scholarly journals De novo discovery of structural motifs in RNA 3D structures through clustering

2017 ◽  
Author(s):  
Ping Ge ◽  
Shahidul Islam ◽  
Cuncong Zhong ◽  
Shaojie Zhang
Keyword(s):  
De Novo ◽  
Three Dimensional ◽  
Structural Motif ◽  
Alignment Algorithm ◽  
Structural Motifs ◽  
3D Structures ◽  
Rna Structural Motifs ◽  
Downstream Analysis ◽  
Functional Components ◽  
Srp Rna

AbstractAs functional components in three-dimensional conformation of an RNA, the RNA structural motifs provide an easy way to associate the molecular architectures with their biological mechanisms. In the past years, many computational tools have been developed to search motif instances by using the existing knowledge of well-studied families. Recently, with the rapidly increasing number of resolved RNA 3D structures, there is an urgent need to discover novel motifs with the newly presented information. In this work, we classify all the loops in non-redundant RNA 3D structures to detect plausible RNA structural motif families by using a clustering pipeline. Compared with other clustering approaches, our method has two benefits: first, the underlying alignment algorithm is tolerant to the variations in 3D structures; second, sophisticated downstream analysis has been performed to ensure the clusters are valid and easily applied to further research. The final clustering results contain many interesting new variants of known motif families, such as GNAA tetraloop, kink-turn, sarcin-ricin, and T-loop. We have also discovered potential novel functional motifs conserved in ribosomal RNA, sgRNA, SRP RNA, riboswitch, and ribozyme.

scholarly journals De novo discovery of structural motifs in RNA 3D structures through clustering

2018 ◽  
Vol 46 (9) ◽  
pp. 4783-4793 ◽  
Author(s):  
Ping Ge ◽  
Shahidul Islam ◽  
Cuncong Zhong ◽  
Shaojie Zhang
Keyword(s):  
De Novo ◽  
Structural Motifs ◽  
3D Structures

scholarly journals Three-Dimensional Printing of Proteinaceous Structures by Aqueous Solvent-Directed Molecular Assembly

2019 ◽  
Author(s):  
Xuan Mu ◽  
Yu Wang ◽  
Chengchen Guo ◽  
Yamin Li ◽  
Shengjie Ling ◽  
...  
Keyword(s):  
3D Printing ◽  
Mechanical Performance ◽  
De Novo ◽  
Three Dimensional ◽  
Small Diameter ◽  
Molecular Assembly ◽  
Single Step ◽  
Ambient Conditions ◽  
Aqueous Solvent ◽  
Functional Components

<p>Hierarchical molecular assembly directed by cell-regulated aqueous solvent is a fundamental strategy for manufacturing various proteinaceous structures that are of intense interest for nanotechnology, sustainable manufacturing and regenerative medicine. However, to translate the natural strategy into advanced digital manufacturing like three-dimensional (3D) printing remains a tremendous technical and theoretical challenge. This work presents a 3D printing technique of a particular protein, silk fibroin, by rationally designing an<i> de novo </i>aqueous salt bath capable of directing the hierarchical assembly of the protein molecules. This technique, conducted under aqueous and ambient conditions, results in 3D proteinaceous architectures characterized by intrinsic biocompatibility/biodegradability and remarkable mechanical performance. The versatility of this method is shown in a diversity of 3D shapes and a range of functional components integrated into the 3D prints. Exceptional manufacturing capability and one promising application is exemplified by the single-step construction of perfusable microfluidic chips, also an analogy of small-diameter vascular grafts, which eliminates the use of supporting or sacrificial materials owing to optimized crosslinking dynamics and compartmentalized printing parameters. The 3D shaping capability of the protein material can benefit a multitude of biomedical devices, from drug delivery to surgical implants to tissue scaffolds.</p>

scholarly journals Three-Dimensional Printing of Proteinaceous Structures by Aqueous Solvent-Directed Molecular Assembly

2019 ◽  
Author(s):  
Xuan Mu ◽  
Yu Wang ◽  
Chengchen Guo ◽  
Yamin Li ◽  
Shengjie Ling ◽  
...  
Keyword(s):  
3D Printing ◽  
Mechanical Performance ◽  
De Novo ◽  
Three Dimensional ◽  
Small Diameter ◽  
Molecular Assembly ◽  
Single Step ◽  
Ambient Conditions ◽  
Aqueous Solvent ◽  
Functional Components

<p>Hierarchical molecular assembly directed by cell-regulated aqueous solvent is a fundamental strategy for manufacturing various proteinaceous structures that are of intense interest for nanotechnology, sustainable manufacturing and regenerative medicine. However, to translate the natural strategy into advanced digital manufacturing like three-dimensional (3D) printing remains a tremendous technical and theoretical challenge. This work presents a 3D printing technique of a particular protein, silk fibroin, by rationally designing an<i> de novo </i>aqueous salt bath capable of directing the hierarchical assembly of the protein molecules. This technique, conducted under aqueous and ambient conditions, results in 3D proteinaceous architectures characterized by intrinsic biocompatibility/biodegradability and remarkable mechanical performance. The versatility of this method is shown in a diversity of 3D shapes and a range of functional components integrated into the 3D prints. Exceptional manufacturing capability and one promising application is exemplified by the single-step construction of perfusable microfluidic chips, also an analogy of small-diameter vascular grafts, which eliminates the use of supporting or sacrificial materials owing to optimized crosslinking dynamics and compartmentalized printing parameters. The 3D shaping capability of the protein material can benefit a multitude of biomedical devices, from drug delivery to surgical implants to tissue scaffolds.</p>

scholarly journals Structure of Looped Regions in β-α- and α-β-Arches in Abcd-Units of Globular Proteins

2016 ◽  
Vol 11 (2) ◽  
pp. 159-169
Author(s):  
Е.В. Бражников ◽  
E.V. Brazhnikov
Keyword(s):  
Amino Acid ◽  
De Novo ◽  
Protein Structures ◽  
Three Dimensional ◽  
Structural Motif ◽  
Dimensional Structure ◽  
Amino Acid Residues ◽  
Homologous Proteins ◽  
Reverse Turn ◽  
Structure Of Proteins

Conformations of about 600 looped regions (loops) in β-α- and α-β-arches of a structural motif occurring in the abCd-unit of proteins were analyzed. On the whole, 258 abCd-units with a reverse turn of the polypeptide chain (236 PDB files) and 69 abCd-units with a direct turn (65 PDB files) were selected in non-homologous proteins. Four types of arches were studied: β-α- and α-β-ones at a direct turn of the chain; β-α- and α-β-ones at a reverse turn of the chain. For each type of arches, frequencies of loops occurrence of different lengths were determined and corresponding histograms were plotted. It was found that abCd-units with loops up to three amino acid residues long occur most frequently (57 %). In β-α-arches with a direct turn of the chain, loops consisting of two amino acid residues occur most often (44 %) and in 86% cases they have the βmαβαn - conformation. They have no Gly and Pro residues, and in position β there is an Asn residue. In such type of arches, the loops of one residue (βmεαn- or βmαLαn- conformation) contain the Gly residue most frequently. α-β-Arches with a direct turn of the chain have most commonly (18 %) loops of four amino acid residues. In this case, there is no predominant conformation of the loops. In β-α-arches with a reverse turn of the chain, most common are loops of seven amino acid residues (17%), and most part of them (88 %) have the βmαLββααββαn - conformation. α-β-Arches with a reverse turn of the chain contain most frequently (32%) loops of one amino acid residue (all Gly ones) with arch conformations αmεβn or αmαLβn. The above structural analysis of the abCd-unit has useful information for prediction of the three-dimensional structure of proteins and for molecular simulation of the de novo design of protein structures.

From Levinthal’s Paradox to the Effects of Cell Environmental Perturbation on Protein Folding

2020 ◽  
Vol 26 (42) ◽  
pp. 7537-7554 ◽  
Author(s):  
Juan Zeng ◽  
Zunnan Huang
Keyword(s):  
Protein Folding ◽  
Posttranslational Modifications ◽  
Three Dimensional ◽  
Rational Drug Design ◽  
Basic Knowledge ◽  
Sequence Evolution ◽  
3D Structures ◽  
Folding Mechanism ◽  
Cellular Environment ◽  
Environment Temperature

Background: The rapidly increasing number of known protein sequences calls for more efficient methods to predict the Three-Dimensional (3D) structures of proteins, thus providing basic knowledge for rational drug design. Understanding the folding mechanism of proteins is valuable for predicting their 3D structures and for designing proteins with new functions and medicinal applications. Levinthal’s paradox is that although the astronomical number of conformations possible even for proteins as small as 100 residues cannot be fully sampled, proteins in nature normally fold into the native state within timescales ranging from microseconds to hours. These conflicting results reveal that there are factors in organisms that can assist in protein folding. Methods: In this paper, we selected a crowded cell-like environment and temperature, and the top three Posttranslational Modifications (PTMs) as examples to show that Levinthal’s paradox does not reflect the folding mechanism of proteins. We then revealed the effects of these factors on protein folding. Results: The results summarized in this review indicate that a crowded cell-like environment, temperature, and the top three PTMs reshape the Free Energy Landscapes (FELs) of proteins, thereby regulating the folding process. The balance between entropy and enthalpy is the key to understanding the effect of the crowded cell-like environment and PTMs on protein folding. In addition, the stability/flexibility of proteins is regulated by temperature. Conclusion: This paper concludes that the cellular environment could directly intervene in protein folding. The long-term interactions of the cellular environment and sequence evolution may enable proteins to fold efficiently. Therefore, to correctly understand the folding mechanism of proteins, the effect of the cellular environment on protein folding should be considered.

scholarly journals De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1342
Author(s):  
Shaghayegh Mehravi ◽  
Gholam Ali Ranjbar ◽  
Ghader Mirzaghaderi ◽  
Anita Alice Severn-Ellis ◽  
Armin Scheben ◽  
...  
Keyword(s):  
De Novo ◽  
Genetic Relationships ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Genomic Resources ◽  
High Quality Snps ◽  
The Family ◽  
Double Digestion ◽  
Flanking Sequences ◽  
Downstream Analysis

The species of Pimpinella, one of the largest genera of the family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used to identify single nucleotide polymorphisms (SNPs) in eight Pimpinella species from Iran. After double-digestion with the enzymes HpyCH4IV and HinfI, a total of 334,702,966 paired-end reads were de novo assembled into 1,270,791 loci with an average of 28.8 reads per locus. After stringent filtering, 2440 high-quality SNPs were identified for downstream analysis. Analysis of genetic relationships and population structure, based on these retained SNPs, indicated the presence of three major groups. Gene ontology and pathway analysis were determined by using comparison SNP-associated flanking sequences with a public non-redundant database. Due to the lack of genomic resources in this genus, our present study is the first report to provide high-quality SNPs in Pimpinella based on a de novo analysis pipeline using ddRAD-seq. This data will enhance the molecular knowledge of the genus Pimpinella and will provide an important source of information for breeders and the research community to enhance breeding programs and support the management of Pimpinella genomic resources.

scholarly journals Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment

2011 ◽  
Vol 40 (3) ◽  
pp. 1307-1317 ◽  
Author(s):  
Cuncong Zhong ◽  
Shaojie Zhang
Keyword(s):  
Structural Alignment ◽  
Ribosomal Rnas ◽  
Structural Motifs ◽  
Rna Structural Motifs

128 The “physiological” behaviour of DNA/RNA structural motifs in gas phase

2015 ◽  
Vol 33 (sup1) ◽  
pp. 82-83 ◽  
Author(s):  
Massimiliano Porrini ◽  
Valentina D’Atri ◽  
Josephine Abi-Ghanem ◽  
Frédéric Rosu ◽  
Valérie Gabelica
Keyword(s):  
Gas Phase ◽  
Structural Motifs ◽  
Rna Structural Motifs
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