Translational and Rotational Diffusion of Proteins

Smith, Pieter E. S.; Gunsteren, Wilfred F. van

doi:10.1006/jmbi.1994.1172

Cited by 82 publications

(78 citation statements)

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“…The latter quantity was calculated in a recent simulation of BPTI at 4°C (Brunne et al, 1993); an average over all surface water molecules gave t res S /t res bulk 1 3. Bearing in mind that our estimate of N S is somewhat arbitrary, and that the protein-water pair potentials used in simulations are of uncertain quality (Smith & van Gunsteren, 1994), the agreement is reassuring.…”

Section: Surface Watermentioning

confidence: 66%

Protein Hydration Dynamics in Aqueous Solution: A Comparison of Bovine Pancreatic Trypsin Inhibitor and Ubiquitin by Oxygen-17 Spin Relaxation Dispersion

Денисов

Halle

1995

Journal of Molecular Biology

162

177

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Water oxygen-17 spin relaxation was used to study hydration and dynamics Condensed Matter Magnetic Resonance Group, Chemical of the globular proteins bovine pancreatic trypsin inhibitor (BPTI) and ubiquitin in aqueous solution. The frequency dispersion of the longitudinal Center, Lund University P. O. Box 124, S-22100 Lund and transverse relaxation rates was measured over the Larmor frequency Sweden range 2.6 to 49 MHz in the pD range 2 to 11 at 27°C. While the protein-induced relaxation enhancement was similar for the two proteins at high frequencies, it was an order of magnitude smaller for ubiquitin than for BPTI at low frequencies. This difference was ascribed to the abscence, in ubiquitin, of highly ordered internal water molecules, which are known to be present in BPTI and in most other globular proteins. These observations demonstrate that the water relaxation dispersion in protein solutions is essentially due to a few structural water molecules buried within the protein matrix, but exchanging rapidly with the external water. The relaxation data indicate that the internal water molecules of BPTI exchange with bulk water on the time-scale 10 −8 to 10 −6 second thus lowering the recently reported upper bound on the residence time of these internal water molecules by four orders of magnitude, and implying that local unfolding occurs on the submicrosecond time-scale. The water molecules residing at the surface of the two proteins were found to be highly mobile, with an average rotational correlation time of approximately 20 picoseconds. For both proteins, the oxygen-17 relaxation depended only very weakly on pD, showing that ionic residues do not perturb hydration water dynamics more than other surface residues. We believe that the present results resolve the long-standing controversy regarding the mechanism behind the spin relaxation dispersion of water nuclei in protein solutions, thus establishing oxygen-17 relaxation as a powerful tool for studies of structurally and functionally important water molecules in proteins and other biomolecules.

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Section: Surface Watermentioning

confidence: 66%

Protein Hydration Dynamics in Aqueous Solution: A Comparison of Bovine Pancreatic Trypsin Inhibitor and Ubiquitin by Oxygen-17 Spin Relaxation Dispersion

Денисов

Halle

1995

Journal of Molecular Biology

162

177

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“…Considering the scales of time and molecular displacement, many viscosity-dependent steps are needed to explain the viscosity-dependent slowing of gating. Assuming that the diffusion of soluble proteins will give a maximum value of time over which a segment displacement takes place under the mechanical stress, because the diffusion itself is also the result of many Brownian movements, it appears clear that even a 1 nm displacement of a rigid particle to close the channel pore takes only 1 ns in a viscous solution of several millipascal seconds (Smith & van Gunsteren, 1994). In order to explain the viscosity-dependent conformational change of sodium channel gating in a few hundreds of microseconds, there may be many viscosity-dependent steps.…”

Section: Discussionmentioning

confidence: 99%

Solvent‐dependent rate‐limiting steps in the conformational change of sodium channel gating in squid giant axon.

Kukita

1997

The Journal of Physiology

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1. The time course of sodium currents (INa) in squid giant axon was analysed using viscous non-electrolyte solutions on both sides of the axolemma. It slowed reversibly as the nonelectrolyte concentration increased. The activation, deactivation (closing) and inactivation processes were slowed in a similar manner. showing that the basic gating mechanism did not change in these solutions and only a slight increase in the activation free energy was one of the main causes of slowing. 4. Eight non-electrolytes, formamide, ethylene glycol, glycerol, erythritol, glucose, sorbitol, sucrose and polyethylene glycol (mean molecular weight 600) were used. The amount of slowing was correlated with the gram concentration (g Fl) of non-electrolytes, but not with molar concentration (M) and solution osmolarity (osmol Fl). 6. Values of a and y deviated frequently from those in an ideal case, i.e. 100% for a and 1 for y, and they scattered, having a tendency to decrease as a function of molecular weight. 7. The slowing was also expressed as an exponential function of the solution osmolarity.A predicted solute-inaccessible volume V. ranged (in nm3 per molecule) between 0 09 and 1 45. The value of Va increased as a logarithmic function of the molecular weight of the nonelectrolyte. 8. This solute-inaccessible volume should be distributed in all hydrophilic parts of the sodium channel protein, but is not located in the channel conducting pore itself. The slowing of gating could be explained by a model in which a rate-limiting step is a hydration process that occurs after local small structural changes have exposed new, unhydrated faces (transient hydrated-states model).9. Considering the opposite dependencies of parameters a (or y) and fi on the molecular weight, sodium channel gating is likely to reflect a combination of these two models, which are coupled in microscopic segment movements. We emphasize with this combination of models that fluctuating hydrophilic structures play an important role in determining time constants in the gating process.

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“…Secondly, the description of the protein-water interactions may need an optimization. This argument has been raised as an explanation for the fact that overall rotation of peptides and proteins is too fast in simulation by a factor of 3.54, 55 Improvement may involve a fine-tuning of the interaction function parameters and refined interaction paradigms, e.g., polarizability of solvent and solute. Van Belle and W~d a k~~ have found that a polarizable water model (PSPC)57 displays a less pronounced retardation effect than SPC water in the vicinity of nonpolar solutes.…”

Section: Lifetimes Of Neighborhood Relationsmentioning

confidence: 98%

The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation

1996

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Translational and Rotational Diffusion of Proteins

Cited by 82 publications

References 0 publications

Protein Hydration Dynamics in Aqueous Solution: A Comparison of Bovine Pancreatic Trypsin Inhibitor and Ubiquitin by Oxygen-17 Spin Relaxation Dispersion

Protein Hydration Dynamics in Aqueous Solution: A Comparison of Bovine Pancreatic Trypsin Inhibitor and Ubiquitin by Oxygen-17 Spin Relaxation Dispersion

Solvent‐dependent rate‐limiting steps in the conformational change of sodium channel gating in squid giant axon.

The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation

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