Secondary structures of synthetic polypeptide polymers

2018 ◽  
Vol 9 (13) ◽  
pp. 1517-1529 ◽  
Author(s):  
Colin Bonduelle
Keyword(s):  
Secondary Structure ◽  
Self Assembly ◽  
Synthetic Peptide ◽  
Polymeric Materials ◽  
Secondary Structures ◽  
Review Article ◽  
Synthetic Polypeptide

Synthetic peptide-based polymers can fold into different secondary structures in the same way as do proteins. This review article presents how tuning the polypeptide secondary structure could be a key step to modulate various properties in advanced polymeric materials (size, rigidity, self-assembly,etc.).

Preparation of BSA Nanoparticles by Desolvation Technique Using Acetone as Desolvating Agent

2012 ◽  
Vol 5 (1) ◽  
pp. 1643-1647
Author(s):  
Krishna Sailaja A ◽  
Amareshwar P
Keyword(s):  
Aqueous Solution ◽  
Standard Deviation ◽  
Process Parameters ◽  
Self Assembly ◽  
Size Control ◽  
Polymeric Materials ◽  
Preparation Condition ◽  
Assembly Process ◽  
Average Size

In order to see the functionality and toxicity of nanoparticles in various food and drug applications, it is important to establish procedures to prepare nanoparticles of a controlled size. Desolvation is a thermodynamically driven self-assembly process for polymeric materials. In this study, we prepared BSA nanoparticles using the desolvation technique using acetone as desolvating agent. Acetone was added intermittently into 1% BSA solution at different pH under stirring at 700 rpm. Amount of acetone added, intermittent timeline of acetone addition, and pH of solution were considered as process parameters to be optimized. The effect of the process parameters on size of the nanoparticles was studied. The results indicated that the size control of BSA nanoparticles was achieved by adding acetone intermittently. The standard deviation of average size of BSA nanoparticles at each preparation condition was minimized by adding acetone intermittently. The intermittent addition in polymeric aqueous solution can be useful for size control for food or drug applications.  

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 Recent Developments in Lignin- and Tannin-Based Non-Isocyanate Polyurethane Resins for Wood Adhesives—A Review

2021 ◽  
Vol 11 (9) ◽  
pp. 4242
Author(s):  
Manggar Arum Aristri ◽  
Muhammad Adly Rahandi Lubis ◽  
Sumit Manohar Yadav ◽  
Petar Antov ◽  
Antonios N. Papadopoulos ◽  
...  
Keyword(s):  
Automotive Industry ◽  
Polymeric Materials ◽  
Review Article ◽  
Future Perspectives ◽  
Wood Adhesives ◽  
Adhesion Properties ◽  
Lighting Industry ◽  
Renewable Natural Resources ◽  
Recent Developments ◽  
Strong Adhesion

This review article aims to summarize the potential of using renewable natural resources, such as lignin and tannin, in the preparation of NIPUs for wood adhesives. Polyurethanes (PUs) are extremely versatile polymeric materials, which have been widely used in numerous applications, e.g., packaging, footwear, construction, the automotive industry, the lighting industry, insulation panels, bedding, furniture, metallurgy, sealants, coatings, foams, and wood adhesives. The isocyanate-based PUs exhibit strong adhesion properties, excellent flexibility, and durability, but they lack renewability. Therefore, this study focused on the development of non-isocyanate polyurethane lignin and tannin resins for wood adhesives. PUs are commercially synthesized using polyols and polyisocyanates. Isocyanates are toxic, costly, and not renewable; thus, a search of suitable alternatives in the synthesis of polyurethane resins is needed. The reaction with diamine compounds could result in NIPUs based on lignin and tannin. The research on bio-based components for PU synthesis confirmed that they have good characteristics as an alternative for the petroleum-based adhesives. The advantages of improved strength, low curing temperatures, shorter pressing times, and isocyanate-free properties were demonstrated by lignin- and tannin-based NIPUs. The elimination of isocyanate, associated with environmental and human health hazards, NIPU synthesis, and its properties and applications, including wood adhesives, are reported comprehensively in this paper. The future perspectives of NIPUs’ production and application were also outlined.

scholarly journals Orderly aligned manganese-based nanotube arrays with controllable secondary structures

RSC Advances ◽  
2021 ◽  
Vol 11 (14) ◽  
pp. 8277-8281
Author(s):  
Xiaoyan Huang ◽  
Zhuoxi Liang ◽  
Jiqiu Wen ◽  
Yong Liu ◽  
Ayoub Taallah ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Secondary Structures ◽  
Nanotube Arrays ◽  
Negative Growth

The collaboration of nanochannel confinement and dynamic negative growth creates orderly aligned manganese-based nanotube arrays decorated with nanopores as a secondary structure.

Anion-Directed Self-Assembly of Coordination Polymer into Tunable Secondary Structure

2004 ◽  
Vol 126 (22) ◽  
pp. 7009-7014 ◽  
Author(s):  
Ho-Joong Kim ◽  
Wang-Cheol Zin ◽  
Myongsoo Lee
Keyword(s):  
Secondary Structure ◽  
Coordination Polymer ◽  
Self Assembly

Use of synchrotron-based FTIR microspectroscopy to determine protein secondary structures of raw and heat-treated brown and golden flaxseeds: A novel approach

2005 ◽  
Vol 85 (4) ◽  
pp. 437-448 ◽  
Author(s):  
P. Yu ◽  
J. J. McKinnon ◽  
H. W. Soita ◽  
C. R. Christensen ◽  
D. A. Christensen
Keyword(s):  
Secondary Structure ◽  
Matrix Protein ◽  
Protein Secondary Structure ◽  
Secondary Structures ◽  
Heat Processing ◽  
Lower Percentage ◽  
Protein Secondary Structures ◽  
Novel Approach ◽  
Α Helix ◽  
Β Sheet

The objectives of the study were to use synchrotron Fourier transform infrared microspectroscopy (S-FTIR) as a novel approach to: (1) reveal ultra-structural chemical features of protein secondary structures of flaxseed tissues affected by variety (golden and brown) and heat processing (raw and roasted), and (2) quantify protein secondary structures using Gaussian and Lorentzian methods of multi-component peak modeling. By using multi-component peak modeling at protein amide I region of 1700–1620 cm-1, the results showed that the golden flaxseed contained relatively higher percentage of α-helix (47.1 vs. 36.9%), lower percentage of β-sheet (37.2 vs. 46.3%) and higher (P < 0.05) ratio of α-helix to β-sheet than the brown flaxseed (1.3 vs. 0.8). The roasting reduced (P < 0.05) percentage of α-helix (from 47.1 to 36.1%), increased percentage of β-sheet (from 37.2 to 49.8%) and reduced α-helix to β-sheet ratio (1.3 to 0.7) of the golden flaxseed tissues. However, the roasting did not affect percentage and ratio of α-helix and β-sheet in the brown flaxseed tissue. No significant differences were found in quantification of protein secondary structures between Gaussian and Lorentzian methods. These results demonstrate the potential of highly spatially resolved S-FTIR to localize relatively pure protein in the tissue and reveal protein secondary structures at a cellular level. The results indicated relative differences in protein secondary structures between flaxseed varieties and differences in sensitivities of protein secondary structure to the heat processing. Further study is needed to understand the relationship between protein secondary structure and protein digestion and utilization of flaxseed and to investigate whether the changes in the relative amounts of protein secondary structures are primarily responsible for differences in protein availability. Key words: Synchrotron, FTIR microspectrosopy, flaxseeds, intrinsic structural matrix, protein secondary structures, protein nutritive value

scholarly journals Amount of RNA secondary structure required to induce an alternative splice.

1987 ◽  
Vol 7 (9) ◽  
pp. 3194-3198 ◽  
Author(s):  
D Solnick ◽  
S I Lee
Keyword(s):  
Alternative Splicing ◽  
Secondary Structure ◽  
Alternative Splice ◽  
Rna Secondary Structure ◽  
Secondary Structures ◽  
Splice Sites ◽  
Perfect Complementarity ◽  
Set Up

We set up an alternative splicing system in vitro in which the relative amounts of two spliced RNAs, one containing and the other lacking a particular exon, were directly proportional to the length of an inverted repeat inserted into the flanking introns. We then used the system to measure the effect of intramolecular complementarity on alternative splicing in vivo. We found that an alternative splice was induced in vivo only when the introns contained more than approximately 50 nucleotides of perfect complementarity, that is, only when the secondary structure was much more stable than most if not all possible secondary structures in natural mRNA precursors. We showed further that intron insertions containing long complements to splice sites and a branch point inhibited splicing in vitro but not in vivo. These results raise the possibility that in cells most pre-mRNA secondary structures either are not maintained long enough to influence splicing choices, or never form at all.

scholarly journals Self-assembly of alkyl chains of fatty acids in papermaking systems: A review of related pitch issues, hydrophobic sizing, and pH effects

BioResources ◽  
2020 ◽  
Vol 15 (2) ◽  
pp. 4591-4635
Author(s):  
Martin A. Hubbe ◽  
Douglas S. McLean ◽  
Karen R. Stack ◽  
Xiaomin Lu ◽  
Anders Strand ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Self Assembly ◽  
Review Article ◽  
Ph Effects ◽  
Monolayer Films ◽  
Alkyl Chains ◽  
Ph Values ◽  
Self Association ◽  
Long Chain

This review article considers the role of fatty acids and the mutual association of their long-chain (e.g. C18) alkyl and alkenyl groups in some important aspects of papermaking. In particular, published findings suggest that interactions involving fatty acids present as condensed monolayer films can play a controlling role in pitch deposition problems. Self-association among the tails of fatty acids and their soaps also helps to explain some puzzling aspects of hydrophobic sizing of paper. When fatty acids and their soaps are present as monolayers in papermaking systems, the pH values associated with their dissociation, i.e. their pKa values, tend to be strongly shifted. Mutual association also appears to favor non-equilibrium multilayer structures that are tacky and insoluble, possibly serving as a nucleus for deposition of wood extractives, such, as resins and triglyceride fats, in pulp and paper systems.

scholarly journals RNA secondary structure prediction using deep learning with thermodynamic integration

2020 ◽  
Author(s):  
Kengo Sato ◽  
Manato Akiyama ◽  
Yasubumi Sakakibara
Keyword(s):  
Deep Learning ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Rna Secondary Structure ◽  
Secondary Structure Prediction ◽  
Secondary Structures ◽  
Thermodynamic Integration ◽  
Rna Secondary Structure Prediction ◽  
Rna Secondary Structures ◽  
Non Coding Rnas

RNA secondary structure prediction is one of the key technologies for revealing the essential roles of functional non-coding RNAs. Although machine learning-based rich-parametrized models have achieved extremely high performance in terms of prediction accuracy, the risk of overfitting for such models has been reported. In this work, we propose a new algorithm for predicting RNA secondary structures that uses deep learning with thermodynamic integration, thereby enabling robust predictions. Similar to our previous work, the folding scores, which are computed by a deep neural network, are integrated with traditional thermodynamic parameters to enable robust predictions. We also propose thermodynamic regularization for training our model without overfitting it to the training data. Our algorithm (MXfold2) achieved the most robust and accurate predictions in computational experiments designed for newly discovered non-coding RNAs, with significant 2–10 % improvements over our previous algorithm (MXfold) and standard algorithms for predicting RNA secondary structures in terms of F-value.

Sign in / Sign up

Export Citation Format

Share Document