An Eye Lens Protein–Water Structure: 1.2 Å Resolution Structure of γB-Crystallin at 150 K

Kumaraswamy, V. Sagar; Lindley, P.F.; Slingsby, C.; Glover, I. D.

doi:10.1107/s0907444995014302

Cited by 52 publications

(37 citation statements)

References 25 publications

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“…A fraction of the protein crystals which diffract to atomic resolution contain only a very small region of disordered solvent. Two examples of this are crambin (Stec et al, 1995;Teeter, 1992) and B-crystallin (Kumaraswamy et al, 1996). In these structures, virtually all the water molecules making up the solvent volume of the crystal are well ordered and are therefore explicitly present in the structural model.…”

Section: Anisotropy Of Water Molecules Associated With the Protein Stmentioning

confidence: 99%

Expanding the model: anisotropic displacement parameters in protein structure refinement

Merritt

1999

Acta Crystallogr D Biol Crystallogr

148

168

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Ethan Merritt ®rst encountered crystallography as a graduate student in computer science, and was delighted to have found a research ®eld offering a wide scope for developing and applying computational techniques in pursuit of biological goals. He earned a PhD in the group of M. Sundaralingam in Madison, dividing his efforts between macromolecular graphics, conformational modeling of nucleotides and the use of anomalous scattering to determine the stereospeci®city of metal/nucleotide coordination in ATP-binding enzymes. He then joined the research staff of the Stanford Synchrotron Radiation Laboratory, where he worked to implement the X-ray optics, beamline-control systems and data-processing software needed to turn MAD phasing from a promising idea into a routine technique for structure determination. This effort culminated in a series of collaborations, notably with Hans Freeman and Wayne Hendrickson, which yielded the ®rst protein structure determinations entirely from MAD phasing. In 1989, he moved to the University of Washington Medical School in Seattle. There his research interests have included structure-based drug design, development of the Raster3D graphics package and the improved exploitation of synchrotron radiation in protein crystallography. The review presented here grew from a convergence of these interests.# 1999 International Union of Crystallography Printed in Denmark ± all rights reserved Recent technological improvements in crystallographic data collection have led to a surge in the number of protein structures being determined at atomic or near-atomic resolution. At this resolution, structural models can be expanded to include anisotropic displacement parameters (ADPs) for individual atoms. New protocols and new tools are needed to re®ne, analyze and validate such models optimally. One such tool, PARVATI, has been used to examine all protein structures (peptide chains >50 residues) for which expanded models including ADPs are available from the Protein Data Bank. The distribution of anisotropy within each of these re®ned models is broadly similar across the entire set of structures, with a mean anisotropy A in the range 0.4±0.5. This is a signi®cant departure from a purely isotropic model and explains why the inclusion of ADPs yields a substantial improvement in the crystallographic residuals R and R free . The observed distribution of anisotropy may prove useful in the validation of very high resolution structures. A more complete understanding of this distribution may also allow the development of improved protein structural models, even at lower resolution.

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Section: Anisotropy Of Water Molecules Associated With the Protein Stmentioning

confidence: 99%

Expanding the model: anisotropic displacement parameters in protein structure refinement

Merritt

1999

Acta Crystallogr D Biol Crystallogr

148

168

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“…12 and described there; briefly, d 11 corresponds to the diameter of a sphere with the volume of one molecule of γB-crystallin. With use of the value for γB-crystallin 5 of v eff = 0.71 cm 3 /g, typical of globular proteins, together with the known molecular weight M W ,γ of bovine γB-crystallin, 20 993 g/mol, 58 one obtains d 11 = 36.2 Å. However, the sticky-sphere model light scattering predictions can be written so that the diameter values enter in terms of ratios, and so we take d 11 = 1 in Table I.…”

Section: A Molecular Parameters For γB and α-Crystallinmentioning

confidence: 99%

Statistical-thermodynamic model for light scattering from eye lens protein mixtures

Bell

Ross

Bautista

et al. 2017

The Journal of Chemical Physics

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We model light-scattering cross sections of concentrated aqueous mixtures of the bovine eye lens proteins γB-and α-crystallin by adapting a statistical-thermodynamic model of mixtures of spheres with short-range attractions. The model reproduces measured static light scattering cross sections, or Rayleigh ratios, of γB-α mixtures from dilute concentrations where light scattering intensity depends on molecular weights and virial coefficients, to realistically high concentration protein mixtures like those of the lens. The model relates γB-γB and γB-α attraction strengths and the γB-α size ratio to the free energy curvatures that set light scattering efficiency in tandem with protein refractive index increments. The model includes (i) hard-sphere α-α interactions, which create short-range order and transparency at high protein concentrations, (ii) short-range attractive plus hard-core γ-γ interactions, which produce intense light scattering and liquid-liquid phase separation in aqueous γ-crystallin solutions, and (iii) short-range attractive plus hard-core γ-α interactions, which strongly influence highly non-additive light scattering and phase separation in concentrated γ-α mixtures. The model reveals a new lens transparency mechanism, that prominent equilibrium composition fluctuations can be perpendicular to the refractive index gradient. The model reproduces the concave-up dependence of the Rayleigh ratio on α/γ composition at high concentrations, its concave-down nature at intermediate concentrations, non-monotonic dependence of light scattering on γ-α attraction strength, and more intricate, temperature-dependent features. We analytically compute the mixed virial series for light scattering efficiency through third order for the sticky-sphere mixture, and find that the full model represents the available light scattering data at concentrations several times those where the second and third mixed virial contributions fail. The model indicates that increased γ-γ attraction can raise γ-α mixture light scattering far more than it does for solutions of γ-crystallin alone, and can produce marked turbidity tens of degrees celsius above liquid-liquid separation. Published by AIP Publishing.

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“…In those works, X-ray data were sometimes collected at freezing temperature to reduce the irradiation damage of crystals and to extend the resolution. [13][14][15] On the other hand, Sevcik et al 16 have reported the refinement of ribonuclease at atomic resolution using the data measured at room temperature. In the present paper, we deal with crystals of two chicken type lysozymes, turkey egg lysozyme (TEL) and human lysozyme (HL).…”

Section: Introductionmentioning

confidence: 98%

Full-matrix least-squares refinement of lysozymes and analysis of anisotropic thermal motion

1998

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Crystal structures of turkey egg lysozyme (TEL) and human lysozyme (HL) were refined by full-matrix least-squares method using anisotropic temperature factors. The refinement converged at the conventional R-values of 0.104 (TEL) and 0.115 (HL) for reflections with Fo > 0 to the resolution of 1.12 A and 1.15 A, respectively. The estimated r.m.s. coordinate errors for protein atoms were 0.031 A (TEL) and 0.034 A (HL). The introduction of anisotropic temperature factors markedly reduced the R-value but did not significantly affect the main chain coordinates. The degree of anisotropy of atomic thermal motion has strong positive correlation with the square of distance from the molecular centroid. The ratio of the radial component of thermal ellipsoid to the r.m.s. magnitude of three principal components has negative correlation with the distance from the molecular centroid, suggesting the domination of libration rather than breathing motion. The TLS model was applied to elucidate the characteristics of the rigid-body motion. The TLS tensors were determined by the least-squares fit to observed temperature factors. The profile of the magnitude of reproduced temperature factors by the TLS method well fitted to that of observed B(eqv). However, considerable disagreement was observed in the shape and orientation of thermal ellipsoid for atoms with large temperature factors, indicating the large contribution of local motion. The upper estimate of the external motion, 67% (TEL) and 61% (HL) of B(eqv), was deduced from the plot of the magnitude of TLS tensors determined for main chain atoms which were grouped into shells according to the distance from the center of libration. In the external motion, the translational portion is predominant and the contribution of libration and screw motion is relatively small. The internal motion, estimated by subtracting the upper estimate of the external motion from the observed temperature factor, is very similar between TEL and HL in spite of the difference in 54 of 130 amino acid residues and in crystal packing, being suggested to reflect the intrinsic internal motion of chicken-type lysozymes.

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An Eye Lens Protein–Water Structure: 1.2 Å Resolution Structure of γB-Crystallin at 150 K

Cited by 52 publications

References 25 publications

Expanding the model: anisotropic displacement parameters in protein structure refinement

Expanding the model: anisotropic displacement parameters in protein structure refinement

Statistical-thermodynamic model for light scattering from eye lens protein mixtures

Full-matrix least-squares refinement of lysozymes and analysis of anisotropic thermal motion

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