Insights into the secondary structures of lactam N-substituted stapled peptides

2020 ◽  
Vol 18 (20) ◽  
pp. 3838-3842
Author(s):  
Aldrin V. Vasco ◽  
Celia G. Moya ◽  
Stefan Gröger ◽  
Wolfgang Brandt ◽  
Jochen Balbach ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Secondary Structure ◽  
Secondary Structures ◽  
Dynamics Simulation ◽  
Stapled Peptides ◽  
Lactam Bridge ◽  
Cd Studies

NMR and CD studies together with molecular dynamics simulation reveal new insights into the s-cis/s-trans isomerism and the effect of the lactam bridge N-substituent on the secondary structure of stapled peptides.

Molecular Dynamics Study on an Adipokinetic Hormone Peptide in Aqueous Solution

2000 ◽  
Vol 55 (1-2) ◽  
pp. 125-128 ◽  
Author(s):  
Igor Z. Zubrzycki
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulation ◽  
Secondary Structure ◽  
Room Temperature ◽  
Dynamics Simulation ◽  
Red Pigment ◽  
Adipokinetic Hormone ◽  
Extended Conformation ◽  
Flying Insects

Lom-AKH-I is a member of the adipokinetic hormone/ red pigment concentrating hormone (AKH / RPCH) family of peptides found in flying insects. A molecular dynamics simulation at room temperature (293 K) in water has been performed to survey the folding path of the Lom-AKH-I peptide in water and to establish the secondary structure of Lom-AKH-I. The obtained results indicate the presence of an undefined extended conformation.

scholarly journals Screening of druggable conformers of α-synuclein using molecular dynamics simulation

2020 ◽  
Vol 10 (3) ◽  
pp. 5338-5347
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Secondary Structure ◽  
Surface Area ◽  
Accessible Surface Area ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area ◽  
Binding Pockets ◽  
Accessible Surface ◽  
Solvent Accessible Surface

Intrinsically disordered proteins (IDPs) are becoming an engaging prospect for therapeutic intervention by small drug-like molecules. IDPs structural binding pockets and their flexibility exist as a challenging target for standard druggable approaches. Hence, in this study, we have performed and identified the most probable druggable conformers from molecular dynamics simulation on α-synuclein based on the structural parameters: radius of gyration (Rg), solvent accessible surface area (SASA) and the standard secondary structure content. We found the conformers showing lower solvent accessible surface area and higher secondary structure content of α-helical are defined to be suitable binding pockets for druggability.

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