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Garcia-Sacristan C, Gisbert VG, Klein K, Šarić A, Garcia R. In Operando Imaging Electrostatic-Driven Disassembly and Reassembly of Collagen Nanostructures. ACS NANO 2024. [PMID: 38958189 DOI: 10.1021/acsnano.4c03839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Collagen is the most abundant protein in tissue scaffolds in live organisms. Collagen can self-assemble in vitro, which has led to a number of biotechnological and biomedical applications. To understand the dominant factors that participate in the formation of collagen nanostructures, here we study in real time and with nanoscale resolution the disassembly and reassembly of collagens. We implement a high-speed force microscope, which provides in situ high spatiotemporal resolution images of collagen nanostructures under changing pH conditions. The disassembly and reassembly are dominated by the electrostatic interactions among amino-acid residues of different molecules. Acidic conditions favor disassembly by neutralizing negatively charged residues. The process sets a net repulsive force between collagen molecules. A neutral pH favors the presence of negative and positively charged residues along the collagen molecules, which promotes their electrostatic attraction. Molecular dynamics simulations reproduce the experimental behavior and validate the electrostatic-based model of the disassembly and reassembly processes.
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Affiliation(s)
- Clara Garcia-Sacristan
- Instituto de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
| | - Victor G Gisbert
- Instituto de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
| | - Kevin Klein
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Anđela Šarić
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
| | - Ricardo Garcia
- Instituto de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
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2
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Xu G, Cheng K, Liu M, Li C. Studying protein stability in crowded environments by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2024; 140-141:42-48. [PMID: 38705635 DOI: 10.1016/j.pnmrs.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 05/07/2024]
Abstract
Most proteins perform their functions in crowded and complex cellular environments where weak interactions are ubiquitous between biomolecules. These complex environments can modulate the protein folding energy landscape and hence affect protein stability. NMR is a nondestructive and effective method to quantify the kinetics and equilibrium thermodynamic stability of proteins at an atomic level within crowded environments and living cells. Here, we review NMR methods that can be used to measure protein stability, as well as findings of studies on protein stability in crowded environments mimicked by polymer and protein crowders and in living cells. The important effects of chemical interactions on protein stability are highlighted and compared to spatial excluded volume effects.
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Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China.
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3
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Zhang Z, Zhao Q, Gong Z, Du R, Liu M, Zhang Y, Zhang L, Li C. Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology. JACS AU 2024; 4:369-383. [PMID: 38425916 PMCID: PMC10900494 DOI: 10.1021/jacsau.3c00712] [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: 11/14/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 03/02/2024]
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.
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Affiliation(s)
- Zeting Zhang
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qun Zhao
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Zhou Gong
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ruichen Du
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
- University
of Chinese Academy of Sciences, Beijing 10049, China
| | - Maili Liu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yukui Zhang
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Conggang Li
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
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4
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Wang M, Song X, Chen J, Chen X, Zhang X, Yang Y, Liu Z, Yao L. Intracellular environment can change protein conformational dynamics in cells through weak interactions. SCIENCE ADVANCES 2023; 9:eadg9141. [PMID: 37478178 PMCID: PMC10361600 DOI: 10.1126/sciadv.adg9141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/21/2023] [Indexed: 07/23/2023]
Abstract
Conformational dynamics is important for protein functions, many of which are performed in cells. How the intracellular environment may affect protein conformational dynamics is largely unknown. Here, loop conformational dynamics is studied for a model protein in Escherichia coli cells by using nuclear magnetic resonance (NMR) spectroscopy. The weak interactions between the protein and surrounding macromolecules in cells hinder the protein rotational diffusion, which extends the dynamic detection timescale up to microseconds by the NMR spin relaxation method. The loop picosecond to microsecond dynamics is confirmed by nanoparticle-assisted spin relaxation and residual dipolar coupling methods. The loop interactions with the intracellular environment are perturbed through point mutation of the loop sequence. For the sequence of the protein that interacts stronger with surrounding macromolecules, the loop becomes more rigid in cells. In contrast, the mutational effect on the loop dynamics in vitro is small. This study provides direct evidence that the intracellular environment can modify protein loop conformational dynamics through weak interactions.
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Affiliation(s)
- Mengting Wang
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangfei Song
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Jingfei Chen
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Xiaoxu Chen
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueying Zhang
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Yang
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Zhijun Liu
- National Facility for Protein Science, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Lishan Yao
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
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Liu Z, Zheng X, Wang J. Bioinspired Ice-Binding Materials for Tissue and Organ Cryopreservation. J Am Chem Soc 2022; 144:5685-5701. [PMID: 35324185 DOI: 10.1021/jacs.2c00203] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cryopreservation of tissues and organs can bring transformative changes to medicine and medical science. In the past decades, limited progress has been achieved, although cryopreservation of tissues and organs has long been intensively pursued. One key reason is that the cryoprotective agents (CPAs) currently used for cell cryopreservation cannot effectively preserve tissues and organs because of their cytotoxicity and tissue destructive effect as well as the low efficiency in controlling ice formation. In stark contrast, nature has its unique ways of controlling ice formation, and many living organisms can effectively prevent freezing damage. Ice-binding proteins (IBPs) are regarded as the essential materials identified in these living organisms for regulating ice nucleation and growth. Note that controversial results have been reported on the utilization of IBPs and their mimics for the cryopreservation of tissues and organs, that is, some groups revealed that IBPs and mimics exhibited unique superiorities in tissues cryopreservation, while other groups showed detrimental effects. In this perspective, we analyze possible reasons for the controversy and predict future research directions in the design and construction of IBP inspired ice-binding materials to be used as new CPAs for tissue cryopreservation after briefly introducing the cryo-injuries and the challenges of conventional CPAs in the cryopreservation of tissues and organs.
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Affiliation(s)
- Zhang Liu
- Key Laboratory of Green Printing, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Xia Zheng
- Key Laboratory of Green Printing, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jianjun Wang
- Key Laboratory of Green Printing, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, PR China.,School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100190, PR China
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Chu IT, Stewart CJ, Speer SL, Pielak GJ. A Difference between In Vitro and In-Cell Protein Dimer Formation. Biochemistry 2022; 61:409-412. [PMID: 35188746 DOI: 10.1021/acs.biochem.1c00780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The high concentration of macromolecules in cells affects the stability of proteins and protein complexes via hard repulsions and chemical interactions, yet few studies have focused on chemical interactions. We characterized the domain-swapped dimer of the B1 domain of protein G in buffer and Escherichia coli cells by using heteronuclear, multidimensional nuclear magnetic resonance spectroscopy. In buffer, the monomer is a partially folded molten globule, but that species is not observed in cells. Experiments using urea suggest that the monomer is unfolded in cells, but again, the molten-globule form of the monomer is absent. The data suggest that attractive chemical interactions in the cytoplasm unfold the molten globule. We conclude that the intracellular environment not only modulates the stability of protein complexes but also can change the species present, reinforcing the idea that chemical interactions are more important than hard repulsions in cells.
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Affiliation(s)
- I-Te Chu
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Claire J Stewart
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Shannon L Speer
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Gary J Pielak
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States.,Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States.,Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
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