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.

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 Open-Bundle Structure as the Unfolding Intermediate of Cytochrome c’ Revealed by Small Angle Neutron Scattering

2021 ◽  
Author(s):  
Takahide Yamaguchi ◽  
Kouhei Akao ◽  
Alexandros Koutsioubas ◽  
Henrich Frielinghaus ◽  
Takamitsu Kohzuma
Keyword(s):  
Cytochrome C ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Alpha Helix ◽  
Random Coil ◽  
Radius Of Gyration ◽  
Alpha Helices ◽  
Cyt C ◽  
Bundle Structure

The open-bundle structure of cytochrome c&rsquo; as an unfolding intermediate was determined by small-angle neutron scattering experiment (SANS). The four-&alpha;-helix bundle structure of Cyt c&rsquo; at neutral pH was transited to an open-bundle structure (at pD ~13), which is a joint-clubs consisting of four clubs (&alpha;-helices) connected by short loops. The compactly folded structure of Cyt c&rsquo; (radius of gyration, Rg = 18 &Aring; for the Cyt c&rsquo; dimer) at neutral or mildly alkaline pD transitioned to a remarkably larger &ldquo;open-bundle&rdquo; structure at pD ~13 (Rg = 25 &Aring; for the Cyt c&rsquo; monomer). Cyt c&rsquo; adopts an unstructured random coil structure at pD = 1.7 (Rg = 25 &Aring; for the Cyt c&rsquo; monomer). Numerical partial scattering function analysis (joint-clubs) and ab initio modelling gave structures similar to the &ldquo;open-bundle&rdquo;, which retains the &alpha;-helices but loses the bundle structure.

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.

scholarly journals Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion proteins

1993 ◽  
Vol 90 (23) ◽  
pp. 10962-10966 ◽  
Author(s):  
K M Pan ◽  
M Baldwin ◽  
J Nguyen ◽  
M Gasset ◽  
A Serban ◽  
...  
Keyword(s):  
Chemical Modification ◽  
Prion Protein ◽  
Conformational Transition ◽  
Prion Proteins ◽  
Limited Proteolysis ◽  
Alpha Helix ◽  
Beta Sheets ◽  
Cellular Prion Protein ◽  
Beta Sheet ◽  
Alpha Helices

Prions are composed largely, if not entirely, of prion protein (PrPSc in the case of scrapie). Although the formation of PrPSc from the cellular prion protein (PrPC) is a post-translational process, no candidate chemical modification was identified, suggesting that a conformational change features in PrPSc synthesis. To assess this possibility, we purified both PrPC and PrPSc by using nondenaturing procedures and determined the secondary structure of each. Fourier-transform infrared (FTIR) spectroscopy demonstrated that PrPC has a high alpha-helix content (42%) and no beta-sheet (3%), findings that were confirmed by circular dichroism measurements. In contrast, the beta-sheet content of PrPSc was 43% and the alpha-helix 30% as measured by FTIR. As determined in earlier studies, N-terminally truncated PrPSc derived by limited proteolysis, designated PrP 27-30, has an even higher beta-sheet content (54%) and a lower alpha-helix content (21%). Neither PrPC nor PrPSc formed aggregates detectable by electron microscopy, while PrP 27-30 polymerized into rod-shaped amyloids. While the foregoing findings argue that the conversion of alpha-helices into beta-sheets underlies the formation of PrPSc, we cannot eliminate the possibility that an undetected chemical modification of a small fraction of PrPSc initiates this process. Since PrPSc seems to be the only component of the "infectious" prion particle, it is likely that this conformational transition is a fundamental event in the propagation of prions.

scholarly journals Secondary Structure Preferences of Mn2+ Binding Sites in Bacterial Proteins

2014 ◽  
Vol 2014 ◽  
pp. 1-14 ◽  
Author(s):  
Tatyana Aleksandrovna Khrustaleva
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Glutamic Acid ◽  
Gc Content ◽  
Alpha Helix ◽  
Random Coil ◽  
Amino Acid Residues ◽  
Alpha Helices ◽  
Beta Strand ◽  
Genomic Gc Content

3D structures of proteins with coordinated Mn2+ ions from bacteria with low, average, and high genomic GC-content have been analyzed (149 PDB files were used). Major Mn2+ binders are aspartic acid (6.82% of Asp residues), histidine (14.76% of His residues), and glutamic acid (3.51% of Glu residues). We found out that the motif of secondary structure “beta strand-major binder-random coil” is overrepresented around all the three major Mn2+ binders. That motif may be followed by either alpha helix or beta strand. Beta strands near Mn2+ binding residues should be stable because they are enriched by such beta formers as valine and isoleucine, as well as by specific combinations of hydrophobic and hydrophilic amino acid residues characteristic to beta sheet. In the group of proteins from GC-rich bacteria glutamic acid residues situated in alpha helices frequently coordinate Mn2+ ions, probably, because of the decrease of Lys usage under the influence of mutational GC-pressure. On the other hand, the percentage of Mn2+ sites with at least one amino acid in the “beta strand-major binder-random coil” motif of secondary structure (77.88%) does not depend on genomic GC-content.

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 The Influence of Flanking Secondary Structures on Amino Acid Content and Typical Lengths of 3/10 Helices

2014 ◽  
Vol 2014 ◽  
pp. 1-13 ◽  
Author(s):  
Vladislav Victorovich Khrustalev ◽  
Eugene Victorovich Barkovsky ◽  
Tatyana Aleksandrovna Khrustaleva
Keyword(s):  
Amino Acid ◽  
Gc Content ◽  
Amino Acid Content ◽  
Alpha Helix ◽  
Major Elements ◽  
Random Coil ◽  
Amino Acid Residues ◽  
Alpha Helices ◽  
Beta Strand ◽  
Bacterial Proteins

We used 3D structures of a highly redundant set of bacterial proteins encoded by genes of high, average, and low GC-content. Four types of connecting bridges—regions situated between any of two major elements of secondary structure (alpha helices and beta strands)—containing a pure random coil were compared with connecting bridges containing 3/10 helices. We included discovered trends in the original “VVTAK Connecting Bridges” algorithm, which is able to predict more probable conformation for a given connecting bridge. The highest number of significant differences in amino acid usage was found between 3/10 helices containing bridges connecting two beta strands (they have increased Phe, Tyr, Met, Ile, Leu, Val, and His usages but decreased usages of Asp, Asn, Gly, and Pro) and those without 3/10 helices. The typical (most common) length of 3/10 helices situated between two beta strands and between beta strand and alpha helix is equal to 5 amino acid residues. The preferred length of 3/10 helices situated between alpha helix and beta strand is equal to 3 residues. For 3/10 helices situated between two alpha helices, both lengths (3 and 5 amino acid residues) are typical.

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 1, 4 Alpha Glucan Branching Enzyme and Substrate Docking Studies

2020 ◽  
Vol 17 (1) ◽  
pp. 40-50
Author(s):  
Farzane Kargar ◽  
Amir Savardashtaki ◽  
Mojtaba Mortazavi ◽  
Masoud Torkzadeh Mahani ◽  
Ali Mohammad Amani ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
In Silico ◽  
Alpha Helix ◽  
In Silico Analysis ◽  
Glycogen Storage ◽  
Docking Studies ◽  
Random Coil ◽  
Special Topic ◽  
Industrial Biotechnology ◽  
In Silico Study

Background: The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server. Methods: For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina. Results: By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence. Conclusion: By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.

A novel dextranase gene from the marine bacterium Bacillus aquimaris S5 and its expression and characteristics

2021 ◽  
Vol 368 (3) ◽  
Author(s):  
Dongxue Dong ◽  
Xuelian Wang ◽  
Tian Deng ◽  
Zhe Ning ◽  
Xiaopeng Tian ◽  
...  
Keyword(s):  
Dental Plaque ◽  
Marine Bacterium ◽  
3D Structure ◽  
Great Promise ◽  
Glycoside Hydrolase Family ◽  
Alpha Helices ◽  
Random Coils ◽  
Pharmaceutical Industries ◽  
Bacterium Bacillus ◽  
Hydrolase Family

ABSTRACT Dextranase specifically hydrolyzes dextran and is used to produce functional isomalto-saccharide prebiotics. Moreover, dextranase is used as an additive in mouthwash to remove dental plaque. We cloned and expressed the dextranase gene of the marine bacterium Bacillus aquimaris S5. The length of the BaDex gene was 1788 bp, encoding 573 amino acids. Using bioinformatics to predict and analyze the amino acid sequence of BaDex, we found the isoelectric point and instability coefficient to be 4.55 and 29.22, respectively. The average hydrophilicity (GRAVY) was −0.662. The secondary structure of BaDex consisted of 145 alpha helices, accounting for 25.31% of the protein; 126 extended strands, accounting for 21.99%; and 282 random coils, accounting for 49.21%. The 3D structure of the BaDex protein was predicted and simulated using SWISS-MODEL, and BaDex was classified as a Glycoside Hydrolase Family 66 protein. The optimal temperature and pH for BaDex activity were 40°C and 6.0, respectively. The hydrolysates had excellent antioxidant activity, and 8 U/mL of BaDex could remove 80% of dental plaque in MBRC experiment. This recombinant protein thus has great promise for applications in the food and pharmaceutical industries.

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