Dataset Information

Extent and relevance of stacking disorder in "ice I(c)".

ABSTRACT: A solid water phase commonly known as "cubic ice" or "ice I(c)" is frequently encountered in various transitions between the solid, liquid, and gaseous phases of the water substance. It may form, e.g., by water freezing or vapor deposition in the Earth's atmosphere or in extraterrestrial environments, and plays a central role in various cryopreservation techniques; its formation is observed over a wide temperature range from about 120 K up to the melting point of ice. There was multiple and compelling evidence in the past that this phase is not truly cubic but composed of disordered cubic and hexagonal stacking sequences. The complexity of the stacking disorder, however, appears to have been largely overlooked in most of the literature. By analyzing neutron diffraction data with our stacking-disorder model, we show that correlations between next-nearest layers are clearly developed, leading to marked deviations from a simple random stacking in almost all investigated cases. We follow the evolution of the stacking disorder as a function of time and temperature at conditions relevant to atmospheric processes; a continuous transformation toward normal hexagonal ice is observed. We establish a quantitative link between the crystallite size established by diffraction and electron microscopic images of the material; the crystallite size evolves from several nanometers into the micrometer range with progressive annealing. The crystallites are isometric with markedly rough surfaces parallel to the stacking direction, which has implications for atmospheric sciences.

SUBMITTER: Kuhs WF

PROVIDER: S-EPMC3535660 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature

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Extent and relevance of stacking disorder in "ice I(c)".

Kuhs Werner F WF Sippel Christian C Falenty Andrzej A Hansen Thomas C TC

Proceedings of the National Academy of Sciences of the United States of America 20121211 52

A solid water phase commonly known as "cubic ice" or "ice I(c)" is frequently encountered in various transitions between the solid, liquid, and gaseous phases of the water substance. It may form, e.g., by water freezing or vapor deposition in the Earth's atmosphere or in extraterrestrial environments, and plays a central role in various cryopreservation techniques; its formation is observed over a wide temperature range from about 120 K up to the melting point of ice. There was multiple and comp ...[more]

PMID: 23236184

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Project description:Most homodimeric proteins have symmetric structure. Although symmetry is known to confer structural and functional advantage, asymmetric organization is also observed. Using a non-redundant dataset of 223 high-resolution crystal structures of biologically relevant homodimers, we address questions on the prevalence and significance of asymmetry. We used two measures to quantify global and interface asymmetry, and assess the correlation of several molecular and structural parameters with asymmetry. We have identified rare cases (11/223) of biologically relevant homodimers with pronounced global asymmetry. Asymmetry serves as a means to bring about 2:1 binding between the homodimer and another molecule; it also enables cellular signalling arising from asymmetric macromolecular ligands such as DNA. Analysis of these cases reveals two possible mechanisms by which possible infinite array formation is prevented. In case of homodimers associating via non-topologically equivalent surfaces in their tertiary structures, ligand-dependent mechanisms are used. For stable dimers binding via large surfaces, ligand-dependent structural change regulates polymerisation/depolymerisation; for unstable dimers binding via smaller surfaces that are not evolutionarily well conserved, dimerisation occurs only in the presence of the ligand. In case of homodimers associating via interaction surfaces with parts of the surfaces topologically equivalent in the tertiary structures, steric hindrance serves as the preventive mechanism of infinite array. We also find that homodimers exhibiting grossly symmetric organization rarely exhibit either perfect local symmetry or high local asymmetry. Binding of small ligands at the interface does not cause any significant variation in interface asymmetry. However, identification of biologically relevant interface asymmetry in grossly symmetric homodimers is confounded by the presence of similar small magnitude changes caused due to artefacts of crystallisation. Our study provides new insights regarding accommodation of asymmetry in homodimers.

Dataset Information

Extent and relevance of stacking disorder in "ice I(c)".

Publications

Extent and relevance of stacking disorder in "ice I(c)".

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