Comparative analysis of rigidity across protein families

We present a comparative study in which 'pebble game' rigidity analysis is applied to multiple protein crystal structures, for each of six different protein families. We find that the main-chain rigidity of a protein structure at a given hydrogen bond energy cutoff is quite sensitive to small structural variations, and conclude that the hydrogen bond constraints in rigidity analysis should be chosen so as to form and test specific hypotheses about the rigidity of a particular protein. Our comparative approach highlights two different characteristic patterns ('sudden' or 'gradual') for protein rigidity loss as constraints are removed, in line with recent results on the rigidity transitions of glassy networks

"Quiet Food Sovereignty” as Food Sovereignty without Movements? Understanding Food Sovereignty in Post-Socialist Russia

What does food sovereignty look like in settings where rural social movements are weak or non-existent, such as in countries with post-socialist, semi-authoritarian regimes? Focusing on Russia, we present a divergent form of food sovereignty. Building on the concept of ‘quiet sustainability’, we present a dispersed, muted, but clearly bottom-up variant we term ‘quiet food sovereignty’. In the latter, the role of the very productive smallholdings is downplayed by the state and partly by the smallholders themselves. Those smallholdings are not seen as an alternative to industrial agriculture, but subsidiary to it (although superior in terms of sociality and healthy, environmentally friendly produce). As such, ‘quiet food sovereignty’ deviates from the overt struggle frequently associated with food sovereignty. We discuss the prospects of the ‘quiet food sovereignty’ to develop into a full food sovereignty movement, and stress the importance of studying implicit everyday forms of food sovereignty

Hybrid Orthorhombic Carbon Flakes Intercalated with Bimetallic Au-Ag Nanoclusters: Influence of Synthesis Parameters on Optical Properties

Until recently, planar carbonaceous structures such as graphene did not show any birefringence under normal incidence. In contrast, a recently reported novel orthorhombic carbonaceous structure with metal nanoparticle inclusions does show intrinsic birefringence, outperforming other natural orthorhombic crystalline materials. These flake-like structures self-assemble during a laser-induced growth process. In this article, we explore the potential of this novel material and the design freedom during production. We study in particular the dependence of the optical and geometrical properties of these hybrid carbon-metal flakes on the fabrication parameters. The influence of the laser irradiation time, concentration of the supramolecular complex in the solution, and an external electric field applied during the growth process are investigated. In all cases, the self-assembled metamaterial exhibits a strong linear birefringence in the visible spectral range, while the wavelength-dependent attenuation was found to hinge on the concentration of the supramolecular complex in the solution. By varying the fabrication parameters one can steer the shape and size of the flakes. This study provides a route towards fabrication of novel hybrid carbon-metal flakes with tailored optical and geometrical properties

Ways to Transfer Oil and Oil Products in Heating Conditions and Methods for Their Enhancement

© Published under licence by IOP Publishing Ltd. This paper discusses the methods of oil transportation through pipelines. Particular attention is paid to the processes of complex rheological behavior of high-paraffin crude oils. Optimal methods applicable for transportation of heavy oil with the help of intensifiers are revealed

Theoretical Studies of the Magnetic Anisotropy of Cobalt Films Separated by a Copper Plate

In this work, we studied the energy and magnetic properties of the Co/Cu/Co system. Calculations have shown that for the (100) and (111) faces, direction of magnetic moments parallel to the film plane is energetically favorable. For the (110) face, a weak perpendicular magnetoanisotropy was obtainedИсследование выполнено при финансовой поддержке Минобрнауки РФ (соглашение 0741-2020-0002)

Canonical and noncanonical sites determine NPT2A binding selectivity to NHERF1 PDZ1

Na+/H+ Exchanger Regulatory Factor-1 (NHERF1) is a scaffolding protein containing 2 PDZ domains that coordinates the assembly and trafficking of transmembrane receptors and ion channels. Most target proteins harboring a C-terminus recognition motif bind more-or-less equivalently to the either PDZ domain, which contain identical core-binding motifs. However some substrates such as the type II sodium-dependent phosphate co-transporter (NPT2A), uniquely bind only one PDZ domain. We sought to define the structural determinants responsible for the specificity of interaction between NHERF1 PDZ domains and NPT2A. By performing all-atom/explicit-solvent molecular dynamics (MD) simulations in combination with biological mutagenesis, fluorescent polarization (FP) binding assays, and isothermal titration calorimetry (ITC), we found that in addition to canonical interactions of residues at 0 and -2 positions, Arg at the -1 position of NPT2A plays a critical role in association with Glu43 and His27 of PDZ1 that are absent in PDZ2. Experimentally introduced mutation in PDZ1 (Glu43Asp and His27Asn) decreased binding to NPT2A. Conversely, introduction of Asp183Glu and Asn167His mutations in PDZ2 promoted the formation of favorable interactions yielding micromolar KDs. The results describe novel determinants within both the PDZ domain and outside the canonical PDZ-recognition motif that are responsible for discrimination of NPT2A between two PDZ domains. The results challenge general paradigms for PDZ recognition and suggest new targets for drug development

STUDY OF THE Fe1/3TiS2 INTERCALATION SYSTEM USING EVOLUTIONARY ALGORITHMS AND FIRST-PRINCIPLE CALCULATIONS

The FexTiS2 intercalation system with atom Fe concentration x=1/3 was studied using first-principle calculations and evolutionary algorithms. Calculations were performed for a single unit cell for various magnetic and nonmagnetic configurations with changes in the shape and volume of the unit cell.Исследования проведены с использованием ресурсов Центра коллективного пользования научным оборудованием «Центр обработки и хранения научных данных ДВО РАН», финансируемого Минобрнауки России по соглашению № 075-15-2021-663