2N9A

3D Structure of Decoralin-NH2 by Solution NMR

Summary for 2N9A

• Entry DOI: 10.2210/pdb2n9a/pdb
• NMR Information: BMRB: 25898
• Descriptor: Decoralin (1 entity in total)
• Functional Keywords: antimicrobial peptides, leishmanicidal activity, membrane targeting peptides, antimicrobial protein
• Biological source: Oreumenes decoratus (Potter wasp)
• Cellular location: Secreted : P85870
• Total number of polymer chains: 1
• Total formula weight: 1256.60

Authors

Fadel, V.,Cabrera, M.P.S. (deposition date: 2015-11-12, release date: 2016-11-16, Last modification date: 2024-11-20)

Primary citation

Guerra, M.E.R.,Fadel, V.,Maltarollo, V.G.,Baldissera, G.,Honorio, K.M.,Ruggiero, J.R.,Dos Santos Cabrera, M.P.
MD simulations and multivariate studies for modeling the antileishmanial activity of peptides.
Chem Biol Drug Des, 90:501-510, 2017

PubMed Abstract: Leishmaniasis, a protozoan-caused disease, requires alternative treatments with minimized side-effects and less prone to resistance development. Antimicrobial peptides represent a possible choice to be developed. We report on the prospection of structural parameters of 23 helical antimicrobial and leishmanicidal peptides as a tool for modeling and predicting the activity of new peptides. This investigation is based on molecular dynamic simulations (MD) in mimetic membrane environment, as most of these peptides share the feature of interacting with phospholipid bilayers. To overcome the lack of experimental data on peptides' structures, we started simulations from designed 100% α-helices. This procedure was validated through comparisons with NMR data and the determination of the structure of Decoralin-amide. From physicochemical features and MD results, descriptors were raised and statistically related to the minimum inhibitory concentration against Leishmania by the multivariate data analysis technique. This statistical procedure confirmed five descriptors combined by different loadings in five principal components. The leishmanicidal activity depends on peptides' charge, backbone solvation, volume, and solvent-accessible surface area. The generated model possesses good predictability (q  = 0.715, r  = 0.898) and is indicative for the most and the least active peptides. This is a novel theoretical path for structure-activity studies combining computational methods that identify and prioritize the promising peptide candidates.

PubMed: 28267894
DOI: 10.1111/cbdd.12970

Experimental method

SOLUTION NMR