scholarly journals Lasso Proteins—Unifying Cysteine Knots and Miniproteins

Polymers ◽  
2021 ◽  
Vol 13 (22) ◽  
pp. 3988
Author(s):  
Bartosz Ambroży Greń ◽  
Pawel Dabrowski-Tumanski ◽  
Wanda Niemyska ◽  
Joanna Ida Sulkowska
Keyword(s):  
Disulfide Bridges ◽  
Antimicrobial Proteins ◽  
Considerable Fraction ◽  
Lasso Peptides ◽  
Topological Features ◽  
Biological Compounds ◽  
The Stability

Complex lasso proteins are a recently identified class of biological compounds that are present in considerable fraction of proteins with disulfide bridges. In this work, we look at complex lasso proteins as a generalization of well-known cysteine knots and miniproteins (lasso peptides). In particular, we show that complex lasso proteins with the same crucial topological features—cysteine knots and lasso peptides—are antimicrobial proteins, which suggests that they act as a molecular plug. Based on an analysis of the stability of the lasso piercing residue, we also introduce a method to determine which lasso motif is potentially functional. Using this method, we show that the lasso motif in antimicrobial proteins, as well in that in cytokines, is functionally relevant. We also study the evolution of lasso motifs, their conservation, and the usefulness of the lasso fingerprint, which extracts all topologically non-triviality concerning covalent loops. The work is completed by the presentation of extensive statistics on complex lasso proteins to analyze, in particular, the strange propensity for “negative” piercings. We also identify 21 previously unknown complex lasso proteins with an ester and a thioester bridge.

Applications of random graphs

2017 ◽  
Author(s):  
A.C.C. Coolen ◽  
A. Annibale ◽  
E.S. Roberts
Keyword(s):  
Social Networks ◽  
Random Graphs ◽  
Interaction Network ◽  
Power Grids ◽  
Protein Protein Interaction ◽  
Topological Features ◽  
First Case ◽  
The Stability ◽  
Protein Protein Interaction Network

This chapter reviews graph generation techniques in the context of applications. The first case study is power grids, where proposed strategies to prevent blackouts have been tested on tailored random graphs. The second case study is in social networks. Applications of random graphs to social networks are extremely wide ranging – the particular aspect looked at here is modelling the spread of disease on a social network – and how a particular construction based on projecting from a bipartite graph successfully captures some of the clustering observed in real social networks. The third case study is on null models of food webs, discussing the specific constraints relevant to this application, and the topological features which may contribute to the stability of an ecosystem. The final case study is taken from molecular biology, discussing the importance of unbiased graph sampling when considering if motifs are over-represented in a protein–protein interaction network.

scholarly journals Deciphering functional redundancy in the human microbiome

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Liang Tian ◽  
Xu-Wen Wang ◽  
Ang-Kun Wu ◽  
Yuhang Fan ◽  
Jonathan Friedman ◽  
...  
Keyword(s):  
Fecal Microbiota Transplantation ◽  
Human Microbiome ◽  
Functional Redundancy ◽  
Fecal Microbiota ◽  
Taxonomic Composition ◽  
Topological Features ◽  
Its Gene ◽  
The Stability ◽  
Stability And Resilience ◽  
Analyze Data

AbstractAlthough the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved — implying an ecological property known as functional redundancy. Such functional redundancy has been hypothesized to underlie the stability and resilience of the human microbiome, but this hypothesis has never been quantitatively tested. The origin of functional redundancy is still elusive. Here, we investigate the basis for functional redundancy in the human microbiome by analyzing its genomic content network — a bipartite graph that links microbes to the genes in their genomes. We find that this network exhibits several topological features that favor high functional redundancy. Furthermore, we develop a simple genome evolution model to generate genomic content network, finding that moderate selection pressure and high horizontal gene transfer rate are necessary to generate genomic content networks with key topological features that favor high functional redundancy. Finally, we analyze data from two published studies of fecal microbiota transplantation (FMT), finding that high functional redundancy of the recipient’s pre-FMT microbiota raises barriers to donor microbiota engraftment. This work elucidates the potential ecological and evolutionary processes that create and maintain functional redundancy in the human microbiome and contribute to its resilience.

Chemical synthesis of disulfide surrogate peptides by using beta-carbon dimethyl modified diaminodiacids

2021 ◽  
Author(s):  
jibin cui ◽  
xiaoxiong wei ◽  
Rui Zhao ◽  
Huixia Zhu ◽  
Jing Shi ◽  
...  
Keyword(s):  
Chemical Synthesis ◽  
Reducing Agents ◽  
Disulfide Bridges ◽  
Promising Strategy ◽  
The Stability

The replacement of disulfide bridges with metabolically stable isosteres is a promising strategy to improve the stability of disulfide-rich polypeptides towards reducing agents and isomerases. Diaminodiacid-based strategy is one of...

scholarly journals A theoretical study of the stability of disulfide bridges in various β-sheet structures of protein segment models

2014 ◽  
Vol 593 ◽  
pp. 48-54 ◽  
Author(s):  
Natalie J. Galant ◽  
Heeyeon Cheryl Song ◽  
Imre Jákli ◽  
Bela Viskolcz ◽  
Imre G. Csizmadia ◽  
...  
Keyword(s):  
Theoretical Study ◽  
Disulfide Bridges ◽  
Protein Segment ◽  
The Stability ◽  
Β Sheet

On the competition between centrifugal and shear instability in spiral Poiseuille flow

2002 ◽  
Vol 455 ◽  
pp. 129-148 ◽  
Author(s):  
A. MESEGUER ◽  
F. MARQUES
Keyword(s):  
Poiseuille Flow ◽  
Critical Values ◽  
Shear Instability ◽  
Critical Surface ◽  
Neutral Stability ◽  
Topological Features ◽  
Centrifugal Instability ◽  
Axial Pressure Gradient ◽  
Wide Range ◽  
The Stability

A numerical exploration of the linear stability of a fluid confined between two coaxial cylinders rotating independently and with an imposed axial pressure gradient (spiral Poiseuille flow) is presented. The investigation covers a wide range of experimental parameters, being focused on co-rotation situations. The exploration is made for a wide gap case in order to compare the numerical results with previous experimental data available. The competition between shear and centrifugal instability mechanisms affects the topological features of the neutral stability curves and the critical surface is observed to exhibit zeroth-order discontinuities. These curves may exhibit disconnected branches which lower the critical values of instability considerably. The same phenomenon has been reported in similar fluid flows where shear and centrifugal instability mechanisms compete. The stability analysis of the rigid-body rotation case is studied in detail and the asymptotic critical values are found to be qualitatively similar to those obtained in rotating Hagen-Poiseuille and spiral Couette flows. The results are in good agreement with the previous experimental explorations.

A persistent homological analysis of network data flow malfunctions

2017 ◽  
Vol 5 (6) ◽  
pp. 884-892 ◽  
Author(s):  
Nicholas A Scoville ◽  
Karthik Yegnesh
Keyword(s):  
Data Flow ◽  
Persistent Homology ◽  
Topological Data Analysis ◽  
Network Data ◽  
Packet Delivery ◽  
Topological Features ◽  
Algorithmic Construction ◽  
The Stability ◽  
Novel Applications ◽  
Persistence Diagrams

Abstract Persistent homology has recently emerged as a powerful technique in topological data analysis for analysing the emergence and disappearance of topological features throughout a filtered space, shown via persistence diagrams. In this article, we develop an application of ideas from the theory of persistent homology and persistence diagrams to the study of data flow malfunctions in networks with a certain hierarchical structure. In particular, we formulate an algorithmic construction of persistence diagrams that parameterize network data flow errors, thus enabling novel applications of statistical methods that are traditionally used to assess the stability of persistence diagrams corresponding to homological data to the study of data flow malfunctions. We conclude with an application to network packet delivery systems.

Charge and energy redistribution in sulfonamides undergoing conformational changes. Hybridization as a controlling influence over conformer stability

1996 ◽  
Vol 74 (6) ◽  
pp. 1271-1282 ◽  
Author(s):  
Curt M. Breneman ◽  
Lawrence W. Weber
Keyword(s):  
Electron Density ◽  
Conformational Changes ◽  
Energy Flow ◽  
Energy Redistribution ◽  
Topological Features ◽  
Rotational Barriers ◽  
Density Analysis ◽  
The Stability ◽  
Electron Density Analysis ◽  
Internal Rotational Barriers

The redistribution of charge and electronic kinetic energy was studied during rotation about the S—N bonds of sulfonamide and fluorosulfonamide. The rotational potentials and electronic topological features of both compounds were evaluated at the HF/6-3 1G* level of theory and their electron densities partitioned into atomic contributions using FASTINT, an updated version of the PROAIM program. The results indicate that the stability of each rotamer is strongly dependent upon the hybridization of the sulfonamide nitrogen. The hybridization of the nitrogen was determined by examination of the positions and magnitudes of the electrostatic and Laplacian minima in the nonbonded region of the sulfonamide nitrogen atom. Independent assessments of hybridization were made using nitrogen pyramidalization altitudes. The rotational barriers in these compounds were found to arise mainly from energetic penalties resulting from adding electrons to already electron-rich sulfonyl oxygens while removing electron density from other more electronegative atoms. The fluorine-substituted analogue provided an example in which the sulfur and oxygen atoms were much less electron rich, causing an enhancement of the nitrogen rehybridization effects. The extent of covalent bonding between pertinent pairs of atoms in sulfonamide and fluorosulfonamide was assessed throughout the rotational pathway using the BONDER program. In contrast with much existing dogma, all of these findings were consistent with the same general model of charge and energy flow that has been shown to determine the internal rotational barriers in amides. Key words: sulfonamide, electron density analysis, rotational barrier, hybridization, atoms-in-molecules calculations.

Charge density in crystalline citrinin from X-ray diffraction at 19 K

1996 ◽  
Vol 74 (6) ◽  
pp. 1145-1161 ◽  
Author(s):  
Pietro Roversi ◽  
Felicita Merati ◽  
Riccardo Destro ◽  
Mario Barzaghi
Keyword(s):  
Electron Density ◽  
Chemical Reactivity ◽  
Topological Analysis ◽  
X Ray Diffraction ◽  
X Ray ◽  
Bond Path ◽  
Topological Features ◽  
Path Lengths ◽  
The Stability ◽  
Experimental Electron Density

For the fungal metabolite citrinin, C13H14O5, the total experimental electron distribution ρ(r) and its Laplacian [Formula: see text] have been obtained from an extensive set (36 564 measurements) of single-crystal X-ray diffracted intensities at a temperature of 19 ± 2 K. Relevant steps in data collection and processing are reported. The resulting 7698 independent intensity data have been analysed with a multipole (pseudoatoms) formalism. The topological properties of ρ(r) have been determined according to the quantum theory of atoms in molecules. CC and CO bond path lengths have been obtained by numerical integration; their values are found to be well correlated with those of the electron density at the bond critical points. Topological features have been used to characterize the extension of the conjugated system of the molecule, and to confirm the stability of its rings, particularly the two formed by intramolecular H bonds. Maps of [Formula: see text] are presented, showing details in the valence charge distribution and providing a very sensitive tool for analysing dependence of the density on the model adopted to interpret X-ray data. The known chemical reactivity of the molecule towards nucleophiles at a Csp2 atom is confirmed by the shape of the molecular reactive surface (the zero envelope of [Formula: see text]). Key words: experimental electron density, low-temperature X-ray diffraction, topological analysis, Laplacian of ρ.

scholarly journals Electrocomposite Developed with Chitosan and Ionic Liquids Using Screen-Printed Carbon Electrodes Useful to Detect Rutin in Tropical Fruits

Sensors ◽  
2018 ◽  
Vol 18 (9) ◽  
pp. 2934
Author(s):  
Lili Muñoz ◽  
Verónica Arancibia ◽  
Olimpo García-Beltrán ◽  
Edgar Nagles ◽  
John Hurtado
Keyword(s):  
Modified Electrode ◽  
Electrochemical Impedance ◽  
Limit Of Detection ◽  
Stripping Voltammetry ◽  
Carbon Electrodes ◽  
Tropical Fruits ◽  
Relative Standard ◽  
Biological Compounds ◽  
Constant Potential ◽  
The Stability

This work reports the development of a composite of the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]BP4) and chitosan (CS) described in previous reports through a new method using cyclic voltammetry with 10 cycles at a scan rate of 50.0 mV s−1. This method is different from usual methods such as casting, deposition, and constant potential, and it allows the development of an electroactive surface toward the oxidation of rutin by stripping voltammetry applied to the detection in tropical fruits such as orange, lemon, and agraz (Vaccinium meridionale Swartz), with results similar to those reported in previous studies. In addition, the surface was characterized by electrochemical impedance spectroscopy (EIS), scanning electron microscopy (SEM), and Raman spectroscopy. The limit of detection was 0.07 µmol L−1 and the relative standard deviation (RSD) of 10 measurements using the same modified electrode was 0.86%. Moreover, the stability of the sensor was studied for six days using the same modified electrode, where the variation of the signal using a known concentration of rutin (RT) was found to be less than 5.0%. The method was validated using a urine chemistry control spiked with known amounts of RT and possible interference was studied using ten substances including organic and biological compounds, metal ions, and dyes. The results obtained in this study demonstrated that this electrodeveloped composite was sensitive, selective, and stable.

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