scholarly journals Computational identification of fertility functions of bovine Reprimo gene

2020 ◽  
Vol 42 (1) ◽  
Author(s):  
S. O. Durosara ◽  
A. O. Adebambo ◽  
A. J. Sanda ◽  
O. Olowofeso ◽  
S. O. Osho ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Growth Hormone ◽  
Protein Structure ◽  
Amino Acid ◽  
Root Mean Square ◽  
Growth Hormone Gene ◽  
Mean Square ◽  
Tertiary Structures ◽  
Structure Comparison ◽  
Fertility Genes

Improvement in fertility is possible through gene assisted selection. Cattle fertility and genes underlying it should be thoroughly studied and exploited to find solution to declining cattle fertility. Reprimo (RPRM) gene is a pleiotropic gene involved in suppression of cancer, regulation of mitotic cell cycle, cell cycle arrest and regulation of survival. Comparison of protein tertiary structures is important in inferring functional characteristics of new proteins. This study used computational approach to identify some fertility functions of bovine RPRM gene using motif prediction and protein structure comparison. Amino acid sequences of bovine RPRM gene and some other cattle fertility genes were retrieved from GenBank. Motifs in the amino acid sequence of bovine RPRM gene were predicted using PROSITE software. The domain structure of bovine RPRM protein was predicted using simple modular architecture research tool (SMART). Protein tertiary structures (3D structures) of bovine RPRM gene and other cattle fertility genes were predicted with Phyre2 software. To have structural and functional similarity, it has been found that protein structure after superimposition should have Root Mean Square Deviation (RMSD) value less than or equal to 2Å. The protein 3D structures of other cattle fertility genes were superposed against the protein 3D structure of bovine RPRM gene using SuperPose web server and the proteins with RMSD value of 2Å or less were predicted as proteins with similar functions and structures as bovine RPRM gene. The predicted motifs (N-glycosylation site, N-myristoylation site, and cAMP and cGMP-dependent protein kinase phosphorylation site) and protein structure comparison revealed that, bovine RPRM gene and bovine growth hormone gene have the same fertility function with alpha carbon and backbone root mean square deviations of 1.94 Å and 1.81 Å, respectively. It follows therefore that other fertility functions of bovine RPRM gene included sexual maturation, steroidogenesis, gametogenesis, gonadal differentiation and gonadotrophin secretion which are the functions of growth hormone gene.

How root-mean-square distance (r.m.s.d.) values depend on the resolution of protein structures that are compared

2003 ◽  
Vol 36 (1) ◽  
pp. 125-128 ◽  
Author(s):  
Oliviero Carugo
Keyword(s):  
Protein Structure ◽  
Root Mean Square ◽  
Protein Pair ◽  
Protein Structures ◽  
Structural Similarity ◽  
Protein Crystal ◽  
Mean Square ◽  
Root Mean Square Distance ◽  
Open Question ◽  
Mean Square Distance

The most popular estimator of structural similarity is the root-mean-square distance (r.m.s.d.) between equivalent atoms, computed after optimal superposition of the two structures that are compared. It is known that r.m.s.d. values do not depend only on conformational differences but also on other features, for example the dimensions of the structures that are compared. An open question is how they might depend on the accuracy of the experimentally determined protein structures. Given that the accuracy of the protein crystal structures is generally estimated through the crystallographic resolution, it is important to know the dependence of the r.m.s.d. on the crystallographic resolution of the two structures that are compared. 14458 protein structure pairs of identical sequence were compared and the resulting r.m.s.d. values were normalized to 100-residue length to avoid the bias introduced by the dependence of the r.m.s.d. values on the protein-pair dimensions. On average, smaller r.m.s.d. values are associated with protein structure pairs at better resolution and the r.m.s.d. values tend to increase if the two proteins that are compared have been refined at different resolutions. For crystallographic resolutions ranging between 1.6 and 2.9 Å, both relationships appear to be linear: r.m.s.d. = −0.73 + 0.48 resolution and delta_r.m.s.d. = 0.20 + 0.30 delta_resolution (`delta' indicating difference). Although the linearity of these relationships is not expected to hold outside the 1.6–2.9 Å resolution range, they are useful in making the r.m.s.d. values more reliable.

The 2.8 Å resolution structure of Streptomyces griseus protease B and its homology with α-chymotrypsin and Streptomyces griseus protease A

1979 ◽  
Vol 57 (2) ◽  
pp. 135-144 ◽  
Author(s):  
Louis T. J. Delbaere ◽  
Gary D. Brayer ◽  
Michael N. G. James
Keyword(s):  
Root Mean Square ◽  
Root Mean Square Deviation ◽  
Active Site ◽  
Heavy Atom ◽  
Streptomyces Griseus ◽  
Mean Square ◽  
Mean Square Deviation ◽  
Tertiary Structures ◽  
Protease B ◽  
Resolution Structure

The 2.8 Å (1 Å = 0.1 nm) resolution structure of the crystalline orthorhombic form of the microbial serine protease Streptomyces griseus protease B (SGPB) has been solved by the method of multiple isomorphous replacement using five heavy-atom derivatives. The geometrical arrangement of the active site quartet, Ser-214, Asp-102, His-57, and Ser-195, is similar to that found for pancreatic α-chymotrypsin. SGPB and α-chymotrypsin have only 18% identity of primary structure but their tertiary structures are 63% topologically equivalent within a root mean square deviation of 2.07 Å. The major tertiary structural differences between the bacterial enzyme SGPB and the pancreatic enzymes is due to the zymogen requirement of the multicellular organisms in order to protect themselves against autolytic degradation. The two pronase enzymes, SGPB and Streptomyces griseus protease A (SGPA), have 61% identity of sequence and their tertiary structures are 85% topologically equivalent within a root mean square deviation of 1.46 Å. The active site regions of SGPA and SGPB are similar and their tertiary structures differ only in three minor regions of surface loops.

scholarly journals IDENTIFICATION OF GROWTH HORMONE GENE OF Pangasionodon hypophthalmus

2009 ◽  
Vol 4 (1) ◽  
pp. 9
Author(s):  
Raden Roro Sri Pudji Sinarni Dewi ◽  
Agus Oman Sudrajat ◽  
Alimuddin Alimuddin ◽  
Komar Sumantadinata
Keyword(s):  
Growth Hormone ◽  
Amino Acid ◽  
Rna Extraction ◽  
Pcr Amplification ◽  
Transgenic Fish ◽  
Nucleotide Sequencing ◽  
Tryptophan Residue ◽  
Growth Hormone Gene ◽  
Reading Frame ◽  
Gh Gene

Identification of growth hormone (GH) gene in a target fish is the first step in the construction of “all fish genes transfer vector” to generate transgenic fish. The research was done to identify and characterize the GH gene of Pangasionodon hypophthalmus. There were several activities performed in identifying the GH gene: RNA extraction, cDNA synthesis, PCR amplification, and DNA fragment isolation. The characterizations were done using the nucleotide sequencing engine ABIPRISM 3100. The results were then analyzed using BLASTN/P and GENETYX version 7 program. The full-length GH gene of P. hypophthalmus was 1151 bp in length, coding for an open reading frame (ORF) of 603 bp. The 5’ and 3’ untranslated regions of the GH gene were 22 bp and 526 bp long, respectively. The GH gene of P. hypophthalmus had some common characteristics that are owned by GH genes, such as single tryptophan residue (W) on the 104th amino acid, 5 cysteine residues (C) on the amino acid 71, 135, 173, 190, and 198 and a motif of Asn-Xaa-Thr on C terminus which is the potential location for N-linked glycosilation. Polyadenylation signal (aataaa) was on the 14 bp at the upstream of polyadenylation location. Growth hormone of P. hypophthalmus consisted of over 200 amino acids from GH cDNA deduction. The highest proportion of amino acid composition was leusin (14%) while the lowest was tryptophan (0.5%).

scholarly journals Molecular Dynamics Study of Insulin Mutants

2021 ◽  
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Secondary Structure ◽  
Root Mean Square ◽  
Human Insulin ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area ◽  
Mean Square ◽  
Wild Type ◽  
Secondary Structure Content

Human insulin, a small protein hormone consisting of A-chain (21 residues) and B-chain (30 residues) linked by three disulfide bonds, is crucial for controlling the hyperglycemia in type I diabetes. In the present work molecular dynamics simulation (MD) with human insulin and its mutants was used to assess the influence of 10 point mutations (HisA8, ValA10, AspB10, GlnB17, AlaB17, GlnB18, AspB25, ThrB26, GluB27, AspB28), 6 double mutations (GluA13+GluB10, SerA13+GluB27, GluB1+GluB27, SerB2+AspB10, AspB9+GluB27, GluB16+GluB27) and one triple mutation (GluA15+AspA18+AspB3) in the protein sequence on the structure and dynamics of human insulin. A series of thermal unfolding MD simulations with wild type (WT) human insulin and its mutants was performed at 400 K with GROMACS software (version 5.1) using the CHARMM36m force field. The MD results have been analyzed in terms of the parameters characterizing both the global and local protein structure, such as the backbone root mean-square deviation, gyration radius, solvent accessible surface area, the root mean-square fluctuations and the secondary structure content. The MD simulation data showed that depending on time evolution of integral characteristics, the examined mutants can be tentatively divided into three groups: 1) the mutants HisA8, ValA10, AlaB17, AspB25, ThrB26, GluB27, GluA13+GluB10, GluB1+GluB27 and GluB16+GluB27, which exert stabilizing effect on the protein structure in comparison with wild type insulin; 2) the mutants GlnB17, AspB10, SerB2+AspB10 and GluA15+AspA18+AspB3 that did not significantly affect the dynamical properties of human insulin with a minimal stabilizing impact; 3) the mutants AspB28, AspB9+GluB27 and SerA13+GluB27, GlnB18, destabilizing the protein structure. Analysis of the secondary structure content provided evidence for the influence of AspB28, AspB9+GluB27 and SerA13+GluB27, GlnB18 on the insulin unfolding. Our MD results indicate that the replacement of superficial nonpolar residues in the insulin structure by hydrophilic ones gives rise to the increase in protein stability in comparison with the wild type protein.

scholarly journals A novel hyperthermophilic methylglyoxal synthase: molecular dynamic analysis on the regional fluctuations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gyo-Yeon Seo ◽  
Hoe-Suk Lee ◽  
Hyeonsoo Kim ◽  
Sukhyeong Cho ◽  
Jeong-Geol Na ◽  
...  
Keyword(s):  
Protein Structure ◽  
Hydrogen Bonds ◽  
Root Mean Square ◽  
Residual Activity ◽  
Dynamics Simulation ◽  
Mean Square ◽  
Salt Bridges ◽  
Optimum Activity ◽  
Regional Fluctuations ◽  
Methylglyoxal Synthase

AbstractTwo putative methylglyoxal synthases, which catalyze the conversion of dihydroxyacetone phosphate to methylglyoxal, from Oceanithermus profundus DSM 14,977 and Clostridium difficile 630 have been characterized for activity and thermal stability. The enzyme from O. profundus was found to be hyperthermophilic, with the optimum activity at 80 °C and the residual activity up to 59% after incubation of 15 min at 95 °C, whereas the enzyme from C. difficile was mesophilic with the optimum activity at 40 °C and the residual activity less than 50% after the incubation at 55 °C or higher temperatures for 15 min. The structural analysis of the enzymes with molecular dynamics simulation indicated that the hyperthermophilic methylglyoxal synthase has a rigid protein structure with a lower overall root-mean-square-deviation value compared with the mesophilic or thermophilic counterparts. In addition, the simulation results identified distinct regions with high fluctuations throughout those of the mesophilic or thermophilic counterparts via root-mean-square-fluctuation analysis. Specific molecular interactions focusing on the hydrogen bonds and salt bridges in the distinct regions were analyzed in terms of interatomic distances and positions of the individual residues with respect to the secondary structures of the enzyme. Key interactions including specific salt bridges and hydrogen bonds between a rigid beta-sheet core and surrounding alpha helices were found to contribute to the stabilisation of the hyperthermophilic enzyme by reducing the regional fluctuations in the protein structure. The structural information and analysis approach in this study can be further exploited for the engineering and industrial application of the enzyme.

scholarly journals Protein structure validation by generalized linear model root-mean-square deviation prediction

2012 ◽  
Vol 21 (2) ◽  
pp. 229-238 ◽  
Author(s):  
Anurag Bagaria ◽  
Victor Jaravine ◽  
Yuanpeng J. Huang ◽  
Gaetano T. Montelione ◽  
Peter Güntert
Keyword(s):  
Protein Structure ◽  
Linear Model ◽  
Root Mean Square ◽  
Root Mean Square Deviation ◽  
Generalized Linear Model ◽  
Mean Square ◽  
Mean Square Deviation ◽  
Structure Validation ◽  
Protein Structure Validation

Sequencing and Polymorphism detection in growth hormone gene in Najdi Sheep and their association with milk production

2018 ◽  
Author(s):  
Faisal M. Aqlan ◽  
Yaaser Q. Almulaiky ◽  
Mohammed Alkhaled ◽  
Aisha A.M. Alayafi ◽  
Haytham A. Ali ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Amino Acid ◽  
Milk Production ◽  
Milk Yield ◽  
Growth Hormone Gene ◽  
Gh Gene ◽  
Najdi Sheep ◽  
Daily Milk Yield ◽  
The Relationship ◽  
Daily Milk

This study was aimed to evaluate the relationship between growth hormone (GH) gene polymorphism and milk production in Najdi sheep. Two hundred Najdi ewes were used to determine the daily milk yield (DMY). The complete CDS of the Najdi sheep GH gene is1950 in length, GenBank acc. no. KU310891.1. Najdi sheep GH protein consists of 217 amino acids GenBank ALT22407.1 with conversion amino acid arginine number 121 to amino acid lysine (R121K). A novel five SNPs were detected in Najdi sheep GH gene (G871A, A1259C, G1383A, A1486G and A1509G). A significant association between the detected SNPs genotypes and daily milk yield was found in this study. The regression analysis indicated the positive effect of genotype and SNPs on DMY. Individuals carrying homozygote mutant alleles had the highest DMY. Consequently, these SNP may be useful indicators in the selection of ewes for milk production.

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