Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology

Overview

Journal JACS Au

Publisher American Chemical Society

Specialty Chemistry

Date 2024 Mar 1

PMID 38425916

Authors

Zeting Zhang

Qun Zhao

Zhou Gong

Ruichen Du

Maili Liu

Yukui Zhang

Lihua Zhang

Conggang Li

Affiliations

Soon will be listed here.

Abstract

The validity of protein structures and interactions, whether determined under ideal laboratory conditions or predicted by AI tools such as Alphafold2, to precisely reflect those found in living cells remains to be examined. Moreover, understanding the changes in protein structures and interactions in response to stimuli within living cells, under both normal and disease conditions, is key to grasping proteins' functionality and cellular processes. Nevertheless, achieving high-resolution identification of these protein structures and interactions within living cells presents a technical challenge. In this Perspective, we summarize the recent advancements in in-cell nuclear magnetic resonance (NMR) and in vivo cross-linking mass spectrometry (XL-MS) for studying protein structures and interactions within a cellular context. Additionally, we discuss the challenges, opportunities, and potential benefits of integrating in-cell NMR and in vivo XL-MS in future research to offer an exhaustive approach to studying proteins in their natural habitat.

Citing Articles

π-HuB: the proteomic navigator of the human body.

He F, Aebersold R, Baker M, Bian X, Bo X, Chan D Nature. 2024; 636(8042):322-331.

PMID: 39663494 DOI: 10.1038/s41586-024-08280-5.

Recent Advances in Mass Spectrometry-Based Protein Interactome Studies.

Wu S, Zhang S, Liu C, Fernie A, Yan S Mol Cell Proteomics. 2024; 24(1):100887.

PMID: 39608603 PMC: 11745815. DOI: 10.1016/j.mcpro.2024.100887.

References

Gryk M, Hoch J . Local knowledge helps determine protein structures. Proc Natl Acad Sci U S A. 2008; 105(12):4533-4. PMC: 2290792. DOI: 10.1073/pnas.0801069105. View

Ghosh R, Xiao Y, Kragelj J, Frederick K . In-Cell Sensitivity-Enhanced NMR of Intact Viable Mammalian Cells. J Am Chem Soc. 2021; 143(44):18454-18466. PMC: 8961430. DOI: 10.1021/jacs.1c06680. View

Muntener T, Haussinger D, Selenko P, Theillet F . In-Cell Protein Structures from 2D NMR Experiments. J Phys Chem Lett. 2016; 7(14):2821-5. DOI: 10.1021/acs.jpclett.6b01074. View

Primikyri A, Sayyad N, Quilici G, Vrettos E, Lim K, Chi S . Probing the interaction of a quercetin bioconjugate with Bcl-2 in living human cancer cells with in-cell NMR spectroscopy. FEBS Lett. 2018; 592(20):3367-3379. DOI: 10.1002/1873-3468.13250. View

Xu G, Cheng K, Wu Q, Liu M, Li C . Confinement Alters the Structure and Function of Calmodulin. Angew Chem Int Ed Engl. 2016; 56(2):530-534. DOI: 10.1002/anie.201609639. View

Pell A, Pintacuda G, Grey C . Paramagnetic NMR in solution and the solid state. Prog Nucl Magn Reson Spectrosc. 2019; 111:1-271. DOI: 10.1016/j.pnmrs.2018.05.001. View

Xie H, Zhao Y, Zhao W, Chen Y, Liu M, Yang J . Solid-state NMR structure determination of a membrane protein in cellular inner membrane. Sci Adv. 2023; 9(44):eadh4168. PMC: 10619923. DOI: 10.1126/sciadv.adh4168. View

Monteith W, Cohen R, Smith A, Guzman-Cisneros E, Pielak G . Quinary structure modulates protein stability in cells. Proc Natl Acad Sci U S A. 2015; 112(6):1739-42. PMC: 4330749. DOI: 10.1073/pnas.1417415112. View

Muller F, Graziadei A, Rappsilber J . Quantitative Photo-crosslinking Mass Spectrometry Revealing Protein Structure Response to Environmental Changes. Anal Chem. 2019; 91(14):9041-9048. PMC: 6639777. DOI: 10.1021/acs.analchem.9b01339. View

10.

Gronenborn A . Small, but powerful and attractive: F in biomolecular NMR. Structure. 2022; 30(1):6-14. PMC: 8797020. DOI: 10.1016/j.str.2021.09.009. View

11.

Zheng W, Zhang Z, Ye Y, Wu Q, Liu M, Li C . Phosphorylation dependent α-synuclein degradation monitored by in-cell NMR. Chem Commun (Camb). 2019; 55(75):11215-11218. DOI: 10.1039/c9cc05662a. View

12.

Chai Z, Wu Q, Cheng K, Liu X, Zhang Z, Jiang L . Visualizing Proteins in Human Cells at Near-Physiological Concentrations with Sensitive F NMR Chemical Tags. Angew Chem Int Ed Engl. 2023; 62(22):e202300318. DOI: 10.1002/anie.202300318. View

13.

An Y, Zhao Q, Gao H, Zhao L, Li X, Zhang X . Selective Removal of Unhydrolyzed Monolinked Peptides from Enriched Crosslinked Peptides To Improve the Coverage of Protein Complex Analysis. Anal Chem. 2022; 94(9):3904-3913. DOI: 10.1021/acs.analchem.1c04927. View

14.

Song X, Wang M, Chen X, Zhang X, Yang Y, Liu Z . Quantifying Protein Electrostatic Interactions in Cells by Nuclear Magnetic Resonance Spectroscopy. J Am Chem Soc. 2021; 143(46):19606-19613. DOI: 10.1021/jacs.1c10154. View

15.

Pinto C, Mance D, Julien M, Daniels M, Weingarth M, Baldus M . Studying assembly of the BAM complex in native membranes by cellular solid-state NMR spectroscopy. J Struct Biol. 2017; 206(1):1-11. DOI: 10.1016/j.jsb.2017.11.015. View

16.

Narasimhan S, Scherpe S, Lucini Paioni A, van der Zwan J, Folkers G, Ovaa H . DNP-Supported Solid-State NMR Spectroscopy of Proteins Inside Mammalian Cells. Angew Chem Int Ed Engl. 2019; 58(37):12969-12973. PMC: 6772113. DOI: 10.1002/anie.201903246. View

17.

Boczek E, Fursch J, Niedermeier M, Jawerth L, Jahnel M, Ruer-Gruss M . HspB8 prevents aberrant phase transitions of FUS by chaperoning its folded RNA-binding domain. Elife. 2021; 10. PMC: 8510580. DOI: 10.7554/eLife.69377. View

18.

Liu F, Rijkers D, Post H, Heck A . Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry. Nat Methods. 2015; 12(12):1179-84. DOI: 10.1038/nmeth.3603. View

19.

Beriashvili D, Yao R, DAmico F, Krafcikova M, Gurinov A, Safeer A . A high-field cellular DNP-supported solid-state NMR approach to study proteins with sub-cellular specificity. Chem Sci. 2023; 14(36):9892-9899. PMC: 10510770. DOI: 10.1039/d3sc02117c. View

20.

Ni Q, Daviso E, Can T, Markhasin E, Jawla S, Swager T . High frequency dynamic nuclear polarization. Acc Chem Res. 2013; 46(9):1933-41. PMC: 3778063. DOI: 10.1021/ar300348n. View