are normally found in Shaker, and just like in cysteine-based methods, fluorescent probes could be easily attached to the AHAs in this membrane protein. Shaker is a protein that allows potassium ions to flow across the cell membrane by changing shape in response to the membrane voltage. The fluorescence from those probes also changed with the membrane voltage in a way that was comparable to cysteine-mediated approaches. This indicated that the AHA modification could also be used to track structural changes in the Shaker protein. Finally, Gupta et al. showed that AHA- and cysteine-mediated labeling approaches could be combined to attach two different fluorescent probes onto the Shaker protein. This method will expand the toolbox for researchers studying the relationship between the structure and function of membrane proteins in live cells. In future, it could be applied more widely once the properties of the fluorescent probes for AHA-mediated labeling can be optimized.
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Affiliation(s)
- Kanchan Gupta
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, United States
| | - Gilman Es Toombes
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, United States
| | - Kenton J Swartz
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, United States
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Raghuraman H, Chatterjee S, Das A. Site-Directed Fluorescence Approaches for Dynamic Structural Biology of Membrane Peptides and Proteins. Front Mol Biosci 2019; 6:96. [PMID: 31608290 PMCID: PMC6774292 DOI: 10.3389/fmolb.2019.00096] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Membrane proteins mediate a number of cellular functions and are associated with several diseases and also play a crucial role in pathogenicity. Due to their importance in cellular structure and function, they are important drug targets for ~60% of drugs available in the market. Despite the technological advancement and recent successful outcomes in determining the high-resolution structural snapshot of membrane proteins, the mechanistic details underlining the complex functionalities of membrane proteins is least understood. This is largely due to lack of structural dynamics information pertaining to different functional states of membrane proteins in a membrane environment. Fluorescence spectroscopy is a widely used technique in the analysis of functionally-relevant structure and dynamics of membrane protein. This review is focused on various site-directed fluorescence (SDFL) approaches and their applications to explore structural information, conformational changes, hydration dynamics, and lipid-protein interactions of important classes of membrane proteins that include the pore-forming peptides/proteins, ion channels/transporters and G-protein coupled receptors.
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Affiliation(s)
- H. Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, Kolkata, India
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Wong ZC, Fan WY, Chwee TS. Computational modelling of singlet excitation energy transfer: a DFT/TD-DFT study of the ground and excited state properties of a syn bimane dimer system using non-empirically tuned range-separated functionals. NEW J CHEM 2018. [DOI: 10.1039/c8nj02920b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Range-tuned DFT/TD-DFT improves predicted properties for the sequence of events leading to excitation energy transfer (EET) in bimanes.
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Affiliation(s)
- Z. C. Wong
- Institute of High Performance Computing
- Agency for Science, Technology and Research (A*STAR)
- Singapore
- NUS Graduate School for Integrative Sciences and Engineering
- National University of Singapore
| | - W. Y. Fan
- Department of Chemistry
- National University of Singapore
- Singapore
| | - T. S. Chwee
- Institute of High Performance Computing
- Agency for Science, Technology and Research (A*STAR)
- Singapore
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Smith DA, Sessions AL, Dawson KS, Dalleska N, Orphan VJ. Rapid quantification and isotopic analysis of dissolved sulfur species. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:791-803. [PMID: 28249106 DOI: 10.1002/rcm.7846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 01/06/2017] [Accepted: 02/23/2017] [Indexed: 06/06/2023]
Abstract
RATIONALE Dissolved sulfur species are of significant interest, both as important substrates for microbial activities and as key intermediaries in biogeochemical cycles. Species of intermediate oxidation state such as sulfite, thiosulfate, and thiols are of particular interest but are notoriously difficult to analyze, because of low concentrations and rapid oxidation during storage and analysis. METHODS Dissolved sulfur species are reacted with monobromobimane which yields a fluorescent bimane derivative that is stable to oxidation. Separation by Ultra-Performance Liquid Chromatography (UPLC) on a C18 column yields baseline resolution of analytes in under 5 min. Fluorescence detection (380 nm excitation, 480 nm emission) provides highly selective and sensitive quantitation, and Time-of-Flight Mass Spectrometry (TOF-MS) is used to quantify isotopic abundance, providing the ability to detect stable isotope tracers (either 33 S or 34 S). RESULTS Sulfite, thiosulfate, methanethiol, and bisulfide were quantified with on-column detection limits of picomoles (μM concentrations). Other sulfur species with unshared electrons are also amenable to analysis. TOF-MS detection of 34 S enrichment was accurate and precise to within 0.6% (relative) when sample and standard had similar isotope ratios, and was able to detect enrichments as small as 0.01 atom%. Accuracy was validated by comparison to isotope-ratio mass spectrometry. Four example applications are provided to demonstrate the utility of this method. CONCLUSIONS Derivatization of aqueous sulfur species with bromobimane is easily accomplished in the field, and protects analytes from oxidation during storage. UPLC separation with fluorescence detection provides low-μM detection limits. Using high-resolution TOF-MS, accurate detection of as little as 0.01% 34 S label incorporation into multiple species is feasible. This provides a useful new analytical window into microbial sulfur cycling. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Derek A Smith
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | - Alex L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | - Katherine S Dawson
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | - Nathan Dalleska
- Environmental Science and Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
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12
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Wong ZC, Fan WY, Chwee TS, Sullivan MB. Modelling fluorescence lifetimes with TD-DFT: a case study with syn-bimanes. RSC Adv 2016. [DOI: 10.1039/c6ra11495d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Syn-bimanes are a class of fluorophores that are widely used for labelling thiol containing biological systems. We used TD-DFT to study their absorption, emission, solvatochromism, and fluorescence lifetimes.
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Affiliation(s)
- Z. C. Wong
- Institute of High Performance Computing
- Agency for Science
- Technology and Research (A*STAR)
- Singapore
- NUS Graduate School for Integrative Sciences and Engineering
| | - W. Y. Fan
- Department of Chemistry
- National University of Singapore
- Singapore
| | - T. S. Chwee
- Institute of High Performance Computing
- Agency for Science
- Technology and Research (A*STAR)
- Singapore
| | - M. B. Sullivan
- Institute of High Performance Computing
- Agency for Science
- Technology and Research (A*STAR)
- Singapore
- Department of Chemistry
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Sujaree K, Kitjaruwankul S, Boonamnaj P, Supunyabut C, Sompornpisut P. Transmembrane Helix Assembly by Max-Min Ant System Algorithm. Chem Biol Drug Des 2015; 86:1360-72. [PMID: 26058409 DOI: 10.1111/cbdd.12600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/27/2015] [Accepted: 05/25/2015] [Indexed: 11/29/2022]
Abstract
Because of the rapid progress in biochemical and structural studies of membrane proteins, considerable attention has been given on developing efficient computational methods for solving low-to-medium resolution structures using sparse structural data. In this study, we demonstrate a novel algorithm, max-min ant system (MMAS), designed to find an assembly of α-helical transmembrane proteins using a rigid helix arrangement guided by distance constraints. The new algorithm generates a large variety with finite number of orientations of transmembrane helix bundle and finds the solution that is matched with the provided distance constraints based on the behavior of ants to search for the shortest possible path between their nest and the food source. To demonstrate the efficiency of the novel search algorithm, MMAS is applied to determine the transmembrane packing of KcsA and MscL ion channels from a limited distance information extracted from the crystal structures, and the packing of KvAP voltage sensor domain using a set of 10 experimentally determined constraints, and the results are compared with those of two popular used stochastic methods, simulated annealing Monte Carlo method and genetic algorithm.
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Affiliation(s)
- Kanon Sujaree
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.,Graduate School of Nanoscience and Technology, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunan Kitjaruwankul
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.,Graduate School of Nanoscience and Technology, Chulalongkorn University, Bangkok 10330, Thailand
| | - Panisak Boonamnaj
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chirayut Supunyabut
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Pornthep Sompornpisut
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
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14
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Supunyabut C, Fuklang S, Sompornpisut P. Continuum electrostatic approach for evaluating positions and interactions of proteins in a bilayer membrane. J Mol Graph Model 2015; 59:81-91. [DOI: 10.1016/j.jmgm.2015.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 04/02/2015] [Accepted: 04/03/2015] [Indexed: 01/08/2023]
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15
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16
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Pérez-Madrigal MM, del Valle LJ, Armelin E, Michaux C, Roussel G, Perpète EA, Alemán C. Polypyrrole-supported membrane proteins for bio-inspired ion channels. ACS APPLIED MATERIALS & INTERFACES 2015; 7:1632-43. [PMID: 25585165 DOI: 10.1021/am507142f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Biomedical platforms constructed by immobilizing membrane proteins in matrixes made of synthetic organic polymers is a challenge because the structure and function of these proteins are affected by environmental conditions. In this work, an operative composite that regulates the diffusion of alkali ions has been prepared by functionalizing a supporting matrix made of poly(N-methylpyrrole) (PNMPy) with a β-barrel membrane protein (Omp2a) that forms channels and pores. The protein has been unequivocally identified in the composite, and its structure has been shown to remain unaltered. The PNMPy-Omp2a platform fulfills properties typically associated with functional bio-interfaces with biomedical applications (e.g., biocompatibility, biodegrabadility, and hydrophilicity). The functionality of the immobilized protein has been examined by studying the passive ion transport response in the presence of electrolytic solutions with Na(+) and K(+) concentrations close to those found in blood. Although the behavior of PNMPy and PNMPy-Omp2a is very similar for solutions with very low concentration, the resistance of the latter decreases drastically when the concentration of ions increases to ∼100 mM. This reduction reflects an enhanced ion exchange between the biocomposite and the electrolytic medium, which is not observed in PNMPy, evidencing that PNMPy-Omp2a is particularly well suited to prepare bioinspired channels and smart biosensors.
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Affiliation(s)
- Maria M Pérez-Madrigal
- Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya , Avda. Diagonal 647, Barcelona E-08028, Spain
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17
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Różycki B, Boura E. Large, dynamic, multi-protein complexes: a challenge for structural biology. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:463103. [PMID: 25335513 DOI: 10.1088/0953-8984/26/46/463103] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Structural biology elucidates atomic structures of macromolecules such as proteins, DNA, RNA, and their complexes to understand the basic mechanisms of their functions. Among proteins that pose the most difficult problems to current efforts are those which have several large domains connected by long, flexible polypeptide segments. Although abundant and critically important in biological cells, such proteins have proven intractable by conventional techniques. This gap has recently led to the advancement of hybrid methods that use state-of-the-art computational tools to combine complementary data from various high- and low-resolution experiments. In this review, we briefly discuss the individual experimental techniques to illustrate their strengths and limitations, and then focus on the use of hybrid methods in structural biology. We describe how representative structures of dynamic multi-protein complexes are obtained utilizing the EROS hybrid method that we have co-developed.
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Affiliation(s)
- Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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18
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Lu B, Zhang B, Qi W, Zhu Y, Zhao Y, Zhou N, Sun R, Bao J, Wu C. Conformational study reveals amino acid residues essential for hemagglutinating and anti-proliferative activities of Clematis montana lectin. Acta Biochim Biophys Sin (Shanghai) 2014; 46:923-34. [PMID: 25239139 DOI: 10.1093/abbs/gmu085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clematis montana lectin (CML), a novel mannose-binding lectin purified from C. montana Buch.-Ham stem (Ranunculaceae), has been proved to have hemagglutinating activity in rabbit erythrocytes and apoptosis-inducing activity in tumor cells. However, the biochemical properties of CML have not revealed and its structural information still needs to be elucidated. In this study, it was found that CML possessed quite good thermostability and alkaline resistance, and its hemagglutinating activity was bivalent metal cation dependent. In addition, hemagglutination test and fluorescence spectroscopy proved that GuHCl, urea, and sodium dodecyl sulfate could change the conformation of CML and further caused the loss of hemagglutination activity. Moreover, the changes of fluorescence spectrum indicated that the tryptophan (Trp) microenvironment conversion might be related to the conformation and bioactivities of CML. In addition, it was also found that Trp residues, arginine (Arg) residues, and sulfhydryl were important for the hemagglutinating activity of CML, but only Trp was proved to be crucial for the CML conformation. Furthermore, the Trp, Arg, and sulfhydryl-modified CML exhibited 97.17%, 76.99%, and 49.64% loss of its anti-proliferative activity, respectively, which was consistent with the alterations of its hemagglutinating activity. Given these findings, Trp residues on the surface of CML are essential for the active center to form substrate-accessible conformation and suitable environment for carbohydrate binding.
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Affiliation(s)
- Bangmin Lu
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Bin Zhang
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Wei Qi
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Yanan Zhu
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Yan Zhao
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Nan Zhou
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Rong Sun
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Jinku Bao
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Chuanfang Wu
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
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19
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Jones Brunette AM, Farrens DL. Distance mapping in proteins using fluorescence spectroscopy: tyrosine, like tryptophan, quenches bimane fluorescence in a distance-dependent manner. Biochemistry 2014; 53:6290-301. [PMID: 25144569 PMCID: PMC4196733 DOI: 10.1021/bi500493r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Tryptophan-induced quenching of fluorophores
(TrIQ) uses intramolecular
fluorescence quenching to assess distances in proteins too small (<15
Å) to be easily probed by traditional Forster resonance energy
transfer methods. A powerful aspect of TrIQ is its ability to obtain
an ultrafast snapshot of a protein conformation, by identifying “static
quenching” (contact between the Trp and probe at the moment
of light excitation). Here we report new advances in this site-directed
fluorescence labeling (SDFL) approach, gleaned from recent studies
of T4 lysozyme (T4L). First, we show that like TrIQ, tyrosine-induced
quenching (TyrIQ) occurs for the fluorophore bimane in a distance-dependent
fashion, although with some key differences. The Tyr “sphere
of quenching” for bimane (≤10 Å) is smaller than
for Trp (≤15 Å, Cα–Cα distance), and
the size difference between the quenching residue (Tyr) and control
(Phe) differs by only a hydroxyl group. Second, we show how TrIQ and
TyrIQ can be used together to assess the magnitude and energetics
of a protein movement. In these studies, we placed a bimane (probe)
and Trp or Tyr (quencher) on opposite ends of a “hinge”
in T4L and conducted TrIQ and TyrIQ measurements. Our results are
consistent with an ∼5 Å change in Cα–Cα
distances between these sites upon substrate binding, in agreement
with the crystal structures. Subsequent Arrhenius analysis suggests
the activation energy barrier (Ea) to
this movement is relatively low (∼1.5–2.5 kcal/mol).
Together, these results demonstrate that TyrIQ, used together with
TrIQ, significantly expands the power of quenching-based distance
mapping SDFL studies.
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Affiliation(s)
- Amber M Jones Brunette
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University , Portland, Oregon 97239-3098, United States
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20
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Göbl C, Madl T, Simon B, Sattler M. NMR approaches for structural analysis of multidomain proteins and complexes in solution. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 80:26-63. [PMID: 24924266 DOI: 10.1016/j.pnmrs.2014.05.003] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/14/2014] [Indexed: 05/22/2023]
Abstract
NMR spectroscopy is a key method for studying the structure and dynamics of (large) multidomain proteins and complexes in solution. It plays a unique role in integrated structural biology approaches as especially information about conformational dynamics can be readily obtained at residue resolution. Here, we review NMR techniques for such studies focusing on state-of-the-art tools and practical aspects. An efficient approach for determining the quaternary structure of multidomain complexes starts from the structures of individual domains or subunits. The arrangement of the domains/subunits within the complex is then defined based on NMR measurements that provide information about the domain interfaces combined with (long-range) distance and orientational restraints. Aspects discussed include sample preparation, specific isotope labeling and spin labeling; determination of binding interfaces and domain/subunit arrangements from chemical shift perturbations (CSP), nuclear Overhauser effects (NOEs), isotope editing/filtering, cross-saturation, and differential line broadening; and based on paramagnetic relaxation enhancements (PRE) using covalent and soluble spin labels. Finally, the utility of complementary methods such as small-angle X-ray or neutron scattering (SAXS, SANS), electron paramagnetic resonance (EPR) or fluorescence spectroscopy techniques is discussed. The applications of NMR techniques are illustrated with studies of challenging (high molecular weight) protein complexes.
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Affiliation(s)
- Christoph Göbl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Tobias Madl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Molecular Biology, University of Graz, Graz, Austria.
| | - Bernd Simon
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Michael Sattler
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.
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21
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Goldberg JM, Batjargal S, Chen BS, Petersson EJ. Thioamide quenching of fluorescent probes through photoinduced electron transfer: mechanistic studies and applications. J Am Chem Soc 2013; 135:18651-8. [PMID: 24266520 DOI: 10.1021/ja409709x] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Previously we have shown that thioamides can be incorporated into proteins as minimally perturbing fluorescence-quenching probes to study protein dynamics, folding, and aggregation. Here, we show that the spontaneity of photoinduced electron transfer between a thioamide and an excited fluorophore is governed by the redox potentials of each moiety according to a Rehm-Weller-type model. We have used this model to predict thioamide quenching of various common fluorophores, and we rigorously tested more than a dozen examples. In each case, we found excellent agreement between our theoretical predictions and experimental observations. In this way, we have been able to expand the scope of fluorophores quenched by thioamides to include dyes suitable for microscopy and single-molecule studies, including fluorescein, Alexa Fluor 488, BODIPY FL, and rhodamine 6G. We describe the photochemistry of these systems and explore applications that demonstrate the utility of thioamide quenching of fluorescein to studying protein folding and proteolysis.
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Affiliation(s)
- Jacob M Goldberg
- Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104-6323, United States
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22
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Kapus A, Janmey P. Plasma membrane--cortical cytoskeleton interactions: a cell biology approach with biophysical considerations. Compr Physiol 2013; 3:1231-81. [PMID: 23897686 DOI: 10.1002/cphy.c120015] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
From a biophysical standpoint, the interface between the cell membrane and the cytoskeleton is an intriguing site where a "two-dimensional fluid" interacts with an exceedingly complex three-dimensional protein meshwork. The membrane is a key regulator of the cytoskeleton, which not only provides docking sites for cytoskeletal elements through transmembrane proteins, lipid binding-based, and electrostatic interactions, but also serves as the source of the signaling events and molecules that control cytoskeletal organization and remolding. Conversely, the cytoskeleton is a key determinant of the biophysical and biochemical properties of the membrane, including its shape, tension, movement, composition, as well as the mobility, partitioning, and recycling of its constituents. From a cell biological standpoint, the membrane-cytoskeleton interplay underlies--as a central executor and/or regulator--a multitude of complex processes including chemical and mechanical signal transduction, motility/migration, endo-/exo-/phagocytosis, and other forms of membrane traffic, cell-cell, and cell-matrix adhesion. The aim of this article is to provide an overview of the tight structural and functional coupling between the membrane and the cytoskeleton. As biophysical approaches, both theoretical and experimental, proved to be instrumental for our understanding of the membrane/cytoskeleton interplay, this review will "oscillate" between the cell biological phenomena and the corresponding biophysical principles and considerations. After describing the types of connections between the membrane and the cytoskeleton, we will focus on a few key physical parameters and processes (force generation, curvature, tension, and surface charge) and will discuss how these contribute to a variety of fundamental cell biological functions.
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Affiliation(s)
- András Kapus
- Keenan Research Center, Li Ka Shing Knowledge Institute, St. Michael's Hospital and Department of Surgery, University of Toronto, Ontario, Canada.
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23
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Cheng CY, Han S. Dynamic Nuclear Polarization Methods in Solids and Solutions to Explore Membrane Proteins and Membrane Systems. Annu Rev Phys Chem 2013; 64:507-32. [DOI: 10.1146/annurev-physchem-040412-110028] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Membrane proteins regulate vital cellular processes, including signaling, ion transport, and vesicular trafficking. Obtaining experimental access to their structures, conformational fluctuations, orientations, locations, and hydration in membrane environments, as well as the lipid membrane properties, is critical to understanding their functions. Dynamic nuclear polarization (DNP) of frozen solids can dramatically boost the sensitivity of current solid-state nuclear magnetic resonance tools to enhance access to membrane protein structures in native membrane environments. Overhauser DNP in the solution state can map out the local and site-specific hydration dynamics landscape of membrane proteins and lipid membranes, critically complementing the structural and dynamics information obtained by electron paramagnetic resonance spectroscopy. Here, we provide an overview of how DNP methods in solids and solutions can significantly increase our understanding of membrane protein structures, dynamics, functions, and hydration in complex biological membrane environments.
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Affiliation(s)
- Chi-Yuan Cheng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
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24
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Yu X, Wu X, Bermejo GA, Brooks BR, Taraska JW. Accurate high-throughput structure mapping and prediction with transition metal ion FRET. Structure 2012; 21:9-19. [PMID: 23273426 DOI: 10.1016/j.str.2012.11.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/15/2012] [Accepted: 11/17/2012] [Indexed: 11/28/2022]
Abstract
Mapping the landscape of a protein's conformational space is essential to understanding its functions and regulation. The limitations of many structural methods have made this process challenging for most proteins. Here, we report that transition metal ion FRET (tmFRET) can be used in a rapid, highly parallel screen, to determine distances from multiple locations within a protein at extremely low concentrations. The distances generated through this screen for the protein maltose binding protein (MBP) match distances from the crystal structure to within a few angstroms. Furthermore, energy transfer accurately detects structural changes during ligand binding. Finally, fluorescence-derived distances can be used to guide molecular simulations to find low energy states. Our results open the door to rapid, accurate mapping and prediction of protein structures at low concentrations, in large complex systems, and in living cells.
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Affiliation(s)
- Xiaozhen Yu
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiongwu Wu
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Guillermo A Bermejo
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin W Taraska
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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25
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Cheng CY, Goor OJ, Han S. Quantitative analysis of molecular transport across liposomal bilayer by J-mediated 13C Overhauser dynamic nuclear polarization. Anal Chem 2012; 84:8936-40. [PMID: 23072518 PMCID: PMC4656247 DOI: 10.1021/ac301932h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We introduce a new NMR technique to dramatically enhance the solution-state (13)C NMR sensitivity and contrast at 0.35 T and at room temperature by actively transferring the spin polarization from Overhauser dynamic nuclear polarization (ODNP)-enhanced (1)H to (13)C nuclei through scalar (J) coupling, a method that we term J-mediated (13)C ODNP. We demonstrate the capability of this technique by quantifying the permeability of glycine across negatively charged liposomal bilayers composed of dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylglycerol (DPPG). The permeability coefficient of glycine across this DPPC/DPPG bilayer is measured to be (1.8 ± 0.1) × 10(-11)m/s, in agreement with the literature value. We further observed that the presence of 20 mol % cholesterol within the DPPC/DPPG lipid membrane significantly retards the permeability of glycine by a factor of 4. These findings demonstrate that the high sensitivity and contrast of J-mediated (13)C ODNP affords the measurement of the permeation kinetics of small hydrophilic molecules across lipid bilayers, a quantity that is difficult to accurately measure with existing techniques.
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Affiliation(s)
- Chi-Yuan Cheng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Olga J.G.M. Goor
- Department of Biomedical Engineering, Laboratory of Chemical Biology, and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, the Netherlands
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
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