scholarly journals Secondary structures and some related combinatorial objects

2017 ◽  
Author(s):  
Ivica Martinjak ◽  
Ivana Zubac
Keyword(s):  
Secondary Structures ◽  
Combinatorial Objects

scholarly journals Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Michela Quadrini
Keyword(s):  
Hydrogen Bonding ◽  
Secondary Structure ◽  
Nucleotide Sequence ◽  
Thermus Thermophilus ◽  
Three Dimensional ◽  
Secondary Structures ◽  
Structural Effect ◽  
Biological Processes ◽  
Structural Pattern ◽  
Rna Molecules

Abstract RNA molecules play crucial roles in various biological processes. Their three-dimensional configurations determine the functions and, in turn, influences the interaction with other molecules. RNAs and their interaction structures, the so-called RNA–RNA interactions, can be abstracted in terms of secondary structures, i.e., a list of the nucleotide bases paired by hydrogen bonding within its nucleotide sequence. Each secondary structure, in turn, can be abstracted into cores and shadows. Both are determined by collapsing nucleotides and arcs properly. We formalize all of these abstractions as arc diagrams, whose arcs determine loops. A secondary structure, represented by an arc diagram, is pseudoknot-free if its arc diagram does not present any crossing among arcs otherwise, it is said pseudoknotted. In this study, we face the problem of identifying a given structural pattern into secondary structures or the associated cores or shadow of both RNAs and RNA–RNA interactions, characterized by arbitrary pseudoknots. These abstractions are mapped into a matrix, whose elements represent the relations among loops. Therefore, we face the problem of taking advantage of matrices and submatrices. The algorithms, implemented in Python, work in polynomial time. We test our approach on a set of 16S ribosomal RNAs with inhibitors of Thermus thermophilus, and we quantify the structural effect of the inhibitors.

scholarly journals Properties of Journal Bearing Materials That Determine Their Wear Resistance on the Example of Aluminum-Based Alloys

Materials ◽  
2021 ◽  
Vol 14 (3) ◽  
pp. 535
Author(s):  
Alexander Mironov ◽  
Iosif Gershman ◽  
Eugeniy Gershman ◽  
Pavel Podrabinnik ◽  
Ekaterina Kuznetsova ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Wear Resistance ◽  
Journal Bearing ◽  
Tribological Behavior ◽  
Secondary Structures ◽  
Magnesium Content ◽  
Wear Rates ◽  
Relative Extension ◽  
Bearing Materials ◽  
Antifriction Alloys

Potential relations of tribological characteristics of aluminum antifriction alloys with their compositions and mechanical properties were investigated. In this regard, the properties of eight aluminum alloys containing tin from 5.4% to 11% doped with lead, copper, silicon, zinc, magnesium, and titanium were studied. Mechanical properties such as hardness, strength, relative extension, and impact strength were analyzed. Within the tribological tests seizure load and wear of material were evaluated and secondary structures were studied afterwards. The absence of a definitive correlation between tribological behavior and mechanical properties was shown. It was determined that doping tin over 6% is excessive. The seizure load of the alloys increases with the magnesium content. Secondary structures of the alloys with higher wear rates contain one order less magnesium and tin.

scholarly journals Deciphering the Role of π-Interactions in Polyelectrolyte Complexes Using Rationally Designed Peptides

Polymers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 2074
Author(s):  
Sara Tabandeh ◽  
Cristina Elisabeth Lemus ◽  
Lorraine Leon
Keyword(s):  
Hydrogen Bonding ◽  
Phase Separation ◽  
Liquid Phase ◽  
Charge Density ◽  
Secondary Structures ◽  
Liquid Phase Separation ◽  
Polyelectrolyte Complexes ◽  
Π Interactions ◽  
Liquid Liquid Phase Separation

Electrostatic interactions, and specifically π-interactions play a significant role in the liquid-liquid phase separation of proteins and formation of membraneless organelles/or biological condensates. Sequence patterning of peptides allows creating protein-like structures and controlling the chemistry and interactions of the mimetic molecules. A library of oppositely charged polypeptides was designed and synthesized to investigate the role of π-interactions on phase separation and secondary structures of polyelectrolyte complexes. Phenylalanine was chosen as the π-containing residue and was used together with lysine or glutamic acid in the design of positively or negatively charged sequences. The effect of charge density and also the substitution of fluorine on the phenylalanine ring, known to disrupt π-interactions, were investigated. Characterization analysis using MALDI-TOF mass spectroscopy, H NMR, and circular dichroism (CD) confirmed the molecular structure and chiral pattern of peptide sequences. Despite an alternating sequence of chirality previously shown to promote liquid-liquid phase separation, complexes appeared as solid precipitates, suggesting strong interactions between the sequence pairs. The secondary structures of sequence pairs showed the formation of hydrogen-bonded structures with a β-sheet signal in FTIR spectroscopy. The presence of fluorine decreased hydrogen bonding due to its inhibitory effect on π-interactions. π-interactions resulted in enhanced stability of complexes against salt, and higher critical salt concentrations for complexes with more π-containing amino acids. Furthermore, UV-vis spectroscopy showed that sequences containing π-interactions and increased charge density encapsulated a small charged molecule with π-bonds with high efficiency. These findings highlight the interplay between ionic, hydrophobic, hydrogen bonding, and π-interactions in polyelectrolyte complex formation and enhance our understanding of phase separation phenomena in protein-like structures.

Changes in the secondary structures and zeta potential of soybean peptide and its calcium complexes in cell membrane medium

2021 ◽  
Author(s):  
He Liu ◽  
Ying Lv ◽  
Jingting Xu ◽  
Chen Chen ◽  
Shuntang Guo
Keyword(s):  
Enzymatic Hydrolysis ◽  
Cell Membrane ◽  
Zeta Potential ◽  
Calcium Binding ◽  
Binding Capacity ◽  
Secondary Structures ◽  
High Calcium ◽  
Calcium Complexes

In this study, soybean peptides (10-30kDa) with high calcium binding capacity were prepared by enzymatic hydrolysis and ultrafiltration. The results of cell experiments showed that the peptide could transport calcium...

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