Molecular Dynamics Investigations on the Effect ofdAmino Acid Substitution in a Triple-Helix Structure and the Stability of Collagen

2009 ◽  
Vol 113 (26) ◽  
pp. 8983-8992 ◽  
Author(s):  
V. Punitha ◽  
S. Sundar Raman ◽  
R. Parthasarathi ◽  
V. Subramanian ◽  
J. Raghava Rao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Triple Helix ◽  
Helix Structure ◽  
The Stability

Molecular dynamics investigations of the polysaccharide scleroglucan: first study on the triple helix structure

2005 ◽  
Vol 340 (13) ◽  
pp. 2154-2162 ◽  
Author(s):  
Antonio Palleschi ◽  
Gianfranco Bocchinfuso ◽  
Tommasina Coviello ◽  
Franco Alhaique
Keyword(s):  
Molecular Dynamics ◽  
Triple Helix ◽  
Helix Structure

Design of potential IKK-β inhibitors using molecular docking and molecular dynamics techniques for their anti-cancer potential

2020 ◽  
Vol 16 ◽  
Author(s):  
Salam Pradeep Singh ◽  
Iftikar Hussain ◽  
Bolin Kumar Konwar ◽  
Ramesh Chandra Deka ◽  
Chingakham Brajakishor Singh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Md Simulation ◽  
Inflammatory Diseases ◽  
Binding Free Energy ◽  
Anti Cancer ◽  
Dietary Phytochemicals ◽  
Toxicity Analysis ◽  
The Stability ◽  
Stable Trajectory

Aim and Objective: To evaluate a set of seventy phytochemicals for their potential ability to bind the inhibitor of nuclear factor kappaB kinase beta (IKK-β) which is a prime target for cancer and inflammatory diseases. Materials and Methods: Seventy phytochemicals were screened against IKK-β enzyme using DFT-based molecular docking technique and the top docking hits were carried forward for molecular dynamics (MD) simulation protocols. The adme-toxicity analysis was also carried out for the top docking hits. Results: Sesamin, matairesinol and resveratrol were found to be the top docking hits with a total score of -413 kJ/mol, -398.11 kJ/mol and 266.73 kJ/mol respectively. Glu100 and Gly102 were found to be the most common interacting residues. The result from MD simulation observed a stable trajectory with a binding free energy of -107.62 kJ/mol for matairesinol, -120.37 kJ/mol for sesamin and -40.56 kJ/mol for resveratrol. The DFT calculation revealed the stability of the compounds. The ADME-Toxicity prediction observed that these compounds fall within the permissible area of Boiled-Egg and it does not violate any rule for pharmacological criteria, drug-likeness etc. Conclusion: The study interprets that dietary phytochemicals are potent inhibitors of IKK-β enzyme with favourable binding affinity and less toxic effects. In fact, there is a gradual rise in the use of plant-derived molecules because of its lesser side effects compared to chemotherapy. The study has also provided an insight by which the phytochemicals inhibited the IKK-β enzyme. The investigation would also provide in understanding the inhibitory mode of certain dietary phytochemicals in treating cancer.

scholarly journals A neutral polysaccharide with a triple helix structure from ginger: Characterization and immunomodulatory activity

2021 ◽  
Vol 350 ◽  
pp. 129261
Author(s):  
Xiaolong Yang ◽  
Siqing Wei ◽  
Xiaoming Lu ◽  
Xuguang Qiao ◽  
Jesus Simal-Gandara ◽  
...  
Keyword(s):  
Triple Helix ◽  
Immunomodulatory Activity ◽  
Helix Structure

scholarly journals Hoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix

RNA ◽  
2016 ◽  
Vol 22 (5) ◽  
pp. 743-749 ◽  
Author(s):  
Jessica A. Brown ◽  
Charles G. Kinzig ◽  
Suzanne J. DeGregorio ◽  
Joan A. Steitz
Keyword(s):  
Triple Helix ◽  
The Stability ◽  
And Function ◽  
Rna Triple Helix

Bis(β-diketonate) ligands for the synthesis of bimetallic complexes of TiIII, VIII, MnIII and FeIII with a triple-helix structure

1997 ◽  
pp. 1561-1562 ◽  
Author(s):  
Vincent A. Grillo ◽  
Elisa J. Seddon ◽  
Craig M. Grant ◽  
Guillem Aromí ◽  
John C. Bollinger ◽  
...  
Keyword(s):  
Triple Helix ◽  
Bimetallic Complexes ◽  
Helix Structure

scholarly journals Structural Properties of G,T-Parallel Duplexes

2010 ◽  
Vol 2010 ◽  
pp. 1-11 ◽  
Author(s):  
Anna Aviñó ◽  
Elena Cubero ◽  
Raimundo Gargallo ◽  
Carlos González ◽  
Modesto Orozco ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Properties ◽  
Theoretical Calculations ◽  
Md Simulations ◽  
Theoretical Studies ◽  
Duplex Structure ◽  
Strong Stabilization ◽  
The Stability ◽  
The Impact

The structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD) simulations and UV- and CD spectroscopies. In addition the impact of the substitution of adenine by 8-aminoadenine and guanine by 8-aminoguanine is analyzed. The presence of 8-aminoadenine and 8-aminoguanine stabilizes the parallel duplex structure. Binding of these oligonucleotides to their target polypyrimidine sequences to form the corresponding G,T-parallel triplex was not observed. Instead, when unmodified parallel-stranded duplexes were mixed with their polypyrimidine target, an interstrand Watson-Crick duplex was formed. As predicted by theoretical calculations parallel-stranded duplexes carrying 8-aminopurines did not bind to their target. The preference for the parallel-duplex over the Watson-Crick antiparallel duplex is attributed to the strong stabilization of the parallel duplex produced by the 8-aminopurines. Theoretical studies show that the isomorphism of the triads is crucial for the stability of the parallel triplex.

Triple-Helix Conformation of a Polysaccharide Determined with Light Scattering, AFM, and Molecular Dynamics Simulation

2018 ◽  
Vol 51 (24) ◽  
pp. 10150-10159 ◽  
Author(s):  
Yan Meng ◽  
Xiaodan Shi ◽  
Liqin Cai ◽  
Shihai Zhang ◽  
Kan Ding ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Light Scattering ◽  
Molecular Dynamics Simulation ◽  
Triple Helix ◽  
Dynamics Simulation ◽  
Helix Conformation
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