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Publications

Quantifying radiation damage in biomolecular small-angle X-ray scattering

Cornell Affiliated Author(s)
Author
J.B. Hopkins
R.E. Thorne
Abstract

Small-angle X-ray scattering (SAXS) is an increasingly popular technique that provides low-resolution structural information about biological macromolecules in solution. Many of the practical limitations of the technique, such as minimum required sample volume, and of experimental design, such as sample flow cells, are necessary because the biological samples are sensitive to damage from the X-rays. Radiation damage typically manifests as aggregation of the sample, which makes the collected data unreliable.

Journal
Journal of Applied Crystallography
Date Published
Research Area
Group (Lab)
Robert Thorne Group

Thermal contraction of aqueous glycerol and ethylene glycol solutions for optimized protein-crystal cryoprotection:

Cornell Affiliated Author(s)
Author
C. Shen
E.F. Julius
T.J. Tyree
D.W. Moreau
H. Atakisi
R.E. Thorne
Abstract

The thermal contraction of aqueous cryoprotectant solutions on cooling to cryogenic temperatures is of practical importance in protein cryocrystallography and in biological cryopreservation. In the former case, differential contraction on cooling of protein molecules and their lattice relative to that of the internal and surrounding solvent may lead to crystal damage and the degradation of crystal diffraction properties. Here, the amorphous phase densities of aqueous solutions of glycerol and ethylene glycol at T = 77 K have been determined.

Journal
Acta Crystallographica Section D: Structural Biology
Date Published
Research Area
Group (Lab)
Robert Thorne Group

Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

Cornell Affiliated Author(s)
Author
D.A. Keedy
L.R. Kenner
M. Warkentin
R.A. Woldeyes
J.B. Hopkins
M.C. Thompson
A.S. Brewster
A.H.V. Benschoten
E.L. Baxter
M. Uervirojnangkoorn
S.E. McPhillips
J. Song
R. Alonso-Mori
J.M. Holton
W.I. Weis
A.T. Brunger
S.M. Soltis
H. Lemke
A. Gonzalez
N.K. Sauter
A.E. Cohen
H. van den Bedem
R.E. Thorne
J.S. Fraser
Abstract

Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography.

Journal
eLife
Date Published
Research Area
Group (Lab)
Robert Thorne Group

A microfabricated fixed path length silicon sample holder improves background subtraction for cryoSAXS

Cornell Affiliated Author(s)
Author
J.B. Hopkins
A.M. Katz
S.P. Meisburger
M.A. Warkentin
R.E. Thorne
L. Pollack
Abstract

The application of small-angle X-ray scattering (SAXS) for high-throughput characterization of biological macromolecules in solution is limited by radiation damage. By cryocooling samples, radiation damage and required sample volumes can be reduced by orders of magnitude. However, the challenges of reproducibly creating the identically sized vitrified samples necessary for conventional background subtraction limit the widespread adoption of this method. Fixed path length silicon sample holders for cryoSAXS have been microfabricated to address these challenges.

Journal
Journal of Applied Crystallography
Date Published
Research Area
Group (Lab)
Robert Thorne Group

Spatially resolved transient dynamics of charge density waves in NbSe3

Cornell Affiliated Author(s)
Author
E.C. Geil
R.E. Thorne
Abstract

We have developed methods for acquiring temporally and spatially resolved spectrograms of the velocity of sliding charge-density waves (CDWs), allowing unprecedented access to CDW dynamics. Complex transients arising from the interplay between elastic and plastic processes occur when the driving field direction is reversed. A transient spectral component due to shear elasticity can be unambiguously identified, and allows the most direct determination to date of the CDW's shear elastic modulus.

Journal
Physical Review Letters
Date Published
Group (Lab)
Robert Thorne Group

Dynamic correlations in sliding charge-density waves probed by spatially resolved measurements of voltage oscillations

Cornell Affiliated Author(s)
Author
E.C. Geil
R.E. Thorne
Abstract

In sliding charge-density wave (CDW) conductors such as NbSe3, voltage oscillations at a frequency proportional to the local CDW velocity accompany CDW motion and can furnish many insights into the dynamics of these systems. We have used high-performance cryogenic differential amplifiers to make position-dependent measurements of voltage oscillations in the quasisteady state. These measurements yield voltage-voltage and velocity-velocity correlations and the temperature dependence of the CDW's longitudinal and transverse velocity coherence. © 2014 American Physical Society.

Journal
Physical Review B - Condensed Matter and Materials Physics
Date Published
Group (Lab)
Robert Thorne Group

Correcting for surface topography in X-ray fluorescence imaging

Cornell Affiliated Author(s)
Author
E.C. Geil
R.E. Thorne
Abstract

Samples with non-planar surfaces present challenges for X-ray fluorescence imaging analysis. Here, approximations are derived to describe the modulation of fluorescence signals by surface angles and topography, and suggestions are made for reducing this effect. A correction procedure is developed that is effective for trace element analysis of samples having a uniform matrix, and requires only a fluorescence map from a single detector. This procedure is applied to fluorescence maps from an incised gypsum tablet. © 2014 International Union of Crystallography.

Journal
Journal of Synchrotron Radiation
Date Published
Group (Lab)
Robert Thorne Group

Temperature-dependent radiation sensitivity and order of 70S ribosome crystals

Cornell Affiliated Author(s)
Author
M. Warkentin
J.B. Hopkins
J.B. Haber
G. Blaha
R.E. Thorne
Abstract

All evidence to date indicates that at T = 100 K all protein crystals exhibit comparable sensitivity to X-ray damage when quantified using global metrics such as change in scaling B factor or integrated intensity versus dose. This is consistent with observations in cryo-electron microscopy, and results because nearly all diffusive motions of protein and solvent, including motions induced by radiation damage, are frozen out.

Journal
Acta Crystallographica Section D: Biological Crystallography
Date Published
Research Area
Group (Lab)
Robert Thorne Group

Application of X-ray fluorescence imaging to ceramics from the American Southwest

Cornell Affiliated Author(s)
Author
E.C. Geil
S.A. LeBlanc
D.S. Dale
R.E. Thorne
Abstract

We have used synchrotron-based X-ray fluorescence imaging (XRFI) to examine sherds of painted ceramics from prehistoric cultures of the American Southwest. These sherds are very well suited to XRFI analysis. Paints can generally be detected and distinguished by the fluorescence intensities of their constituent elements. Spatial maps of element distributions yield the spatial distribution of pigments.

Journal
Journal of Archaeological Science
Date Published
Group (Lab)
Robert Thorne Group

Critical droplet theory explains the glass formability of aqueous solutions

Cornell Affiliated Author(s)
Author
M. Warkentin
J.P. Sethna
R.E. Thorne
Abstract

When pure water is cooled at ∼106 K/s, it forms an amorphous solid (glass) instead of the more familiar crystalline phase. The presence of solutes can reduce this required (or "critical") cooling rate by orders of magnitude. Here, we present critical cooling rates for a variety of solutes as a function of concentration and a theoretical framework for understanding these rates. For all solutes tested, the critical cooling rate is an exponential function of concentration. The exponential's characteristic concentration for each solute correlates with the solute's Stokes radius.

Journal
Physical Review Letters
Date Published
Group (Lab)
Robert Thorne Group