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. 2011 Nov 1;50(43):9225-36.
doi: 10.1021/bi201287e. Epub 2011 Oct 5.

Exploring weak, transient protein--protein interactions in crowded in vivo environments by in-cell nuclear magnetic resonance spectroscopy

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Exploring weak, transient protein--protein interactions in crowded in vivo environments by in-cell nuclear magnetic resonance spectroscopy

Qinghua Wang et al. Biochemistry. .

Abstract

Biology relies on functional interplay of proteins in the crowded and heterogeneous environment inside cells, and functional protein interactions are often weak and transient. Thus, methods that preserve these interactions and provide information about them are needed. In-cell nuclear magnetic resonance (NMR) spectroscopy is an attractive method for studying a protein's behavior in cells because it may provide residue-level structural and dynamic information, yet several factors limit the feasibility of protein NMR spectroscopy in cells; among them, slow rotational diffusion has emerged as the most important. In this paper, we seek to elucidate the causes of the dramatically slow protein tumbling in cells and in so doing to gain insight into how the intracellular viscosity and weak, transient interactions modulate protein mobility. To address these questions, we characterized the rotational diffusion of three model globular proteins in Escherichia coli cells using two-dimensional heteronuclear NMR spectroscopy. These proteins have a similar molecular size and globular fold but very different surface properties, and indeed, they show very different rotational diffusion in the E. coli intracellular environment. Our data are consistent with an intracellular viscosity approximately 8 times that of water, too low to be a limiting factor for observation of small globular proteins by in-cell NMR spectroscopy. Thus, we conclude that transient interactions with cytoplasmic components significantly and differentially affect the mobility of proteins and therefore their NMR detectability. Moreover, we suggest that an intricate interplay of total protein charge and hydrophobic interactions plays a key role in regulating these weak intermolecular interactions in cells.

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Figures

Figure 1
Figure 1
Effect of protein size on the quality of in-cell NMR spectra. In-cell [1H,15N] HSQC spectra of GB1, NmerA, and GB1-L1-GB1 (dGB1). Spectra were measured with 8, 32, and 16 scans, corresponding to total acquisition times of 10, 40 and 20 minutes for GB1, NmerA, and dGB1, respectively. The boxed regions show sharp peaks arising from flexible NH2 side-chains.
Figure 2
Figure 2
Determination of the apparent intracellular viscosity. (A, C) A representative example of a measured (A) 1HN linewidth, Δν, and (C) difference between 15N TROSY and anti-TROSY linewidths, ΔΔνTAT, as a function of the solution viscosity for residue T43 in GB1. Red, blue and green colors correspond to datasets 1, 2 and 3 (Table S1), respectively. Solid lines show the best linear fit obtained using all titration data (A) or only dataset 1 (C). (B, D) Histograms showing Δν (B) and ΔΔνTAT (D) as a function of GB1 residue number. Colors indicate the bulk viscosity in solution from lowest (red) to highest (yellow). In-cell data are shown by black and labeled.
Figure 3
Figure 3
Apparent intracellular viscosity as a function of residue number, obtained from 1HN linewidth (red) and TROSY/anti-TROSY (black) analysis on GB1.
Figure 4
Figure 4
Effect of intracellular environments and molecular crowding on protein mobility. (A) Average 1HN linewidths in lysate samples of GB1, NmerA, Ubi3A (U3A in the figure), and dGB1 (red), ubiquitin (green), and average 1HN linewidths (black) obtained from glycerol titrations of GB1 and dGB1 lysates from datasets 2 and 3 (Table S1) as a function of an apparent molecular weight, MW app = MWη/η0, where MW, η, and η0 are the protein molecular weight, the apparent sample viscosity, and the viscosity of water, respectively. A solid black line is the best linear fit of GB1/dGB1 glycerol titrations. (B) Average 1HN linewidths for GB1 and dGB1 (blue), and NmerA (red) lysate samples in the presence of 100 and 200 g/L BSA as a function of an apparent molecular weight, MW app = MWη/η0, where MW, η, and η0 are a protein molecular weight, the bulk viscosity and the viscosity of water, respectively. A solid black line is the best linear fit of GB1/dGB1 glycerol titrations (same as in Fig. 4A). (C) Histograms showing experimental 1HN linewidths, Δν, as a function of NmerA residue number. Colors indicate viscosity in solution from lowest (red) to highest (yellow). Horizontal lines show the average 1HN linewidths for in-cell GB1 and dGB1 samples. A black solid line shows theoretically predicted NmerA linewidths expected for intracellular environment 11 times as viscous as water.

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