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Nonlinear temperature dependence of the crystal structure of lysozyme: correlation between coordinate shifts and thermal factors.

Joti Y, Nakasako M, Kidera A, Go N
Acta Crystallogr D Biol Crystallogr 58 1421-32 (2002)
Related entries: 1iwu, 1iwv, 1iww, 1iwx, 1iwy, 1iwz

Cited: 24 times
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Abstract

The static and dynamic structures of human lysozyme at seven different temperatures ranging from 113 to 178 K were investigated by normal-mode refinement of the cryogenic X-ray diffraction data collected from a single crystal. Normal-mode refinement decomposes the mean-square fluctuations of protein atoms from their average position into the contributions from the internal degrees of freedom, which change the shape of the protein structure, and those from the external degrees of freedom, which generate rigid-body motions in the crystal. While at temperatures below 150 K the temperature dependence of the total mean-square fluctuations shows a small gradient similar to that predicted theoretically by normal-mode analysis, at temperatures above 150 K there is an apparent inflection in the temperature dependence with a higher gradient. The inflection in the temperature dependence at temperatures above 150 K occurs mostly in the external degrees of freedom. Possible causes for the dynamic transition are discussed with respect to the crystal packing and physicochemical properties of crystalline water.

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  1. Hypervalent nonbonded interactions of a divalent sulfur atom. Implications in protein architecture and the functions. Iwaoka M, Isozumi N. Molecules 17 7266-7283 (2012)

Articles - 1iwt mentioned but not cited (5)

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  1. Thermodynamic and dynamic factors involved in the stability of native protein structure in amorphous solids in relation to levels of hydration. Hill JJ, Shalaev EY, Zografi G. J Pharm Sci 94 1636-1667 (2005)
  2. Normal Mode Analysis as a Routine Part of a Structural Investigation. Bauer JA, Pavlović J, Bauerová-Hlinková V. Molecules 24 E3293 (2019)

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  7. Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged. Verma D, Jacobs DJ, Livesay DR. PLoS Comput Biol 8 e1002409 (2012)
  8. Exploring structurally conserved solvent sites in protein families. Bottoms CA, White TA, Tanner JJ. Proteins 64 404-421 (2006)
  9. Ensemble MD simulations restrained via crystallographic data: accurate structure leads to accurate dynamics. Xue Y, Skrynnikov NR. Protein Sci 23 488-507 (2014)
  10. Hydration effect on low-frequency protein dynamics observed in simulated neutron scattering spectra. Joti Y, Nakagawa H, Kataoka M, Kitao A. Biophys J 94 4435-4443 (2008)
  11. Effects of soman inhibition and of structural differences on cholinesterase molecular dynamics: a neutron scattering study. Gabel F, Weik M, Masson P, Renault F, Fournier D, Brochier L, Doctor BP, Saxena A, Silman I, Zaccai G. Biophys J 89 3303-3311 (2005)
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  13. The role of the confined water in the dynamic crossover of hydrated lysozyme powders. Kurzweil-Segev Y, Greenbaum Gutina A, Popov I, Golodnitsky D, Feldman Y. Phys Chem Chem Phys 18 10992-10999 (2016)
  14. Water in the hydrated protein powders: Dynamic and structure. Sasaki K, Popov I, Feldman Y. J Chem Phys 150 204504 (2019)
  15. Cryo-Cooling Effect on DHFR Crystal Studied by Replica-Exchange Molecular Dynamics Simulations. Nagai T, Tama F, Miyashita O. Biophys J 116 395-405 (2019)
  16. 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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