scholarly journals Modalities of Protein Denaturation and Nature of Denaturants

2021 ◽  
Vol 69 (2) ◽  
Author(s):  
Vaishali V. Acharya ◽  
Pratima Chaudhuri
Keyword(s):  
Tertiary Structure ◽  
Protein Denaturation ◽  
Alpha Helix ◽  
Beta Sheets ◽  
Physiological Conditions ◽  
Unfolded Protein ◽  
Irreversible Denaturation ◽  
Folded Proteins ◽  
Chemical Conditions ◽  
Weak Chemical

Denaturation of protein is a biological phenomenon in which a protein loses its native shape due to the breaking or disruption of weak chemical bonds and interactions which makes the protein biologically inactive. It is the process where properly folded proteins formed under physiological conditions is transformed to an unfolded protein under non-physiological conditions. The process of denaturation of proteins can occur under different physiological and chemical conditions. Denaturation can be reversible or irreversible. Denaturation mostly takes places when the protein is subjected under external elements like inorganic solutes, organic solvents, acids or bases, and by heat or irradiations. The denaturing agents or denaturants widely used in protein folding or unfolding experiments are urea and guanidinium chloride (GdmCl). In denaturation, the alpha-helix structure and beta sheets structure of the native protein are disrupted and unfolds it into any random shape. We can also say that denaturation occurs due to the disruption of bonding interactions which are responsible for secondary structure and the tertiary structure of the proteins.

scholarly journals In Silico Structural, Functional, and Phylogenetic Analysis of Cytochrome (CYPD) Protein Family

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Hafiz Ishfaq Ahmad ◽  
Gulnaz Afzal ◽  
Adil Jamal ◽  
Shumaila Kiran ◽  
Musarrat Abbas Khan ◽  
...  
Keyword(s):  
Tertiary Structure ◽  
Alpha Helix ◽  
Beta Sheets ◽  
Random Coil ◽  
Functional Study ◽  
Motif Analysis ◽  
Alpha Helices ◽  
Random Coils ◽  
Metabolic Reactions ◽  
Exogenous Compounds

Cytochrome (CYP) enzymes catalyze the metabolic reactions of endogenous and exogenous compounds. The superfamily of enzymes is found across many organisms, regardless of type, except for plants. Information was gathered about CYP2D enzymes through protein sequences of humans and other organisms. The secondary structure was predicted using the SOPMA. The structural and functional study of human CYP2D was conducted using ProtParam, SOPMA, Predotar 1.03, SignalP, TMHMM 2.0, and ExPASy. Most animals shared five central motifs according to motif analysis results. The tertiary structure of human CYP2D, as well as other animal species, was predicted by Phyre2. Human CYP2D proteins are heavily conserved across organisms, according to the findings. This indicates that they are descended from a single ancestor. They calculate the ratio of alpha-helices to extended strands to beta sheets to random coils. Most of the enzymes are alpha-helix, but small amounts of the random coil were also found. The data were obtained to provide us with a better understanding of mammalian proteins’ functions and evolutionary relationships.

Insights into the Structural Features, Conformational Stability and Functional Activity of the Olneya tesota PF2 Lectin

2020 ◽  
Vol 27 ◽  
Author(s):  
Edgar Acedo-Espinoza ◽  
Irlanda Lagarda-Diaz ◽  
Rosina Cabrera ◽  
Ana M. Guzman-Partida ◽  
Amir Maldonado-Arce ◽  
...  
Keyword(s):  
Tertiary Structure ◽  
Proteolytic Enzymes ◽  
Conformational Stability ◽  
Structural Features ◽  
Beta Sheets ◽  
Hemagglutinating Activity ◽  
Effect Of Temperature ◽  
Hydrodynamic Diameter ◽  
Bioinformatic Tools ◽  
Structural Levels

Background: The O. tesota lectin PF2 is a tetrameric protein with subunits of 33 kDa that recognizes only complex carbohydrates, resistant to proteolytic enzymes and has insecticidal activity against Phaseolus beans pest. Objective: To explore PF2 lectin features at different protein structural levels and to evaluate the effect of temperature and pH on its functionality and conformational stability. Methods: PF2 lectin was purified by affinity chromatography. Its primary structure was resolved by mass spectrometry and analyzed by bioinformatic tools, including its tertiary structure homology modeling. The effect of temperature and pH on its conformational traits and stability was addressed by dynamic light scattering, circular dichroism, and intrinsic fluorescence. The hemagglutinating activity was evaluated using a suspension of peripheral blood erythrocytes. Results: The proposed PF2 folding comprises a high content of beta sheets. At pH 7 and 25 °C, the hydrodynamic diameter (Dh) was found to be 12.3 nm which corresponds to the oligomeric native state of PF2 lectin. Dh increased under the other evaluated pH and temperature conditions, suggesting protein aggregation. At basic pH, PF2 exhibited low conformational stability. The native PF2 (pH 7) retained its full hemagglutinating activity up to 45 °C and exhibited one transition state with a melting temperature of 76.8 °C. Conclusion: PF2 showed distinctive characteristics found in legume lectins. The pH influences the functionality and conformational stability of the protein. PF2 lectin displayed a relatively narrow thermostability to the loss of secondary structure and hemagglutinating activity.

In Silico Study of Secondary Structure of Hemoglobin Protein

2021 ◽  
pp. 6245-6249
Author(s):  
Roma Chandra
Keyword(s):  
Secondary Structure ◽  
Protein Sequence ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Protein Secondary Structure ◽  
Alpha Helix ◽  
Prediction Methods ◽  
Protein Secondary Structures

Protein structure prediction is one of the important goals in the area of bioinformatics and biotechnology. Prediction methods include structure prediction of both secondary and tertiary structures of protein. Protein secondary structure prediction infers knowledge related to presence of helixes, sheets and coils in a polypeptide chain whereas protein tertiary structure prediction infers knowledge related to three dimensional structures of proteins. Protein secondary structures represent the possible motifs or regular expressions represented as patterns that are predicted from primary protein sequence in the form of alpha helix, betastr and and coils. The secondary structure prediction is useful as it infers information related to the structure and function of unknown protein sequence. There are various secondary structure prediction methods used to predict about helixes, sheets and coils. Based on these methods there are various prediction tools under study. This study includes prediction of hemoglobin using various tools. The results produced inferred knowledge with reference to percentage of amino acids participating to produce helices, sheets and coils. PHD and DSC produced the best of the results out of all the tools used.

scholarly journals Glutton: a tool for generating structural ensembles of partly disordered proteins from chemical shifts

2018 ◽  
Vol 35 (7) ◽  
pp. 1234-1236
Author(s):  
Yi He ◽  
Suhani Nagpal ◽  
Mourad Sadqi ◽  
Eva de Alba ◽  
Victor Muñoz
Keyword(s):  
Structure Prediction ◽  
Chemical Shifts ◽  
Disordered Proteins ◽  
Supplementary Information ◽  
Dihedral Angles ◽  
Physiological Conditions ◽  
Accessible Information ◽  
Structural Ensembles ◽  
Folded Proteins ◽  
Partially Disordered Proteins

Abstract Motivation Many proteins are partially disordered in physiological conditions and only fold, fully or partially, upon binding. Their structural analysis is challenging because the accessible information, typically chemical shifts (CS) from nuclear magnetic resonance experiments, are averages over broad ensembles of conformations. We aim to develop a database for the analysis of such data in terms of conformational distributions of the protein backbone rather than of individual high-resolution structures. Results Glutton is the largest available database linking CS and protein 3D structures (5270 entries organized in three levels) and is searchable via a python script. It generates statistical distributions of ϕ−ψ dihedral angles based on CS or vice versa. Such ϕ−ψ distributions are used to calculate structural ensembles of partially disordered proteins from their CS. For folded proteins, such ensembles are excellent starting points for further refinement with additional experimental restraints (structure determination) or computational methods (structure prediction). Availability and implementation Glutton is freely available at https://github.com/YeeHo/Glutton. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Control of the Unfolded Protein Response in Health and Disease

2017 ◽  
Vol 22 (7) ◽  
pp. 787-800 ◽  
Author(s):  
Dimitrios Doultsinos ◽  
Tony Avril ◽  
Stéphanie Lhomond ◽  
Nicolas Dejeans ◽  
Philippe Guédat ◽  
...  
Keyword(s):  
Unfolded Protein Response ◽  
Clinical Trial Design ◽  
Screening Tools ◽  
Unfolded Protein ◽  
Disease States ◽  
Health And Disease ◽  
Folded Proteins ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
Novel Therapeutic

The unfolded protein response (UPR) is an integrated, adaptive biochemical process that is inextricably linked with cell homeostasis and paramount to maintenance of normal physiological function. Prolonged accumulation of improperly folded proteins in the endoplasmic reticulum (ER) leads to stress. This is the driving stimulus behind the UPR. As such, prolonged ER stress can push the UPR past beneficial functions such as reduced protein production and increased folding and clearance to apoptotic signaling. The UPR is thus contributory to the commencement, maintenance, and exacerbation of a multitude of disease states, making it an attractive global target to tackle conditions sorely in need of novel therapeutic intervention. The accumulation of information of screening tools, readily available therapies, and potential pathways to drug development is the cornerstone of informed clinical research and clinical trial design. Here, we review the UPR’s involvement in health and disease and, beyond providing an in-depth description of the molecules found to target the three UPR arms, we compile all the tools available to screen for and develop novel therapeutic agents that modulate the UPR with the scope of future disease intervention.

scholarly journals Sequence analysis and mRNA expression of prolactin receptor gene isoforms in different tissues of sheep during lactation and the post-weaning period

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11868
Author(s):  
Ruochen Yang ◽  
Chunhui Duan ◽  
Yunxia Guo ◽  
Yujing Ma ◽  
Nazi Niu ◽  
...  
Keyword(s):  
Mammary Gland ◽  
Mrna Expression ◽  
Tertiary Structure ◽  
Receptor Gene ◽  
Prolactin Receptor ◽  
Protein Structures ◽  
Alpha Helix ◽  
Ovis Aries ◽  
Random Coils ◽  
Different Tissues

Few studies on mRNA expression of the prolactin receptor (PRLR) isoforms in different tissues of sheep were reported. The objective of this study was to analyze the gene sequence and mRNA expression of PRLR isoforms in the uterus, mammary gland, ovary, spleen and lymph tissue of ewes during the lactation and post-weaning periods. Ten lactating crossbred ewes (Dorper×Hu sheep) with twin lambs were used in this study. Five ewes were chosen randomly and slaughtered at mid-lactation (35 days after lambing). The remaining five ewes were slaughtered on the 5th day after weaning. Samples of uterus, mammary gland, ovary, spleen and lymph tissue were collected from each ewe to determine the mRNA expression of long PRLR (L-PRLR) and short PRLR (S-PRLR) by RT-qPCR. The physical and chemical properties, the similarity of the nucleotides L-PRLR and S-PRLR genes and the secondary and tertiary structure of the L-PRLR and S-PRLR proteins of sheep were analyzed. The results indicated that the predicted protein molecular weights of L-PRLR and S-PRLR are 65235.36 KD and 33847.48 KD, respectively, with isoelectric points of 5.12 and 8.34, respectively. The secondary protein structures of L-PRLR and S-PRLR are different. For L-PRLR these include alpha helix, extended strand and random coils and β-turns for which the content was 16.01%, 21%, 59.55% and 3.44%, respectively, whereas the secondary protein structures of S-PRLR contain only alpha helices, extended strand and random coils, comprising 18.24%, 30.07% and 48.99%, respectively. The L-PRLR and S-PRLR genes of the sheep (Ovis aries) had nucleotide sequences showing much similarity among ruminants. In these sheep, mRNA expression of L-PRLR and S-PRLR was highest in the uterus and differed between the uterus, ovary, mammary gland, spleen and lymph tissue. The mRNA expression of L-PRLR in lymph tissue was higher during lactation than in the post-weaning period (P < 0.01), whereas mRNA expression of S-PRLR in the uterus and the mammary gland was lower during lactation than during the post-weaning period (P < 0.01). In the uterus, mRNA expression of L-PRLR was higher than that of S-PRLR during lactation (P < 0.01) but there were no significant differences (P < 0.05) for the other five tissues. This study that the L-PRLR and S-PRLR proteins in ewes are mainly composed of extended fragments and random coils. The data also indicate that mRNA expression of L-PRLR and S-PRLR genes varies among different tissues in sheep and is higher in the uterus than in the ovary, spleen, mammary gland and lymph tissue throughout lactation and the post-weaning period.

scholarly journals Subpopulations of soluble, misfolded proteins commonly bypass chaperones: How it happens at the molecular level

2021 ◽  
Author(s):  
Ritaban Halder ◽  
Daniel A. Nissley ◽  
Ian Sitarik ◽  
Edward P. O’Brien
Keyword(s):  
Tertiary Structure ◽  
Molecular Level ◽  
Meta Analysis ◽  
Hydrophobic Surface ◽  
Misfolded Proteins ◽  
Similar Degree ◽  
Functional Protein ◽  
Folded Proteins ◽  
And Function

ABSTRACTSubpopulations of soluble, misfolded proteins can bypass chaperones within cells. The scope of this phenomenon and the lifetimes of these states have not been experimentally quantified, and how such misfolding happens at the molecular level is poorly understood. We address the first issue through a meta-analysis of the experimental literature. We find that in all quantitative protein refolding-function studies, there is always a subpopulation of soluble but misfolded and less-functional protein that does not fold in the presence of one or more chaperones. This subpopulation ranges from 8% to 50% of the soluble protein molecules in solution. Fitting the experimental time traces to a kinetic model, we find these chaperone-bypassing misfolded states take months or longer to fold and function in the presence of different chaperones. We next addressed how, at the molecular level, some misfolded proteins can evade chaperones by simulating six different proteins interacting with E. coli’s GroEL and HtpG chaperones when those proteins are in folded, unfolded, or long-lived, soluble, misfolded states. We observe that both chaperones strongly bind the unfolded state and weakly bind the folded and misfolded states to a similar degree. Thus, these chaperones cannot distinguish between the folded and long-lived misfolded states of these proteins. A structural analysis reveals the misfolded states are highly similar to the native state – having a similar size, amount of exposed hydrophobic surface area, and level of tertiary structure formation. These results demonstrate that in vitro it is common for appreciable subpopulations of proteins to remain misfolded, soluble, and evade the refolding action of chaperones for very long times. Further, these results suggest that this happens because these misfolded subpopulations are near-native and therefore interact with chaperones to a similar extent as properly folded proteins. More broadly, these results indicate a mechanism in which long-time scale changes in protein structure and function can persist in cells because some protein’s non-native states can bypass components of the proteostasis machinery.TEASERNear-native, misfolded protein conformations explain why some soluble proteins fail to refold in the presence of chaperones.

scholarly journals ADEP1 activated ClpP1P2 macromolecule of Leptospira, an ideal Achilles’ heel to deregulate proteostasis and hamper the cell survival

2020 ◽  
Author(s):  
Anusua Dhara ◽  
Md Saddam Hussain ◽  
Shankar Prasad Kanaujia ◽  
Manish Kumar
Keyword(s):  
Tertiary Structure ◽  
Bacterial Species ◽  
Small Extent ◽  
The Self ◽  
Site Directed Mutagenesis ◽  
Peptidase Activity ◽  
Serine Residue ◽  
Protein Substrates ◽  
Unfolded Protein

ABSTRACTThe caseinolytic protease (ClpP) complex in Leptospira interrogans is unusual in its functional activation. The genus Leptospira has two ClpPs, ClpP1 and ClpP2, which transcribes independently, regardless it couples to form the active tetradecamer. Acyldepsipeptide (ADEP) antibiotic hampers the growth of numerous bacterial species by activating the target protein ClpP and dysregulating the physiological proteostasis within the cell. In vitro culture of the L. interrogans fortified with the ADEP impeded the spirochete growth accompanied by a more elongated morphology. The chemoactivation of the ClpP is conditional on the duration of the self-compartmentalization of each of the ClpP isoforms. The small extent (10 min) self-assembled ClpP1P2 revealed inhibition in the peptidase activity (7-fold) in the presence of the ADEP due to the self-cleavage of the ClpP subunits. On supplementation of the β-casein or bovine serum albumin, the peptidase activity of the ClpP1P2 (short-incubated) got enhanced by the ADEP, while the ClpP1P2 (long-incubated) activity was retained to the same level. ADEP can also switch on the ClpP1P2 from a strict peptidase into proteolytic machinery that discerns and degrades the unfolded protein substrates autonomous of the cognate chaperone ClpX. In consensus to the most prokaryotes with the multi ClpP variants, the computational prototype of the ClpP1P2 tertiary structure infers that the hydrophobic pocket wherein the ADEPs predominantly docks are present in the ClpP2 heptamer. Additionally, the dynamic light scattering and the site-directed mutagenesis of a catalytic serine residue in either of the ClpP isoforms proposes a second interaction site for the ADEP.

Dynamic Regulation of Mis-Folded N-CoR by Aberrant Protease and Its Implication in UPR-Induced Apoptosis of APL Cells.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4514-4514
Author(s):  
Matiullah Khan
Keyword(s):  
Er Stress ◽  
Protein S ◽  
Spectrometric Analysis ◽  
Insoluble Protein ◽  
Dynamic Regulation ◽  
Paradoxical Response ◽  
Unfolded Protein ◽  
Folded Proteins ◽  
Induced Apoptosis ◽  
Protein Response

Abstract We have recently reported that accumulation of mis-folded N-CoR as insoluble protein aggregates in APL cells induces Endoplasmic Reticulum (ER) stress and activates unfolded protein response (UPR). Although, accumulation of mis-folded proteins is known to trigger UPR-induced cytotoxic cell death in several neurodegenerative disorders, APL cells are notably resistant to UPR-induced apoptosis. The molecular basis for the paradoxical response of APL cells to UPR is not known. Here we report that a glyco-protease, selectively expressed in APL cells, regulates APL cells’ response to UPR-induced apoptosis through processing of mis-folded N-CoR protein. Results show that mis-folded N-CoR is cleaved selectively in APL cells, and cellular extracts of APL cells and human primary APL cells contain activity that cleaves N-CoR protein. Purification and spectrometric analysis of N-CoR cleaving activity from an APL cell line reveals that it is a glycoprotein endopeptidase known as OSGEP. Furthermore, the cleavage of N-CoR in APL cells could be blocked by the broad-spectrum protease inhibitor, AEBSF, and by RNAi-mediated down-regulation of OSGEP expression. AEBSF selectively inhibits growth and promotes apoptosis of APL cells, possibly through a mechanism involving AEBSF-induced accumulation of insoluble N-CoR protein and by triggering ER stress. Taken together, these finding suggest that selective induction of protease activity in APL cells may represent a novel cytoprotective component of UPR, which could be exploited by tumor cells to survive the toxic insult of mis-folded protein(s).

In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals

2019 ◽  
Author(s):  
P.R. Sahoo ◽  
S.R. Mishra ◽  
S. Mohapatra ◽  
Santoswini Sahu ◽  
G. Sahoo ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
In Silico ◽  
Tertiary Structure ◽  
Alpha Helix ◽  
Domestic Animals ◽  
Random Coil ◽  
Local Alignment ◽  
Physiochemical Properties ◽  
Gapdh Gene ◽  
Time Of Divergence

This study has been able to determine the physiochemical properties, secondary and tertiary structure, and phylogenetic analysis of GAPDH among domestic animals under in silico platform. Eighteen nucleotide and protein sequence of GAPDH gene of different mammalian species were retrieved from National Centre for Biotechnology information (NCBI). The percentage of identity and similarity was done by Basic Local Alignment Search Tool (BLAST), physiochemical properties were analyzed by ExPASy”s ProtParam tool, the secondary and 3-D structure was predicted by GOR IV and Swiss modeling respectively. Phylogenetic analysis among the animals was done by Molecular Evolutionary Genetics Analysis. It was found that the percentage of identity and similarity among all animals were almost more than 90%. The physiochemical analysis showed this protein is very stable, hydrophilic and intracytoplasmic in nature. The secondary structure analysis showed that GAPDH has more number of random coil (49.85%) Extended strand (27.93%), alpha helix (22.22%) of the protein. The QMEAN Z score was found 0.33 under protein modeling which interfered that this protein is of comparable quality. The phylogenetic analysis of this gene showed that the highest time of divergence occurred between sheep and common chimpanzee but least time of divergence observed between killer whale and dolphin. So it can be concluded that the GAPDH gene is highly conserved along all animal species.

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