Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method

Proteins are vital components of living systems, serving as building blocks, molecular machines, enzymes, receptors, ion channels, sensors, and transporters. Protein-protein interactions (PPIs) are a key part of their function. There are more than 645,000 reported disease-relevant PPIs in the human interactome, but drugs have been developed for only 2% of these targets. The advances in PPI-focused drug discovery are highly dependent on the availability of structural data and accurate computational tools for analysis of this data. Quantum mechanical approaches are often too expensive computationally, but the fragment molecular orbital (FMO) method offers an excellent solution that combines accuracy, speed and the ability to reveal key interactions that would otherwise be hard to detect. FMO provides essential information for PPI drug discovery, namely, identification of key interactions formed between residues of two proteins, including their strength (in kcal/mol) and their chemical nature (electrostatic or hydrophobic). In this chapter, we have demonstrated how three different FMO-based approaches (pair interaction energy analysis (PIE analysis), subsystem analysis (SA) and analysis of protein residue networks (PRNs)) have been applied to study PPI in three protein-protein complexes

Terrestrial trophic dynamics in the Canadian Arctic

The Swedish Tundra Northwest Expedition of 1999 visited 17 sites throughout the Canadian Arctic. At 12 sites that were intensively sampled we estimated the standing crop of plants and the densities of herbivores and predators with an array of trapping, visual surveys, and faecal-pellet transects. We developed a trophic-balance model using ECOPATH to integrate these observations and determine the fate of primary and secondary production in these tundra ecosystems, which spanned an 8-fold range of standing crop of plants. We estimated that about 13% of net primary production was consumed by herbivores, while over 70% of small-herbivore production was estimated to flow to predators. Only 9% of large-herbivore production was consumed by predators. Organization of Canadian Arctic ecosystems appears to be more top-down than bottom-up. Net primary production does not seem to be herbivore-limited at any site. This is the first attempt to integrate trophic dynamics over the entire Canadian Arctic

The boundary integral theory for slow and rapid curved solid/liquid interfaces propagating into binary systems

The boundary integral method for propagating solid/liquid interfaces is detailed with allowance for the thermo-solutal Stefan-type models. Two types of mass transfer mechanisms corresponding to the local equilibrium (parabolic-type equation) and local non-equilibrium (hyperbolic-type equation) solidification conditions are considered. A unified integro-differential equation for the curved interface is derived. This equation contains the steady-state conditions of solidification as a special case. The boundary integral analysis demonstrates how to derive the quasi-stationary Ivantsov and Horvay–Cahn solutions that, respectively, define the paraboloidal and elliptical crystal shapes. In the limit of highest Péclet numbers, these quasi-stationary solutions describe the shape of the area around the dendritic tip in the form of a smooth sphere in the isotropic case and a deformed sphere along the directions of anisotropy strength in the anisotropic case. A thermo-solutal selection criterion of the quasi-stationary growth mode of dendrites which includes arbitrary Péclet numbers is obtained. To demonstrate the selection of patterns, computational modelling of the quasi-stationary growth of crystals in a binary mixture is carried out. © 2018 The Author(s) Published by the Royal Society. All rights reserved.Russian Science Foundation, RSF: 16-11-1009550WM1541Data accessibility. This article has no additional data. Authors’ contributions. All authors contributed equally to the present review paper. Competing interests. The authors declare that they have no competing interests. Funding. This work was supported by the Russian Science Foundation (grant no. 16-11-10095) and the German Space Center Space Management under contract no. 50WM1541