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Ultrahigh-resolution study of protein atomic displacement parameters at cryotemperatures obtained with a helium cryostat.

Petrova T, Ginell S, Mitschler A, Hazemann I, Schneider T, Cousido A, Lunin VY, Joachimiak A, Podjarny A
Acta Crystallogr D Biol Crystallogr 62 1535-44 (2006)
Cited: 9 times
EuropePMC logo PMID: 17139089

Abstract

Two X-ray data sets for a complex of human aldose reductase (h-AR) with the inhibitor IDD 594 and the cofactor NADP(+) were collected from two different parts of the same crystal to a resolution of 0.81 A at 15 and 60 K using cold helium gas as cryogen. The contribution of temperature to the atomic B values was estimated by comparison of the independently refined models. It was found that although being slightly different for different kinds of atoms, the differences (deltaB) in the isotropic equivalents B of atomic displacement parameters (ADPs) were approximately constant (about 1.7 A(2)) for well ordered atoms as the temperature was increased from 15 to 60 K. The mean value of this difference varied according to the number of non-H atoms covalently bound to the parent atom. Atoms having a B value of higher than 8 A(2) at 15 K showed much larger deviations of deltaB from the average value, which might reflect partial occupancy of atomic sites. An analysis of the anisotropy of ADPs for individual atoms revealed an increase in the isotropy of ADPs with the increase of the temperature from 15 to 60 K. In a separate experiment, a 0.93 A resolution data set was collected from a different crystal of the same complex at 100 K using cold nitrogen as a cryogen. The effects of various errors on the atomic B values were estimated by comparison of the refined models and the temperature-dependent component was inferred. It was found that both decreasing the data redundancy and increasing the resolution cutoff led to an approximately constant increase in atomic B values for well ordered atoms.

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Articles citing this publication (8)

  1. Could MM-GBSA be accurate enough for calculation of absolute protein/ligand binding free energies? Mulakala C, Viswanadhan VN. J Mol Graph Model 46 41-51 (2013)
  2. Crystal packing modifies ligand binding affinity: the case of aldose reductase. Cousido-Siah A, Petrova T, Hazemann I, Mitschler A, Ruiz FX, Howard E, Ginell S, Atmanene C, Van Dorsselaer A, Sanglier-Cianférani S, Joachimiak A, Podjarny A. Proteins 80 2552-2561 (2012)
  3. X-ray-induced deterioration of disulfide bridges at atomic resolution. Petrova T, Ginell S, Mitschler A, Kim Y, Lunin VY, Joachimiak G, Cousido-Siah A, Hazemann I, Podjarny A, Lazarski K, Joachimiak A. Acta Crystallogr D Biol Crystallogr 66 1075-1091 (2010)
  4. Protein dynamics of a beta-sheet protein. Schmidt M, Achterhold K, Prusakov V, Parak FG. Eur Biophys J 38 687-700 (2009)
  5. X-ray-radiation-induced cooperative atomic movements in protein. Petrova T, Lunin VY, Ginell S, Hazemann I, Lazarski K, Mitschler A, Podjarny A, Joachimiak A. J Mol Biol 387 1092-1105 (2009)
  6. A physical picture of protein dynamics and conformational changes. Parak FG, Achterhold K, Croci S, Schmidt M. J Biol Phys 33 371-387 (2007)
  7. On the reduction in the effects of radiation damage to two-dimensional crystals of organic and biological molecules at liquid-helium temperature. Naydenova K, Kamegawa A, Peet MJ, Henderson R, Fujiyoshi Y, Russo CJ. Ultramicroscopy 237 113512 (2022)
  8. Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase. Plapp BV, Gakhar L, Subramanian R. Acta Crystallogr D Struct Biol 78 1221-1234 (2022)


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