Structural similarity of loops in protein families: toward the understanding of protein evolution

BACKGROUND: Protein evolution and protein classification are usually inferred by comparing protein cores in their conserved aligned parts. Structurally aligned protein regions are separated by less conserved loop regions, where sequence and structure locally deviate from each other and do not superimpose well. RESULTS: Our results indicate that even longer protein loops can not be viewed as "random coils" and for the majority of protein families in our test set there exists a linear correlation between the measures of sequence similarity and loop structural similarity. Results suggest that distance matrices derived from the loop (dis)similarity measure may produce in some cases more reliable cluster trees compared to the distance matrices based on the conventional measures of sequence and structural (dis)similarity. CONCLUSIONS: We show that by considering "dissimilar" loop regions rather than only conserved core regions it is possible to improve our understanding of protein evolution

Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners

Recent advances in high-throughput experimental methods for the identification of protein interactions have resulted in a large amount of diverse data that are somewhat incomplete and contradictory. As valuable as they are, such experimental approaches studying protein interactomes have certain limitations that can be complemented by the computational methods for predicting protein interactions. In this review we describe different approaches to predict protein interaction partners as well as highlight recent achievements in the prediction of specific domains mediating protein-protein interactions. We discuss the applicability of computational methods to different types of prediction problems and point out limitations common to all of them

The effect of thermal cycling and stress-assistant ageing two-way shape memory effect in [123]-oriented Co40Ni33Al27 single crystals

The effect of thermal cycling through an interval of B2-L10 martensitic transformation (MT) under action of external stress and tensile stress-assistant ageing on the two-way shape memory effect in [bar 123]-oriented Co40Ni33Al27 (at.%) single crystals are investigated. For the first time it is experimentally established that tensile stress-assistant 100 MPa ageing at 573 K for 1 h along [bar 123]-direction of Co40Ni33Al27 single crystals creates the necessary conditions for two-way shape memory effect (TWSME) with the reversible strain up to epsilon=2.4 (±0.3)% at cooling/heating. The TWSME in quenched [bar 123]-oriented Co40Ni33Al27 single crystals can be induced by thermal cycling through an interval of B2-L10 MT under action of constant external stress 50 MPa with the reversible strain less than 1%

Regulatory Justification of the Fundamental Concepts of Ergonomics in Wheeled Agricultural Machinery

A single-seated man-machine system (MMS) is formed when a person starts controlling a technical device or unit, while undergoing production processes. Production tasks for MMS are developed by the senior system and contain output work parameters, which are determined by the properties of the human operator and the technical subsystem. The purpose of the paper is to demonstrate the process of ensuring the working conditions of a single-seated MMS, the difficulties that arise upon performing tasks, including the content of regulatory acts, which are the technical foundation for the formation of the quality of operation of a single-seated MMS. Study results indicate external and internal restrictions that influence the efficient work of the human operator and are not provided for in regulatory standards, including ways to solve existing restrictions

Long-term trends in evolution of indels in protein sequences

BACKGROUND: In this paper we describe an analysis of the size evolution of both protein domains and their indels, as inferred by changing sizes of whole domains or individual unaligned regions or "spacers". We studied relatively early evolutionary events and focused on protein domains which are conserved among various taxonomy groups. RESULTS: We found that more than one third of all domains have a statistically significant tendency to increase/decrease in size in evolution as judged from the overall domain size distribution as well as from the size distribution of individual spacers. Moreover, the fraction of domains and individual spacers increasing in size is almost twofold larger than the fraction decreasing in size. CONCLUSION: We showed that the tolerance to insertion and deletion events depends on the domain's taxonomy span. Eukaryotic domains are depleted in insertions compared to the overall test set, namely, the number of spacers increasing in size is about the same as the number of spacers decreasing in size. On the other hand, ancient domain families show some bias towards insertions or spacers which grow in size in evolution. Domains from several Gene Ontology categories also demonstrate certain tendencies for insertion or deletion events as inferred from the analysis of spacer sizes

Investigation of the two-way shape memory effect in [001]-oriented Co35Ni35Al30 single crystals

For the first time, a study of the two-way shape memory effect (the TWSME) for the quenched and aged at 673 K for 0.5 h [001]-oriented Co35Ni35Al30 single crystals in compression was carried out. In the quenched CoNiAl crystals, the TWSME with a reversible strain of (-3.1 ± 0.3) % was induced by training procedure in the superelasticity temperature range. The physical reason of the TWSME is the creation of internal stress fields due to the formation of dislocations next to γ-phase particles, and an interface between the B2-matrix and the γ-phase in the quenched crystals. It was experimentally shown that aging at 673 K for 0.5 h under a compressive stress of 100 MPa along the [110] direction creates the conditions necessary for observing the TWSME, without additional training with a reversible strain of (+2.2 ± 0.3) %. The conditions for observing the TWSME are determined by the action of the internal stress fields of 25 MPa created by the oriented arrangement of the dispersed particles in the stress-assisted aged crystals. The TWSME is not observed in the stress-free aged crystals with non-oriented precipitation of particles, both before and after training

Stress-induced martensitic transformation in high-strength [236]-oriented Ni51Ti36.5Hf12.5 single crystals

The effects of heat treatment on the stress-induced B2-B19' martensitic transformations in the Ni51.0Ti36.5Hf12.5 single crystals oriented along [236] direction are studied. It is shown that in the annealed at 1323K for 4 h crystals, the temperature range of superelasticity increase almost twofold from 75K up to 135K as compared to the as-grown single crystal contained disperse particles of H-phase. The [236]-oriented Ni51.0Ti36.5Hf12.5 single crystals are characterized with high levels of applied compressive stress up to 1700 MPa in the as-grown state and 1900 MPa in annealed crystals for the completely reversible stress- induced B2-B19' martensitic transformation with reversible strain up to |εSE| =1.4%