Impeded Rotation of a Protein in a Sol−Gel Matrix

Gottfried, David; Kagan, Anna; Hoffman, and Brian M.; Friedman, Joel M.

doi:10.1021/jp9840230

Cited by 82 publications

(83 citation statements)

References 23 publications

(49 reference statements)

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“…Actually, the discrepancy should only be a factor 2, as for most other proteins (see Table 1 and Fig. 1); a more accurate experimental value, determined by fluorescence depolarization (45), is D R expt ϭ 15 s Ϫ1 (at 20°C). As discussed above, most of this factor-2 discrepancy should be attributed not to hydration but to the fact that myoglobin is not a compact sphere.…”

Section: Discussionmentioning

confidence: 99%

Biomolecular hydration: From water dynamics to hydrodynamics

Halle

Davidovic²

2003

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

180

197

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Thermally driven rotational and translational diffusion of proteins and other biomolecules is governed by frictional coupling to their solvent environment. Prediction of this coupling from biomolecular structures is a longstanding biophysical problem, which cannot be solved without knowledge of water dynamics in an interfacial region comparable to the dry protein in volume. Efficient algorithms have been developed for solving the hydrodynamic equations of motion for atomic-resolution biomolecular models, but experimental diffusion coefficients can be reproduced only by postulating hundreds of rigidly bound water molecules. This static picture of biomolecular hydration is fundamentally inconsistent with magnetic relaxation dispersion experiments and molecular dynamics simulations, which both reveal a highly dynamic interface where rotation and exchange of nearly all water molecules are several orders of magnitude faster than biomolecular diffusion. Here, we resolve this paradox by means of a dynamic hydration model that explicitly links protein hydrodynamics to hydration dynamics. With the aid of this model, bona fide structure-based predictions of global biomolecular dynamics become possible, as demonstrated here for a set of 16 proteins for which accurate experimental rotational diffusion coefficients are available.T he translational and rotational motions of a protein molecule are three or more orders of magnitude slower than the relaxation of its linear and angular momenta and can therefore be described accurately by diffusion equations (1). Such global dynamics is thus characterized by isotropic translational (D T ) and rotational (D R ) diffusion coefficients, or by the corresponding tensors. The dynamic protein-solvent coupling is embodied in Einstein's fluctuation-dissipation theorem D T,R ϭ k B T͞ T,R (2). When this equation is combined with the results of macroscopic continuum hydrodynamics (3) for the friction coefficients of a sphere of radius a undergoing steady translation or rotation in a solvent of shear viscosity 0 , one obtains the celebrated Stokes-Einstein (SE) relationsMore elaborate expressions have been derived for ellipsoidal solutes (4). When applied to globular proteins, these expressions severely overestimate the diffusion coefficients. As an example, consider the rotation of hen egg-white lysozyme (HEWL). By using either the crystal structure or the partial specific volume in solution, one obtains a molecular volume of 16 nm 3 . Inserted into Eq. 1, this yields D R ϭ 42 s Ϫ1 in H 2 O at 20°C. If the elongated shape of HEWL is modeled by a prolate spheroid of aspect ratio 1.5, D R is reduced to 40 s Ϫ1 , still a factor 2 above the experimental value of 20 Ϯ 1 s Ϫ1 (5). Early workers attributed such discrepancies to ''bound'' water that migrates with the protein and therefore contributes to its hydrodynamic volume (6, 7). Measurements of transport coefficients like D T or D R thus became established as a method for quantifying protein hydration. Proteins, of course, do not have ellipsoid...

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Section: Discussionmentioning

confidence: 99%

Biomolecular hydration: From water dynamics to hydrodynamics

Halle

Davidovic²

2003

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

180

197

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“…The mobilities of glass entrapped proteins have been characterized by fluorescence anisotropy [26,[59][60][61][62], tryptophan phosphorescence [63], and photobleaching experiments [62]. In addition to apoMb, enhanced conformational stability at elevated temperatures has been observed for many glass-entrapped proteins including α-lactalbumin [22], lysozyme [22,24], human serum albumin [24,26,54], creatine kinase [31], monellin [59], oncomodulin [64], cytochrome c [65], and carbonic anhydrase [66].…”

Section: Discussionmentioning

confidence: 99%

Favourable influence of hydrophobic surfaces on protein structure in porous organically-modified silica glasses

et al. 2008

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Organically-modified siloxanes were used as host materials to examine the influence of surface chemistry on protein conformation in a crowded environment. The sol-gel materials were prepared from tetramethoxysilane and a series of monosubstituted alkoxysilanes, RSi(OR′) 3 , featuring alkyl groups of increasing chain length in the R-position. Using circular dichroism spectroscopy in the far-UV region, apomyoglobin was found to transit from an unfolded state to a native-like helical state as the content of the hydrophobic precursor increased from 0-15%. At a fixed molar content of 5% RSi(OR') 3 , the helical structure of apomyoglobin increased with the chain length of the R-group, i.e. methyl < ethyl < n-propyl < n-butyl < n-hexyl. This trend also was observed for the tertiary structure of ribonuclease A, suggesting that protein folding and biological activity are sensitive to the hydrophilic/hydrophobic balance of neighboring surfaces. The observed changes in protein structure did not correlate with total surface area or the average pore size of the modified glasses, but scanning electron microscopy images revealed an interesting relationship between surface morphology and alkyl chain length. The unexpected benefit of incorporating a low content of hydrophobic groups into a hydrophilic surface may lead to materials with improved biocompatibility for use in biosensors and implanted devices.

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“…3,[23][24][25][26][27][28] Fluorescence anisotropy studies have demonstrated that proteins in sol-gel pores experience dramatically hindered rates of rotation due to protein adsorption to the pore walls. 23,29,30 Alternatively, the pore dimensions could influence the protein structural stability by affecting the dynamics of the surrounding solvent, which is intimately coupled to the dynamics of the protein. Water in nanoscopic environments (i.e.…”

Section: Introductionmentioning

confidence: 99%

Dynamics of Proteins Encapsulated in Silica Sol−Gel Glasses Studied with IR Vibrational Echo Spectroscopy

2006

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Spectrally-resolved infrared stimulated vibrational echo spectroscopy is used to measure the fast dynamics of heme-bound CO in carbonmonoxy-myoglobin (MbCO) and hemoglobin (HbCO) embedded in silica sol-gel glasses. On the time scale of ~100 fs to several ps, the vibrational dephasing of the heme-bound CO is measurably slower for both MbCO and HbCO relative to aqueous protein solutions. The fast structural dynamics of MbCO, as sensed by the heme-bound CO, are influenced more by the sol-gel environment than those of HbCO. Longer time scale structural dynamics (tens of ps), as measured by the extent of spectral diffusion, are the same for both proteins encapsulated in sol-gel glasses compared to aqueous solutions. A comparison of the sol-gel experimental results to viscosity dependent vibrational echo data taken on various mixtures of water and fructose shows that the sol-gel encapsulated MbCO exhibits dynamics that are the equivalent to the protein in a solution that is nearly 20 times more viscous than bulk water. In contrast, the HbCO dephasing in the sol-gel reflects only a 2-fold increase in viscosity. Attempts to alter the encapsulating pore size by varying the molar ratio of silane precursor to water (R-value) used to prepare the sol-gel glasses were found to have no effect on the fast or steady-state spectroscopic results. The vibrational echo data are discussed in the context of solvent confinement and protein-pore wall interactions to provide insights into the influence of a confined environment on the fast structural dynamics experienced by a biomolecule.

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Impeded Rotation of a Protein in a Sol−Gel Matrix

Cited by 82 publications

References 23 publications

Biomolecular hydration: From water dynamics to hydrodynamics

Biomolecular hydration: From water dynamics to hydrodynamics

Favourable influence of hydrophobic surfaces on protein structure in porous organically-modified silica glasses

Dynamics of Proteins Encapsulated in Silica Sol−Gel Glasses Studied with IR Vibrational Echo Spectroscopy

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