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Journal articles on the topic 'Ramachandran plot'

Author: Grafiati

Published: 4 June 2021

Last updated: 11 February 2022

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1

Sheik, S. S., P. Sundararajan, A. S. Z. Hussain, and K. Sekar. "Ramachandran plot on the web." Bioinformatics 18, no. 11 (November 1, 2002): 1548–49. http://dx.doi.org/10.1093/bioinformatics/18.11.1548.

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2

Carugo, Oliviero, and Kristina Djinović-Carugo. "A proteomic Ramachandran plot (PRplot)." Amino Acids 44, no. 2 (September 25, 2012): 781–90. http://dx.doi.org/10.1007/s00726-012-1402-z.

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3

K. Gopalakrishnan, G. Sowmiya, S. S. Sheik, and K. Sekar. "Ramachandran Plot on The Web (2.0)." Protein & Peptide Letters 14, no. 7 (July 1, 2007): 669–71. http://dx.doi.org/10.2174/092986607781483912.

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4

Gopalakrishnan, K., S. Saravanan, R. Sarani, and K. Sekar. "RPMS: Ramachandran plot for multiple structures." Journal of Applied Crystallography 41, no. 1 (January 16, 2008): 219–21. http://dx.doi.org/10.1107/s0021889807053708.

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An interactive internet computing server,RPMS(Ramachandran plot for multiple structures) has been developed to visualize the Ramachandran angles of several highly homologous protein structures in a single plot. Options are provided for users to locate the amino acid residues in various regions of the plot. To perform the above, users need to enter the Protein Data Bank (PDB) identification codes. In addition, users can upload the atomic coordinates from the local machine. A Java graphics interface has been deployed and the server has been interfaced with a locally maintained PDB anonymous FTP server, which is updated weekly. The serverRPMScan be accessed through the Bioinformatics web server at http://cluster.physics.iisc.ernet.in/rpms/.

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5

Iwaoka, M., M. Okada, and S. Tomoda. "Quantum Chemical Study of Ramachandran Plot." Seibutsu Butsuri 39, supplement (1999): S115. http://dx.doi.org/10.2142/biophys.39.s115_1.

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6

Hollingsworth, Scott A., and P. Andrew Karplus. "A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins." BioMolecular Concepts 1, no. 3-4 (October 1, 2010): 271–83. http://dx.doi.org/10.1515/bmc.2010.022.

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AbstractThe Ramachandran plot is among the most central concepts in structural biology, seen in publications and textbooks alike. However, with the increasing numbers of known protein structures and greater accuracy of ultra-high resolution protein structures, we are still learning more about the basic principles of protein structure. Here, we use high-fidelity conformational information to explore novel ways, such as geo-style and wrapped Ramachandran plots, to convey some of the basic aspects of the Ramachandran plot and of protein conformation. We point out the pressing need for a standard nomenclature for peptide conformation and propose such a nomenclature. Finally, we summarize some recent conceptual advances related to the building blocks of protein structure. The results for linear groups imply the need for substantive revisions in how the basics of protein structure are handled.

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7

Mannige, Ranjan V. "An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)." PeerJ 5 (May 16, 2017): e3327. http://dx.doi.org/10.7717/peerj.3327.

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The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing the φ and ψ values of a peptide (e.g., is the regular peptide defined by φ = ψ = − 100° left-handed or right-handed?). This report provides a new metric for backbone handedness (h) based on interpreting a peptide backbone as a helix with axial displacement d and angular displacement θ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral angles φ, ψ and ω. In particular, h equals sin(θ)d∕|d|, with range [−1, 1] and negative (or positive) values indicating left(or right)-handedness. The metric h is used to characterize the handedness of every region of the Ramachandran plot for both cis (ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ, ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based on d and θ that serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone including cis and trans backbones. The intuitiveness arises from the fact that d and θ provide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity.

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8

Zhou, Alice Qinhua, Corey S. O'Hern, and Lynne Regan. "Revisiting the Ramachandran plot from a new angle." Protein Science 20, no. 7 (May 31, 2011): 1166–71. http://dx.doi.org/10.1002/pro.644.

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9

Porter, Lauren L., and George D. Rose. "Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints." Proceedings of the National Academy of Sciences 108, no. 1 (December 8, 2010): 109–13. http://dx.doi.org/10.1073/pnas.1014674107.

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A protein backbone has two degrees of conformational freedom per residue, described by its φ,ψ-angles. Accordingly, the energy landscape of a blocked peptide unit can be mapped in two dimensions, as shown by Ramachandran, Sasisekharan, and Ramakrishnan almost half a century ago. With atoms approximated as hard spheres, the eponymous Ramachandran plot demonstrated that steric clashes alone eliminate ¾ of φ,ψ-space, a result that has guided all subsequent work. Here, we show that adding hydrogen-bonding constraints to these steric criteria eliminates another substantial region of φ,ψ-space for a blocked peptide; for conformers within this region, an amide hydrogen is solvent-inaccessible, depriving it of a hydrogen-bonding partner. Yet, this “forbidden” region is well populated in folded proteins, which can provide longer-range intramolecular hydrogen-bond partners for these otherwise unsatisfied polar groups. Consequently, conformational space expands under folding conditions, a paradigm-shifting realization that prompts an experimentally verifiable conjecture about likely folding pathways.

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10

Porter, Lauren L., and George D. Rose. "Comment on “Revisiting the Ramachandran plot from a new angle”." Protein Science 20, no. 11 (October 13, 2011): 1771–73. http://dx.doi.org/10.1002/pro.724.

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11

Chen, Y. W. "A program to generate the Ramachandran plot using Microsoft Excel." Journal of Applied Crystallography 27, no. 4 (August 1, 1994): 660–61. http://dx.doi.org/10.1107/s0021889893014153.

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12

KOLASKAR, A. S., and SANGEETA SAWANT. "Prediction of conformational states of amino acids using a Ramachandran plot." International Journal of Peptide and Protein Research 47, no. 1-2 (January 12, 2009): 110–16. http://dx.doi.org/10.1111/j.1399-3011.1996.tb00817.x.

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13

Parchaňský, Václav, Josef Kapitán, Jakub Kaminský, Jaroslav Šebestík, and Petr Bouř. "Ramachandran Plot for Alanine Dipeptide as Determined from Raman Optical Activity." Journal of Physical Chemistry Letters 4, no. 16 (August 5, 2013): 2763–68. http://dx.doi.org/10.1021/jz401366j.

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14

P., Praveen Reddy. "Modeling and validation of L-asparaginase enzyme, an anticancer agent using the tools of computational biology." International Journal of Research in Medical Sciences 8, no. 1 (December 25, 2019): 211. http://dx.doi.org/10.18203/2320-6012.ijrms20195909.

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Background: The L-Asparaginase is a medically important drug. The L-Asparaginase enzyme, an anticancer agent produced by microorganisms is used for the treatment of patients suffering from lymphoma and leukemia. The L-Asparaginase is economical and its administration is easy when compared to other commercial drugs available in market. Many microbes have been reported to produce the L-Asparaginase.Methods: In the present work the sequence of L-Asparaginase enzyme protein was obtained from the Universal Protein Resource (UNIPROT) server. The sequence of L-Asparaginase was used to generate 3-D model of L-Asparaginase in SWISS MODEL server. The constructed L-Asparaginase model was verified using Ramachandran Plot in PROCHECK server.Results: The FASTA format of L-Asparaginase enzyme of Bacillus subtilis strain 168 was retrieved from UNIPROT server. The FASTA format of L-Asparaginase was submitted to SWISS MODEL and its three-dimensional structural model was developed based on relevant template model. The model structure of L-Asparaginase was validated in PROCHECK server using Ramachandran Plot. The Ramachandran Plot of L-Asparaginase model inferred the reliability of L-Asparaginase structure model developed in SWISS MODEL server. Conclusions: In the present study computational tools were exploited to develop and validate a potent anticancer drug, L-Asparaginase. Further the modeled L-Asparaginase enzyme protein can be improved using advanced bioinformatics tools and the same improved enzyme can be produced by improving the L-Asparaginase producing microbial strains by site-directed mutagenesis in the corresponding gene.

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15

Grygorenko, Oleksandr O., Daryna Demenko, Dmitry M. Volochnyuk, and Igor V. Komarov. "Following Ramachandran 2: exit vector plot (EVP) analysis of disubstituted saturated rings." New Journal of Chemistry 42, no. 11 (2018): 8355–65. http://dx.doi.org/10.1039/c7nj05015a.

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16

Zhou, Alice Qinhua, Corey S. O'Hern, and Lynne Regan. "Reply to: Comment on “Revisiting the Ramachandran plot from a new angle”." Protein Science 20, no. 11 (October 13, 2011): 1774. http://dx.doi.org/10.1002/pro.722.

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17

Hooft, Rob W. W., Chris Sander, and Gerrit Vriend. "Objectively judging the quality of a protein structure from a Ramachandran plot." Bioinformatics 13, no. 4 (1997): 425–30. http://dx.doi.org/10.1093/bioinformatics/13.4.425.

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18

Serov, A. E., E. R. Odintzeva, I. V. Uporov, and V. I. Tishkov. "Use of Ramachandran Plot for Increasing Thermal Stability of Bacterial Formate Dehydrogenase." Biochemistry (Moscow) 70, no. 7 (July 2005): 804–8. http://dx.doi.org/10.1007/s10541-005-0187-z.

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19

Momen, Roya, Alireza Azizi, Lingling Wang, Yang Ping, Tianlv Xu, Steven R. Kirk, Wenxuan Li, Sergei Manzhos, and Samantha Jenkins. "Exploration of the forbidden regions of the Ramachandran plot (ϕ-ψ) with QTAIM." Phys. Chem. Chem. Phys. 19, no. 38 (2017): 26423–34. http://dx.doi.org/10.1039/c7cp05124g.

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Left: Response β is defined as: β = arccos(e̲₂·y̲) with β* = arccos(e̲₁·y̲). Right: QTAIM interpreted Ramachandran plots {(β_ϕ,β_ϕ*)-(β_ψ,β_ψ*)} ‘-’ 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.

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20

Malagón Bernal, Rafael Eduardo, Manuel Alejandro Fernández Navas, and Orlando Emilio Acevedo Sarmiento. "Modelo molecular teórico del receptor serotoninérgico 5HT2A acoplado a proteína G." Universitas Scientiarum 17, no. 2 (June 1, 2012): 119. http://dx.doi.org/10.11144/javeriana.sc17-2.tmmo.

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<strong>Objective</strong> Build a theoretical molecular model of the tertiary structure of the Homo sapiens 5HT2A receptor from experimentally obtained structures as templates. <strong>Materials</strong> <strong>and methods</strong> In the construction of the theoretical model we considered the protocol established by Ballesteros and Weinstein for the construction of the G-protein coupled receptor, by the alignment of the amino acid sequence, hydrophobicity profiles, refinement of loops by spatial restrictions and energy minimization with the force field OPLS_2005. <strong>Results</strong> The resulting model was validated by the Ramachandran plot with 91.7% of amino acids within the limits set for angles phi and psi and a RMSD of 0.95 Å with respect to bovine rhodopsin. <strong>Conclusions</strong> We obtained a validated theoretical model useful in studies of ligand-receptor docking.<br /><strong>Key words</strong>: G protein receptor, hydrophobicity profile, Ramachandran plot, orthosteric site, molecular modelling.

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21

SZABADKA, ZOLTÁN, RAFAEL ÖRDÖG, and VINCE GROLMUSZ. "THE RAMACHANDRAN MAP OF MORE THAN 6,500 PERFECT POLYPEPTIDE CHAINS." Biophysical Reviews and Letters 02, no. 03n04 (October 2007): 267–71. http://dx.doi.org/10.1142/s1793048007000519.

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The Protein Data Bank (PDB) is the most important depository of protein structural information, containing more than 45,000 deposited entries today. Because of its inhomogeneous structure, its fully automated processing is almost impossible. In a previous work, we cleaned and re-structured the entries in the Protein Data Bank, and from the result we have built the RS-PDB database. Using the RS-PDB database, we draw a Ramachandran-plot from 6,593 "perfect" polypeptide chains found in the PDB, containing 1,192,689 residues. This is a more than tenfold increase in the size of data analyzed before this work. The density of the data points makes it possible to draw a logarithmic heat map enhanced Ramachandran map, showing the fine inner structure of the right-handed α-helix region.

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22

Gopukumar, S. T., Sreeya G. Nair, R. Radha, N. V. Sugathan, Anooj E. S, and Lekshmi Gangadhar. "Three dimensional structure modeling and ramachandran plot analysis of autographa californica nucleopolyhdro viral protein." Annals of Tropical Medicine and Public Health 23, no. 06 (2020): 207–14. http://dx.doi.org/10.36295/asro.2020.23626.

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23

Gromiha, M. Michael, Motohisa Oobatake, Hidetoshi Kono, Hatsuho Uedaira, and Akinori Sarai. "Importance of mutant position in Ramachandran plot for predicting protein stability of surface mutations." Biopolymers 64, no. 4 (June 3, 2002): 210–20. http://dx.doi.org/10.1002/bip.10125.

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24

Jiang, Zhongming, Malgorzata Biczysko, and Nigel W. Moriarty. "Accurate geometries for “Mountain pass” regions of the Ramachandran plot using quantum chemical calculations." Proteins: Structure, Function, and Bioinformatics 86, no. 3 (January 12, 2018): 273–78. http://dx.doi.org/10.1002/prot.25451.

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25

Gromiha, M. Michael, M. Oobatake, H. Kono, H. Uedaira, and A. Sarai. "Importance of Mutant Position in Ramachandran Plot for Predicting Protein Stability upon Surface Mutations." Seibutsu Butsuri 40, supplement (2000): S117. http://dx.doi.org/10.2142/biophys.40.s117_2.

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26

Cao, Chen, Lincong Wang, Xiaoyang Chen, Shuxue Zou, Guishen Wang, and Shutan Xu. "Amino Acids in Nine Ligand-Prefer Ramachandran Regions." BioMed Research International 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/757495.

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Several secondary structures, such asπ-helix and left-handed helix, have been frequently identified at protein ligand-binding sites. A secondary structure is considered to be constrained to a specific region of dihedral angles. However, a comprehensive analysis of the correlation between main chain dihedral angles and ligand-binding sites has not been performed. We undertook an extensive analysis of the relationship between dihedral angles in proteins and their distance to ligand-binding sites, frequency of occurrence, molecular potential energy, amino acid composition, van der Waals contacts, and hydrogen bonds with ligands. The results showed that the values of dihedral angles have a strong preference for ligand-binding sites at certain regions in the Ramachandran plot. We discovered that amino acids preceding the ligand-preferϕ/ψbox residues are exposed more to solvents, whereas amino acids following ligand-preferϕ/ψbox residues form more hydrogen bonds and van der Waals contacts with ligands. Our method exhibited a similar performance compared with the program Ligsite-csc for both ligand-bound structures and ligand-free structures when just one ligand-binding site was predicted. These results should be useful for the prediction of protein ligand-binding sites and for analysing the relationship between structure and function.

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27

Ho, Bosco K., Annick Thomas, and Robert Brasseur. "Revisiting the Ramachandran plot: Hard-sphere repulsion, electrostatics, and H-bonding in the α-helix." Protein Science 12, no. 11 (January 1, 2009): 2508–22. http://dx.doi.org/10.1110/ps.03235203.

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28

Pandit, Rakesh K. R., Dinesh Gupta, and Tapan K. Mukherjee. "IDENTIFICATION OF POTENTIAL SALMONELLA TYPHI BETA-LACTAMASE TEM 1 INHIBITORS USING PEPTIDOMIMETICS, VIRTUAL SCREENING, AND MOLECULAR DYNAMICS SIMULATIONS." International Journal of Pharmacy and Pharmaceutical Sciences 10, no. 1 (January 1, 2018): 91. http://dx.doi.org/10.22159/ijpps.2018v10i1.21520.

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Objective: The purpose of this study was to identify a potential peptidomimetic S. typhi Beta-lactamase TEM 1 inhibitor to tackle the antibiotic resistance among S. typhi.Methods: The potential peptidomimetic inhibitor was identified by in silico docking of the small peptide WFRKQLKW with S. typhi Beta-lactamase TEM 1. The 3D coordinate geometry of the residues of small peptide interacting with the active site of the receptor was generated and mimics were identified using PEP: MMs: MIMIC server. All the identified mimics were docked at the active site of the receptor using Autodock 4.2 and the best-docked complex was selected on the basis of binding energy and number of H-bonds. The complex was then subjected to molecular dynamics simulations of 30 ns using AMBER 12 software package. The stereochemical stability of the Beta-lactamase TEM 1-WFRKQLKW complex was estimated with the help of Ramachandran plot using PROCHECK tool.Results: In the present study, a new potential peptidomimetic inhibitor (ZINC05839264) of Beta-lactamase TEM 1 has been identified based on antimicrobial peptide WFRKQLKW by virtual screening of the MMsINC database. The docking and molecular simulation studies revealed that the mimic binds more tightly to the active site of the receptor than the peptide. The Ramachandran plot also shows that the Beta-lactamase TEM 1-mimic complex is stereo chemically more stable than Beta-lactamase TEM 1-WFRKQLKW complex as more number of residues (93.6%) are falling under the core region of the plot in case of the former.Conclusion: The study shows that the peptidomimetic compound can act as a potential inhibitor of S. typhi Beta-lactamase TEM 1 and further it can be developed into more effective therapeutic to tackle the problem of antibiotic resistance.

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29

Torshin, Ivan Yu, Natalya G. Esipova, and Vladimir G. Tumanyan. "Alternatingly twisted β-hairpins and nonglycine residues in the disallowed II′ region of the Ramachandran plot." Journal of Biomolecular Structure and Dynamics 32, no. 2 (February 5, 2013): 198–208. http://dx.doi.org/10.1080/07391102.2012.759451.

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30

Maxwell, Peter I., and Paul L. A. Popelier. "Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective." Journal of Computational Chemistry 38, no. 29 (August 25, 2017): 2459–74. http://dx.doi.org/10.1002/jcc.24904.

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31

Callahan, T., W. B. Gleason, and T. P. Lybrand. "PAP: a protein analysis package." Journal of Applied Crystallography 23, no. 5 (October 1, 1990): 434–36. http://dx.doi.org/10.1107/s0021889890004228.

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A program package has been assembled for the analysis of protein coordinates which are in the Brookhaven Protein Data Bank (PDB) format. These programs can be used to make two types of φ–ψ plots: a Ramachandran-style scatter plot, and a plot of φ and ψ values as a function of the linear sequence. Programs are also available for the display of distance diagonal plots for proteins. Two protein structures can be compared and the resulting r.m.s. differences in the structures plotted as a function of sequence. Temperature factors can be analyzed and plotted as a function of the linear sequence. In addition, various utilities are supplied for splitting PDB files which contain multiple subunits into individual files and also for renumbering PDB files. A utility is also provided for converting Amber-style PDB files into standard PDB files. Priestle's program RIBBON [J. Appl. Cryst. (1988), 21, 572–576] has been converted to run in a stand-alone mode with interactive rotation of the three-dimensional ribbon picture. Programs are Silicon Graphics four-dimensional level and have been tested on 4D70/GT and personal Iris workstations, although programs which give Postscript output have been converted to run on Digital Equipment Corporation VAX computers and Sun workstations.

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32

van Beusekom, Bart, George Damaskos, Maarten L. Hekkelman, Fernando Salgado-Polo, Yoshitaka Hiruma, Anastassis Perrakis, and Robbie P. Joosten. "LAHMA: structure analysis through local annotation of homology-matched amino acids." Acta Crystallographica Section D Structural Biology 77, no. 1 (January 1, 2021): 28–40. http://dx.doi.org/10.1107/s2059798320014473.

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Comparison of homologous structure models is a key step in analyzing protein structure. With a wealth of homologous structures, comparison becomes a tedious process, and often only a small (user-biased) selection of data is used. A multitude of structural superposition algorithms are then typically used to visualize the structures together in 3D and to compare them. Here, the Local Annotation of Homology-Matched Amino acids (LAHMA) website (https://lahma.pdb-redo.eu) is presented, which compares any structure model with all of its close homologs from the PDB-REDO databank. LAHMA displays structural features in sequence space, allowing users to uncover differences between homologous structure models that can be analyzed for their relevance to chemistry or biology. LAHMA visualizes numerous structural features, also allowing one-click comparison of structure-quality plots (for example the Ramachandran plot) and `in-browser' structural visualization of 3D models.

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33

Coe, James V., Steven V. Nystrom, Zhaomin Chen, Ran Li, Dominique Verreault, Charles L. Hitchcock, Edward W. Martin, and Heather C. Allen. "Extracting Infrared Spectra of Protein Secondary Structures Using a Library of Protein Spectra and the Ramachandran Plot." Journal of Physical Chemistry B 119, no. 41 (September 30, 2015): 13079–92. http://dx.doi.org/10.1021/acs.jpcb.5b08052.

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34

Nazari-Robati, Mahdieh, Khosro Khajeh, Mahdi Aminian, Nasrin Mollania, and Abolfazl Golestani. "Enhancement of thermal stability of chondroitinase ABC I by site-directed mutagenesis: An insight from Ramachandran plot." Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1834, no. 2 (February 2013): 479–86. http://dx.doi.org/10.1016/j.bbapap.2012.11.002.

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35

Krebs, Frederik C., and Mikkel Jørgensen. "On the Conformational Properties of [n]Cyclophanes. A New Application of the Ramachandran Plot Using Crystallographic Data." Journal of Organic Chemistry 65, no. 12 (June 2000): 3846–49. http://dx.doi.org/10.1021/jo000166i.

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36

Tam, Benjamin, Siddharth Sinha, and San Ming Wang. "Combining Ramachandran plot and molecular dynamics simulation for structural-based variant classification: Using TP53 variants as model." Computational and Structural Biotechnology Journal 18 (2020): 4033–39. http://dx.doi.org/10.1016/j.csbj.2020.11.041.

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37

Keating, Kevin S., Elisabeth L. Humphris, and Anna Marie Pyle. "A new way to see RNA." Quarterly Reviews of Biophysics 44, no. 4 (May 18, 2011): 433–66. http://dx.doi.org/10.1017/s0033583511000059.

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AbstractUnlike proteins, the RNA backbone has numerous degrees of freedom (eight, if one counts the sugar pucker), making RNA modeling, structure building and prediction a multidimensional problem of exceptionally high complexity. And yet RNA tertiary structures are not infinite in their structural morphology; rather, they are built from a limited set of discrete units. In order to reduce the dimensionality of the RNA backbone in a physically reasonable way, a shorthand notation was created that reduced the RNA backbone torsion angles to two (η and θ, analogous to φ and ψ in proteins). When these torsion angles are calculated for nucleotides in a crystallographic database and plotted against one another, one obtains a plot analogous to a Ramachandran plot (the η/θ plot), with highly populated and unpopulated regions. Nucleotides that occupy proximal positions on the plot have identical structures and are found in the same units of tertiary structure. In this review, we describe the statistical validation of the η/θ formalism and the exploration of features within the η/θ plot. We also describe the application of the η/θ formalism in RNA motif discovery, structural comparison, RNA structure building and tertiary structure prediction. More than a tool, however, the η/θ formalism has provided new insights into RNA structure itself, revealing its fundamental components and the factors underlying RNA architectural form.

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38

Vyshnavi, Hima, Aswin Mohan, Shahanas Naisam, Suvanish Kumar, and Nidhin Sreekumar. "Homology Modeling and Evaluation of Sars-Cov-2 Spike Protein Mutant." International Journal of Quantitative Structure-Property Relationships 6, no. 4 (October 2021): 38–55. http://dx.doi.org/10.4018/ijqspr.2021100103.

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Severe acute respiratory syndrome coronavirus 2 (SARS‐Cov-2), a global pandemic, affected the world, increasing every day. A mutated variant D614G, showing more virulence and transmission, was studied for forecasting the emergence of more virulent and pathogenic viral strains. This study focuses on structure modeling and validation. Characterization of proteins homologous to wild spike protein was done, and homology models of the mutated variant were modeled using these proteins. Validation of models was done using Ramachandran plot and ERRAT plot. Molecular dynamics simulation was used to validate the stability of the models, and binding affinity of these models were estimated by molecular docking with an approved antiviral drug. Docked complexes were studied and the best model was selected. Molecular dynamics simulation was used to estimate the stability of the docked complex. The model of 6VXX, a homologous of wild spike protein, was found to be stable with the interaction of the antiviral drug from this study.

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39

Valli S, Abiraami, and Mythili T. "BIOINFORMATIC STUDY OF AN ANTITUMOR PROTEIN, AZURIN." Asian Journal of Pharmaceutical and Clinical Research 11, no. 6 (June 7, 2018): 169. http://dx.doi.org/10.22159/ajpcr.2018.v11i6.23339.

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Objective: The main objective of this study is to analyze the structure and function of an antitumor protein, azurin, thereby giving validation to the protein structure and existing physicochemical properties in the anticancer protein which are responsible for the anticancer activity.Methods: Protein sequence analysis was done using Basic Local Alignment Search Tool (BLAST) with ten different randomly selected species of Pseudomonas obtained from GenBank. The physicochemical properties, prediction of secondary structure, identification of motifs and domains, three-dimensional (3-D) structure of the antitumor protein, validation through Ramachandran plot, multiple sequence alignment (MSA), and phylogenetic analysis were studied and functional property was confirmed through in silico docking.Results: The similarity search (BLAST-P analysis) for the primary sequence from GenBank carried out showed 86% similarity to the second sequence, azurin (Pseudomonas nitroreducens). The ProtParam, ExPASy tool server indicated the presence of essential physicochemical properties in azurin. Secondary structure prediction revealed random coil, extended strand, alpha helix, and beta turn. The study on domains indicated the presence of one domain in azurin responsible for the anticancer activity. The 3-D structural analysis revealed azurin as metalloprotein, of length-128, and polymer-1 with α-helices, β-sheets, and β-barrels. The validation carried out through Ramachandran plot showed the presence of two outliers (phi and psi). The biological relationship between the input sequences was studied through MSA and phylogenetic analysis. Further, azurin docked against the target protein (p53 tumor suppressor) showed the maximum binding affinity confirming its functional property of causing apoptosis.Conclusion: All the properties analyzed in the present study revealed that the azurin protein can act as a very good anticancer agent, and through the phylogenetic analysis, it was identified that Pseudomonas nitroreducens was closely related to the test organism Pseudomonas aeruginosa.

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Anil, Burcu, Benben Song, Yuefeng Tang, and Daniel P. Raleigh. "Exploiting the Right Side of the Ramachandran Plot: Substitution of Glycines byd-Alanine Can Significantly Increase Protein Stability." Journal of the American Chemical Society 126, no. 41 (October 2004): 13194–95. http://dx.doi.org/10.1021/ja047119i.

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Vega, M. Cristina, Luis Serrano, and Jose C. Martínez. "Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II′ region of the Ramachandran plot." Protein Science 9, no. 12 (2000): 2322–28. http://dx.doi.org/10.1110/ps.9.12.2322.

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Puiggalí, Jordi, and Juan A. Subirana. "An experimental Ramachandran plot for retropeptide derivatives: Conformational features of derivatives of GEM-diamino and malonyl amino acids." Biopolymers 45, no. 2 (February 1998): 149–55. http://dx.doi.org/10.1002/(sici)1097-0282(199802)45:2<149::aid-bip5>3.0.co;2-s.

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Wang, Wei, Minxuan Xia, Jie Chen, Fenni Deng, Rui Yuan, Xiaopei Zhang, and Fafu Shen. "Data set for phylogenetic tree and RAMPAGE Ramachandran plot analysis of SODs in Gossypium raimondii and G. arboreum." Data in Brief 9 (December 2016): 345–48. http://dx.doi.org/10.1016/j.dib.2016.05.025.

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Croll, Tristan Ian. "The rate ofcis–transconformation errors is increasing in low-resolution crystal structures." Acta Crystallographica Section D Biological Crystallography 71, no. 3 (February 26, 2015): 706–9. http://dx.doi.org/10.1107/s1399004715000826.

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Cis-peptide bonds (with the exception ofX-Pro) are exceedingly rare in native protein structures, yet a check for these is not currently included in the standard workflow for some common crystallography packages nor in the automated quality checks that are applied during submission to the Protein Data Bank. This appears to be leading to a growing rate of inclusion of spuriouscis-peptide bonds in low-resolution structures both in absolute terms and as a fraction of solved residues. Most concerningly, it is possible for structures to contain very large numbers (>1%) of spuriouscis-peptide bonds while still achieving excellent quality reports fromMolProbity, leading to concerns that ignoring such errors is allowing software to overfit maps without producing telltale errors in, for example, the Ramachandran plot.

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PUIGGALI, J., and J. A. SUBIRANA. "ChemInform Abstract: An Experimental Ramachandran Plot for Retropeptide Derivatives: Conformational Features of Derivatives of gem-Diamino and Malonyl Amino Acids." ChemInform 29, no. 21 (June 22, 2010): no. http://dx.doi.org/10.1002/chin.199821275.

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Momen, Roya, Alireza Azizi, Lingling Wang, Ping Yang, Tianlv Xu, Steven R. Kirk, Wenxuan Li, Sergei Manzhos, and Samantha Jenkins. "The role of weak interactions in characterizing peptide folding preferences using a QTAIM interpretation of the Ramachandran plot (ϕ-ψ)." International Journal of Quantum Chemistry 118, no. 2 (August 17, 2017): e25456. http://dx.doi.org/10.1002/qua.25456.

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Tharuni, Boya, T. Sathish, G. Nadana Raja Vadivu, and K. Vasumathi. "IN SILICO ANALYSIS OF DELTA 6 DESATURASE - A KEY ENZYME FOR OMEGA Â€“3/6Â€“ FATTY ACID PRODUCTION." International Journal of Advanced Research 9, no. 02 (February 28, 2021): 818–23. http://dx.doi.org/10.21474/ijar01/12519.

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Delta 6 desaturase is a key enzyme involved in the production of omega 3/6 fatty acids and it is the rate-limiting step. The study aims to characterize the delta 6 desaturase enzyme and to find the binding affinity of various ligand with the protein by docking. It is found that delta 6 desaturase enzyme sequence is very unique and has less similarity with the other desaturase protein. The structural analysis was performed by Ramachandran plot and SCOPe structure prediction. Modeller is used to determine the DOPE score of the selected enzyme. The lowest DOPE score protein is chosen to determine the binding affinity of ligand molecules. Three different ligands were selected and its interaction was determined by the PyRX - Autodock Vina. These studies will give a better idea of the interaction of various molecules, which help to deduce its function by further experimentation.

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KARPAGAVALLI, Muthuramalingam, Muthusamy THANGARAJ, Duraisamy ANNADURAI, Thangappan AJITHKUMAR, Mahapathra GYANAPRAKASH, and Raman SURABI. "Phylogenetic Analysis and In Silico Characterization of Cytochrome P450 1A (Cyp1A) Protein from the African Catfish, Clarias gariepinus (Burchell, 1822)." Notulae Scientia Biologicae 11, no. 4 (December 24, 2019): 368–72. http://dx.doi.org/10.15835/nsb11410475.

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The CYP family enzymes are broadly used as biomarkers because of their pattern of expression. This study describes the application of in silico tools to predict the physico-chemical characters of CYP1A protein from the catfish, Clarias gariepinus. The nucleotide sequence analysis of C. gariepinus CYP1A gene showed higher similarity with C. batrachus and reflected in the phylogenetic tree. The comparative modelling results showed this CYP1A protein was highly similar with the 3-D crystal structure of human Cytochrome p450 1A1 (PDB: 1BE3). The prediction results depicted that most of the amino acids formed alpha helix. The predicted pI was 9.10, hydropathycity was -0.226, exposed and buried residues were 61.67, 38.33% respectively. Ramachandran plot analysis showed that most of the amino acids falling on the favoured region and exhibited right- handed alpha helices as the most stable secondary structure. Some amino acids were also found to form loops to interconnect different helices. The CYP1A protein was predicted to be localized in the mitochondrion of the eukaryotic cell.

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Saikat, Abu Saim Mohammad, Rabiul Islam, Shahriar Mahmud, Md Abu Sayeed Imran, Mohammad Shah Alam, Mahmudul Hasan Masud, and Md Ekhlas Uddin. "Structural and Functional Annotation of Uncharacterized Protein NCGM946K2_146 of Mycobacterium Tuberculosis: An In-Silico Approach." Proceedings 66, no. 1 (December 30, 2020): 13. http://dx.doi.org/10.3390/proceedings2020066013.

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The human pathogen Mycobacterium tuberculosis (MTB) is indeed one of the renowned, important, longtime infectious diseases, tuberculosis (TB). Interestingly, MTB infection has become one of the world’s leading causes of human death. In trehalose synthase, the protein NCGM 946K2 146 found in MTB has an important role. For carbohydrate transport and metabolism, trehalose synthase is required. The protein is not clarified yet, though. In this research, an in silico approach was, therefore, formulated for functional and structural documentation of the uncharacterized protein NCGM946K2_146.Three distinct servers, including Modeller, Phyre2, and Swiss Model, were used to evaluate the predicted tertiary structure. The top materials are selected using structural evaluations conducted with the analysis of Ramachandran Plot, Swiss-Model Interactive Workplace, ProSA-web, Verify 3D, and Z scores. This analysis aimed to uncover the value of the NCGM946K2_146 protein of MTB. This research will, therefore, improve our pathogenesis awareness and give us a chance to target the protein compound.

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Mahato, Jayprakash. "Molecular Modeling of Cathepsin B protein in different Leishmania strains." Journal of Drug Delivery and Therapeutics 8, no. 6-s (December 15, 2018): 224–26. http://dx.doi.org/10.22270/jddt.v8i6-s.2118.

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Cathepsin B like cysteine proteases representing a major component of the lysosomal proteolytic repertoire plays an important role in intracellular protein degradation. Comparative models of cathepsin B (CatB) protein of six different Leishmania strains were developed using MODELLER. The modeled three-dimensional (3-D) structure has the correct stereochemistry as gauged from the Ramachandran plot and good 3-D structure compatibility as assessed by PROCHECK and the DOPE score (DS2.1, Accelrys). The modeled proteins were energy minimized and validated using standard dynamic cascade protocol (DS 2.1). Seven different disulfide bonding sites are predicted in CatB protein of Leishmania. Two domains were identified and different motifs are present in catB protein of Leishmania like aspargine glycosylation site, protein kinase phosphorylation site, Protein kinase C activation site, N-myristoylation site. Considering that cathepsin B is essential for survival of Leishmania, including for virulence to the mammalian host, it may be viewed as an attractive drug target. Keyword: Molecular Modelling, Leishmania, Discover Studio, Protein Binding.

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