Chiral Ramachandran Plots II: General Trends and Protein Chirality Spectra

Biochemistry ◽  
2018 ◽  
Vol 57 (45) ◽  
pp. 6395-6403 ◽  
Author(s):  
Huan Wang ◽  
David Avnir ◽  
Inbal Tuvi-Arad
Keyword(s):  
Ramachandran Plots

scholarly journals Characterization of squalene synthase gene from Gymnema sylvestre R. Br.

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Kuldeepsingh A. Kalariya ◽  
Ram Prasnna Meena ◽  
Lipi Poojara ◽  
Deepa Shahi ◽  
Sandip Patel
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Competitive Inhibition ◽  
Sequence Data ◽  
Homology Model ◽  
Squalene Synthase ◽  
Gymnema Sylvestre ◽  
Gardenia Jasminoides ◽  
Ramachandran Plots ◽  
Flanking Regions

Abstract Background Squalene synthase (SQS) is a rate-limiting enzyme necessary to produce pentacyclic triterpenes in plants. It is an important enzyme producing squalene molecules required to run steroidal and triterpenoid biosynthesis pathways working in competitive inhibition mode. Reports are available on information pertaining to SQS gene in several plants, but detailed information on SQS gene in Gymnema sylvestre R. Br. is not available. G. sylvestre is a priceless rare vine of central eco-region known for its medicinally important triterpenoids. Our work aims to characterize the GS-SQS gene in this high-value medicinal plant. Results Coding DNA sequences (CDS) with 1245 bp length representing GS-SQS gene predicted from transcriptome data in G. sylvestre was used for further characterization. The SWISS protein structure modeled for the GS-SQS amino acid sequence data had MolProbity Score of 1.44 and the Clash Score 3.86. The quality estimates and statistical score of Ramachandran plots analysis indicated that the homology model was reliable. For full-length amplification of the gene, primers designed from flanking regions of CDS encoding GS-SQS were used to get amplification against genomic DNA as template which resulted in approximately 6.2-kb sized single-band product. The sequencing of this product through NGS was carried out generating 2.32 Gb data and 3347 number of scaffolds with N50 value of 457 bp. These scaffolds were compared to identify similarity with other SQS genes as well as the GS-SQSs of the transcriptome. Scaffold_3347 representing the GS-SQS gene harbored two introns of 101 and 164 bp size. Both these intronic regions were validated by primers designed from adjoining outside regions of the introns on the scaffold representing GS-SQS gene. The amplification took place when the template was genomic DNA and failed when the template was cDNA confirmed the presence of two introns in GS-SQS gene in Gymnema sylvestre R. Br. Conclusion This study shows GS-SQS gene was very closely related to Coffea arabica and Gardenia jasminoides and this gene harbored two introns of 101 and 164 bp size.

Dissociation Behavior of Doubly-Charged Tryptic Peptides:  Correlation of Gas-Phase Cleavage Abundance with Ramachandran Plots

2004 ◽  
Vol 126 (10) ◽  
pp. 3034-3035 ◽  
Author(s):  
Yingying Huang ◽  
Joseph M. Triscari ◽  
Ljiljana Pasa-Tolic ◽  
Gordon A. Anderson ◽  
Mary S. Lipton ◽  
...  
Keyword(s):  
Gas Phase ◽  
Tryptic Peptides ◽  
Ramachandran Plots ◽  
Doubly Charged

Exploration of the forbidden regions of the Ramachandran plot (ϕ-ψ) with QTAIM

2017 ◽  
Vol 19 (38) ◽  
pp. 26423-26434 ◽  
Author(s):  
Roya Momen ◽  
Alireza Azizi ◽  
Lingling Wang ◽  
Yang Ping ◽  
Tianlv Xu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Peptide Structure ◽  
Ramachandran Plot ◽  
Left Response ◽  
Forbidden Regions ◽  
Dark Green ◽  
Ramachandran Plots ◽  
Pale Green

Left: Response β is defined as: β = arccos(e̲2·y̲) with β* = arccos(e̲1·y̲). Right: QTAIM interpreted Ramachandran plots {(βϕ,βϕ*)-(βψ,βψ*)} ‘-’ is a hyphen and not a subtraction sign. Pale green and dark green crosses indicate the glycine, pink and red pluses represent the remaining amino acids (a.a.) in the magainin peptide structure.

scholarly journals Proteopedia entry: Ramachandran plots

2010 ◽  
Vol 38 (6) ◽  
pp. 430-430 ◽  
Author(s):  
Karl Oberholser
Keyword(s):  
Ramachandran Plots

scholarly journals 3D Structure of VP1 Structural Protein on Enterovirus A71 Using Swiss-Model

BIOEDUSCIENCE ◽  
2020 ◽  
Vol 4 (1) ◽  
pp. 37-47
Author(s):  
Suprianto ◽  
Made Budiarsa ◽  
Fatmah Dhafir
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Stable Structure ◽  
Target Protein ◽  
Dimensional Structure ◽  
Structural Protein ◽  
Three Dimensional Structure ◽  
Enterovirus A71 ◽  
And Function ◽  
Ramachandran Plots

Background: VP1 structural protein plays a role as a key player in the pathogenesis, has a uniqueness that is interesting enough to be studied by studying the nature and function of structural proteins VP1. This study aims to predict the three-dimensional structure of proteins VP1 on EV-A71. Methods: The target protein is obtained from UniProt server with an access code A0A097EV89using templates 4cey.1.A (PDB ID) were analyzed in silico by homology method using SWISS-MODEL server. Results: Analysis showed the target protein and the template has 95.29% identity and is composed of 297 amino acids with a value of -2.15 QMEAN. Structural protein VP1 in Ramachandran Plots have a stable structure, non-glycine residue in the outlier regions only around 0.34% (A53 ALA) Rated rotamer outliers 1.61%.    Conclusion: The three-dimensional structure model of the protein studied has a stable structure and the information obtained is useful for further research in developing vaccines for diseases caused by EV-A71.  

STUDY OF TWO BIOACTIVE PEPTIDES IN VACUUM AND SOLVENT BY MOLECULAR MODELING

2006 ◽  
Vol 17 (06) ◽  
pp. 825-839
Author(s):  
F. YAŞAR ◽  
K. DEMIR
Keyword(s):  
Molecular Modeling ◽  
Three Dimensional ◽  
Helical Structures ◽  
Surface Areas ◽  
Solvent Model ◽  
Letter Code ◽  
End Distance ◽  
Accessible Surface ◽  
High Level ◽  
Ramachandran Plots

The thermodynamic and structural properties of Tyrosine-Glycine-Leusine-Phenylalanine (YGLF, in a one letter code) and Lysine-Valine-Leusine-Proline-Valine-Proline-Glutamine (KVLPVPQ) peptide sequences were studied by three-dimensional molecular modeling in vacuum and solution. All the three-dimensional conformations of each peptide sequences were obtained by multicanonical simulations with using ECEPP/2 force field and each simulation started from completely random initial conformation. Solvation contributions are included by a term that is proportional to solvent-accessible surface areas of peptides. In the present study, we calculated the average values of total energy, specific heat, fourth-order cumulant and end-to-end distance for two peptide sequences of milk protein as a function of temperature. With using major advantage of this simulation technique, Ramachandran plots were prepared and analysed to predict the relative occurrence probabilities of β-turn, γ-turn and helical structures. Although structural predictions of these sequences indicate both the presence of high level of γ-turns and low level of β-turns in vacuum and solvent, it was observed that these probabilities in vacuum were higher than the ones in solvent model.

MOLECULAR MODELING OF TWO HEXAPEPTIDE REPEAT MOTIFS OF HMW GLUTENIN SUBUNITS

2001 ◽  
Vol 12 (02) ◽  
pp. 281-292 ◽  
Author(s):  
HANDAN ARKIN ◽  
FATİH YAŞAR ◽  
TARIK ÇELİK ◽  
SÜEDA ÇELİK ◽  
HAMİT KÖKSEL
Keyword(s):  
Three Dimensional ◽  
Glutenin Subunits ◽  
Central Domain ◽  
Hmw Glutenin Subunits ◽  
Simulation Procedure ◽  
Helical State ◽  
Letter Code ◽  
Hmw Glutenin ◽  
High Level ◽  
Ramachandran Plots

The three-dimensional structures of two hexapeptide repeat motifs (PGQGQQ and SGQGQQ, in one letter code) in the repetitive central domain of HMW glutenin subunits are investigated by using the multicanonical simulation procedure. Ramachandran plots were prepared and analyzed to predict the relative occurrence probabilities of β-turn and γ-turn structures and helical state. Structural predictions of PGQGQQ repeat motif indicated the presence of high level of β-turns and considerable level of γ-turns. Simulations of the repeat motifs in the repetitive central domain of HMW glutenin subunits indicated that these structures take important part in the three-dimensional structures of repeat motifs.

scholarly journals Identification and Computational Analysis of 3D-Structure Of MOCS1

2021 ◽  
Author(s):  
Maham Hamid ◽  
uzma habib ◽  
Javeria Batool ◽  
Arshemah Qaisar ◽  
Rehan Zafar Paracha
Keyword(s):  
Binding Sites ◽  
Biosynthetic Pathway ◽  
Computational Analysis ◽  
Tertiary Structure ◽  
3D Structure ◽  
Structure And Function ◽  
Molybdenum Cofactor ◽  
Recognition Method ◽  
And Function ◽  
Ramachandran Plots

Abstract Cyclic pyranopterin monophosphate (cPMP) is one of the most stable intermediates in Molybdenum cofactor (MoCo) biosynthetic pathway. In humans, synthesis of cPMP from Guanosine triphosphate (GTP) requires functional genes i.e. Molybdenum Cofactor Synthesis-1 (MOCS1) genes that contains for two catalytic proteins MOCS1A and MOCS1B. Importance of MOCS1A and MOCS1B for biosynthesis of MoCo reveals from the fact that its deficiency leads to MoCo type A deficiency. As there is no structure available for MOCS1 genes in the literature, tertiary structure of MOCS1 genes were investigated in this research via threading or folds recognition method by i-TASSER and validation was done using ERRAT, Verify3D and Ramachandran plots. Binding sites were predicted and validated. Docking of MOCS1A with GTP and MOCS1B with 3, 8 dihydroguanosine was done using Autodock via PyRx. Apart from this, highly confident mutations were also predicted using SIFT and polyphen2 that can alter the structure and function of MOCS1 gene.

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