Moving an atom by swapping places across a crystal lattice without vacancies

The mechanism of moving an atom through a crystal lattice without vacancies is considered. This situation can be observed when all sites of the lattice are occupied by atoms of the same type, or when some of them are occupied by isotopes of the same atoms. It is shown that in a three-dimensional crystal lattice constructed from identical atoms without vacancies, one-dimensional motion of the own atom along the lattice chain is possible. This movement is realized as a Frenkel-Kontorova soliton.

Graphene-Assisted Electrochemical Sensor for Detection of Pancreatic Cancer Markers

Pancreatic cancer is a highly lethal gastrointestinal malignancy. Most patients are already in the middle to advanced stages of pancreatic cancer at the time of diagnosis and cannot be treated completely. As a single-atom planar two-dimensional crystal, graphene’s unusual electronic structure, specific electronic properties and excellent electron transport capacity make it uniquely advantageous in the field of electrochemical sensing. In this mini-review, we summarize the potential application of graphene in pancreatic cancer detection. K-Ras gene, CEA and MicroRNA are important in the early diagnosis of pancreatic cancer.

Metastability relationship between two- and three-dimensional crystal structures: a case study of the Cu-based compounds

Some of the three-dimensional (3D) crystal structures are constructed by stacking two-dimensional (2D) layers. To study whether this geometric concept, i.e., using 2D layers as building blocks for 3D structures, can be applied to computational materials design, we theoretically investigate the dynamical stability of copper-based compounds CuX (a metallic element X) in the B$$_h$$ h and L1$$_1$$ 1 structures constructed from the buckled honeycomb (BHC) structure and in the B2 and L1$$_0$$ 0 structures constructed from the buckled square (BSQ) structure. We demonstrate that (i) if CuX in the BHC structure is dynamically stable, those in the B$$_h$$ h and L1$$_1$$ 1 structures are also stable. Using molecular dynamics simulations, we particularly show that CuAu in the B$$_h$$ h and L1$$_1$$ 1 structures withstand temperatures as high as 1000 K. Although the interrelationship of the metastability between the BSQ and the 3D structures (B2 and L1$$_0$$ 0 ) is not clear, we find that (ii) if CuX in the B2 (L1$$_0$$ 0 ) structure is dynamically stable, that in the L1$$_0$$ 0 (B2) is unstable. This is rationalized by the tetragonal Bain path calculations.

Structural and mechanistic insight into CRISPR-Cas9 inhibition by anti-CRISPR protein AcrIIC4

Phages, plasmids, and other mobile genetic elements express inhibitors of CRISPR-Cas immune systems, known as anti-CRISPR proteins, to protect themselves from targeted destruction. These anti-CRISPRs have been shown to function through very diverse mechanisms. In this work we investigate the activity of an anti-CRISPR isolated from a prophage in Haemophilus parainfluenzae that blocks CRISPR-Cas9 DNA cleavage activity. We determine the three-dimensional crystal struture of AcrIIC4 and show that it binds to the Cas9 Recognition Domain. This binding does not prevent the Cas9-anti-CRISPR complex from interacting with target DNA but does inhibit DNA cleavage. AcrIIC4 likely acts by blocking the conformational changes that allow the HNH and RuvC endonuclease domains to contact the DNA sites to be nicked.

Enzymatic and structural characterization of HAD5, an essential phosphomannomutase of malaria parasites

The malaria parasite Plasmodium falciparum is responsible for over 200 million infections and 400,000 deaths per year. At multiple stages during its complex life cycle, P. falciparum expresses several essential proteins tethered to its surface by glycosylphosphatidylinositol (GPI) anchors, which are critical for biological processes such as parasite egress and reinvasion of host red blood cells. Targeting this pathway therapeutically has the potential to broadly impact parasite development across several life stages. Here, we characterize an upstream component of GPI anchor biosynthesis, the putative phosphomannomutase (EC 5.4.2.8) of the parasites, HAD5 (PF3D7_1017400). We confirm the phosphomannomutase and phosphoglucomutase activity of purified recombinant HAD5. By regulating expression of HAD5 in transgenic parasites, we demonstrate that HAD5 is required for malaria parasite egress and erythrocyte reinvasion. Finally, we determine the three-dimensional crystal structure of HAD5 and identify a substrate analog that specifically inhibits HAD5, compared to orthologous human phosphomannomutases. These findings demonstrate that the GPI anchor biosynthesis pathway is exceptionally sensitive to inhibition, and that HAD5 has potential as a multi-stage antimalarial target.