A Novel Correlation for Protein Diffusion Coefficients Based on Molecular Weight and Radius of Gyration

He, Li; Niemeyer, Bernd

doi:10.1021/bp0256059

Cited by 145 publications

(110 citation statements)

References 21 publications

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“…A modified version of the Stokes-Einstein relationship can be used to predict the solvent viscosity η solvent (in centipoise; cP) for freely diffusing spherical and cylindrical FPs in an aqueous solution (44):…”

Section: Methodsmentioning

confidence: 99%

Solute diffusion is hindered in the mitochondrial matrix

Dieteren

Gielen

Nijtmans

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Intracellular chemical reactions generally constitute reaction-diffusion systems located inside nanostructured compartments like the cytosol, nucleus, endoplasmic reticulum, Golgi, and mitochondrion. Understanding the properties of such systems requires quantitative information about solute diffusion. Here we present a novel approach that allows determination of the solvent-dependent solute diffusion constant (D solvent ) inside cell compartments with an experimentally quantifiable nanostructure. In essence, our method consists of the matching of synthetic fluorescence recovery after photobleaching (FRAP) curves, generated by a mathematical model with a realistic nanostructure, and experimental FRAP data. As a proof of principle, we assessed D solvent of a monomeric fluorescent protein (AcGFP1) and its tandem fusion (AcGFP1 2 ) in the mitochondrial matrix of HEK293 cells. Our results demonstrate that diffusion of both proteins is substantially slowed by barriers in the mitochondrial matrix (cristae), suggesting that cells can control the dynamics of biochemical reactions in this compartment by modifying its nanostructure. molecular dynamics | quantitative random-walk model | systems biology A major challenge facing biochemistry is to understand the dynamics of chemical reactions within inhomogeneous cell compartments like the cytosol, nucleus, endoplasmic reticulum (ER), Golgi, and mitochondrion (1). In general, intracompartment reactions involve the conversion of (im)mobile substrates by (im)mobile enzymes into (im)mobile products and therefore constitute reaction-diffusion systems. Obviously, gaining insight into the behavior of such systems requires quantitative information about solute diffusion. The latter depends on solvent and solute properties, the dimensions and shape of the compartment, and the internal structure of the compartment (2-6).A widely used strategy to investigate solute diffusion involves expressing a fluorescent tracer protein (FP) in the compartment of interest. Next, FP mobility is measured using FCS (fluorescence correlation spectroscopy) or FRAP (fluorescence recovery after photobleaching). This is then followed by curve fitting and/ or mathematical modeling of the experimental data to obtain the diffusion constant of the FP (7-16). However, these analysis methods generally do not include realistic (i.e., experimentally determined) information concerning the spatial dimensions and nanostructure of the compartment. Moreover, the temporal scale of most FRAP models does not quantitatively match with that of FRAP experiments. Therefore it was already recognized some time ago (8-17) that the above approaches will only yield an "apparent" (biased) value for the diffusion constant (D app ) of a given FP, which represents an underestimation of the "real" (i.e., purely solvent-dependent) diffusion constant (D solvent ).In this study we present a strategy to determine D solvent inside cell compartments with an experimentally accessible nanostructure. Our method consists of matching synthetic FRA...

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Section: Methodsmentioning

confidence: 99%

Solute diffusion is hindered in the mitochondrial matrix

Dieteren

Gielen

Nijtmans

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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“…A modified Svedberg equation can be used to predict the sedimentation coefficient from the molecular weight and the diffusion coefficient [32]. Using a previously established correlation [10], the diffusion coefficient of VAA can be estimated from its molecular weight (135 kDa) and radius of gyration (54.5 Å without ligand and 49.5 Å with ligand). SANS data thus predicted the sedimentation coefficients of 5.8 S and 6.1 S for VAA in the absence and presence of ligand, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…The scattering curves can be processed using the ab initio method to calculate the proteins' shape [8]. Because hydrodynamic parameters such as sedimentation and diffusion coefficients can be predicted from protein structures [9,10], respective methods (e.g. ultracentrifugation or dynamic light scattering) play a valuable role in validating structure model obtained from SAS data [11].…”

Section: Introductionmentioning

confidence: 99%

Small angle neutron scattering as sensitive tool to detect ligand-dependent shape changes in a plant lectin with β-trefoil folding and their dependence on the nature of the solvent

André

Garamus

et al. 2008

Glycoconj J

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The galactoside-specific Viscum album L. agglutinin (VAA) is a potent biohazard akin to ricin and a mitogen for immune and tumor cells. These activities depend on cell surface binding to glycans. It is an open question whether the process of ligand binding alters the lectin's shape. Small angle neutron scattering (SANS) experiments revealed that the carbohydrate ligand lactose induced a decrease of the radius of gyration of dimeric VAA from 54.5±1 to 49.5±1 Å in water. Apparently, VAA in aqueous solution and at the concentrations tested at 3.6 mg/ml and above adopts a compacted structure as response to ligand binding. In contrast to the behavior in aqueous solution, lactose binding in DMSO resulted in an increase of the lectin's radius of gyration from 49±1 to 55.5±1 Å. Because shape changes may be reflected in the thermostability of the protein, this parameter was examined by activity assays of protein exposed to 60°C and 70°C and by differential scanning calorimetry (DSC). In line with the lactose-induced conformational alterations revealed by the SANS experiments, lactose presence enhanced the thermostability of VAA in water. Thus, binding of the carbohydrate ligand in solution can entail changes in shape and thermostability in the case of the tested plant lectin.

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“…B. die Einstellung der Hydrophilie/Hydrophobie der Oberfläche sowie der Anbindung niedermolekularer Liganden eingestellt. Bei der Adsorption aus der flüssigen Phase und besonders bei groß-volumigen biotechnologischen Wertstoffen spielt die Diffusion eine wichtige Rolle [3,4]. Darüber hinaus kommt es durch die stärkere Einbindung des Fluids in die Oberflä-chenprozesse zu Wechselwirkungen zwischen der flüssigen Phase und dem Adsorptiv (Zielstoff) sowie zwischen der flüssigen Phase und dem Adsorbens.…”

Section: Anwendungenunclassified

Effective Separation of Gas and Fluid Phases by Means of Selective Adsorption

Rosenfeld¹,

Peper

Täffner

et al. 2011

Chemie Ingenieur Technik

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Effective Separation of Gas and Fluid Phases by Means of Selective AdsorptionAdsorption is a versatile tool for the separation of low abundant molecules from complex mixtures. The affinity and selectivity of the adsorbents are crucial parameters for the efficiency of the separation process. This work provides an overview of the basic adsorption mechanisms and illustrates their relevance for technical applications based on own experimental data in bioprocess, environmental and safety engineering. Distinctive features between the adsorption from the gas and fluid phase, respectively, the differences between small molecules and interacting biomacromolecules are presented.

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A Novel Correlation for Protein Diffusion Coefficients Based on Molecular Weight and Radius of Gyration

Cited by 145 publications

References 21 publications

Solute diffusion is hindered in the mitochondrial matrix

Solute diffusion is hindered in the mitochondrial matrix

Small angle neutron scattering as sensitive tool to detect ligand-dependent shape changes in a plant lectin with β-trefoil folding and their dependence on the nature of the solvent

Effective Separation of Gas and Fluid Phases by Means of Selective Adsorption

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