Osmolytes Can Destabilize Proteins in Cells by Modulating Electrostatics and Quinary Interactions

Song, Xiangfei; An, Liaoyuan; Wang, Mengting; Chen, Jingfei; Liu, Zhijun; Yao, Lishan

doi:10.1021/acschembio.1c00024

Cited by 5 publications

(11 citation statements)

References 68 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…E. coli BL21(DE3) cells containing 15 N-labeled GB3MutX and other mutations (Table S2) were prepared as described previously. , Briefly, cells were grown in 250 mL of LB medium at 37 °C until the optical density at 600 nm, OD 600 ≈ 0.6. The cells were harvested by centrifugation (1000 g , 20 min, 4 °C).…”

Section: Methodsmentioning

confidence: 99%

Quantifying Protein Electrostatic Interactions in Cells by Nuclear Magnetic Resonance Spectroscopy

et al. 2021

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Methodsmentioning

confidence: 99%

Quantifying Protein Electrostatic Interactions in Cells by Nuclear Magnetic Resonance Spectroscopy

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…More recently, Yao and colleagues acquired series of 2D 1 H-15 N-HSQC-T1/T2 spectra of the model GB3 proteins in E. coli, which yielded the same conclusions from the 1/T1*1/T2 product: transient interactions occur with cellular components. 181,515 Gierasch and colleagues recorded 2D 1 H-15 N-TROSY spectra of GB1 in E. coli to analyze the socalled TROSY and anti-TROSY peaks: the ratio of their 15 N linewidths informs about the apparent size of the protein, and is not affected by µs-ms events. They also measured 1 H T2 relaxation from their peak linewidth in 2D 1 H-15 N-HSQC spectra; they concluded that these 1 H peaks were broader than what was expected from the molecular size extracted from the TROSY/anti-TROSY peaks.…”

Section: Paramagnetic Centers For Distance and Orientation Measuremen...mentioning

confidence: 99%

In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

Theillet

2022

Chem. Rev.

View full text Add to dashboard Cite

In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promises 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 NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET…) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidences 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. CONTENTS 5.1.1. In-cell EPR 5.1.2. In-cell FRET microscopy 5.1.3. Mass-spectrometry 5.1.4. Cryo-ET 5.2. The specific benefits of in-cell NMR 5.3. The future technical challenges of in-cell NMR 6. Conclusion Author Information

show abstract

“…However, no molecule is completely inert and non‐specific interactions can arise between the molecule of interest and the crowded milieu. To this end, recent work has started to investigate the contribution of such interactions in the crowded cellular environment [19–24] . A large body of work, both experimental and theoretical, has provided quantitative insights on how crowding impacts folding and binding of structured proteins [25–46] .…”

Section: Introductionmentioning

confidence: 99%

“…To this end, recent work has started to investigate the contribution of such interactions in the crowded cellular environment. [19][20][21][22][23][24] A large body of work, both experimental and theoretical, has provided quantitative insights on how crowding impacts folding and binding of structured proteins. Here, we aim to provide a succinct yet detailed description of how crowding can impact disordered proteins and how, viewing the phenomenon through the lens of polymer physics, can help in rationalizing the mechanisms at play.…”

Section: Introductionmentioning

confidence: 99%

Macromolecular Crowding and Intrinsically Disordered Proteins: A Polymer Physics Perspective

Cubuk

Soranno

2022

ChemSystemsChem

View full text Add to dashboard Cite

The cell is a crowded environment where a relevant fraction of the available space is occupied by proteins, nucleic acids, and metabolites. Here we discuss recent advancements in the understanding of crowding effects on intrinsically disordered proteins. Differently from their structured counterparts, these proteins do not adopt a stable three-dimensional structure and remain flexible and dynamic in solution. The physics of polymers and colloids provides a framework to interpret how crowding modulates conformations, dynamics, and interactions of disordered proteins. Flory-Huggins models enable rationalizing the different degree of compaction induced by crowding agents in terms of depletion interactions. The same interactions modulate the diffusion of the disordered proteins in a crowded milieu and the association and dissociation rates when interacting with a ligand. Altogether, this theoretical framework provides new insights into the interpretation of the effects of the cellular environment on disordered proteins.

show abstract

Osmolytes Can Destabilize Proteins in Cells by Modulating Electrostatics and Quinary Interactions

Cited by 5 publications

References 68 publications

Quantifying Protein Electrostatic Interactions in Cells by Nuclear Magnetic Resonance Spectroscopy

Quantifying Protein Electrostatic Interactions in Cells by Nuclear Magnetic Resonance Spectroscopy

In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

Macromolecular Crowding and Intrinsically Disordered Proteins: A Polymer Physics Perspective

Contact Info

Product

Resources

About