scholarly journals Clustering and Differentiation of glr-3 Gene Function and Its Homologous Proteins

2021 ◽  
Vol 3 (3) ◽  
Author(s):  
Yue Ma ◽  
Tiantian Guo ◽  
Yihe Wang ◽  
Xinna Li ◽  
Jingyu Zhang
Keyword(s):  
Secondary Structure ◽  
Protein Glycosylation ◽  
Random Coil ◽  
Homologous Gene ◽  
Phosphorylation Sites ◽  
Homologous Proteins ◽  
Homologous Genes ◽  
Glycosylation Sites ◽  
Α Helix ◽  
Cold Sensing

In order to adapt to the low temperature environment, organisms transmitexcitement to the central system through the thermal sensing system, whichis a classic reflex reaction. The cold receptor GLR-3 perceives cold and produces cold avoidance behavior through peripheral sensory neurons ASER.In order to further understand the gene encoding of the cold sensing glr-3gene and the evolution of its homologous gene group function and proteinfunction, the nucleotide sequence and amino acid sequence of the glr-3gene and its homologous gene in 24 species were obtained and compared.By clustering with the GRIK2 gene sequence of Rana chensinensis, the bioinformatics method was used to predict and sequence analyze the change ofgene, evolution rate, physical and chemical properties of protein, glycosylation sites, phosphorylation sites, secondary structure and tertiary structureof protein. The analysis results show that the glr-3 gene and its homologousgene have obvious positive selection effect. The protein prediction analysisshowed that the glr-3 gene and its homologous genes encoded proteinsin these 25 species were hydrophilic proteins, and the proportion of sidechains of aliphatic amino acids was high. The transmembrane helix waswidespread and there were more N-glycosylation sites and O-glycosylationsites. The protein phosphorylation sites encoded were serine, threonine andtyrosine phosphorylation sites. Secondary structure prediction showed thatthe secondary structure units of the encoded protein were α-helix, β-turn,random coil and extended chain, and the proportion of α-helix was the largest. This study provides useful information on the evolution and function ofthe cold sensing gene glr-3 and its homologous genes.

Bioinformatic Analysis and Characteristics of Glycoprotein L(gL) Encoded by UL1 Gene of Duck Plague Virus

2013 ◽  
Vol 647 ◽  
pp. 250-257
Author(s):  
Ling Jie Zuo ◽  
An Chun Cheng ◽  
Ming Shu Wang
Keyword(s):  
Secondary Structure ◽  
Physicochemical Properties ◽  
Evolutionary Relationship ◽  
Alpha Helix ◽  
Bioinformatic Analysis ◽  
Random Coil ◽  
Phosphorylation Sites ◽  
Duck Plague Virus ◽  
Online Tools ◽  
Glycosylation Sites

Glycoprotein L(gL) is encoded by UL1 gene of duck plague virus (DPV). Through predicting and analyzing the structure and physicochemical properties of DPV gL protein by using some software and online tools to gain more information of DPV gL protein. The phylogenetic tree shows that DPV gL protein has close evolutionary relationship with the genus Simplexvirus. The online analysis of the physicochemical properties demonstrates that the protein has ten potential phosphorylation sites and five potential O-linked glycosylation sites, and without both the signal peptide and the transmembrance region. In addition, the subcellular localization of gL protein largely locates at mitochondrial with 47.8%. The secondary structure results reveal that random coil dominate among secondary structure elements followed by alpha helix, extended strand and β-turn for all sequences. All the data will help a basis for further functional and physiological features study of the DPV gL protein.

scholarly journals Secondary Structure of Bovine Albumin as Studied by Polarization-Sensitive Multiplex CARS Spectroscopy

1996 ◽  
Vol 50 (1) ◽  
pp. 78-85 ◽  
Author(s):  
Artemy Voroshilov ◽  
Cees Otto ◽  
Jan Greve
Keyword(s):  
Secondary Structure ◽  
Raman Spectra ◽  
Random Coil ◽  
Background Suppression ◽  
Good Correspondence ◽  
Bovine Albumin ◽  
Suppression Technique ◽  
Polarized Raman ◽  
Α Helix ◽  
Anti Stokes

The first application of polarization-sensitive multiplex coherent anti-Stokes Raman spectroscopy (MCARS) in the absence of resonance enhancement to the resolution of the secondary structure of a protein in solution is reported. Polarization MCARS spectra of bovine albumin in D2O were obtained in the range 1370 to 1730 cm−1 with the aid of the background suppression technique. The spectra were fitted simultaneously with a single set of parameters (band positions, bandwidths, amplitudes, and depolarization ratios). Polarized Raman spectra simulated with these parameters revealed a good correspondence with the spontaneous Raman spectra measured. The broad amide I′ band was decomposed assuming the three major secondary conformations of protein, of which the contribution of β-sheet structure was found to be negligible. Relative weights of α-helix and random coil conformations agree well with the estimates obtained with Raman and circular dichroism (CD) spectroscopies.

scholarly journals Structural Dynamics of the N-Extension of Cardiac Troponin I Complexed with Troponin C by Site-Directed Spin Labeling Electron Paramagnetic Resonance

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Chenchao Zhao ◽  
Takayasu Somiya ◽  
Shinji Takai ◽  
Shoji Ueki ◽  
Toshiaki Arata
Keyword(s):  
Secondary Structure ◽  
Cardiac Troponin ◽  
Troponin I ◽  
Cardiac Troponin I ◽  
Spin Labels ◽  
Phosphorylation Sites ◽  
Paramagnetic Resonance ◽  
Single Spin ◽  
Site Directed Spin Labeling ◽  
Α Helix

Abstract The secondary structure of the N-extension of cardiac troponin I (cTnI) was determined by measuring the distance distribution between spin labels attached to the i and i + 4 residues: 15/19, 23/27, 27/31, 35/39, and 43/47. All of the EPR spectra of these regions in the monomeric state were broadened and had a amplitude that was reduced by two-thirds of that of the single spin-labeled spectra and was fit by two residual distance distributions, with a major distribution one spreading over the range from 1 to 2.5 nm and the other minor peak at 0.9 nm. Only slight or no obvious changes were observed when the extension was bound to cTnC in the cTnI-cTnC complex at 0.2 M KCl. However, at 0.1 M KCl, residues 43/47, located at the PKC phosphorylation sites Ser42/44 on the boundary of the extension, exclusively exhibited a 0.9 nm peak, as expected from α-helix in the crystal structure, in the complex. Furthermore, 23/27, which is located on the PKA phosphorylation sites Ser23/24, showed that the major distribution was markedly narrowed, centered at 1.4 nm and 0.5 nm wide, accompanying the spin label immobilization of residue 27. Residues 35 and 69 at site 1 and 2 of cTnC exhibited partial immobilization of the attached spin labels upon complex formation. The results show that the extension exhibited a primarily partially folded or unfolded structure equilibrated with a transiently formed α-helix-like short structure over the length. We hypothesize that the structure binds at least near sites 1 and 2 of cTnC and that the specific secondary structure of the extension on cTnC becomes uncovered when decreasing the ionic strength demonstrating that only the phosphorylation regions of cTnI interact stereospecifically with cTnC.

High-Pressure FTIR Studies of the Secondary Structure of Proteins

1996 ◽  
Author(s):  
Yoshihiro Taniguchi ◽  
Naohiro Takeda
Keyword(s):  
High Pressure ◽  
Secondary Structure ◽  
Cytochrome C ◽  
Ribonuclease A ◽  
Random Coil ◽  
Absorbance Spectroscopy ◽  
Α Helix ◽  
Bovine Pancreas ◽  
Β Sheet ◽  
Denaturation Of Proteins

Infrared spectra of five globular proteins (bovine pancreas ribonuclease A, horse skeletal muscle myoglobin, bovine pancreas insulin, horse heart cytochrome c, egg white lysozyme) in 5% D2O solutions (pD 7.0) were measured as a function of pressure up to 1470 MPa at 30 °C. According to the second-derivative spectral changes in the observed amide I band of the proteins, which indicate that the α-helix and β-sheet substructures of the secondary structures break dramatically into the random coil conformation, ribonuclease A and myoglobin are denatured reversibly at 850 MPa and 350 MPa, respectively. Lysozyme denatures partially and reversibly at 670 MPa, as shown by decrease in the α-helix and β-turn substructures, but no change occurs in the random coil and β-sheet substructures. The secondary structure of cytochrome c is not disrupted at pressures up to 1470 MPa, and partial transformation of the α-helix of insulin to random coil starts at 960 MPa. Hydrogen-deuterium exchange of protons on the amide groups in the protein interior is increased by external pressure and is associated with the pressure-induced protein conformational changes. A number of studies on the effects of pressure on protein denaturation have been carried out using various high-pressure detection methods: ultraviolet absorbance spectroscopy (Brandts et al., 1970; Hawley, 1971), visible absorbance spectroscopy (Zipp & Kauzmann, 1973), fluorescence intensity spectroscopy (Li et al., 1976), polarization fluorescence spectroscopy (Chryssomallis et al., 1981), and enzyme activity assays (Taniguchi & Suzuki, 1983; Makimoto et al., 1989). These techniques have the great advantage of being applicable to pressure-induced reversible denaturation of proteins to identify the thermodynamic parameters, especially the volume change and compressibility of a protein in solution, because the experiments can be run under dilute conditions at a protein concentration of less than 0.05% w/v. Therefore, these data reflect the intramolecular phenomena of reversible pressure changes and provide the volume changes accompanying the denaturation of proteins, which are due to the difference in partial molal (specific) volume between the native and denatured proteins in solution.

scholarly journals The Molecular Properties of Peanut Protein: Impact of Temperature, Relative Humidity and Vacuum Packaging during Storage

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2618 ◽  
Author(s):  
Xiaotong Sun ◽  
Hua Jin ◽  
Yangyang Li ◽  
Haiying Feng ◽  
Chunhong Liu ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Functional Properties ◽  
Surface Hydrophobicity ◽  
Protein Isolate ◽  
Peanut Protein ◽  
Molecular Properties ◽  
Random Coil ◽  
Bivariate Correlation ◽  
Protein Particle ◽  
Α Helix

This study aimed to investigate the variation of molecular functional properties of peanut protein isolate (PPI) over the storage process and reveal the correlation between the PPI secondary structure and properties in the storage procedure. After storage, the molecular properties of PPI changed significantly (p < 0.05). Extending storage time resulted in a decrease in free sulfhydryl content, fluorescence intensity, surface hydrophobicity and emulsifying properties, which was accompanied by an increase in protein particle size. The results of infrared spectroscopy suggested the content decline of α-helix and β-sheet, and the content rise of β-turn and random coil. Based on bivariate correlation analysis, it was revealed that surface hydrophobicity and emulsifying activity of PPI was significantly affected by α-helix and by β-turn (p < 0.05), respectively. This research supplied more information for the relationship between the peanut protein’s secondary structure and functional properties over the stored process.

Effect of High Pressure Microfluidization on Secondary Structure of Wheat Gluten in Different Solvents

2013 ◽  
Vol 781-784 ◽  
pp. 770-773
Author(s):  
Zhao Xi Fang ◽  
Nai Jun Yan ◽  
Guo Qin Liu
Keyword(s):  
High Pressure ◽  
Secondary Structure ◽  
Acid Treatment ◽  
Wheat Gluten ◽  
Control Sample ◽  
Random Coil ◽  
Comprehensive Treatment ◽  
Gluten Protein ◽  
Α Helix ◽  
Β Sheet

Far-UV circular dichroism (CD) spectroscopy was used to study the conformation of wheat gluten protein treatmented by dynamic high pressure microfluidization (DHPM), acid treatment and its comprehensive treatment in two solvents. The results showed, the secondary structure of control sample are mainly consist of α-helix and random-coil in phosphate-buffered saline (PBS) and phosphate buffered solution with SDS(SDS), the secondary structure of control sample are mainly consist of β-Sheet and random-coil. The CD data also showed that SDS interacts with the gluten protein and modifies the protein conformation, which switched the conformation from α-helix and β-Turn to β-sheet and random-coil. However, the CD analysis also indicated that some of the ordered structures of α-helix, β-Turn and β-sheet were destroyed and converted random-coil coped with acid in two solvents, in other words, the acid treatment can directed change the secondary structure. Furthermore, the effect of comprehensive treatment (DHPM plus acid) is not equal to the simple sum of the individual treatment effect.

Ultrasonication-Induced Rapid Gelation of Wild Silkworm Silk Fibroins

2013 ◽  
Vol 634-638 ◽  
pp. 1165-1169 ◽  
Author(s):  
Gui Yang Liu ◽  
Si Yong Xiong ◽  
Ren Chuan You ◽  
Ling Shuang Wang ◽  
Ming Zhong Li
Keyword(s):  
Secondary Structure ◽  
Silk Fibroin ◽  
Gelation Time ◽  
Random Coil ◽  
X Ray Diffraction ◽  
Freeze Dried ◽  
Silk Fibroins ◽  
Wild Silkworm ◽  
Α Helix ◽  
Silkworm Silk

Silk fibroin （SF） hydrogels of the wild silkworm species Antheraea pernyi and Antheraea yamamai were obtained from aqueous SF solutions at room temperature. Both A. pernyi and A. yamamai solutions were slow to gelate. Hydrogels of the two species of wild silkworm were obtained rapidly following ultrasonicaton at 400–500 W. The secondary structure of the freeze-dried SF hydrogels was measured by X-ray diffraction and Fourier transform infrared spectroscopy. Ultrasonication did not change the main secondary structure of the hydrogels, but it accelerated the structural transformation of silk fibroin molecules from random coil or α helix to β sheet and reduced the gelation time.

scholarly journals Secondary structure of NADPH: protochlorophyllide oxidoreductase examined by circular dichroism and prediction methods*

1996 ◽  
Vol 317 (2) ◽  
pp. 549-555 ◽  
Author(s):  
Simon J. BIRVE ◽  
Eva SELSTAM ◽  
Lennart B.-Å. JOHANSSON
Keyword(s):  
Secondary Structure ◽  
Fluorescence Emission ◽  
Random Coil ◽  
Prolamellar Body ◽  
Interfacial Region ◽  
Protochlorophyllide Oxidoreductase ◽  
Loop Region ◽  
Rossmann Fold ◽  
Α Helix ◽  
Β Sheet

To study the secondary structure of the enzyme NADPH: protochlorophyllide oxidoreductase (PCOR), a novel method of enzyme isolation was developed. The detergent isotridecyl poly(ethylene glycol) ether (Genapol X-080) selectively solubilizes the enzyme from a prolamellar-body fraction isolated from wheat (Triticum aestivumL.). The solubilized fraction was further purified by ion-exchange chromatography. The isolated enzyme was studied by fluorescence spectroscopy at 77 K, and by CD spectroscopy. The fluorescence-emission spectra revealed that the binding properties of the substrate and co-substrate were preserved and that photo-reduction occurred. The CD spectra of PCOR were analysed for the relative amounts of the secondary structures, α-helix, β-sheet, turn and random coil. The secondary-structure composition was estimated to be 33% α-helix, 19% β-sheet, 20% turn and 28% random coil. These values are in agreement with those predicted by the Predict Heidelberg Deutschland and self-optimized prediction method from alignments methods. The enzyme has some amino acid identity with other NADPH-binding enzymes containing the Rossmann fold. The Rossmann-fold fingerprint motif is localized in the N-terminal region and at the expected positions in the predicted secondary structure. It is suggested that PCOR is anchored to the interfacial region of the membrane by either a β-sheet or an α-helical region containing tryptophan residues. A hydrophobic loop-region could also be involved in membrane anchoring.

Influence of the secondary structure on the AIE-related emission behavior of an amphiphilic polypeptide containing a hydrophobic fluorescent terminal and hydrophilic pendant groups

2016 ◽  
Vol 7 (1) ◽  
pp. 153-163 ◽  
Author(s):  
Li-Yang Lin ◽  
Po-Chiao Huang ◽  
Deng-Jie Yang ◽  
Jhen-Yan Gao ◽  
Jin-Long Hong
Keyword(s):  
Secondary Structure ◽  
Secondary Structures ◽  
Random Coil ◽  
Emission Behavior ◽  
Α Helix ◽  
Β Sheet

AIE-related emission of polypeptide containing an AIE-active terminal is correlated with secondary structures (α-helix, β-sheet and random coil) of the peptide chains.

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

2019 ◽  
Vol 26 (7) ◽  
pp. 532-541 ◽  
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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