The structure of concanavalin A and its bound solvent determined with small-molecule accuracy at 0.94 [Aring ]resolution

Deacon, Ashley M.; Gleichmann, T.; Kalb, A. Joseph; Price, H.J.; Raftery, James; Bradbrook, Gail M.; Yariv, J.; Helliwell, John R.

doi:10.1039/a704140c

Cited by 152 publications

(158 citation statements)

References 22 publications

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“…as a result of X-ray damage), then case studies document the bounds or range of structural change (e.g. Deacon et al 1997) that occur on freezing. Such changes produce more multipleoccupancy side chains and, associated with these, bound-water movements.…”

Section: Discussionmentioning

confidence: 99%

Protein hydration dynamics in solution: a critical survey

Halle

2004

Phil. Trans. R. Soc. Lond. B

499

576

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The properties of water in biological systems have been studied for well over a century by a wide range of physical techniques, but progress has been slow and erratic. Protein hydration-the perturbation of water structure and dynamics by the protein surface-has been a particularly rich source of controversy and confusion. Our aim here is to critically examine central concepts in the description of protein hydration, and to assess the experimental basis for the current view of protein hydration, with the focus on dynamic aspects. Recent oxygen-17 magnetic relaxation dispersion (MRD) experiments have shown that the vast majority of water molecules in the protein hydration layer suffer a mere twofold dynamic retardation compared with bulk water. The high mobility of hydration water ensures that all thermally activated processes at the protein-water interface, such as binding, recognition and catalysis, can proceed at high rates. The MRD-derived picture of a highly mobile hydration layer is consistent with recent molecular dynamics simulations, but is incompatible with results deduced from intermolecular nuclear Overhauser effect spectroscopy, dielectric relaxation and fluorescence spectroscopy. It is also inconsistent with the common view of hydration effects on protein hydrodynamics. Here, we show how these discrepancies can be resolved.

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Section: Discussionmentioning

confidence: 99%

Protein hydration dynamics in solution: a critical survey

Halle

2004

Phil. Trans. R. Soc. Lond. B

499

576

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“…This fact is probably widely appreciated within the crystallography community, although rarely stated explicitly. With a few notable exceptions (6)(7)(8)(9)(10)(11)(12), it is usually taken for granted that the cryostructure is quenched at ambient temperature (T* ϭ T 0 in our notation) and, therefore, that the only structural effect of the low temperature is to sharpen the atomic displacement distributions without significantly displacing the mean atomic positions [apart from a more-or-less uniform contraction of the protein (6-9)]. In contrast to this conventional wisdom, the present analysis indicates that many degrees of freedom are quenched at temperatures near 200 K, where local conformational and association equilibria may be strongly shifted toward low-enthalpy states.…”

Section: Discussionmentioning

confidence: 99%

“…Whatever the cause, these findings raise concerns about the validity of cryostructures of biomolecular complexes (9). Significant conformational differences between cryogenic and room-temperature protein structures have been reported also for solvent-exposed side chains (not located at crystal contacts) and associated water molecules (10)(11)(12), sometimes in the catalytic site of enzymes.…”

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confidence: 95%

Biomolecular cryocrystallography: Structural changes during flash-cooling

Halle

2004

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

191

143

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To minimize radiation damage, crystal structures of biological macromolecules are usually determined after rapid cooling to cryogenic temperatures, some 150 -200 K below the normal physiological range. The biological relevance of such structures relies on the assumption that flash-cooling is sufficiently fast to kinetically trap the macromolecule and associated solvent in a room-temperature equilibrium state. To test this assumption, we use a two-state model to calculate the structural changes expected during rapid cooling of a typical protein crystal. The analysis indicates that many degrees of freedom in a flash-cooled protein crystal are quenched at temperatures near 200 K, where local conformational and association equilibria may be strongly shifted toward low-enthalpy states. Such cryoartifacts should be most important for strongly solvent-coupled processes, such as hydration of nonpolar cavities and surface regions, conformational switching of solventexposed side chains, and weak ligand binding. The dynamic quenching that emerges from the model considered here can also rationalize the glass transition associated with the atomic fluctuations in the protein.protein structure ͉ protein hydration ͉ protein glass transition ͉ x-ray diffraction

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“…This work has been developed by higher resolution studies of the mannose and glucose complexes (Naismith et al, 1994;Harrop et al, 1996). The lectin itself has now been studied at atomic resolution (Deacon et al, 1997).…”

Section: Introductionmentioning

confidence: 99%

A general method for co-crystallization of concanavalin A with carbohydrates

Moothoo

Naismith

1999

Acta Crystallogr D Biol Cryst

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A small grid of conditions has been developed for co-crystallization of the plant lectin concanavalin A (conA) and polysaccharides. Crystals have been obtained of complexes of conA with 1-2 mannobiose, 1-methyl 1-2 mannobiose, fructose, a trisaccharide and a pentasaccharide. The crystals diffract to resolutions of 1.75±2.7 A Ê using a copper rotating-anode source. The crystals are grown in the presence of polyethylene glycol 6K [10±20%(w/v)] at around pH 6.0. Optimization for each particular carbohydrate requires small adjustments in the conditions; however, all complexes give some crystalline precipitate in this limited grid. The 1-2 mannobiose complex crystals diffract to 1.75 A Ê with space group I222 and cell dimensions a = 91.7, b = 86.8, c = 66.6 A Ê . One monomer is present in the asymmetric unit. The 1-methyl 1-2 mannobioside complex crystallizes in space group P2 1 2 1 2 1 , cell dimensions a = 119.7, b = 119.7, c = 68.9 A Ê and diffract to 2.75 A Ê . One tetramer is present in the asymmetric unit. Two crystal forms of the conA±fructose complex have been obtained. The ®rst has space group P2 1 2 1 2 1 , cell dimensions a = 121.7, b = 119.9, c = 67.3 A Ê with a tetramer in the asymmetric unit and diffracts to 2.6 A Ê . The second crystallizes in space group C222 1 , cell dimensions a = 103.3, b = 117.9, c = 254.3 A Ê with two dimers in the asymmetric unit and diffracts to 2.42 A Ê . Structures and crystallization of the trisaccharide±conA and pentasaccharide±conA complexes have already been reported. In all complexes, the protein is found as a tetramer, although varying combinations of non-crystallographic and crystallographic symmetry are involved in generating the tetramer. The precise packing of the tetramer varies from crystal to crystal and it is likely that this variability facilitates crystallization.

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The structure of concanavalin A and its bound solvent determined with small-molecule accuracy at 0.94 [Aring ]resolution

Cited by 152 publications

References 22 publications

Protein hydration dynamics in solution: a critical survey

Protein hydration dynamics in solution: a critical survey

Biomolecular cryocrystallography: Structural changes during flash-cooling

A general method for co-crystallization of concanavalin A with carbohydrates

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