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Publications

Hypothesis for a mechanism of beam-induced motion in cryo-electron microscopy

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

Estimates of heat-transfer rates during plunge-cooling and the patterns of ice observed in cryo-EM samples indicate that the grid bars cool much more slowly than do the support foil and sample near the middle of the grid openings. The resulting transient temperature differences generate transient tensile stresses in the support foil. Most of this foil stress develops while the sample is liquid and cooling toward its glass transition T g, and so does not generate tensile sample stress.

Journal
IUCrJ
Date Published
Group (Lab)
Robert Thorne Group

Starting Dynamics of a Linear Mamyshev Oscillator

Cornell Affiliated Author(s)
Author
Y.-H. Chen
P. Sidorenko
R. Thorne
F. Wise
Abstract

We investigate the starting dynamics of an environmentally-stable linear Mamyshev oscillator that is started by modulation of the pump power. A moving filter is implemented to generate 21-nJ and 65-fs pulses. © 2020 OSA.

Conference Name
Conference
Date Published
Group (Lab)
Robert Thorne Group

Resolution and dose dependence of radiation damage in biomolecular systems

Cornell Affiliated Author(s)
Author
H. Atakisi
L. Conger
D.W. Moreau
R.E. Thorne
Abstract

The local Fourier-space relation between diffracted intensity I, diffraction wavevector q and dose D, , is key to probing and understanding radiation damage by X-rays and energetic particles in both diffraction and imaging experiments. The models used in protein crystallography for the last 50 years provide good fits to experimental I(q) versus nominal dose data, but have unclear physical significance. More recently, a fit to diffraction and imaging experiments suggested that the maximum tolerable dose varies as q -1 or linearly with resolution.

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

Solvent flows, conformation changes and lattice reordering in a cold protein crystal

Cornell Affiliated Author(s)
Author
D.W. Moreau
H. Atakisi
R.E. Thorne
Abstract

When protein crystals are abruptly cooled, the unit-cell, protein and solvent-cavity volumes all contract, but the volume of bulk-like internal solvent may expand. Outflow of this solvent from the unit cell and its accumulation in defective interior crystal regions has been suggested as one cause of the large increase in crystal mosaicity on cooling. It is shown that when apoferritin crystals are abruptly cooled to temperatures between 220 and 260 K, the unit cell contracts, solvent is pushed out and the mosaicity grows.

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

Ice formation and solvent nanoconfinement in protein crystals

Cornell Affiliated Author(s)
Author
D.W. Moreau
H. Atakisi
R.E. Thorne
Abstract

Ice formation within protein crystals is a major obstacle to the cryocrystallographic study of protein structure, and has limited studies of how the structural ensemble of a protein evolves with temperature in the biophysically interesting range from ∼260K to the protein-solvent glass transition near 200K. Using protein crystals with solvent cavities as large as ∼70Å, time-resolved X-ray diffraction was used to study the response of protein and internal solvent during rapid cooling.

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

Density and electron density of aqueous cryoprotectant solutions at cryogenic temperatures for optimized cryoprotection and diffraction contrast

Cornell Affiliated Author(s)
Author
T.J. Tyree
R. Dan
R.E. Thorne
Abstract

The glass-phase densities at T = 77 K of aqueous solutions of the common cryoprotective agents (CPAs) methanol, ethanol, 2-propanol, glycerol, 2-methyl-2,4-pentanediol (MPD), ethylene glycol, polyethylene glycol 200 and polypropylene glycol 425 were measured as a function of CPA concentration. Individual drops with volumes as small as ∼65 pl were rapidly cooled to achieve the glass phase, and their densities at T = 77 K were determined by cryoflotation.

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

Effects of protein-crystal hydration and temperature on side-chain conformational heterogeneity in monoclinic lysozyme crystals

Cornell Affiliated Author(s)
Author
H. Atakisi
D.W. Moreau
R.E. Thorne
Abstract

The modulation of main-chain and side-chain conformational heterogeneity and solvent structure in monoclinic lysozyme crystals by dehydration (related to water activity) and temperature is examined. Decreasing the relative humidity (from 99 to 11%) and decreasing the temperature both lead to contraction of the unit cell, to an increased area of crystal contacts and to remodeling of primarily contact and solvent-exposed residues. Both lead to the depopulation of some minor side-chain conformers and to the generation of new conformations.

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

Lifetimes and spatio-temporal response of protein crystals in intense X-ray microbeams

Cornell Affiliated Author(s)
Author
M.A. Warkentin
H. Atakisi
J.B. Hopkins
D. Walko
R.E. Thorne
Abstract

Serial synchrotron-based crystallography using intense microfocused X-ray beams, fast-framing detectors and protein microcrystals held at 300 K promises to expand the range of accessible structural targets and to increase overall structure-pipeline throughputs. To explore the nature and consequences of X-ray radiation damage under microbeam illumination, the time-, dose- and temperature-dependent evolution of crystal diffraction have been measured with maximum dose rates of 50 MGy s-1.

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

Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase

Cornell Affiliated Author(s)
Author
K. Sen
S. Horrell
D. Kekilli
C.W. Yong
T.W. Keal
H. Atakisi
D.W. Moreau
R.E. Thorne
M.A. Hough
R.W. Strange
Abstract

Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site.

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

Measuring the densities of aqueous glasses at cryogenic temperatures

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

We demonstrate a method for determining the vitreous phase cryogenic temperature densities of aqueous mixtures, and other samples that require rapid cooling, to prepare the desired cryogenic temperature phase. Microliter to picoliter size drops are cooled by projection into a liquid nitrogen-argon (N2-Ar) mixture. The cryogenic temperature phase of the drop is evaluated using a visual assay that correlates with X-ray diffraction measurements. The density of the liquid N2-Ar mixture is adjusted by adding N2 or Ar until the drop becomes neutrally buoyant.

Journal
Journal of Visualized Experiments
Date Published
Group (Lab)
Robert Thorne Group