Properties of liquids in small pores

Bishop, William H.; Richards, Frederic M.

doi:10.1016/0022-2836(68)90389-6

Cited by 40 publications

(23 citation statements)

References 17 publications

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“…The time necessary for equilibration between a crystal and a cryoprotective buffer of a given concentration depends on the size of the crystal, the nature of the solvent channels within the crystal, the temperature, the diffusioff coefficient of the cryoprotectant and a number of other factors (Bishop & Richards, 1968). For small cryoprotective agents such as glycerol, soaking times of less than I min can be sufficient (Schneider, 1996a), whereas for larger cryoprotectants such as PEGs, soaking times of several minutes might be necessary to achieve equilibrium (Bishop & Richards, 1968;Fink & Petsko, 1981;Ray, Bolin, Puvathingal, Minor, Liu & Muchmore, 1991).…”

Section: Hkl D (~) I/~ Hkl D (~) I/~mentioning

confidence: 99%

“…For small cryoprotective agents such as glycerol, soaking times of less than I min can be sufficient (Schneider, 1996a), whereas for larger cryoprotectants such as PEGs, soaking times of several minutes might be necessary to achieve equilibrium (Bishop & Richards, 1968;Fink & Petsko, 1981;Ray, Bolin, Puvathingal, Minor, Liu & Muchmore, 1991). Characteristic linear dimensions of loosely 'folded' PEG molecules with mean molecular weights of 1000 and higher are of the order of 60 A or larger (Knoll & Hermans, 1983), making it difficult for such molecules to diffuse in solvent channels of crystals.…”

Section: Hkl D (~) I/~ Hkl D (~) I/~mentioning

confidence: 99%

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Macromolecular Cryocrystallography

Garman¹,

Schneider²

1997

J Appl Crystallogr

344

289

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The current techniques for X-ray-diffraction data collection from macromolecular crystals at cryogenic temperatures are reviewed. The development of the experimental methods is outlined and the basic concepts pertaining to radiation damage and cryoprotection are summarized. Emphasis is placed on the practical aspects important to the success of the techniques, and a detailed account of these is presented.

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Section: Hkl D (~) I/~ Hkl D (~) I/~mentioning

confidence: 99%

Section: Hkl D (~) I/~ Hkl D (~) I/~mentioning

confidence: 99%

Macromolecular Cryocrystallography

Garman¹,

Schneider²

1997

J Appl Crystallogr

344

289

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“…Although a small molecule which is not bound by the enzyme may diffuse through a 0.5 mm crystal in a few seconds, the diffusion of molecules bound by the enzyme may take hours or days to reach equilibrium (31).…”

Section: Limitations Of the X·ray Diffraction Techniquementioning

confidence: 99%

X-Ray Diffraction Studies of Enzymes

Blow¹,

Steitz²

1970

Annu. Rev. Biochem.

200

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“…When proteins make up the lining of small pores, water and ions affect the passage of substances through such pores [5,6]. With this prospect, the pore structure of a protein crystal offers a useful test system for investigating dynamics of water and ion motion in a confined biological region [6][7][8]. Protein crystals contain biological nanopores that range in width from approximately 0.3 nm up to 10 nm, and occupy 25-75% of the crystal volume.…”

Section: Introductionmentioning

confidence: 99%

“…Dynamic properties (e.g., mobility and structural organization) of water and counter-ions at the protein-water interface differ from those in the bulk [2,5]. When proteins make up the lining of small pores, water and ions affect the passage of substances through such pores [5,6]. With this prospect, the pore structure of a protein crystal offers a useful test system for investigating dynamics of water and ion motion in a confined biological region [6][7][8].…”

Section: Introductionmentioning

confidence: 99%

Diffusion of water and sodium counter-ions in nanopores of a β-lactoglobulin crystal: a molecular dynamics study

Malek¹,

Odijk²,

Coppens³

2005

Nanotechnology

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The dynamics of water and sodium counter-ions (Na + ) in a C222 1 orthorhombic β-lactoglobulin crystal is investigated by means of 5 ns molecular dynamics simulations. The effect of the fluctuation of the protein atoms on the motion of water and sodium ions is studied by comparing simulations in a rigid and in a flexible lattice. The electrostatic interactions of sodium ions with the positively charged LYS residues inside the crystal channels significantly influence the ionic motion. According to our results, water molecules close to the protein surface undergo an anomalous diffusive motion. On the other hand, the motion of water molecules further away from the protein surface is normal diffusive. Protein fluctuations affect the diffusion constant of water, which increases from 0.646 ± 0.108 to 0.887 ± 0.41 nm 2 ns −1 , when protein fluctuations are taken into account. The pore size (0.63-1.05 nm) and the water diffusivities are in good agreement with previous experimental results. The dynamics of sodium ions is disordered. LYS residues inside the pore are the main obstacles to the motion of sodium ions. However, the simulation time is still too short for providing a precise description of anomalous diffusion of sodium ions. The results are not only of interest for studying ion and water transport through biological nanopores, but may also elucidate water-protein and ion-protein interactions in protein crystals.

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Properties of liquids in small pores

Cited by 40 publications

References 17 publications

Macromolecular Cryocrystallography

Macromolecular Cryocrystallography

X-Ray Diffraction Studies of Enzymes

Diffusion of water and sodium counter-ions in nanopores of a β-lactoglobulin crystal: a molecular dynamics study

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