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Protocol | Open Access

Driving force of biomolecular liquid–liquid phase separation probed by nuclear magnetic resonance spectroscopy

Hanyu Zhang1Weiwei Fan1Gilbert Nshogoza2Yaqian Liu1Jia Gao1Jihui Wu1Yunyu Shi1Xiaoming Tu1( )Jiahai Zhang1( )Ke Ruan1( )
Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China
Department of Applied Chemistry, College of Science and Technology, University of Rwanda, Kigali, Rwanda
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Abstract

The assembly of biomolecular condensates is driven by liquid–liquid phase separation. To understand the structure and functions of these condensates, it is essential to characterize the underlying driving forces, e.g., protein–protein and protein–RNA interactions. As both structured and low-complexity domains are involved in the phase separation process, NMR is probably the only technique that can be used to depict the binding topology and interaction modes for the structured and nonstructured domains simultaneously. Atomic-resolution analysis for the intramolecular and intermolecular interactions between any pair of components sheds light on the mechanism for phase separation and biomolecular condensate assembly and disassembly. Herein, we describe the procedures used for the most extensively employed NMR techniques to characterize key interactions for biomolecular phase separation.

References

 

Ambadipudi S, Reddy JG, Biernat J, Mandelkow E, Zweckstetter M (2019) Residue-specific identification of phase separation hot spots of Alzheimer's-related protein tau. Chem Sci 10(26): 6503−6507

 

Antoniou C, Fung LWM (2008) Potential artifacts in using a glutathione S-transferase fusion protein system and spin labeling eiectron paramagnetic resonance methods to study protein-protein interactions. Anal Biochem 376(1): 160−162

 

Aue WP, Bartholdi E, Ernst RR (1976) Two-dimensional spectroscopy. Application to nuclear magnetic-resonance. J Chem Phys 64(5): 2229−2246

 

Bermel W, Bertini I, Felli IC, Lee YM, Luchinat C, Pierattelli R (2006a) Protonless NMR experiments for sequence-specific assignment of backbone nuclei in unfolded proteins. J Am Chem Soc 128(12): 3918−3919

 

Bermel W, Bertini I, Felli IC, Piccioli M, Pierattelli R (2006b) C-13-detected protonless NMR spectroscopy of proteins in solution. Prog Nucl Magn Reson Sp 48(1): 25−45

 

Bertini I, Felli IC, Gonnelli L, Kumar MVV, Pierattelli R (2011) C-13 direct-detection biomolecular NMR spectroscopy in living cells. Angew Chem Int Ed 50(10): 2339−2341

 
Borcherds W, Bremer A, Borgia MB, Mittag T (2021) How do intrinsically disordered protein regions encode a driving force for liquid-liquid phase separation? Curr Opin Struct Biol 67: 41-50
 

Clore GM, Iwahara J (2009) Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes. Chem Rev 109(9): 4108−4139

 

Conicella AE, Dignon GL, Zerze GH, Schmidt HB, D'Ordine AM, Kim YC, Rohatgi R, Ayala YM, Mittal J, Fawzi NL (2020) TDP-43 alpha-helical structure tunes liquid-liquid phase separation and function. Proc Natl Acad Sci USA 117(11): 5883−5894

 

Conicella AE, Zerze GH, Mittal J, Fawzi NL (2016) ALS mutations disrupt phase separation mediated by alpha-helical structure in the TDP-43 low-complexity C-terminal domain. Structure 24(9): 1537−1549

 
Courchaine EM, Lu A, Neugebauer KM (2016) Droplet organelles? EMBO J 35(15): 1603-1612
 

Eletsky A, Moreira O, Kovacs H, Pervushin K (2003) A novel strategy for the assignment of side-chain resonances in completely deuterated large proteins using C-13 spectroscopy. J Biomol NMR 26(2): 167−179

 

Grzesiek S, Bax A (1992a) Correlating backbone amide and side-chain resonances in larger proteins by multiple relayed triple resonance NMR. J Am Chem Soc 114(16): 6291−6293

 

Grzesiek S, Bax A (1992b) An efficient experiment for sequential backbone assignment of medium-sized isotopically enriched proteins. J Magn Reson 99(1): 201−207

 

Grzesiek S, Bax A (1992c) Improved 3D triple-resonance NMR techniques applied to a 31-kDa protein. J Magn Reson 96(2): 432−440

 

Grzesiek S, Bax A (1993) Amino-acid type determination in the sequential assignment procedure of uniformly C-13/N-15-enriched proteins. J Biomol NMR 3(2): 185−204

 

Ikura M, Kay LE, Bax A (1990a) A novel-approach for sequential assignment of H-1, C-13, and N-15 spectra of larger proteins: heteronuclear triple-resonance 3-dimensional NMR-spectroscopy. Application to calmodulin. Biochemistry 29(19): 4659−4667

 

Ikura M, Marion D, Kay LE, Shih H, Krinks M, Klee CB, Bax A (1990b) Heteronuclear 3D NMR and isotopic labeling of calmodulin — Towards the complete assignment of the H-1-NMR spectrum. Biochem Pharmacol 40(1): 153−160

 

Iwahara J, Tang C, Clore GM (2007) Practical aspects of H-1 transverse paramagnetic relaxation enhancement measurements on macromolecules. J Magn Reson 184(2): 185−195

 

Jeener J, Meier BH, Bachmann P, Ernst RR (1979) Investigation of exchange processes by 2-dimensional NMR-spectroscopy. J Chem Phys 71(11): 4546−4553

 

Jensen MR, Zweckstetter M, Huang JR, Backledge M (2014) Exploring free-energy landscapes of intrinsically disordered proteins at atomic resolution using NMR spectroscopy. Chem Rev 114(13): 6632−6660

 

Jonas S, Izaurralde E (2013) The role of disordered protein regions in the assembly of decapping complexes and RNP granules. Genes Dev 27(24): 2628−2641

 

Kay LE, Xu GY, Singer AU, Muhandiram DR, Formankay JD (1993) A gradient-enhanced HCCH TOCSY experiment for recording side-chain H-1 and C-13 correlations in H2O samples of proteins. J Magn Reson B 101(3): 333−337

 

Kay LE, Xu GY, Yamazaki T (1994) Enhanced-sensitivity triple-resonance spectroscopy with minimal H2O saturation. J Magn Reson A 109(1): 129−133

 

Kim HJ, Kim NC, Wang YD, Scarborough EA, Moore J, Diaz Z, MacLea KS, Freibaum B, Li S, Molliex A, Kanagaraj AP, Carter R, Boylan KB, Wojtas AM, Rademakers R, Pinkus JL, Greenberg SA, Trojanowski JQ, Traynor BJ, Smith BN, Topp S, Gkazi AS, Miller J, Shaw CE, Kottlors M, Kirschner J, Pestronk A, Li YR, Ford AF, Gitler AD, Benatar M, King OD, Kimonis VE, Ross ED, Weihl CC, Shorter J, Taylor JP (2013) Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS. Nature 495(7442): 467−473

 

Kovacs H, Moskau D, Spraul M (2005) Cryogenically cooled probes — A leap in NMR technology. Prog Nucl Magn Reson Sp 46(2-3): 131−155

 

Lin Y, Protter DS, Rosen MK, Parker R (2015) Formation and maturation of phase-separated liquid droplets by RNA-binding proteins. Mol Cell 60(2): 208−219

 

Luna RE, Akabayov SR, Ziarek JJ, Wagner G (2014) Examining weak protein-protein interactions in start codon recognition via NMR spectroscopy. FEBS J 281(8): 1965−1973

 

Matsuo H, Li HJ, Wagner G (1996) A sensitive HN(CA)CO experiment for deuterated proteins. J Magn Reson B 110(1): 112−115

 

McKee AC, Gavett BE, Stern RA, Nowinski CJ, Cantu RC, Kowall NW, Perl DP, Hedley-Whyte ET, Price B, Sullivan C, Morin P, Lee HS, Kubilus CA, Daneshvar DH, Wulff M, Budson AE (2010) TDP-43 proteinopathy and motor neuron disease in chronic traumatic encephalopathy. J Neuropathol Exp Neurol 69(9): 918−929

 

Montelione GT, Lyons BA, Emerson SD, Tashiro M (1992) An efficient triple resonance experiment using C-13 isotropic mixing for determining sequence-specific resonance assignments of isotopically-enriched proteins. J Am Chem Soc 114(27): 10974−10975

 

Muhandiram DR, Kay LE (1994) Gradient-enhanced triple-resonance 3-dimensional NMR experiments with improved sensitivity. J Magn Reson B 103(3): 203−216

 

Murthy AC, Dignon GL, Kan Y, Zerze GH, Parekh SH, Mittal J, Fawzi NL (2019) Molecular interactions underlying liquid-liquid phase separation of the FUS low-complexity domain. Nat Struct Mol Biol 26(7): 637−648

 

Murthy AC, Fawzi NL (2020) The (un)structural biology of biomolecular liquid-liquid phase separation using NMR spectroscopy. J Biol Chem 295(8): 2375−2384

 

Musielak B, Janczyk W, Rodriguez I, Plewka J, Sala D, Magiera-Mularz K, Holak T (2020) Competition NMR for detection of hit/lead inhibitors of protein-protein interactions. Molecules 25(13): 3017. https://doi.org/10.3390/molecules25133017

 

Nagayama K, Kumar A, Wuthrich K, Ernst RR (1980) Experimental-techniques of two-dimensional correlated spectroscopy. J Magn Reson 40(2): 321−334

 

Nott TJ, Petsalaki E, Farber P, Jervis D, Fussner E, Plochowietz A, Craggs TD, Bazett-Jones DP, Pawson T, Forman-Kay JD, Baldwin AJ (2015) Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles. Mol Cell 57(5): 936−947

 

Pervushin K, Eletsky A (2003) A new strategy for backbone resonance assignment in large proteins using a MQ-HACACO experiment. J Biomol NMR 25(2): 147−152

 

Piotto M, Saudek V, Sklenar V (1992) Gradient-tailored excitation for single-quantum NMR-spectroscopy of aqueous-solutions. J Biomol NMR 2(6): 661−665

 

Ribbeck K, Gorlich D (2002) The permeability barrier of nuclear pore complexes appears to operate via hydrophobic exclusion. EMBO J 21(11): 2664−2671

 

Ryan VH, Dignon GL, Zerze GH, Chabata CV, Silva R, Conicella AE, Amaya J, Burke KA, Mittal J, Fawzi NL (2018) Mechanistic view of hnRNPA2 low-complexity domain structure, interactions, and phase separation altered by mutation and arginine methylation. Mol Cell 69(3): 465−479

 

Schwalbe H, Rexroth A, Eggenberger U, Geppert T, Griesinger C (1993) Measurement of C', C coupling-constants in C-13-labeled proteins — A new method for the stereospecific assignment of gamma-methyl groups in valine residues. J Am Chem Soc 115(17): 7878−7879

 

Serber Z, Richter C, Dotsch V (2001) Carbon-detected NMR experiments to investigate structure and dynamics of biological macromolecules. Chembiochem 2(4): 247−251

 

Serber Z, Richter C, Moskau D, Bohlen JM, Gerfin T, Marek D, Haberli M, Baselgia L, Laukien F, Stern AS, Hoch JC, Dotsch V (2000) New carbon-detected protein NMR experiments using CryoProbes. J Am Chem Soc 122(14): 3554−3555

 

Shin Y, Chang YC, Lee DSW, Berry J, Sanders DW, Ronceray P, Wingreen NS, Haataja M, Brangwynne CP (2018) Liquid nuclear condensates mechanically sense and restructure the genome. Cell 175(6): 1481−1491

 

Sklenar V, Piotto M, Leppik R, Saudek V (1993) Gradient-tailored water suppression for H-1-N-15 HSQC experiments optimized to retain full sensitivity. J Magn Reson A 102(2): 241−245

 

Takeuchi K, Frueh DP, Hyberts SG, Sun ZYJ, Wagner G (2010a) High-resolution 3D CANCA NMR experiments for complete mainchain assignments using C-alpha direct detection. J Am Chem Soc 132(9): 2945−2951

 

Takeuchi K, Heffron G, Sun ZYJ, Frueh DP, Wagner G (2010b) Nitrogen-detected CAN and CON experiments as alternative experiments for main chain NMR resonance assignments. J Biomol NMR 47(4): 271−282

 

Takeuchi K, Sun Z-YJ, Wagner G (2008) Alternate C-13-C-12 labeling for complete mainchain resonance assignments using C alpha direct-detection with applicability toward fast relaxing protein systems. J Am Chem Soc 130(51): 17210−17211

 

Teixeira D, Sheth U, Valencia-Sanchez MA, Brengues M, Parker R (2005) Processing bodies require RNA for assembly and contain nontranslating mRNAs. RNA 11(4): 371−382

 

Tsai WC, Gayatri S, Reineke LC, Sbardella G, Bedford MT, Lloyd RE (2016) Arginine demethylation of G3BP1 promotes stress granule assembly. J Biol Chem 291(43): 22671−22685

 

Vaynberg J, Qin J (2006) Weak protein-protein interactions as probed by NMR spectroscopy. Trends Biotechnol 24(1): 22−27

 

Vernon RM, Chong PA, Tsang B, Kim TH, Bah A, Farber P, Lin H, Forman-Kay JD (2018) Pi-Pi contacts are an overlooked protein feature relevant to phase separation. Elife 7: e31486. https://doi.org/10.7554/eLife.31486

 

Wagner R, Berger S (1996) Gradient-selected NOESY — A fourfold reduction of the measurement time for the NOESY experiment. J Magn Reson A 123(1): 119−121

 

Yamazaki T, Lee W, Arrowsmith CH, Muhandiram DR, Kay LE (1994a) A suite of triple-resonance NMR experiments for the backbone assignment of N-15, C-13, H-2 labeled proteins with high-sensitivity. J Am Chem Soc 116(26): 11655−11666

 

Yamazaki T, Lee W, Revington M, Mattiello DL, Dahlquist FW, Arrowsmith CH, Kay LE (1994b) An hnca pulse scheme for the backbone assignment of N-15, C-13, H-2-labeled proteins — Application to a 37-kDa TRP repressor DNA complex. J Am Chem Soc 116(14): 6464−6465

 

Zhang H, Ji X, Li PL, Liu C, Lou JZ, Wang Z, Wen WY, Xiao Y, Zhang MJ, Zhu XL (2020) Liquid-liquid phase separation in biology: mechanisms, physiological functions and human diseases. Sci China Life Sci 63(7): 953−985

Biophysics Reports
Pages 90-99
Cite this article:
Zhang H, Fan W, Nshogoza G, et al. Driving force of biomolecular liquid–liquid phase separation probed by nuclear magnetic resonance spectroscopy. Biophysics Reports, 2022, 8(2): 90-99. https://doi.org/10.52601/bpr.2022.210034

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Received: 31 July 2021
Accepted: 29 October 2021
Published: 21 January 2022
© The Author(s) 2022

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