1
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Wen L, Zheng J, Ke Z, Dong J. Macromolecular crowding effect on the β-galactosidase cascade reaction under multivalency and chain overlapping conditions of glycopolymers. Int J Biol Macromol 2025; 313:144343. [PMID: 40389007 DOI: 10.1016/j.ijbiomac.2025.144343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2025] [Revised: 05/10/2025] [Accepted: 05/16/2025] [Indexed: 05/21/2025]
Abstract
Enzymes catalyze cascade reactions in a crowded cellular environment where as much as half of cell volume is occupied by various macromolecules. Nonspecific interaction between enzymes and crowders and excluded volume of the crowders can superimpose on each other and complicate catalytic activity of the enzymes. This study investigates the interaction between a β-galactosidase (β-Gal) and glycosylated acrylamide polymer (P(Glc-β-EAAm)) and unravels the macromolecular crowding effect of the glycopolymer on enzymatic cascade catalysis consisting of β-Gal, glucose oxidase and hydrogen peroxidase. Binding of the glycopolymer induced conformational alterations in β-Gal and gave rise to static fluorescence quenching and stable complex formation with β-Gal via nonspecific interaction. Fluorescence resonance energy transfer assays further demonstrated a compact association between β-Gal and glycopolymer crowders, with binding affinity correlating with the molecular weight of glycopolymer. The reduction of the apparent kinetic constants of the catalysis with the glycopolymer size showed the role of the multivalent effect in enzyme-substrate interactions. The kinetics also depended on the chain overlapping conditions of the crowders. Therefore, the macromolecular crowding effect on the cascade reaction is jointly associated with the crowder's multivalent effect, chain overlapping conditions of the crowders, in addition to the volume exclusion effect of the crowders.
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Affiliation(s)
- Li Wen
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, Zhejiang Province 312000, China
| | - Jinxia Zheng
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, Zhejiang Province 312000, China
| | - Zhijie Ke
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, Zhejiang Province 312000, China
| | - Jian Dong
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, Zhejiang Province 312000, China.
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2
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Streit JO, Chan SHS, Daya S, Christodoulou J. Rational design of 19F NMR labelling sites to probe protein structure and interactions. Nat Commun 2025; 16:4300. [PMID: 40341366 PMCID: PMC12062419 DOI: 10.1038/s41467-025-59105-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Accepted: 04/11/2025] [Indexed: 05/10/2025] Open
Abstract
Proteins are investigated in increasingly more complex biological systems, where 19F NMR is proving highly advantageous due to its high gyromagnetic ratio and background-free spectra. Its application has, however, been hindered by limited chemical shift dispersions and an incomprehensive relationship between chemical shifts and protein structure. Here, we exploit the sensitivity of 19F chemical shifts to ring currents by designing labels with direct contact to a native or engineered aromatic ring. Fifty protein variants predicted by AlphaFold and molecular dynamics simulations show 80-90% success rates and direct correlations of their experimental chemical shifts with the magnitude of the engineered ring current. Our method consequently improves the chemical shift dispersion and through simple 1D experiments enables structural analyses of alternative conformational states, including ribosome-bound folding intermediates, and in-cell measurements of protein-protein interactions and thermodynamics. Our strategy thus provides a simple and sensitive tool to extract residue contact restraints from chemical shifts for previously intractable systems.
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Affiliation(s)
- Julian O Streit
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, UK.
| | - Sammy H S Chan
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, UK.
| | - Saifu Daya
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, UK.
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3
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Markle JM, Neal TD, Kantzer HS, Pielak GJ. Crowding-induced stabilization and destabilization in a single protein. Protein Sci 2025; 34:e70126. [PMID: 40260960 PMCID: PMC12012844 DOI: 10.1002/pro.70126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2025] [Revised: 03/28/2025] [Accepted: 04/03/2025] [Indexed: 04/24/2025]
Abstract
The protein concentration in cells can reach 300 g/L. These crowded conditions affect protein stability. Classic crowding theories predict entropically driven stabilization, which occurs via steric repulsion, but growing evidence shows a role for non-covalent chemical interactions. To aid our understanding of physiologically relevant crowding, we used NMR-detected 1H-2H exchange to examine a simple, semi-reductionist system: protein self-crowding at the residue level using the widely studied model globular protein, GB1 (the B1 domain streptococcal protein G) at concentrations up to its solubility limit, 100 g/L. The surprising result is that self-crowding stabilizes some residues but destabilizes others, contradicting predictions. Two other observations are also contradictory. First, temperature-dependence data show that stabilization can arise enthalpically, not just entropically. Second, concentration-dependence data show destabilization often increases with increasing concentration. These results show a key role for chemical interactions. More specifically, self-crowding increases the free energy required to expose those residues that are only exposed upon complete unfolding, and stabilization of these globally unfolding residues increases with GB1 concentration, a result we attribute to repulsive chemical interactions between GB1 molecules. On the other hand, residues exposed upon local unfolding tend to be destabilized, with destabilization increasing with concentration, a result we attribute to attractive chemical interactions between GB1 molecules.
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Affiliation(s)
- Jordyn M. Markle
- Department of ChemistryUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
| | - Tarynn D. Neal
- Department of ChemistryUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
| | - Hania S. Kantzer
- Department of ChemistryUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
| | - Gary J. Pielak
- Department of ChemistryUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
- Department of Biochemistry & BiophysicsUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
- Lineberger Cancer CenterUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
- Integrative Program for Biological and Genome SciencesUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
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4
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Chen X, Zhang X, Chen J, Wang M, Yang Y, An L, Liu Z, Song X, Yao L. Quantification of CH and NH/π-Stacking Interactions in Cells Using Nuclear Magnetic Resonance Spectroscopy. Anal Chem 2024; 96:14354-14362. [PMID: 39177663 DOI: 10.1021/acs.analchem.4c00688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
π-Stacking, a type of noncovalent interactions involving aromatic residues, plays an important role in protein folding and function. In this work, an attempt has been made to measure CH/π and NH/π stacking interactions in a protein in Escherichia coli cells using a combined double-mutant cycle and nuclear magnetic resonance spectroscopy method. The results show that the CH/π and NH/π stacking interactions are generally weaker in cells than those in the buffer. The transient intermolecular noncovalent interactions between the protein and the complex cellular environment may compete with and thus weaken the stacking interactions in the protein. The weakening of stacking interactions can enhance the local conformational opening of proteins in E. coli cells. This is evident from the faster rates of amide hydrogen/deuterium exchange observed in cells than in the buffer, for residues that undergo local conformational opening. This study highlights the influence of the cellular environment on π-stacking and the conformational dynamics of proteins.
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Affiliation(s)
- Xiaoxu Chen
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xueying Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfei Chen
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Mengting Wang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Yang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Liaoyuan An
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Zhijun Liu
- National Facility for Protein Science, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Xiangfei Song
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Lishan Yao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
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5
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Chen X, Zhang X, Qin M, Chen J, Wang M, Liu Z, An L, Song X, Yao L. Protein Allostery Study in Cells Using NMR Spectroscopy. Anal Chem 2024; 96:7065-7072. [PMID: 38652079 DOI: 10.1021/acs.analchem.4c00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Protein allostery is commonly observed in vitro. But how protein allostery behaves in cells is unknown. In this work, a protein monomer-dimer equilibrium system was built with the allosteric effect on the binding characterized using NMR spectroscopy through mutations away from the dimer interface. A chemical shift linear fitting method was developed that enabled us to accurately determine the dissociation constant. A total of 28 allosteric mutations were prepared and grouped to negative allosteric, nonallosteric, and positive allosteric modulators. ∼ 50% of mutations displayed the allosteric-state changes when moving from a buffered solution into cells. For example, there were no positive allosteric modulators in the buffered solution but eight in cells. The change in protein allostery is correlated with the interactions between the protein and the cellular environment. These interactions presumably drive the surrounding macromolecules in cells to transiently bind to the monomer and dimer mutational sites and change the free energies of the two species differently which generate new allosteric effects. These surrounding macromolecules create a new protein allostery pathway that is only present in cells.
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Affiliation(s)
- Xiaoxu Chen
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xueying Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingming Qin
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Jingfei Chen
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Mengting Wang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Zhijun Liu
- National Facility for Protein Science, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Liaoyuan An
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xiangfei Song
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Lishan Yao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
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6
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Saha D, Kothari S, Kulkarni SD, Thambiraja M, Yennamalli RM, Das DK. Genetic heterogeneity and respiratory chain enzyme analysis in pediatric Indian patients with mitochondrial disorder: Report of novel variants in POLG1 gene and their functional implication using molecular dynamic simulation. Mitochondrion 2024; 76:101870. [PMID: 38471579 DOI: 10.1016/j.mito.2024.101870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/14/2024]
Abstract
Mitochondrial disorders are a heterogeneous group of disorders caused by mutations in the mitochondrial DNA or in nuclear genes encoding the mitochondrial proteins and subunits. Polymerase Gamma (POLG) is a nuclear gene and mutation in the POLG gene are one of the major causes of inherited mitochondrial disorders. In this study, 15 pediatric patients, with a wide spectrum of clinical phenotypes were screened using blood samples (n = 15) and muscle samples (n = 4). Respiratory chain enzyme analysis in the muscle samples revealed multi-complex deficiencies with Complex I deficiency present in (1/4) patients, Complex II (2/4), Complex III (3/4) and Complex IV (2/4) patients. Multiple large deletions were observed in 4/15 patients using LR-PCR. Whole exome sequencing (WES) revealed a compound heterozygous mutation consisting of a POLG1 novel variant (NP_002684.1:p.Trp261X) and a missense variant (NP_002684.1:p. Leu304Arg) in one patient and another patient harboring a novel homozygous POLG1 variant (NP_002684.1:p. Phe750Val). These variants (NP_002684.1:p. Leu304Arg) and (NP_002684.1:p. Phe750Val) and their interactions with DNA were modelled using molecular docking and molecular dynamics (MD) simulation studies. The protein conformation was analyzed as root mean square deviation (RMSD), root mean square fluctuation (RMSF) which showed local fluctuations in the mutants compared to the wildtype. However, Solvent Accessible Surface Area (SASA) significantly increased for NP_002684.1:p.Leu304Arg and decreased in NP_002684.1:p.Phe750Val mutants. Further, Contact Order analysis indicated that the Aromatic-sulfur interactions were destabilizing in the mutants. Overall, these in-silico analysis has revealed a destabilizing mutations suggesting pathogenic variants in POLG1 gene.
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Affiliation(s)
- Debolina Saha
- Stem Cell Biology Department, ICMR-National Institute for Research in Reproductive and Child Health, JM Street, Parel, Mumbai 400012, India
| | - Sonam Kothari
- Department of Pediatric Neurology, Bai Jerbai Wadia Hospital for Children, Acharya Donde Marg, Parel, Mumbai, Maharashtra 400012, India
| | - Shilpa Duttaprasanna Kulkarni
- Department of Pediatric Neurology, Bai Jerbai Wadia Hospital for Children, Acharya Donde Marg, Parel, Mumbai, Maharashtra 400012, India
| | - Menaka Thambiraja
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamilnadu 613401, India
| | - Ragothaman M Yennamalli
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamilnadu 613401, India.
| | - Dhanjit K Das
- Stem Cell Biology Department, ICMR-National Institute for Research in Reproductive and Child Health, JM Street, Parel, Mumbai 400012, India.
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7
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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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8
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Yu I, Mori T, Matsuoka D, Surblys D, Sugita Y. SPANA: Spatial decomposition analysis for cellular-scale molecular dynamics simulations. J Comput Chem 2024; 45:498-505. [PMID: 37966727 DOI: 10.1002/jcc.27260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023]
Abstract
The rapid increase in computational power with the latest supercomputers has enabled atomistic molecular dynamics (MDs) simulations of biomolecules in biological membrane, cytoplasm, and other cellular environments. These environments often contain a million or more atoms to be simulated simultaneously. Therefore, their trajectory analyses involve heavy computations that can become a bottleneck in the computational studies. Spatial decomposition analysis (SPANA) is a set of analysis tools in the Generalized-Ensemble Simulation System (GENESIS) software package that can carry out MD trajectory analyses of large-scale biological simulations using multiple CPU cores in parallel. SPANA applies the spatial decomposition of a large biological system to distribute structural and dynamical analyses into individual CPU cores, which reduces the computational time and the memory size, significantly. SPANA opens new possibilities for detailed atomistic analyses of biomacromolecules as well as solvent water molecules, ions, and metabolites in MD simulation trajectories of very large biological systems containing more than millions of atoms in cellular environments.
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Affiliation(s)
- Isseki Yu
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Department of Bioinformatics, Maebashi Institute of Technology, Maebashi, Gunma, Japan
| | - Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Daisuke Matsuoka
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Donatas Surblys
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
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9
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Alfano C, Fichou Y, Huber K, Weiss M, Spruijt E, Ebbinghaus S, De Luca G, Morando MA, Vetri V, Temussi PA, Pastore A. Molecular Crowding: The History and Development of a Scientific Paradigm. Chem Rev 2024; 124:3186-3219. [PMID: 38466779 PMCID: PMC10979406 DOI: 10.1021/acs.chemrev.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.
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Affiliation(s)
- Caterina Alfano
- Structural
Biology and Biophysics Unit, Fondazione
Ri.MED, 90100 Palermo, Italy
| | - Yann Fichou
- CNRS,
Bordeaux INP, CBMN UMR 5248, IECB, University
of Bordeaux, F-33600 Pessac, France
| | - Klaus Huber
- Department
of Chemistry, University of Paderborn, 33098 Paderborn, Germany
| | - Matthias Weiss
- Experimental
Physics I, Physics of Living Matter, University
of Bayreuth, 95440 Bayreuth, Germany
| | - Evan Spruijt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Simon Ebbinghaus
- Lehrstuhl
für Biophysikalische Chemie and Research Center Chemical Sciences
and Sustainability, Research Alliance Ruhr, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Giuseppe De Luca
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Valeria Vetri
- Dipartimento
di Fisica e Chimica − Emilio Segrè, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Annalisa Pastore
- King’s
College London, Denmark
Hill Campus, SE5 9RT London, United Kingdom
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10
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Ben‐Ishay Y, Barak Y, Feintuch A, Ouari O, Pierro A, Mileo E, Su X, Goldfarb D. Exploring the dynamics and structure of PpiB in living Escherichia coli cells using electron paramagnetic resonance spectroscopy. Protein Sci 2024; 33:e4903. [PMID: 38358137 PMCID: PMC10868451 DOI: 10.1002/pro.4903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
The combined effects of the cellular environment on proteins led to the definition of a fifth level of protein structural organization termed quinary structure. To explore the implication of potential quinary structure for globular proteins, we studied the dynamics and conformations of Escherichia coli (E. coli) peptidyl-prolyl cis/trans isomerase B (PpiB) in E. coli cells. PpiB plays a major role in maturation and regulation of folded proteins by catalyzing the cis/trans isomerization of the proline imidic peptide bond. We applied electron paramagnetic resonance (EPR) techniques, utilizing both Gadolinium (Gd(III)) and nitroxide spin labels. In addition to using standard spin labeling approaches with genetically engineered cysteines, we incorporated an unnatural amino acid to achieve Gd(III)-nitroxide orthogonal labeling. We probed PpiB's residue-specific dynamics by X-band continuous wave EPR at ambient temperatures and its structure by double electron-electron resonance (DEER) on frozen samples. PpiB was delivered to E. coli cells by electroporation. We report a significant decrease in the dynamics induced by the cellular environment for two chosen labeling positions. These changes could not be reproduced by adding crowding agents and cell extracts. Concomitantly, we report a broadening of the distance distribution in E. coli, determined by Gd(III)-Gd(III) DEER measurements, as compared with solution and human HeLa cells. This suggests an increase in the number of PpiB conformations present in E. coli cells, possibly due to interactions with other cell components, which also contributes to the reduction in mobility and suggests the presence of a quinary structure.
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Affiliation(s)
- Yasmin Ben‐Ishay
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
| | - Yoav Barak
- Department of Chemical Research SupportWeizmann Institute of ScienceRehovotIsrael
| | - Akiva Feintuch
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
| | - Olivier Ouari
- CNRS, ICR, Institut de Chimie RadicalaireAix‐Marseille UniversitéMarseilleFrance
| | - Annalisa Pierro
- CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des ProtéinesAix Marseille UniversitéMarseilleFrance
- Present address:
Konstanz Research School Chemical Biology, Department of ChemistryUniversity of KonstanzKonstanzGermany
| | - Elisabetta Mileo
- CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des ProtéinesAix Marseille UniversitéMarseilleFrance
| | - Xun‐Cheng Su
- State Key Laboratory of Elemento‐organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular RecognitionCollege of Chemistry, Nankai UniversityTianjinChina
| | - Daniella Goldfarb
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
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11
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Zheng L, Shi S, Sun X, Lu M, Liao Y, Zhu S, Zhang H, Pan Z, Fang P, Zeng Z, Li H, Li Z, Xue W, Zhu F. MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics. Brief Bioinform 2024; 25:bbae006. [PMID: 38305456 PMCID: PMC10835750 DOI: 10.1093/bib/bbae006] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 02/03/2024] Open
Abstract
Protein structure prediction is a longstanding issue crucial for identifying new drug targets and providing a mechanistic understanding of protein functions. To enhance the progress in this field, a spectrum of computational methodologies has been cultivated. AlphaFold2 has exhibited exceptional precision in predicting wild-type protein structures, with performance exceeding that of other methods. However, predicting the structures of missense mutant proteins using AlphaFold2 remains challenging due to the intricate and substantial structural alterations caused by minor sequence variations in the mutant proteins. Molecular dynamics (MD) has been validated for precisely capturing changes in amino acid interactions attributed to protein mutations. Therefore, for the first time, a strategy entitled 'MoDAFold' was proposed to improve the accuracy and reliability of missense mutant protein structure prediction by combining AlphaFold2 with MD. Multiple case studies have confirmed the superior performance of MoDAFold compared to other methods, particularly AlphaFold2.
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Affiliation(s)
- Lingyan Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
| | - Shuiyang Shi
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xiuna Sun
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
| | - Mingkun Lu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
| | - Yang Liao
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Sisi Zhu
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Ziqi Pan
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Pan Fang
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Zhenyu Zeng
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Honglin Li
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhaorong Li
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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12
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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: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [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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13
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Knab E, Davis CM. Chemical interactions modulate λ 6-85 stability in cells. Protein Sci 2023; 32:e4698. [PMID: 37313657 PMCID: PMC10288553 DOI: 10.1002/pro.4698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/26/2023] [Accepted: 06/06/2023] [Indexed: 06/15/2023]
Abstract
Because steric crowding is most effective when the crowding agent is similar in size to the molecule that it acts upon and the average macromolecule inside cells is much larger than a small protein or peptide, steric crowding is not predicted to affect their folding inside cells. On the other hand, chemical interactions should perturb in-cell structure and stability because they arise from interactions between the surface of the small protein or peptide and its environment. Indeed, previous in vitro measurements of the λ-repressor fragment, λ6-85 , in crowding matrices comprised of Ficoll or protein crowders support these predictions. Here, we directly quantify the in-cell stability of λ6-85 and distinguish the contribution of steric crowding and chemical interactions to its stability. Using a FRET-labeled λ6-85 construct, we find that the fragment is stabilized by 5°C in-cells compared to in vitro. We demonstrate that this stabilization cannot be explained by steric crowding because, as anticipated, Ficoll has no effect on λ6-85 stability. We find that the in-cell stabilization arises from chemical interactions, mimicked in vitro by mammalian protein extraction reagent (M-PER™). Comparison between FRET values in-cell and in Ficoll confirms that U-2 OS cytosolic crowding is reproduced at macromolecule concentrations of 15% w/v. Our measurements validate the cytomimetic of 15% Ficoll and 20% M-PER™ that we previously developed for protein and RNA folding studies. However, because the in-cell stability of λ6-85 is reproduced by 20% v/v M-PER™ alone, we predict that this simplified mixture could be a useful tool to predict the in-cell behaviors of other small proteins and peptides.
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Affiliation(s)
- Edward Knab
- Department of ChemistryYale UniversityNew HavenConnecticutUSA
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14
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Liang Q, Zhang Y, Zhang H, Wu S, Gong W, Perrett S. Reversible Redox-Dependent Conformational Switch of the C-Terminal α-Helical Lid of Human Hsp70 Observed by In-Cell NMR. ACS Chem Biol 2023; 18:176-183. [PMID: 36524733 DOI: 10.1021/acschembio.2c00845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Glutathionylation of human stress-inducible Hsp70 (hHsp70) under oxidative stress conditions has been suggested to act as an on/off switch of hHsp70 chaperone activity and thus transfer redox signals to hHsp70 clients through a change in conformation. The mechanism of this switch involves unfolding of the C-terminal α-helical lid, SBDα, upon glutathionylation, which then binds to and blocks the hHsp70 substrate-binding site. This process is reversible and redox-regulated and has been demonstrated for purified protein in solution. Here, we found that this redox-regulated reversible process also occurs in the cellular environment. Using Escherichia coli as a model system, in-cell NMR data clearly indicate that hHsp70 SBDα undergoes a conformational transition from ordered to disordered after diamide stimulation. The disordered SBDα could spontaneously recover back to the helix bundle conformation over time. This oxidative-stress induced process also occurred in cell lysate, with a similar unfolding rate as in cells, but the refolding rate was significantly slower in cell lysate. Increased temperature accelerates this process. Under heat stress alone, unfolding of the SBDα could not be detected in cells. Our in-cell NMR results provide direct support for the molecular switch model of hHsp70 redox regulation and also demonstrate the power of in-cell NMR for real-time study of protein structures during biological processes in living cells.
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Affiliation(s)
- Qihui Liang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yiying Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Si Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Weibin Gong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sarah Perrett
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
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15
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Chen SJ, Hassan M, Jernigan RL, Jia K, Kihara D, Kloczkowski A, Kotelnikov S, Kozakov D, Liang J, Liwo A, Matysiak S, Meller J, Micheletti C, Mitchell JC, Mondal S, Nussinov R, Okazaki KI, Padhorny D, Skolnick J, Sosnick TR, Stan G, Vakser I, Zou X, Rose GD. Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proc Natl Acad Sci U S A 2023; 120:e2214423119. [PMID: 36580595 PMCID: PMC9910419 DOI: 10.1073/pnas.2214423119] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, MO65211
| | - Mubashir Hassan
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH43205
| | - Robert L. Jernigan
- Bioinformatics and Computational Biology Program and Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA50011
| | - Kejue Jia
- Bioinformatics and Computational Biology Program and Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology Iowa State University, Ames, IA50011
| | - Daisuke Kihara
- Department of Biological Sciences, Department of Computer Science Purdue University, West Lafayette, IN79075
| | - Andrzej Kloczkowski
- Department of Pediatrics, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, The Ohio State University, Columbus, OH43205
| | - Sergei Kotelnikov
- Department of Applied Mathematics and Statistics, Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY11794
| | - Dima Kozakov
- Frey Family Foundation, Department of Applied Mathematics and Statistics, Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY11794
| | - Jie Liang
- Richard and Loan Hill Dept of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL60607
| | - Adam Liwo
- Faculty of Chemistry, University of Gdansk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, Gdansk80-308, Poland
| | - Silvina Matysiak
- Fischell Department of Bioengineering, University of Maryland, College Park, MD20742
| | - Jarek Meller
- University of Cincinnati & Cincinnati Children’s Hospital Medical Center, Cincinnati, OH45229
| | - Cristian Micheletti
- SISSA - International School for Advanced Studies, Via Bonomea 265, TriesteI-34136, Italy
| | | | | | - Ruth Nussinov
- Computational Structural Biology Section, National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD21702
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv69978, Israel
| | - Kei-ichi Okazaki
- Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi444-8585, Japan
| | - Dzmitry Padhorny
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY11794
| | - Jeffrey Skolnick
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30332
| | - Tobin R. Sosnick
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL60637
| | - George Stan
- Department of Chemistry, University of Cincinnati, Cincinnati, OH45221
| | - Ilya Vakser
- Computational Biology Program and Center for Computational Biology, Department of Molecular Biosciences, The University of Kansas, Lawrence, KS66045
| | - Xiaoqin Zou
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, Institute for Data Science and Informatics, University of Missouri, Columbia, MO65211
| | - George D. Rose
- Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
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16
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Protein delivery to living cells by thermal stimulation for biophysical investigation. Sci Rep 2022; 12:17190. [PMID: 36229511 PMCID: PMC9561116 DOI: 10.1038/s41598-022-21103-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/22/2022] [Indexed: 01/05/2023] Open
Abstract
Studying biomolecules in their native environment represents the ideal sample condition for structural biology investigations. Here we present a novel protocol which allows to delivery proteins into eukaryotic cells through a mild thermal stimulation. The data presented herein show the efficacy of this approach for delivering proteins in the intracellular environment of mammalian cells reaching a concentration range suitable for successfully applying biophysical methods, such as double electron electron resonance (DEER) measurements for characterising protein conformations.
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17
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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18
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You X, Baiz CR. Importance of Hydrogen Bonding in Crowded Environments: A Physical Chemistry Perspective. J Phys Chem A 2022; 126:5881-5889. [PMID: 35968816 DOI: 10.1021/acs.jpca.2c03803] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cells are heterogeneous on every length and time scale; cytosol contains thousands of proteins, lipids, nucleic acids, and small molecules, and molecular interactions within this crowded environment determine the structure, dynamics, and stability of biomolecules. For decades, the effects of crowding at the atomistic scale have been overlooked in favor of more tractable models largely based on thermodynamics. Crowding can affect the conformations and stability of biomolecules by modulating water structure and dynamics within the cell, and these effects are nonlocal and environment dependent. Thus, characterizing water's hydrogen-bond (H-bond) networks is a critical step toward a complete microscopic crowding model. This perspective provides an overview of molecular crowding and describes recent time-resolved spectroscopy approaches investigating H-bond networks and dynamics in crowded or otherwise complex aqueous environments. Ultrafast spectroscopy combined with atomistic simulations has emerged as a powerful combination for studying H-bond structure and dynamics in heterogeneous multicomponent systems. We discuss the ongoing challenges toward developing a complete atomistic description of macromolecular crowding from an experimental as well as a theoretical perspective.
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Affiliation(s)
- Xiao You
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 19104, United States
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 19104, United States
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19
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Abstract
Human health depends on the correct folding of proteins, for misfolding and aggregation lead to diseases. An unfolded (denatured) protein can refold to its original folded state. How does this occur is known as the protein folding problem. One of several related questions to this problem is that how much more stable is the folded state than the unfolded state. There are several measures of protein stability. In this article, protein stability is given a thermodynamic definition and is measured by Gibbs free energy change ( Δ G D 0 ) associated with the equilibrium, native (N) conformation ↔ denatured (D) conformation under the physiological condition usually taken as dilute buffer (or water) at 25 °C. We show that this thermodynamic quantity ( Δ G D 0 ), where subscript D represents transition between N and D states, and superscript 0 (zero) represents the fact that the transition occurs in the absence of denaturant, can be neither measured nor predicted under physiological conditions. However, Δ G D can be measured in the presence of strong chemical denaturants such as guanidinium chloride and urea which are shown to destroy all noncovalent interactions responsible for maintaining the folded structure. A problem with this measurement is that the estimate of Δ G D 0 comes from the analysis of the plot of Δ G D versus denaturant concentration, which requires a long extrapolation of values of Δ G D , and all the three methods of extrapolation give three different values of Δ G D 0 for a protein. Thus, our confidence in the authentic value of Δ G D 0 is eroded. Another problem with this in vitro measurement of Δ G D 0 is that it is done on the pure protein sample in dilute buffer which is a very large extrapolation of the in vivo conditions, for the crowding effect on protein stability is ignored.
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Affiliation(s)
- Faizan Ahmad
- Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi, India
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20
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Irukuvajjula SS, Reddy JG, Vadrevu R. Crowding by Poly(ethylene glycol) Destabilizes Chemotaxis Protein Y (CheY). Biochemistry 2022; 61:1431-1443. [PMID: 35796609 DOI: 10.1021/acs.biochem.2c00030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The prevailing understanding of various aspects of biochemical processes, including folding, stability, intermolecular interactions, and the binding of metals, substrates, and inhibitors, is derived from studies carried out under dilute and homogeneous conditions devoid of a crowding-related environment. The effect of crowding-induced modulation on the structure and stability of native and magnesium-dependent Chemotaxis Y (CheY), a bacterial signaling protein, was probed in the presence and absence of poly(ethylene glycol) (PEG). A combined analysis from circular dichroism, intrinsic and extrinsic fluorescence, and tryptophan fluorescence lifetime changes indicates that PEG perturbs the structure but leaves the thermal stability largely unchanged. Intriguingly, while the stability of the protein is enhanced in the presence of magnesium under dilute buffer conditions, PEG-induced crowding leads to reduced thermal stability in the presence of magnesium. Nuclear magnetic resonance (NMR) chemical shift perturbations and resonance broadening for a subset of residues indicate that PEG interacts specifically with a subset of hydrophilic and hydrophobic residues found predominantly in α helices, β strands, and in the vicinity of the metal-binding region. Thus, PEG prompted conformational perturbation, presumably provides a different situation for magnesium interaction, thereby perturbing the magnesium-prompted stability. In summary, our results highlight the dominance of enthalpic contributions between PEG and CheY via both hydrophilic and hydrophobic interactions, which can subtly affect the conformation, modulating the metal-protein interaction and stability, implying that in the context of cellular situation, structure, stability, and magnesium binding thermodynamics of CheY may be different from those measured in dilute solution.
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Affiliation(s)
- Shivkumar Sharma Irukuvajjula
- Department of Biological Sciences, Birla Institute of Technology & Science─Pilani, Hyderabad Campus, Jawahar Nagar, Shamirpet, Hyderabad 500078, India
| | - Jithender G Reddy
- NMR Division, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Ministry of Science and Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Technology & Science─Pilani, Hyderabad Campus, Jawahar Nagar, Shamirpet, Hyderabad 500078, India
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21
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Gorensek-Benitez AH, Kirk B, Myers JK. Protein Fibrillation under Crowded Conditions. Biomolecules 2022; 12:biom12070950. [PMID: 35883507 PMCID: PMC9312947 DOI: 10.3390/biom12070950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 12/04/2022] Open
Abstract
Protein amyloid fibrils have widespread implications for human health. Over the last twenty years, fibrillation has been studied using a variety of crowding agents to mimic the packed interior of cells or to probe the mechanisms and pathways of the process. We tabulate and review these results by considering three classes of crowding agent: synthetic polymers, osmolytes and other small molecules, and globular proteins. While some patterns are observable for certain crowding agents, the results are highly variable and often depend on the specific pairing of crowder and fibrillating protein.
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Affiliation(s)
- Annelise H. Gorensek-Benitez
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, CO 80903, USA
- Correspondence: (A.H.G.-B.); (J.K.M.)
| | - Bryan Kirk
- Department of Biology, Davidson College, Davidson, NC 28035, USA;
| | - Jeffrey K. Myers
- Department of Chemistry, Davidson College, Davidson, NC 28035, USA
- Correspondence: (A.H.G.-B.); (J.K.M.)
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22
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Luchinat E, Cremonini M, Banci L. Radio Signals from Live Cells: The Coming of Age of In-Cell Solution NMR. Chem Rev 2022; 122:9267-9306. [PMID: 35061391 PMCID: PMC9136931 DOI: 10.1021/acs.chemrev.1c00790] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Indexed: 12/12/2022]
Abstract
A detailed knowledge of the complex processes that make cells and organisms alive is fundamental in order to understand diseases and to develop novel drugs and therapeutic treatments. To this aim, biological macromolecules should ideally be characterized at atomic resolution directly within the cellular environment. Among the existing structural techniques, solution NMR stands out as the only one able to investigate at high resolution the structure and dynamic behavior of macromolecules directly in living cells. With the advent of more sensitive NMR hardware and new biotechnological tools, modern in-cell NMR approaches have been established since the early 2000s. At the coming of age of in-cell NMR, we provide a detailed overview of its developments and applications in the 20 years that followed its inception. We review the existing approaches for cell sample preparation and isotopic labeling, the application of in-cell NMR to important biological questions, and the development of NMR bioreactor devices, which greatly increase the lifetime of the cells allowing real-time monitoring of intracellular metabolites and proteins. Finally, we share our thoughts on the future perspectives of the in-cell NMR methodology.
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Affiliation(s)
- Enrico Luchinat
- Dipartimento
di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum−Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
- Magnetic
Resonance Center, Università degli
Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Matteo Cremonini
- Magnetic
Resonance Center, Università degli
Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic
Resonance Center, Università degli
Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Dipartimento
di Chimica, Università degli Studi
di Firenze, Via della
Lastruccia 3, 50019 Sesto Fiorentino, Italy
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23
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Brom JA, Pielak GJ. Desiccation-tolerance and globular proteins adsorb similar amounts of water. Protein Sci 2022; 31:e4288. [PMID: 35481639 PMCID: PMC8994485 DOI: 10.1002/pro.4288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 11/11/2022]
Abstract
When exposed to desiccation stress, extremotolerant organisms from all domains of life produce protective disordered proteins with the potential to inform the design of excipients for formulating biologics and industrial enzymes. However, the mechanism(s) of desiccation protection remain largely unknown. To investigate the role of water sorption in desiccation protection, we use thermogravimetric analysis to study water adsorption by two desiccation-tolerance proteins, cytosolic abundant heat soluble protein D from tardigrades and late embryogenesis abundant protein 4 from the anhydrobiotic midge Polypedilum vanderplanki, and, as a control, the globular B1 domain of staphylococcal protein G. All samples adsorb similar amounts of water, suggesting that modulated water retention is not responsible for dehydration protection by desiccation-tolerance proteins.
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Affiliation(s)
- Julia A Brom
- Department of Chemistry, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, North Carolina, USA
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, North Carolina, USA
- Lineberger Cancer Center, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, North Carolina, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, North Carolina, USA
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24
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Rajendran D, Mitra S, Oikawa H, Madhurima K, Sekhar A, Takahashi S, Naganathan AN. Quantification of Entropic Excluded Volume Effects Driving Crowding-Induced Collapse and Folding of a Disordered Protein. J Phys Chem Lett 2022; 13:3112-3120. [PMID: 35357183 PMCID: PMC7612738 DOI: 10.1021/acs.jpclett.2c00316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We investigate the conformational properties of the intrinsically disordered DNA-binding domain of CytR in the presence of the polymeric crowder polyethylene glycol (PEG). Integrating circular dichroism, nuclear magnetic resonance, and single-molecule Förster resonance energy transfer measurements, we demonstrate that disordered CytR populates a well-folded minor conformation in its native ensemble, while the unfolded ensemble collapses and folds with an increase in crowder density independent of the crowder size. Employing a statistical-mechanical model, the effective reduction in the accessible conformational space of a residue in the unfolded state is estimated to be 10% at 300 mg/mL PEG8000, relative to dilute conditions. The experimentally consistent PEG-temperature phase diagram thus constructed reveals that entropic effects can stabilize disordered CytR by 10 kJ mol-1, driving the equilibrium toward folded conformations under physiological conditions. Our work highlights the malleable conformational landscape of CytR, the presence of a folded conformation in the disordered ensemble, and proposes a scaling relation for quantifying excluded volume effects on protein stability.
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Affiliation(s)
- Divya Rajendran
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Shrutarshi Mitra
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Hiroyuki Oikawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Kulkarni Madhurima
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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25
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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26
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Speer SL, Stewart CJ, Sapir L, Harries D, Pielak GJ. Macromolecular Crowding Is More than Hard-Core Repulsions. Annu Rev Biophys 2022; 51:267-300. [PMID: 35239418 DOI: 10.1146/annurev-biophys-091321-071829] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cells are crowded, but proteins are almost always studied in dilute aqueous buffer. We review the experimental evidence that crowding affects the equilibrium thermodynamics of protein stability and protein association and discuss the theories employed to explain these observations. In doing so, we highlight differences between synthetic polymers and biologically relevant crowders. Theories based on hard-core interactions predict only crowding-induced entropic stabilization. However, experiment-based efforts conducted under physiologically relevant conditions show that crowding can destabilize proteins and their complexes. Furthermore, quantification of the temperature dependence of crowding effects produced by both large and small cosolutes, including osmolytes, sugars, synthetic polymers, and proteins, reveals enthalpic effects that stabilize or destabilize proteins. Crowding-induced destabilization and the enthalpic component point to the role of chemical interactions between and among the macromolecules, cosolutes, and water. We conclude with suggestions for future studies. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Shannon L Speer
- Department of Chemistry, University of North Carolina at Chapel Hill, North Carolina, USA;
| | - Claire J Stewart
- Department of Chemistry, University of North Carolina at Chapel Hill, North Carolina, USA;
| | - Liel Sapir
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, USA
| | - Daniel Harries
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem, Israel
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina at Chapel Hill, North Carolina, USA; .,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina, USA.,Lineberger Cancer Research Center, University of North Carolina at Chapel Hill, North Carolina, USA
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27
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Crilly CJ, Brom JA, Warmuth O, Esterly HJ, Pielak GJ. Protection by desiccation-tolerance proteins probed at the residue level. Protein Sci 2022; 31:396-406. [PMID: 34766407 PMCID: PMC8819849 DOI: 10.1002/pro.4231] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 02/03/2023]
Abstract
Extremotolerant organisms from all domains of life produce protective intrinsically disordered proteins (IDPs) in response to desiccation stress. In vitro, many of these IDPs protect enzymes from dehydration stress better than U.S. Food and Drug Administration-approved excipients. However, as with most excipients, their protective mechanism is poorly understood. Here, we apply thermogravimetric analysis, differential scanning calorimetry, and liquid-observed vapor exchange (LOVE) NMR to study the protection of two model globular proteins (the B1 domain of staphylococcal protein G [GB1] and chymotrypsin inhibitor 2 [CI2]) by two desiccation-tolerance proteins (CAHS D from tardigrades and PvLEA4 from an anhydrobiotic midge), as well as by disordered and globular protein controls. We find that all protein samples retain similar amounts of water and possess similar glass transition temperatures, suggesting that neither enhanced water retention nor vitrification is responsible for protection. LOVE NMR reveals that IDPs protect against dehydration-induced unfolding better than the globular protein control, generally protect the same regions of GB1 and CI2, and protect GB1 better than CI2. These observations suggest that electrostatic interactions, charge patterning, and expanded conformations are key to protection. Further application of LOVE NMR to additional client proteins and protectants will deepen our understanding of dehydration protection, enabling the streamlined production of dehydrated proteins for expanded use in the medical, biotechnology, and chemical industries.
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Affiliation(s)
- Candice J. Crilly
- Department of ChemistryUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
| | - Julia A. Brom
- Department of ChemistryUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
| | - Owen Warmuth
- Department of ChemistryUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
| | - Harrison J. Esterly
- Department of ChemistryUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
| | - Gary J. Pielak
- Department of ChemistryUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA,Department of Biochemistry & BiophysicsUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA,Lineberger Cancer CenterUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA,Integrative Program for Biological and Genome SciencesUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
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28
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Song X, Wang M, Chen X, Zhang X, Yang Y, Liu Z, Yao L. Quantifying Protein Electrostatic Interactions in Cells by Nuclear Magnetic Resonance Spectroscopy. J Am Chem Soc 2021; 143:19606-19613. [PMID: 34766768 DOI: 10.1021/jacs.1c10154] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Most proteins perform their functions in cells. How the cellular environment modulates protein interactions is an important question. In this work, electrostatic interactions between protein charges were studied using in-cell nuclear magnetic resonance (NMR) spectroscopy. A total of eight charge pairs were introduced in protein GB3. Compared to the charge pair electrostatic interactions in a buffer, five charge pairs in cells displayed no apparent changes whereas three pairs had the interactions weakened by more than 70%. Further investigation suggests that the transfer free energy is responsible for the electrostatic interaction modulation. Both the transfer free energy of the folded state and that of the unfolded state can contribute to the cellular environmental effect on protein electrostatics, although the latter is generally larger (more negative) than the former. Our work highlights the importance of direct in-cell studies of protein interactions and thus protein function.
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Affiliation(s)
- 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
| | - 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
| | - 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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29
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Kitoka K, Skrabana R, Gasparik N, Hritz J, Jaudzems K. NMR Studies of Tau Protein in Tauopathies. Front Mol Biosci 2021; 8:761227. [PMID: 34859051 PMCID: PMC8632555 DOI: 10.3389/fmolb.2021.761227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Tauopathies, including Alzheimer's disease (AD), are the most troublesome of all age-related chronic conditions, as there are no well-established disease-modifying therapies for their prevention and treatment. Spatio-temporal distribution of tau protein pathology correlates with cognitive decline and severity of the disease, therefore, tau protein has become an appealing target for therapy. Current knowledge of the pathological effects and significance of specific species in the tau aggregation pathway is incomplete although more and more structural and mechanistic insights are being gained using biophysical techniques. Here, we review the application of NMR to structural studies of various tau forms that appear in its aggregation process, focusing on results obtained from solid-state NMR. Furthermore, we discuss implications from these studies and their prospective contribution to the development of new tauopathy therapies.
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Affiliation(s)
- Kristine Kitoka
- Laboratory of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Rostislav Skrabana
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
- AXON Neuroscience R&D Services SE, Bratislava, Slovakia
| | - Norbert Gasparik
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Jozef Hritz
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kristaps Jaudzems
- Laboratory of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
- Faculty of Chemistry, University of Latvia, Riga, Latvia
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30
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Ghosh R, Xiao Y, Kragelj J, Frederick KK. In-Cell Sensitivity-Enhanced NMR of Intact Viable Mammalian Cells. J Am Chem Soc 2021; 143:18454-18466. [PMID: 34724614 DOI: 10.1021/jacs.1c06680] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
NMR has the resolution and specificity to determine atomic-level protein structures of isotopically labeled proteins in complex environments, and with the sensitivity gains conferred by dynamic nuclear polarization (DNP), NMR has the sensitivity to detect proteins at their endogenous concentrations. However, DNP sensitivity enhancements are critically dependent on experimental conditions and sample composition. While some of these conditions are theoretically compatible with cellular viability, the effects of others on cellular sample integrity are unknown. Uncertainty about the integrity of cellular samples limits the utility of experimental outputs of in-cell experiments. Using several measures, we establish conditions that support DNP enhancements that can enable detection of micromolar concentrations of proteins in experimentally tractable times that are compatible with cellular viability. Taken together, we establish DNP-assisted MAS NMR as a technique for structural investigations of biomolecules in intact viable cells that can be phenotyped both before and after NMR experiments.
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Affiliation(s)
- Rupam Ghosh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas 75390-8816, United States
| | - Yiling Xiao
- Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas 75390-8816, United States
| | - Jaka Kragelj
- Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas 75390-8816, United States
| | - Kendra K Frederick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas 75390-8816, United States.,Center for Alzheimer's and Neurodegenerative Disease, UT Southwestern Medical Center, Dallas, Texas 75390, United States
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31
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Jia Bu Y, Nitz M. Incorporation of TePhe into Expressed Proteins is Minimally Perturbing. Chembiochem 2021; 22:2449-2456. [PMID: 34003548 DOI: 10.1002/cbic.202100160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 05/14/2021] [Indexed: 01/24/2023]
Abstract
Tellurium is a versatile heavy chalcogen with numerous applications in chemical biology, providing valuable probes in mass cytometry, fluorescence imaging and structural biology. L-Tellurienylalanine (TePhe) is an analogue of the proteinogenic amino acid L-phenylalanine (Phe) in which the phenyl side chain has been replaced by a 5-membered tellurophene moiety. High incorporation level of TePhe in expressed proteins at defined sites is expected to facilitate studies in proteomics, protein NMR spectroscopy, and structure elucidation. As a model we chose immunoglobulin-binding Protein G, B1 domain (GB1) to validate TePhe as a suitable structural analogue for Phe. We demonstrate that approximately 1 in 2 of all Phe sites within GB1 can be substituted with TePhe through expression in standard non-Phe-auxotrophic E. coli in Phe-deficient media containing glyphosate, an inhibitor of aromatic amino acid biosynthesis. The TePhe content of the GB1 sample can be further increased to 85 % through HPLC. Using NMR and CD spectroscopy, we confirm that the Phe-to-TePhe substitution has negligible impact on the global structure and stability of GB1.
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Affiliation(s)
- Yong Jia Bu
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
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32
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Katava M, Stirnemann G, Pachetti M, Capaccioli S, Paciaroni A, Sterpone F. Specific Interactions and Environment Flexibility Tune Protein Stability under Extreme Crowding. J Phys Chem B 2021; 125:6103-6111. [PMID: 34100611 DOI: 10.1021/acs.jpcb.1c01511] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Macromolecular crowding influences protein mobility and stability in vivo. A precise description of the crowding effect on protein thermal stability requires the estimate of the combined effects of excluded volume, specific protein-environment interactions, as well as the thermal response of the crowders. Here, we explore an ideal model system, the lysozyme protein in powder state, to dissect the factors controlling the melting of the protein under extreme crowding. By deploying state-of-the art molecular simulations, supported by calorimetric experiments, we assess the role of the environment flexibility and of intermolecular electrostatic interactions. In particular, we show that the temperature-dependent flexibility of the macromolecular crowders, along with specific interactions, significantly alleviates the stabilizing contributions of the static volume effect.
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Affiliation(s)
- Marina Katava
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Guillaume Stirnemann
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Maria Pachetti
- Elettra-Sincrotrone Trieste, S.S. 14 km 163.5, Area Science Park, 34149 Trieste, Italy.,Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
| | - Simone Capaccioli
- Dipartimento di Fisica, Universitá di Pisa, largo Pontecorvo 3, 56127 Pisa, Italy.,CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Lungarno Pacinotti 43, I-56127 Pisa, Italy
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia, Universitá di Perugia, via A. Pascoli, 06123 Perugia, Italy
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
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33
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Höfurthner T, Mateos B, Konrat R. On-Cell NMR Contributions to Membrane Receptor Binding Characterization. Chempluschem 2021; 86:938-945. [PMID: 34160899 DOI: 10.1002/cplu.202100134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/28/2021] [Indexed: 12/21/2022]
Abstract
NMR spectroscopy has matured into a powerful tool to characterize interactions between biological molecules at atomic resolution, most importantly even under near to native (physiological) conditions. The field of in-cell NMR aims to study proteins and nucleic acids inside living cells. However, cells interrogate their environment and are continuously modulated by external stimuli. Cell signaling processes are often initialized by membrane receptors on the cell surface; therefore, characterizing their interactions at atomic resolution by NMR, hereafter referred as on-cell NMR, can provide valuable mechanistic information. This review aims to summarize recent on-cell NMR tools that give information about the binding site and the affinity of membrane receptors to their ligands together with potential applications to in vivo drug screening systems.
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Affiliation(s)
- Theresa Höfurthner
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Borja Mateos
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
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34
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Song X, An L, Wang M, Chen J, Liu Z, Yao L. Osmolytes Can Destabilize Proteins in Cells by Modulating Electrostatics and Quinary Interactions. ACS Chem Biol 2021; 16:864-871. [PMID: 33843182 DOI: 10.1021/acschembio.1c00024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although numerous in vitro studies have shown that osmolytes are capable of stabilizing proteins, their effect on protein folding in vivo has been less understood. In this work, we investigated the effect of osmolytes, including glycerol, sorbitol, betaine, and taurine, on the folding of a protein GB3 variant in E. coli cells using NMR spectroscopy. 400 mM osmolytes were added to E. coli cells; only glycerol stabilizes the folded protein, whereas betaine and taurine considerably destabilize the protein through modulating folding and unfolding rates. Further investigation indicates that betaine and taurine can enhance the quinary interaction between the protein and cellular environment and manifestly weaken the electrostatic attraction in protein salt bridges. The combination of the two factors causes destabilization of the protein in E. coli cells. These factors counteract the preferential exclusion mechanism that is adopted by osmolytes to stabilize proteins.
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Affiliation(s)
- Xiangfei Song
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liaoyuan An
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengting Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Zhijun Liu
- National Facility for Protein Science, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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35
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Iwakawa N, Morimoto D, Walinda E, Leeb S, Shirakawa M, Danielsson J, Sugase K. Transient Diffusive Interactions with a Protein Crowder Affect Aggregation Processes of Superoxide Dismutase 1 β-Barrel. J Phys Chem B 2021; 125:2521-2532. [PMID: 33657322 DOI: 10.1021/acs.jpcb.0c11162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Aggregate formation of superoxide dismutase 1 (SOD1) inside motor neurons is known as a major factor in onset of amyotrophic lateral sclerosis. The thermodynamic stability of the SOD1 β-barrel has been shown to decrease in crowded environments such as inside a cell, but it remains unclear how the thermodynamics of crowding-induced protein destabilization relate to SOD1 aggregation. Here we have examined the effects of a protein crowder, lysozyme, on fibril aggregate formation of the SOD1 β-barrel. We found that aggregate formation of SOD1 is decelerated even in mildly crowded solutions. Intriguingly, transient diffusive interactions with lysozyme do not significantly affect the static structure of the SOD1 β-barrel but stabilize an alternative excited "invisible" state. The net effect of crowding is to favor species off the aggregation pathway, thereby explaining the decelerated aggregation in the crowded environment. Our observations suggest that the intracellular environment may have a similar negative (inhibitory) effect on fibril formation of other amyloidogenic proteins in living cells. Deciphering how crowded intracellular environments affect aggregation and fibril formation of such disease-associated proteins will probably become central in understanding the exact role of aggregation in the etiology of these enigmatic diseases.
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Affiliation(s)
- Naoto Iwakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sarah Leeb
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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36
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Gruebele M, Pielak GJ. Dynamical spectroscopy and microscopy of proteins in cells. Curr Opin Struct Biol 2021; 70:1-7. [PMID: 33662744 DOI: 10.1016/j.sbi.2021.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/01/2021] [Indexed: 12/31/2022]
Abstract
With a strong understanding of how proteins fold in hand, it is now possible to ask how in-cell environments modulate their folding, binding and function. Studies accessing fast (ns to s) in-cell dynamics have accelerated over the past few years through a combination of in-cell NMR spectroscopy and time-resolved fluorescence microscopies. Here, we discuss this recent work and the emerging picture of protein surfaces as not just hydrophilic coats interfacing the solvent to the protein's core and functional regions, but as critical components in cells controlling protein mobility, function and communication with post-translational modifications.
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Affiliation(s)
- Martin Gruebele
- Department of Chemistry, Department of Physics, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Gary J Pielak
- Departments of Chemistry, Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.
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37
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Thole JF, Fadero TC, Bonin JP, Stadmiller SS, Giudice JA, Pielak GJ. Danio rerio Oocytes for Eukaryotic In-Cell NMR. Biochemistry 2021; 60:451-459. [PMID: 33534998 DOI: 10.1021/acs.biochem.0c00922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Understanding how the crowded and complex cellular milieu affects protein stability and dynamics has only recently become possible by using techniques such as in-cell nuclear magnetic resonance. However, the combination of stabilizing and destabilizing interactions makes simple predictions difficult. Here we show the potential of Danio rerio oocytes as an in-cell nuclear magnetic resonance model that can be widely used to measure protein stability and dynamics. We demonstrate that in eukaryotic oocytes, which are 3-6-fold less crowded than other cell types, attractive chemical interactions still dominate effects on protein stability and slow tumbling times, compared to the effects of dilute buffer.
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Affiliation(s)
- Joseph F Thole
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Tanner C Fadero
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jeffrey P Bonin
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Samantha S Stadmiller
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jonathan A Giudice
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Gary J Pielak
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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38
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Markel U, Lanvers P, Sauer DF, Wittwer M, Dhoke GV, Davari MD, Schiffels J, Schwaneberg U. A Photoclick-Based High-Throughput Screening for the Directed Evolution of Decarboxylase OleT. Chemistry 2021; 27:954-958. [PMID: 32955127 PMCID: PMC7839715 DOI: 10.1002/chem.202003637] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/15/2020] [Indexed: 11/30/2022]
Abstract
Enzymatic oxidative decarboxylation is an up-and-coming reaction yet lacking efficient screening methods for the directed evolution of decarboxylases. Here, we describe a simple photoclick assay for the detection of decarboxylation products and its application in a proof-of-principle directed evolution study on the decarboxylase OleT. The assay was compatible with two frequently used OleT operation modes (directly using hydrogen peroxide as the enzyme's co-substrate or using a reductase partner) and the screening of saturation mutagenesis libraries identified two enzyme variants shifting the enzyme's substrate preference from long chain fatty acids toward styrene derivatives. Overall, this photoclick assay holds promise to speed-up the directed evolution of OleT and other decarboxylases.
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Affiliation(s)
- Ulrich Markel
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Pia Lanvers
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Daniel F. Sauer
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Malte Wittwer
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Gaurao V. Dhoke
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Mehdi D. Davari
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Johannes Schiffels
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Ulrich Schwaneberg
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
- DWI—Leibniz Institute for Interactive MaterialsForckenbeckstraße 5052074AachenGermany
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39
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Hu Y, Cheng K, He L, Zhang X, Jiang B, Jiang L, Li C, Wang G, Yang Y, Liu M. NMR-Based Methods for Protein Analysis. Anal Chem 2021; 93:1866-1879. [PMID: 33439619 DOI: 10.1021/acs.analchem.0c03830] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a well-established method for analyzing protein structure, interaction, and dynamics at atomic resolution and in various sample states including solution state, solid state, and membranous environment. Thanks to rapid NMR methodology development, the past decade has witnessed a growing number of protein NMR studies in complex systems ranging from membrane mimetics to living cells, which pushes the research frontier further toward physiological environments and offers unique insights in elucidating protein functional mechanisms. In particular, in-cell NMR has become a method of choice for bridging the huge gap between structural biology and cell biology. Herein, we review the recent developments and applications of NMR methods for protein analysis in close-to-physiological environments, with special emphasis on in-cell protein structural determination and the analysis of protein dynamics, both difficult to be accessed by traditional methods.
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Affiliation(s)
- Yunfei Hu
- 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 for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, 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 Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China
| | - Lichun He
- 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 for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Xu 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 for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Bin Jiang
- 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 for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Ling Jiang
- 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 for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, 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 for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Guan Wang
- 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 for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Yunhuang Yang
- 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 for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, 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 for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
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40
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Crilly CJ, Brom JA, Kowalewski ME, Piszkiewicz S, Pielak GJ. Dried Protein Structure Revealed at the Residue Level by Liquid-Observed Vapor Exchange NMR. Biochemistry 2021; 60:152-159. [PMID: 33400518 DOI: 10.1021/acs.biochem.0c00863] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Water is key to protein structure and stability, yet the relationship between protein-water interactions and structure is poorly understood, in part because there are few techniques that permit the study of dehydrated protein structure at high resolution. Here, we describe liquid-observed vapor exchange (LOVE) NMR, a solution NMR-based method that provides residue-level information about the structure of dehydrated proteins. Using the model protein GB1, we show that LOVE NMR measurements reflect the fraction of the dried protein population trapped in a conformation where a given residue is protected from exchange with D2O vapor. Comparisons to solution hydrogen-deuterium exchange data affirm that the dried protein structure is strongly influenced by local solution stability and that the mechanism of dehydration protection exerted by the widely used protectant trehalose differs from its mechanism of stabilization in solution. Our results highlight the need for refined models of cosolute-mediated dehydration protection and demonstrate the ability of LOVE NMR to inform such models.
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Affiliation(s)
- Candice J Crilly
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Julia A Brom
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Mark E Kowalewski
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Samantha Piszkiewicz
- 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, United States.,Lineberger Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Integrative Program for Biological & Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7100, United States
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41
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Schnatwinkel J, Herrmann C. The interaction strength of an intrinsically disordered protein domain with its binding partner is little affected by very different cosolutes. Phys Chem Chem Phys 2020; 22:27903-27911. [PMID: 33284914 DOI: 10.1039/d0cp03040f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A common feature of intrinsically disordered proteins (IDPs) is a disorder-to-order transition upon binding to other proteins, which has been tied to multiple benefits, including accelerated association rates or binding with low affinity, yet high specificity. Given the balanced equilibrium concentrations of folded and unfolded state of an IDP we asked the question if changes in the chemical environment, such as the presence of osmolytes or crowding agents, have a strong influence on the interaction of an IDP. Here, we demonstrate the impact of cosolutes on the interaction of the intrinsically disordered transcription factor c-Myb and its binding partner, the kinase-inducible interaction domain (KIX) of the CREB-binding protein. Temperature jump relaxation kinetics and microscale thermophoresis were employed in order to quantify the rate constants and the binding affinity of the c-Myb/KIX complex, respectively, in the presence of various cosolutes. We find the binding free energy of the c-Myb/KIX complex only marginally modulated by cosolutes, whereas the enthalpy and entropy of the interaction are very sensitive to the respective solvent conditions. For different cosolutes we observe substantial changes in enthalpy, both favorable and unfavorable, which are going with entropy changes largely compensating the enthalpy effects in each case. These characteristics might reflect a potential mechanism by which c-Myb offsets changes in the physico-chemical environment to maintain a roughly unaltered binding affinity.
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Affiliation(s)
- Jan Schnatwinkel
- Physical Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, D-44780 Bochum, Germany.
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42
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Grosas AB, Rekas A, Mata JP, Thorn DC, Carver JA. The Aggregation of αB-Crystallin under Crowding Conditions Is Prevented by αA-Crystallin: Implications for α-Crystallin Stability and Lens Transparency. J Mol Biol 2020; 432:5593-5613. [PMID: 32827531 DOI: 10.1016/j.jmb.2020.08.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 02/08/2023]
Abstract
One of the most crowded biological environments is the eye lens which contains a high concentration of crystallin proteins. The molecular chaperones αB-crystallin (αBc) with its lens partner αA-crystallin (αAc) prevent deleterious crystallin aggregation and cataract formation. However, some forms of cataract are associated with structural alteration and dysfunction of αBc. While many studies have investigated the structure and function of αBc under dilute in vitro conditions, the effect of crowding on these aspects is not well understood despite its in vivo relevance. The structure and chaperone ability of αBc under conditions that mimic the crowded lens environment were investigated using the polysaccharide Ficoll 400 and bovine γ-crystallin as crowding agents and a variety of biophysical methods, principally contrast variation small-angle neutron scattering. Under crowding conditions, αBc unfolds, increases its size/oligomeric state, decreases its thermal stability and chaperone ability, and forms kinetically distinct amorphous and fibrillar aggregates. However, the presence of αAc stabilizes αBc against aggregation. These observations provide a rationale, at the molecular level, for the aggregation of αBc in the crowded lens, a process that exhibits structural and functional similarities to the aggregation of cataract-associated αBc mutants R120G and D109A under dilute conditions. Strategies that maintain or restore αBc stability, as αAc does, may provide therapeutic avenues for the treatment of cataract.
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Affiliation(s)
- Aidan B Grosas
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Agata Rekas
- National Deuteration Facility, Australian Nuclear Science and Technology Organisation (ANSTO), Lucas Heights, NSW 2234, Australia
| | - Jitendra P Mata
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation (ANSTO), Lucas Heights, NSW 2234, Australia
| | - David C Thorn
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - John A Carver
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia.
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43
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In-cell destabilization of a homodimeric protein complex detected by DEER spectroscopy. Proc Natl Acad Sci U S A 2020; 117:20566-20575. [PMID: 32788347 DOI: 10.1073/pnas.2005779117] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The complexity of the cellular medium can affect proteins' properties, and, therefore, in-cell characterization of proteins is essential. We explored the stability and conformation of the first baculoviral IAP repeat (BIR) domain of X chromosome-linked inhibitor of apoptosis (XIAP), BIR1, as a model for a homodimer protein in human HeLa cells. We employed double electron-electron resonance (DEER) spectroscopy and labeling with redox stable and rigid Gd3+ spin labels at three representative protein residues, C12 (flexible region), E22C, and N28C (part of helical residues 26 to 31) in the N-terminal region. In contrast to predictions by excluded-volume crowding theory, the dimer-monomer dissociation constant K D was markedly higher in cells than in solution and dilute cell lysate. As expected, this increase was partially recapitulated under conditions of high salt concentrations, given that conserved salt bridges at the dimer interface are critically required for association. Unexpectedly, however, also the addition of the crowding agent Ficoll destabilized the dimer while the addition of bovine serum albumin (BSA) and lysozyme, often used to represent interaction with charged macromolecules, had no effect. Our results highlight the potential of DEER for in-cell study of proteins as well as the complexities of the effects of the cellular milieu on protein structures and stability.
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44
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Molecular dynamics in cells: A neutron view. Biochim Biophys Acta Gen Subj 2020; 1864:129475. [DOI: 10.1016/j.bbagen.2019.129475] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 11/21/2022]
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45
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Davis CM, Deutsch J, Gruebele M. An in vitro mimic of in-cell solvation for protein folding studies. Protein Sci 2020; 29:1060-1068. [PMID: 31994240 DOI: 10.1002/pro.3833] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 01/15/2023]
Abstract
Ficoll, an inert macromolecule, is a common in vitro crowder, but by itself it does not reproduce in-cell stability or kinetic trends for protein folding. Lysis buffer, which contains ions, glycerol as a simple kosmotrope, and mimics small crowders with hydrophilic/hydrophobic patches, can reproduce sticking trends observed in cells but not the crowding. We previously suggested that the proper combination of Ficoll and lysis buffer could reproduce the opposite in-cell folding stability trend of two proteins: variable major protein-like sequence expressed (VlsE) is destabilized in eukaryotic cells and phosphoglycerate kinase (PGK) is stabilized. Here, to discover a well-characterized solvation environment that mimics in-cell stabilities for these two very differently behaved proteins, we conduct a two-dimensional scan of Ficoll (0-250 mg/ml) and lysis buffer (0-75%) mixtures. Contrary to our previous expectation, we show that mixtures of Ficoll and lysis buffer have a significant nonadditive effect on the folding stability. Lysis buffer enhances the stabilizing effect of Ficoll on PGK and inhibits the stabilizing effect of Ficoll on VlsE. We demonstrate that a combination of 150 mg/ml Ficoll and 60% lysis buffer can be used as an in vitro mimic to account for both crowding and non-steric effects on PGK and VlsE stability and folding kinetics in the cell. Our results also suggest that this mixture is close to the point where phase separation will occur. The simple mixture proposed here, based on commercially available reagents, could be a useful tool to study a variety of cytoplasmic protein interactions, such as folding, binding and assembly, and enzymatic reactions. SIGNIFICANCE STATEMENT: The complexity of the in-cell environment is difficult to reproduce in the test tube. Here we validate a mimic of cellular crowding and sticking interactions in a test tube using two proteins that are differently impacted by the cell: one is stabilized and the other is destabilized. This mimic is a starting point to reproduce cellular effects on a variety of protein and biomolecular interactions, such as folding and binding.
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Affiliation(s)
- Caitlin M Davis
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Jonathan Deutsch
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Martin Gruebele
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
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46
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Kaldmäe M, Leppert A, Chen G, Sarr M, Sahin C, Nordling K, Kronqvist N, Gonzalvo-Ulla M, Fritz N, Abelein A, Laίn S, Biverstål H, Jörnvall H, Lane DP, Rising A, Johansson J, Landreh M. High intracellular stability of the spidroin N-terminal domain in spite of abundant amyloidogenic segments revealed by in-cell hydrogen/deuterium exchange mass spectrometry. FEBS J 2019; 287:2823-2833. [PMID: 31815338 PMCID: PMC7383493 DOI: 10.1111/febs.15169] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/01/2019] [Accepted: 12/05/2019] [Indexed: 12/22/2022]
Abstract
Proteins require an optimal balance of conformational flexibility and stability in their native environment to ensure their biological functions. A striking example is spidroins, spider silk proteins, which are stored at extremely high concentrations in soluble form, yet undergo amyloid-like aggregation during spinning. Here, we elucidate the stability of the highly soluble N-terminal domain (NT) of major ampullate spidroin 1 in the Escherichia coli cytosol as well as in inclusion bodies containing fibrillar aggregates. Surprisingly, we find that NT, despite being largely composed of amyloidogenic sequences, showed no signs of concentration-dependent aggregation. Using a novel intracellular hydrogen/deuterium exchange mass spectrometry (HDX-MS) approach, we reveal that NT adopts a tight fold in the E. coli cytosol and in this manner conceals its aggregation-prone regions by maintaining a tight fold under crowded conditions. Fusion of NT to the unstructured amyloid-forming Aβ40 peptide, on the other hand, results in the formation of fibrillar aggregates. However, HDX-MS indicates that the NT domain is only partially incorporated into these aggregates in vivo. We conclude that NT is able to control its aggregation to remain functional under the extreme conditions in the spider silk gland.
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Affiliation(s)
- Margit Kaldmäe
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - Axel Leppert
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Gefei Chen
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Medoune Sarr
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Cagla Sahin
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - Kerstin Nordling
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Nina Kronqvist
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Marta Gonzalvo-Ulla
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden.,Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nicolas Fritz
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - Axel Abelein
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Sonia Laίn
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - Henrik Biverstål
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden.,Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Hans Jörnvall
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - David P Lane
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - Anna Rising
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden.,Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Johansson
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
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47
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Bashardanesh Z, Elf J, Zhang H, van der Spoel D. Rotational and Translational Diffusion of Proteins as a Function of Concentration. ACS OMEGA 2019; 4:20654-20664. [PMID: 31858051 PMCID: PMC6906769 DOI: 10.1021/acsomega.9b02835] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/14/2019] [Indexed: 05/21/2023]
Abstract
Atomistic simulations of three different proteins at different concentrations are performed to obtain insight into protein mobility as a function of protein concentration. We report on simulations of proteins from diluted to the physiological water concentration (about 70% of the mass). First, the viscosity was computed and found to increase by a factor of 7-9 going from pure water to the highest protein concentration, in excellent agreement with in vivo nuclear magnetic resonance results. At a physiological concentration of proteins, the translational diffusion is found to be slowed down to about 30% of the in vitro values. The slow-down of diffusion found here using atomistic models is slightly more than that of a hard sphere model that neglects the electrostatic interactions. Interestingly, rotational diffusion of proteins is slowed down somewhat more (by about 80-95% compared to in vitro values) than translational diffusion, in line with experimental findings and consistent with the increased viscosity. The finding that rotation is retarded more than translation is attributed to solvent-separated clustering. No direct interactions between the proteins are found, and the clustering can likely be attributed to dispersion interactions that are stronger between proteins than between protein and water. Based on these simulations, we can also conclude that the internal dynamics of the proteins in our study are affected only marginally under crowding conditions, and the proteins become somewhat more stable at higher concentrations. Simulations were performed using a force field that was tuned for dealing with crowding conditions by strengthening the protein-water interactions. This force field seems to lead to a reproducible partial unfolding of an α-helix in one of the proteins, an effect that was not observed in the unmodified force field.
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Affiliation(s)
- Zahedeh Bashardanesh
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
| | - Johan Elf
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
| | - Haiyang Zhang
- Department
of Biological Science and Engineering, School of Chemistry and Biological
Engineering, University of Science and Technology
Beijing, 100083 Beijing, China
| | - David van der Spoel
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
- E-mail: . Phone: +46 18 4714205
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48
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Guin D, Gelman H, Wang Y, Gruebele M. Heat shock-induced chaperoning by Hsp70 is enabled in-cell. PLoS One 2019; 14:e0222990. [PMID: 31557226 PMCID: PMC6762143 DOI: 10.1371/journal.pone.0222990] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Recent work has shown that weak protein-protein interactions are susceptible to the cellular milieu. One case in point is the binding of heat shock proteins (Hsps) to substrate proteins in cells under stress. Upregulation of the Hsp70 chaperone machinery at elevated temperature was discovered in the 1960s, and more recent studies have shown that ATPase activity in one Hsp70 domain is essential for control of substrate binding by the other Hsp70 domain. Although there are several denaturant-based assays of Hsp70 activity, reports of ATP-dependent binding of Hsp70 to a globular protein substrate under heat shock are scarce. Here we show that binding of heat-inducible Hsp70 to phosphoglycerate kinase (PGK) is remarkably different in vitro compared to in-cell. We use fluorescent-labeled mHsp70 and ePGK, and begin by showing that mHsp70 passes the standard β-galactosidase assay, and that it does not self-aggregate until 50°C in presence of ATP. Yet during denaturant refolding or during in vitro heat shock, mHsp70 shows only ATP-independent non-specific sticking to ePGK, as evidenced by nearly identical results with an ATPase activity-deficient K71M mutant of Hsp70 as a control. Addition of Hsp40 (co-factor) or Ficoll (crowder) does not reduce non-specific sticking, but cell lysate does. Therefore, Hsp70 does not act as an ATP-dependent chaperone on its substrate PGK in vitro. In contrast, we observe only specific ATP-dependent binding of mHsp70 to ePGK in mammalian cells, when compared to the inactive Hsp70 K71M mutant. We hypothesize that enhanced in-cell activity is not due to an unknown co-factor, but simply to a favorable shift in binding equilibrium caused by the combination of crowding and osmolyte/macromolecular interactions present in the cell. One candidate mechanism for such a favorable shift in binding equilibrium is the proven ability of Hsp70 to bind near-native states of substrate proteins in vitro. We show evidence for early onset of binding in-cell. Our results suggest that Hsp70 binds PGK preemptively, prior to its full unfolding transition, thus stabilizing it against further unfolding. We propose a "preemptive holdase" mechanism for Hsp70-substrate binding. Given our result for PGK, more proteins than one might think based on in vitro assays may be chaperoned by Hsp70 in vivo. The cellular environment thus plays an important role in maintaining proper Hsp70 function.
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Affiliation(s)
- Drishti Guin
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Hannah Gelman
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Yuhan Wang
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Martin Gruebele
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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49
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Guin D, Gruebele M. Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function. Chem Rev 2019; 119:10691-10717. [PMID: 31356058 DOI: 10.1021/acs.chemrev.8b00753] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In recent years, better instrumentation and greater computing power have enabled the imaging of elusive biomolecule dynamics in cells, driving many advances in understanding the chemical organization of biological systems. The focus of this Review is on interactions in the cell that affect both biomolecular stability and function and modulate them. The same protein or nucleic acid can behave differently depending on the time in the cell cycle, the location in a specific compartment, or the stresses acting on the cell. We describe in detail the crowding, sticking, and quinary structure in the cell and the current methods to quantify them both in vitro and in vivo. Finally, we discuss protein evolution in the cell in light of current biophysical evidence. We describe the factors that drive protein evolution and shape protein interaction networks. These interactions can significantly affect the free energy, ΔG, of marginally stable and low-population proteins and, due to epistasis, direct the evolutionary pathways in an organism. We finally conclude by providing an outlook on experiments to come and the possibility of collaborative evolutionary biology and biophysical efforts.
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Affiliation(s)
- Drishti Guin
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States
| | - Martin Gruebele
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois , Urbana , Illinois 61801 , United States.,Center for Biophysics and Quantitative Biology , University of Illinois , Urbana , Illinois 61801 , United States
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50
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Gnutt D, Sistemich L, Ebbinghaus S. Protein Folding Modulation in Cells Subject to Differentiation and Stress. Front Mol Biosci 2019; 6:38. [PMID: 31179287 PMCID: PMC6544126 DOI: 10.3389/fmolb.2019.00038] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/07/2019] [Indexed: 11/25/2022] Open
Abstract
Cytomimetic media are used to mimic the physicochemical properties of the cellular milieu in an in vitro experiment. The motivation is that compared to entire cells, they can be used efficiently in combination with a broad range of experimental techniques. However, the development and use of cytomimetic media is hampered by the lack of in-cell data that could be used as a hallmark to directly evaluate and improve the performance of cytomimetic media in different applications. Such data must include the study of specific biomolecular reactions in different cell types, different compartments of a single cells and different cellular conditions. In previous studies, model systems such as cancer cell lines, bacteria or oocytes were used. Here we studied how the environment of cells that undergo neuronal differentiation or proteostasis stress modulates the protein folding equilibrium. We found that NGF induced differentiation leads to a decrease of the melting temperature and a change of the folding mechanism. Proteomic changes that occur upon differentiation could explain this effect, however, we found that the crowding effect remained unchanged. Using MG132, a common proteasome inhibitor and inducer of the unfolded protein response, we show that changes to the quality control machinery modulate the folding equilibrium, leading to protein destabilization at prolonged stress exposure. Our study explores the range of protein folding modulation within cells subject to differentiation or stress that must be encountered in the development of cytomimetic media.
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Affiliation(s)
- David Gnutt
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Braunschweig, Germany.,Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany
| | - Linda Sistemich
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Braunschweig, Germany.,Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany
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