Comparative analysis of the secondary structure of non-histone chromatin proteins HMGB1 and HMGB2

Abstract The non-histone chromosomal proteins HMGB1 and HMGB2 were found in the cells of all studied eukaryotes. They are involved in cell decision and many biological processes such as replication, transcription, repair, etc. In this work, the secondary structure of the HMGB1 and HMGB2 proteins was studied by the circular dichroism method. It was shown that, despite the high homology between them, the secondary structure of these proteins is different. The revealed structural features, most likely, should influence their functions in the cell nucleus, in particular, the interaction with DNA and other proteins.

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Characterization of Tamm-Horsfall Urinary Glycoprotein

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010007254x ◽

1973 ◽

Vol 31 ◽

pp. 420-421

Author(s):

John P. Robinson ◽

J. David Puett

Keyword(s):

Electron Microscopy ◽

Circular Dichroism ◽

Secondary Structure ◽

Quaternary Structure ◽

Normal Adult ◽

Morphological Properties ◽

Adult Males ◽

Circular Dichroïsm ◽

Urinary Glycoprotein

Much work has been reported on the chemical, physical and morphological properties of urinary Tamm-Horsfall glycoprotein (THG). Although it was once reported that cystic fibrotic (CF) individuals had a defective THG, more recent data indicate that THG and CF-THG are similar if not identical.No studies on the conformational aspects have been reported on this glycoprotein using circular dichroism (CD). We examined the secondary structure of THG and derivatives under various conditions and have correlated these results with quaternary structure using electron microscopy.THG was prepared from normal adult males and CF-THG from a 16-year old CF female by the method of Tamm and Horsfall. CF female by the method of Tamm and Horsfall.

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Effect of Temperature and pH on the Secondary Structure and Denaturation Process of Jumbo Squid Hepatopancreas Cathepsin D.

Protein and Peptide Letters ◽

10.2174/0929866526666190405124353 ◽

2019 ◽

Vol 26 (7) ◽

pp. 532-541 ◽

Cited By ~ 1

Author(s):

Cadena-Cadena Francisco ◽

Cárdenas-López José Luis ◽

Ezquerra-Brauer Josafat Marina ◽

Cinco-Moroyoqui Francisco Javier ◽

López-Zavala Alonso Alexis ◽

...

Keyword(s):

Circular Dichroism ◽

Secondary Structure ◽

Cathepsin D ◽

Thermal Denaturation ◽

Protein Denaturation ◽

Marine Organisms ◽

Effect Of Temperature ◽

Jumbo Squid ◽

Α Helix ◽

Circular Dichroïsm

Background: Cathepsin D is a lysosomal enzyme that is found in all organisms acting in protein turnover, in humans it is present in some types of carcinomas, and it has a high activity in Parkinson's disease and a low activity in Alzheimer disease. In marine organisms, most of the research has been limited to corroborate the presence of this enzyme. It is known that cathepsin D of some marine organisms has a low thermostability and that it has the ability to have activity at very acidic pH. Cathepsin D of the Jumbo squid (Dosidicus gigas) hepatopancreas was purified and partially characterized. The secondary structure of these enzymes is highly conserved so the role of temperature and pH in the secondary structure and in protein denaturation is of great importance in the study of enzymes. The secondary structure of cathepsin D from jumbo squid hepatopancreas was determined by means of circular dichroism spectroscopy. Objective: In this article, our purpose was to determine the secondary structure of the enzyme and how it is affected by subjecting it to different temperature and pH conditions. Methods: Circular dichroism technique was used to measure the modifications of the secondary structure of cathepsin D when subjected to different treatments. The methodology consisted in dissecting the hepatopancreas of squid and freeze drying it. Then a crude extract was prepared by mixing 1: 1 hepatopancreas with assay buffer, the purification was in two steps; the first step consisted of using an ultrafiltration membrane with a molecular cut of 50 kDa, and the second step, a pepstatin agarose resin was used to purification the enzyme. Once the enzyme was purified, the purity was corroborated with SDS PAGE electrophoresis, isoelectric point and zymogram. Circular dichroism is carried out by placing the sample with a concentration of 0.125 mg / mL in a 3 mL quartz cell. The results were obtained in mdeg (millidegrees) and transformed to mean ellipticity per residue, using 111 g/mol molecular weight/residue as average. Secondary-structure estimation from the far-UV CD spectra was calculated using K2D Dichroweb software. Results: It was found that α helix decreases at temperatures above 50 °C and above pH 4. Heating the enzyme above 70°C maintains a low percentage of α helix and increases β sheet. Far-UV CD measurements of cathepsin D showed irreversible thermal denaturation. The process was strongly dependent on the heating rate, accompanied by a process of oligomerization of the protein that appears when the sample is heated, and maintained a certain time at this temperature. An amount typically between 3 and 4% α helix of their secondary structure remains unchanged. It is consistent with an unfolding process kinetically controlled due to the presence of an irreversible reaction. The secondary structure depends on pH, and a pH above 4 causes α helix structures to be modified. Conclusion: In conclusion, cathepsin D from jumbo squid hepatopancreas showed retaining up to 4% α helix at 80°C. The thermal denaturation of cathepsin D at pH 3.5 is under kinetic control and follows an irreversible model.

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A Systematic Review on Popularity, Application and Characteristics of Protein Secondary Structure Prediction Tools

Current Drug Discovery Technologies ◽

10.2174/1570163815666180227162157 ◽

2019 ◽

Vol 16 (2) ◽

pp. 159-172 ◽

Cited By ~ 3

Author(s):

Elaheh Kashani-Amin ◽

Ozra Tabatabaei-Malazy ◽

Amirhossein Sakhteman ◽

Bagher Larijani ◽

Azadeh Ebrahim-Habibi

Keyword(s):

Systematic Review ◽

Secondary Structure ◽

Structure Prediction ◽

Web Of Science ◽

Secondary Structure Prediction ◽

Structural Information ◽

Protein Secondary Structure ◽

Structural Features ◽

Prediction Tools ◽

Insight Into

Background: Prediction of proteins’ secondary structure is one of the major steps in the generation of homology models. These models provide structural information which is used to design suitable ligands for potential medicinal targets. However, selecting a proper tool between multiple Secondary Structure Prediction (SSP) options is challenging. The current study is an insight into currently favored methods and tools, within various contexts. Objective: A systematic review was performed for a comprehensive access to recent (2013-2016) studies which used or recommended protein SSP tools. Methods: Three databases, Web of Science, PubMed and Scopus were systematically searched and 99 out of the 209 studies were finally found eligible to extract data. Results: Four categories of applications for 59 retrieved SSP tools were: (I) prediction of structural features of a given sequence, (II) evaluation of a method, (III) providing input for a new SSP method and (IV) integrating an SSP tool as a component for a program. PSIPRED was found to be the most popular tool in all four categories. JPred and tools utilizing PHD (Profile network from HeiDelberg) method occupied second and third places of popularity in categories I and II. JPred was only found in the two first categories, while PHD was present in three fields. Conclusion: This study provides a comprehensive insight into the recent usage of SSP tools which could be helpful for selecting a proper tool.

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

Journal of Integrative Bioinformatics ◽

10.1515/jib-2020-0039 ◽

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.

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Identifying Conserved Generic Aspergillus spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics

Journal of Fungi ◽

10.3390/jof7040270 ◽

2021 ◽

Vol 7 (4) ◽

pp. 270

Author(s):

Tim J. H. Baltussen ◽

Jordy P. M. Coolen ◽

Paul E. Verweij ◽

Jan Dijksterhuis ◽

Willem J. G. Melchers

Keyword(s):

Comparative Analysis ◽

Expression Patterns ◽

Biological Processes ◽

Polarized Growth ◽

Black Module ◽

Cross Platform ◽

Gene Modules ◽

Opportunistic Human Pathogen ◽

Dependent Transport ◽

Blue Module

Aspergillus spp. is an opportunistic human pathogen that may cause a spectrum of pulmonary diseases. In order to establish infection, inhaled conidia must germinate, whereby they break dormancy, start to swell, and initiate a highly polarized growth process. To identify critical biological processes during germination, we performed a cross-platform, cross-species comparative analysis of germinating A. fumigatus and A. niger conidia using transcriptional data from published RNA-Seq and Affymetrix studies. A consensus co-expression network analysis identified four gene modules associated with stages of germination. These modules showed numerous shared biological processes between A. niger and A. fumigatus during conidial germination. Specifically, the turquoise module was enriched with secondary metabolism, the black module was highly enriched with protein synthesis, the darkgreen module was enriched with protein fate, and the blue module was highly enriched with polarized growth. More specifically, enriched functional categories identified in the blue module were vesicle formation, vesicular transport, tubulin dependent transport, actin-dependent transport, exocytosis, and endocytosis. Genes important for these biological processes showed similar expression patterns in A. fumigatus and A. niger, therefore, they could be potential antifungal targets. Through cross-platform, cross-species comparative analysis, we were able to identify biologically meaningful modules shared by A. fumigatus and A. niger, which underscores the potential of this approach.

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Investigation by Synchrotron Radiation Circular Dichroism of the Secondary Structure Evolution of Pepsin under Oxidative Environment

Foods ◽

10.3390/foods10050998 ◽

2021 ◽

Vol 10 (5) ◽

pp. 998

Author(s):

Laetitia Théron ◽

Aline Bonifacie ◽

Jérémy Delabre ◽

Thierry Sayd ◽

Laurent Aubry ◽

...

Keyword(s):

Circular Dichroism ◽

Synchrotron Radiation ◽

Secondary Structure ◽

Proteolytic Activity ◽

Digestive Enzyme ◽

Structure Evolution ◽

Food Protein ◽

Maldi Tof ◽

Kinetics Of ◽

Circular Dichroïsm

Food processing affects the structure and chemical state of proteins. In particular, protein oxidation occurs and may impair protein properties. These chemical reactions initiated during processing can develop during digestion. Indeed, the physicochemical conditions of the stomach (oxygen pressure, low pH) favor oxidation. In that respect, digestive proteases may be affected as well. Yet, very little is known about the link between endogenous oxidation of digestive enzymes, their potential denaturation, and, therefore, food protein digestibility. Thus, the objective of this study is to understand how oxidative chemical processes will impact the pepsin secondary structure and its hydrolytic activity. The folding and unfolding kinetics of pepsin under oxidative conditions was determined using Synchrotron Radiation Circular Dichroism. SRCD gave us the possibility to monitor the rapid kinetics of protein folding and unfolding in real-time, giving highly resolved spectral data. The proteolytic activity of control and oxidized pepsin was investigated by MALDI-TOF mass spectrometry on a meat protein model, the creatine kinase. MALDI-TOF MS allowed a rapid evaluation of the proteolytic activity through peptide fingerprint. This study opens up new perspectives by shifting the digestion paradigm taking into account the gastric digestive enzyme and its substrate.

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