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Novel Unexpected Reconstructions of (100) and (111) Surfaces of NaCl: Theoretical Prediction.

ABSTRACT: We have predicted stable reconstructions of the (100) and (111) surfaces of NaCl using the global optimization algorithm USPEX. Several new reconstructions, together with the previously reported ones, are found. For the cleaved bare (100) surface, pure Na and pure Cl are the only stable surface phases. Our study of the (111) surface shows that a newly predicted Na3Cl-(1?×?1) reconstruction is thermodynamically stable in a wide range of chlorine chemical potentials. It has a sawtooth-like profile where each facet reproduces the (100) surface of rock-salt NaCl, hinting on the preferred growth of the (100) surface. We used Bader charge analysis to explain the preferable formation of this sawtooth-like Na3Cl-(1?×?1) reconstruction of the (111) surface of NaCl. We find that at a very high chemical potential of Na, the polar (and normally absent) (111) surface becomes part of the equilibrium crystal morphology. At both very high and very low chemical potentials of Cl, we predict a large decrease of surface energy and fracture toughness (the Rehbinder effect).

SUBMITTER: Kvashnin AG

PROVIDER: S-EPMC6776646 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Novel Unexpected Reconstructions of (100) and (111) Surfaces of NaCl: Theoretical Prediction.

Kvashnin Alexander G AG Kvashnin Dmitry G DG Oganov Artem R AR

Scientific reports 20191003 1

We have predicted stable reconstructions of the (100) and (111) surfaces of NaCl using the global optimization algorithm USPEX. Several new reconstructions, together with the previously reported ones, are found. For the cleaved bare (100) surface, pure Na and pure Cl are the only stable surface phases. Our study of the (111) surface shows that a newly predicted Na<sub>3</sub>Cl-(1 × 1) reconstruction is thermodynamically stable in a wide range of chlorine chemical potentials. It has a sawtooth-l ...[more]

PMID: 31582761

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Project description:Abasic (AP) sites in DNA arise through both endogenous and exogenous mechanisms. Since AP sites can prevent replication and transcription, the cell contains systems for their identification and repair. AP endonuclease (APEX1) cleaves the phosphodiester backbone 5' to the AP site. The cleavage, a key step in the base excision repair pathway, is followed by nucleotide insertion and removal of the downstream deoxyribose moiety, performed most often by DNA polymerase beta (pol-beta). While yeast two-hybrid studies and electrophoretic mobility shift assays provide evidence for interaction of APEX1 and pol-beta, the specifics remain obscure. We describe a theoretical study designed to predict detailed interacting surfaces between APEX1 and pol-beta based on published co-crystal structures of each enzyme bound to DNA. Several potentially interacting complexes were identified by sliding the protein molecules along DNA: two with pol-beta located downstream of APEX1 (3' to the damaged site) and three with pol-beta located upstream of APEX1 (5' to the damaged site). Molecular dynamics (MD) simulations, ensuring geometrical complementarity of interfaces, enabled us to predict interacting residues and calculate binding energies, which in two cases were sufficient (approximately -10.0 kcal/mol) to form a stable complex and in one case a weakly interacting complex. Analysis of interface behavior during MD simulation and visual inspection of interfaces allowed us to conclude that complexes with pol-beta at the 3'-side of APEX1 are those most likely to occur in vivo. Additional multiple sequence analyses of APEX1 and pol-beta in related organisms identified a set of correlated mutations of specific residues at the predicted interfaces. Based on these results, we propose that pol-beta in the open or closed conformation interacts and makes a stable interface with APEX1 bound to a cleaved abasic site on the 3' side. The method described here can be used for analysis in any DNA-metabolizing pathway where weak interactions are the principal mode of cross-talk among participants and co-crystal structures of the individual components are available.

Dataset Information

Novel Unexpected Reconstructions of (100) and (111) Surfaces of NaCl: Theoretical Prediction.

Publications

Novel Unexpected Reconstructions of (100) and (111) Surfaces of NaCl: Theoretical Prediction.

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