scholarly journals Analisis In-Silico Struktur Tiga Dimensi Reseptor Trk A dan Trk B Protein Neurotrophin 3 Pada Gallus gallus (Chicken)

2020 ◽  
Vol 12 (2) ◽  
pp. 78-84
Author(s):  
Muhammad F. Rahman ◽  
Amiruddin Kasim ◽  
Muchlis L. Djirimu ◽  
I. Made Budiarsa
Keyword(s):  
Amino Acids ◽  
In Silico ◽  
Three Dimensional ◽  
Gallus Gallus ◽  
Dimensional Structure ◽  
Neurotrophin 3 ◽  
Trk A ◽  
And Function ◽  
Trk B ◽  
Ucsf Chimera

NT3 protein is expressed by Neurotrophin 3 (NTF-3) which plays a role in the process of differentiation, survival of peripheral and neuropathological of neurons. The information of structure and function of NT-3 proteins is still very limited, especially in Gallus gallus. This study aims to predict the three-dimensional structure of the Trk A and Trk B proteins in Gallus gallus. The target protein obtained from the UniProt server with access codes Q91009 (Trk A) and Q91987 (Trk B) using the 6kzc 1.A (PDB ID) template was analyzed in silico through a homology approach and describing the structural assessment using Chimera UCSF software. The analysis showed that the Trk A protein had a QMEAN value of -0.08, composed of 778 amino acids, mass 87334.30 Daltons, and Seq Identity 79.93%. Trk B had a QMEAN value of 0.16, consisting of 818 amino acids, mass 91732.05 Daltons, and Seq Identity 84.30%. Key words: NT3; homology; UCSF chimera; G. gallus

scholarly journals In Silico Characterization of Surface Glycoprotein [QHD43416] of Severe Acute Respiratory Syndrome-Coronavirus 2

2020 ◽  
Vol 3 (2) ◽  
pp. 32-36
Author(s):  
Rajneesh Prajapat ◽  
◽  
Suman Jain ◽  
Manish K Vaishnav ◽  
Sonal Sogani ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
In Silico ◽  
Three Dimensional ◽  
Surface Glycoprotein ◽  
Dimensional Structure ◽  
Model Quality ◽  
Core Section ◽  
Novel Coronavirus ◽  
And Function ◽  
Tools And Techniques

The novel coronavirus (SARS-CoV-2) reported from Wuhan, China, that spread rapidly and cause severe acute respiratory syndrome. The disease associated with infection of SARS-CoV-2 that is referred as COVID-19 (Coronavirus Disease 2019). In the present study, the surface glycoprotein [QHD43416] of SARS-CoV-2 was characterized for structure analysis and validation to provide information about its three-dimensional structure by using in silico tools and techniques. The surface glycoprotein [QHD43416] sequence of SARS-CoV-2 was retrieved from NCBI and its PDB file was designed by using phyre2 server. The RAMPAGE and UCLA-DOE (Verify 3D) was used for analysis and validation of structure model of protein. The model quality estimation based on the ProSA. Alignment of surface glycoprotein [QHD43416], revealed homology (72% identity) with spike protein of bat coronavirus [BM48-31/BGR/2008]. The model corresponding to probability conformation with 90.5% residue of core section, 9.1 % of allowed section and 0.4 % residue of outer section in φ-ψ plot, that specifies accuracy of prediction model. The Verify 3D results shows that 59.53% residues have average 3D-1D score >= 0.2 this determines compatibility of 3D model with its amino acid sequence (1D). ProSA Z-score -11.19 represents the good quality of the model. The structure and function of coronavirus surface glycoprotein could be predicted by in silico modeling studies. The protein model will be further used for designing of vaccine / drug development against coronavirus infection.

In silico analysis of Nattokinase from Bacillus subtilis sp natto

2017 ◽  
Vol 9 (04) ◽  
Author(s):  
Cambyz Irajie ◽  
Milad Mohkam ◽  
Navid Nezafat ◽  
Fatemeh Mohammadi ◽  
Younes Ghasemi
Keyword(s):  
Bacillus Subtilis ◽  
Serine Protease ◽  
In Silico ◽  
Three Dimensional ◽  
In Silico Analysis ◽  
Dimensional Structure ◽  
Cardiovascular Therapy ◽  
And Function ◽  
Outlier Region ◽  
Silico Analysis

Nattokinase or subtilisin NAT (EC 3.4.21.62) is one of the most remarkable enzymes produced by Bacillus subtilis sp. Natto, which posses direct fibrinolytic activity. The aim of this study is in silico analysis of Nattokinase structure and function. The three-dimensional structure of serine protease Nattokinase from Bacillus subtilis sp. natto was determined using homology modeling performed by Geno3D2 Web Server and refined by ModRefiner. The obtained models were validated via programs such as RAMPAGE, ERRAT, 3D Match and verify 3D for consistency; moreover, functional analysis performed by PFP from Kihara Bioinformatics laboratory. RAMPAGE analysis showed that 96.7% of the residues are located in the favored region, 3.0% in allowed region and 0.4% in outlier region of the Ramachandran plot. The verify 3D value of 0.73 indicates that the environmental sketch of the model is fine. SOPMA and PSIPRED were exploited for computation of the secondary structural properties of serine protease Nattokinase. Active site determination via AADS suggested that this enzyme can be applied as a potent enzyme for cardiovascular therapy. However, these results should be more confirmed by wet lab researches for designing the more active enzyme for better functions on its fibrinolysis activity.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Structural Role of rRNAs on the Ribosomal Subunits from E. Coli by Scanning Transmission Electron Microscopy

1981 ◽  
Vol 39 ◽  
pp. 424-425
Author(s):  
M. Boublik ◽  
N. Robakis ◽  
J.S. Wall
Keyword(s):  
Three Dimensional ◽  
Uranyl Acetate ◽  
Dimensional Structure ◽  
Electron Microscopic ◽  
Ribosomal Subunits ◽  
E Coli ◽  
Freeze Dried ◽  
16S Rna ◽  
Scanning Transmission ◽  
And Function

The three-dimensional structure and function of biological supramolecular complexes are, in general, determined and stabilized by conformation and interactions of their macromolecular components. In the case of ribosomes, it has been suggested that one of the functions of ribosomal RNAs is to act as a scaffold maintaining the shape of the ribosomal subunits. In order to investigate this question, we have conducted a comparative TEM and STEM study of the structure of the small 30S subunit of E. coli and its 16S RNA.The conventional electron microscopic imaging of nucleic acids is performed by spreading them in the presence of protein or detergent; the particles are contrasted by electron dense solution (uranyl acetate) or by shadowing with metal (tungsten). By using the STEM on freeze-dried specimens we have avoided the shearing forces of the spreading, and minimized both the collapse of rRNA due to air drying and the loss of resolution due to staining or shadowing. Figure 1, is a conventional (TEM) electron micrograph of 30S E. coli subunits contrasted with uranyl acetate.

scholarly journals Impact of genetic variation on three dimensional structure and function of proteins

PLoS ONE ◽  
2017 ◽  
Vol 12 (3) ◽  
pp. e0171355 ◽  
Author(s):  
Roshni Bhattacharya ◽  
Peter W. Rose ◽  
Stephen K. Burley ◽  
Andreas Prlić
Keyword(s):  
Genetic Variation ◽  
Three Dimensional ◽  
Structure And Function ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
And Function

The Study on the Clinical Phenotype and Function of HPRT1 Gene

2021 ◽  
Author(s):  
Miao Guo ◽  
Yucai Chen ◽  
Longlong Lin ◽  
Yilin Wang ◽  
Anqi Wang ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Clinical Manifestations ◽  
Protein Translation ◽  
Dimensional Structure ◽  
Normal Individuals ◽  
Second Generation Sequencing ◽  
Self Harm ◽  
And Function ◽  
Neurogenetic Disease ◽  
Generation Sequencing

Abstract Background: Lesch-Nyhan disease (LND) is a rare x-linked purine metabolic neurogenetic disease caused by enzyme hypoxanthine-guanine phosphoriribosyltransferase(HGprt) deficiency, also known as self-destructive appearance syndrome. A series of manifestations are caused by abnormal purine metabolism. The typical clinical manifestations are hyperuricemia, growth retardation, mental retardation, short stature, dance-like athetosis, aggressive behavior, and compulsive self-harm.. Results: we identified a point mutation c.151C > T (p. Arg51*) in a pedigree. We analyzed the clinical characteristics of children in a family, and obtained the blood of their parents and siblings for second-generation sequencing. At the same time, we also analyzed and compared the expression of HPRT1 gene and predicted the three-dimensional structure of the protein. And we analyzed the clinical manifestations caused by the defect of the HPRT1 genethe mutation led to the termination of transcription at the 51st arginine, resulting in the production of truncated protein, and the relative expression of HPRT1 gene in patients was significantly lower than other family members and 10 normal individuals. Conclusion: this mutation leads to the early termination of protein translation and the formation of a truncated HPRT protein, which affects the function of the protein and generates corresponding clinical manifestations.

scholarly journals Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
A.E. Naas ◽  
A.K. MacKenzie ◽  
B. Dalhus ◽  
V.G.H. Eijsink ◽  
P.B. Pope
Keyword(s):  
Active Site ◽  
Three Dimensional ◽  
Structural Features ◽  
Structure And Function ◽  
Dimensional Structure ◽  
Active Site Cleft ◽  
Polysaccharide Utilization Locus ◽  
And Function ◽  
Rumen Metagenome

Abstract Previous gene-centric analysis of a cow rumen metagenome revealed the first potentially cellulolytic polysaccharide utilization locus, of which the main catalytic enzyme (AC2aCel5A) was identified as a glycoside hydrolase (GH) family 5 endo-cellulase. Here we present the 1.8 Å three-dimensional structure of AC2aCel5A and characterization of its enzymatic activities. The enzyme possesses the archetypical (β/α)8-barrel found throughout the GH5 family and contains the two strictly conserved catalytic glutamates located at the C-terminal ends of β-strands 4 and 7. The enzyme is active on insoluble cellulose and acts exclusively on linear β-(1,4)-linked glucans. Co-crystallization of a catalytically inactive mutant with substrate yielded a 2.4 Å structure showing cellotriose bound in the −3 to −1 subsites. Additional electron density was observed between Trp178 and Trp254, two residues that form a hydrophobic “clamp”, potentially interacting with sugars at the +1 and +2 subsites. The enzyme’s active-site cleft was narrower compared to the closest structural relatives, which in contrast to AC2aCel5A, are also active on xylans, mannans and/or xyloglucans. Interestingly, the structure and function of this enzyme seem adapted to less-substituted substrates such as cellulose, presumably due to the insufficient space to accommodate the side-chains of branched glucans in the active-site cleft.

Multiplicity spin, structure, and charge of iron-verdohemeoxygenase complex: A comparison study by the DFT method

2020 ◽  
Vol 24 (10) ◽  
pp. 1208-1214
Author(s):  
Hamideh Tasharofi ◽  
Maryam Daghighi Asli ◽  
Parisa Rajabali Jamaat
Keyword(s):  
Heme Oxygenase ◽  
Density Functional ◽  
Complex Structure ◽  
Three Dimensional ◽  
Dft Method ◽  
Basis Set ◽  
Dimensional Structure ◽  
Central Metal ◽  
Stable States ◽  
And Function

Recently the three-dimensional structure of verdoheme heme oxygenase complex was revealed. However, many parameters of verdoheme heme oxygenase’s complex structure and their role and function on Heme degradation were unknown. In this work the structure of iron verdoheme in complex with heme oxygenase was compared by the density functional theory (DFT)-based B3LYP method using the 6-31G basis set. Many parameters such as charge of verdoheme and iron as central metal, electron distribution, spin multiplicity of the molecule and proximal substituents effects on verdoheme ring stabilization and their arrangement are discussed and compared for twelve different conformations of the molecules to find the most energetically stable states.

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