AI Chat Paper
Discover the SciOpen Platform and Achieve Your Research Goals with Ease.
Search articles, authors, keywords, DOl and etc.
{{expandStatus?'Exit ':''}}Advanced Search
As cryogenic electron microscopy (cryoEM) gains traction in the structural biology community as a method of choice for determining atomic structures of biological complexes, it has been increasingly recognized that many complexes that behave well under conventional negative-stain electron microscopy tend to have preferential orientation, aggregate or simply mysteriously “disappear” on cryoEM grids. However, the reasons for such misbehavior are not well understood, which limits systematic approaches to solving the problem. Here, we have developed a theoretical formulation that explains these observations. Our formulation predicts that all particles migrate to the air–water interface (AWI) to lower the total potential surface energy-rationalizing the use of surfactant, which is a direct solution to reduce the surface tension of the aqueous solution. By performing cryogenic electron tomography (cryoET) on the widely-tested sample, GroEL, we demonstrate that, in a standard buffer solution, nearly all particles migrate to the AWI. Gradually reducing the surface tension by introducing surfactants decreased the percentage of particles exposed to the surface. By conducting single-particle cryoEM, we confirm that suitable surfactants do not damage the biological complex, thus suggesting that they might provide a practical, simple, and general solution to the problem for high-resolution cryoEM. Applying this solution to a real-world AWI adsorption problem involving a more challenging membrane protein, namely, the ClC-1 channel, has resulted in its near-atomic structure determination using cryoEM.
Bai XC, Fernandez IS, McMullan G, Scheres SH (2013) Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles. Elife 2: e0046. https://doi.org/10.7554/eLife.00461
Chamberlain AK, Handel TM, Marqusee S (1996) Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH. Nat Struct Biol 3(9): 782−787
Chen S, Li J, Vinothkumar KR, Henderson R (2022) Interaction of human erythrocyte catalase with air–water interface in cryoEM. Microscopy (Oxf) 71(Supplement_1): i51−i59
Chu CH, Sarangadharan I, Regmi A, Chen YW, Hsu CP, Chang WH, Lee GY, Chyi JI, Chen CC, Shiesh SC, Lee GB, Wang YL (2017) Beyond the Debye length in high ionic strength solution: direct protein detection with field-effect transistors (FETs) in human serum. Sci Rep 7(1): 5256. https://doi.org/10.1038/s41598-017-05426-6
Cieplak M, Allan DB, Leheny RL, Reich DH (2014) Proteins at air-water interfaces: a coarse-grained model. Langmuir 30(43): 12888−12896
Fan H, Wang B, Zhang Y, Zhu Y, Song B, Xu H, Zhai Y, Qiao M, Sun F (2021) A cryo-electron microscopy support film formed by 2D crystals of hydrophobin HFBI. Nat Commun 12(1): 7257. https://doi.org/10.1038/s41467-021-27596-8
Glaeser RM, Han B-G (2017) Opinion: hazards faced by macromolecules when confined to thin aqueous films. Biophys Rep 3(1): 1−7
Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE (2018) UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci 27(1): 14−25
Graham DE, Phillips MC (1979) Proteins at liquid interfaces: I. Kinetics of adsorption and surface denaturation. J Colloid Interface Sci 70(3): 403−414
Han Y, Fan X, Wang H, Zhao F, Tully CG, Kong J, Yao N, Yan N (2020) High-yield monolayer graphene grids for near-atomic resolution cryoelectron microscopy. Proc Natl Acad Sci USA 117(2): 1009−1014
Hauner IM, Deblais A, Beattie JK, Kellay H, Bonn D (2017) The dynamic surface tension of water. J Phys Chem Lett 8(7): 1599−1603
Hoffmann PC, Kreysing JP, Khusainov I, Tuijtel MW, Welsch S, Beck M (2022) Structures of the eukaryotic ribosome and its translational states in situ. Nat Commun 13(1): 7435. https://doi.org/10.1038/s41467-022-34997-w
Hughes TET, Lodowski DT, Huynh KW, Yazici A, Del Rosario J, Kapoor A, Basak S, Samanta A, Han X, Chakrapani S, Zhou ZH, Filizola M, Rohacs T, Han S, Moiseenkova-Bell VY (2018) Structural basis of TRPV5 channel inhibition by econazole revealed by cryo-EM. Nat Struct Mol Biol 25(1): 53−60
Inácio ÂS, Mesquita KA, Baptista M, Ramalho-Santos J, Vaz WLC, Vieira OV (2011) In vitro surfactant structure-toxicity relationships: implications for surfactant use in sexually transmitted infection prophylaxis and contraception. PLoS One 6(5): e19850−e19850
Jain T, Sheehan P, Crum J, Carragher B, Potter CS (2012) Spotiton: a prototype for an integrated inkjet dispense and vitrification system for cryo-TEM. J Struct Biol 179(1): 68−75
Koepf E, Schroeder R, Brezesinski G, Friess W (2017) The film tells the story: physical-chemical characteristics of IgG at the liquid-air interface. Eur J Pharm Biopharm 119: 396−407
Kremer JR, Mastronarde DN, McIntosh JR (1996) Computer visualization of three-dimensional image data using IMOD. J Struct Biol 116(1): 71−76
Liao M, Cao E, Julius D, Cheng Y (2013) Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504(7478): 107−112
Liao W-C, Zatz JL (1979) Surfactant solutions as test liquids for measurement of critical surface tension. J Pharm Sci 68(4): 486−488
Lyumkis D (2019) Challenges and opportunities in cryo-EM single-particle analysis. J Biol Chem 294(13): 5181−5197
MacRitchie F (1985) Desorption of proteins from the air/water interface. J Colloid Interface Sci 105(1): 119−123
Maity H, Maity M, Krishna MMG, Mayne L, Englander SW (2005) Protein folding: the stepwise assembly of foldon units. Proc Natl Acad Sci USA 102(13): 4741−4746
Mastronarde DN (2005) Automated electron microscope tomography using robust prediction of specimen movements. J Struct Biol 152(1): 36−51
Mondal S, Phukan M, Ghatak A (2015) Estimation of solid-liquid interfacial tension using curved surface of a soft solid. Proc Natl Acad Sci USA 112: 12563−12568
Narsimhan G, Uraizee F (1992) Kinetics of adsorption of globular proteins at an air–water interface. Biotechnol Prog. 8(3): 187−196
Naydenova K, Russo CJ (2017) Measuring the effects of particle orientation to improve the efficiency of electron cryomicroscopy. Nature Commun 8(1): 629. https://doi.org/10.1038/s41467-017-00782-3
Noble AJ, Dandey VP, Wei H, Brasch J, Chase J, Acharya P, Tan YZ, Zhang Z, Kim LY, Scapin G, Rapp M, Eng ET, Rice WJ, Cheng A, Negro CJ, Shapiro L, Kwong PD, Jeruzalmi D, des Georges A, Potter CS, Carragher B (2018a) Routine single particle CryoEM sample and grid characterization by tomography. Elife 29(7): e34257. https://doi.org/10.7554/eLife.34257
Noble AJ, Wei H, Dandey VP, Zhang Z, Tan YZ, Potter CS, Carragher B (2018b) Reducing effects of particle adsorption to the air–water interface in cryo-EM. Nat Methods 15(10): 793−795
O'Reilly FJ, Xue L, Graziadei A, Sinn L, Lenz S, Tegunov D, Blotz C, Singh N, Hagen WJH, Cramer P, Stulke J, Mahamid J, Rappsilber J (2020) In-cell architecture of an actively transcribing-translating expressome. Science 369(6503): 554−557
Pantelic RS, Suk JW, Magnuson CW, Meyer JC, Wachsmuth P, Kaiser U, Ruoff RS, Stahlberg H (2011) Graphene: substrate preparation and introduction. J Struct Biol 174(1): 234−238
Park KH, Berrier C, Lebaupain F, Pucci B, Popot JL, Ghazi A, Zito F (2007) Fluorinated and hemifluorinated surfactants as alternatives to detergents for membrane protein cell-free synthesis. Biochem J 403(1): 183−187
Roh S-H, Hryc CF, Jeong H-H, Fei X, Jakana J, Lorimer GH, Chiu W (2017) Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM. Proc Natl Acad Sci USA 114(31): 8259−8264
Russo CJ, Passmore LA (2014) Controlling protein adsorption on graphene for cryo-EM using low-energy hydrogen plasmas. Nat Methods 11(6): 649−652
Russo CJ, Passmore LA (2016) Progress towards an optimal specimen support for electron cryomicroscopy. Curr Opin Struct Biol 37: 81−89
Shuttleworth R (1950) The surface tension of solids. Proc Natl Acad Sci USA 63: 444−457
Stauber T, Weinert S, Jentsch TJ (2012) Cell biology and physiology of CLC chloride channels and transporters. Compr Physiol 2(3): 1701−1744
Taylor KA, Glaeser RM (2008) Retrospective on the early development of cryoelectron microscopy of macromolecules and a prospective on opportunities for the future. J Struct Biol 163(3): 214−223
Tegunov D, Cramer P (2019) Real-time cryo-electron microscopy data preprocessing with Warp. Nat Methods 16(11): 1146−1152
Tribet C, Audebert R, Popot J-L (1996) Amphipols: Polymers that keep membrane proteins soluble in aqueous solutions. Proc Natl Acad Sci USA 93(26): 15047. https://doi.org/10.1073/pnas.93.26.15047
Vinothkumar KR (2015) Membrane protein structures without crystals, by single particle electron cryomicroscopy. Curr Opin Struct Biol 33: 103−114
Wang J, Chen L (2003) Domain motions in GroEL upon binding of an oligopeptide. J Mol Biol. 334(3): 489−499
Wang K, Preisler SS, Zhang L, Cui Y, Missel JW, Gronberg C, Gotfryd K, Lindahl E, Andersson M, Calloe K, Egea PF, Klaerke DA, Pusch M, Pedersen PA, Zhou ZH, Gourdon P (2019) Structure of the human ClC-1 chloride channel. PLoS Biol 17(4): e3000218. https://doi.org/10.1371/journal.pbio.3000218
Wiesbauer J, Prassl R, Nidetzky B (2013) Renewal of the air–water interface as a critical system parameter of protein stability: aggregation of the human growth hormone and its prevention by surface–active compounds. Langmuir 29(49): 15240−15250
Williams RC, Glaeser RM (1972) Ultrathin carbon support films for electron microscopy. Science 175(4025): 1000−1001
Zhao Y, Chwastyk M, Cieplak M (2017) Topological transformations in proteins: effects of heating and proximity of an interface. Sci Rep 7(1): 39851. https://doi.org/10.1038/srep39851
This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
京公网安备11010802044758号