Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model

Biskupek, Iga; Czaplewski, Cezary; Sawicka, Justyna; Iłowska, Emilia; Dzierżyńska, Maria; Rodziewicz-Motowidło, Sylwia; Liwo, Adam

doi:10.3390/biom12081140

Open AccessArticle

Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model

by

Iga Biskupek

,

Cezary Czaplewski

,

Justyna Sawicka

,

Emilia Iłowska

,

Maria Dzierżyńska

,

Sylwia Rodziewicz-Motowidło

and

Adam Liwo

^*

Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland

^*

Author to whom correspondence should be addressed.

Biomolecules 2022, 12(8), 1140; https://doi.org/10.3390/biom12081140

Submission received: 14 July 2022 / Revised: 13 August 2022 / Accepted: 16 August 2022 / Published: 18 August 2022

(This article belongs to the Collection Feature Papers in Bioinformatics and Systems Biology Section)

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Abstract

The UNited RESidue (UNRES) model of polypeptide chains was applied to study the association of 20 peptides with sizes ranging from 6 to 32 amino-acid residues. Twelve of those were potentially aggregating hexa- or heptapeptides excised from larger proteins, while the remaining eight contained potentially aggregating sequences, functionalized by attaching larger ends rich in charged residues. For 13 peptides, the experimental data of aggregation were used. The remaining seven were synthesized, and their properties were measured in this work. Multiplexed replica-exchange simulations of eight-chain systems were conducted at 12 temperatures from 260 to 370 K at concentrations from 0.421 to 5.78 mM, corresponding to the experimental conditions. The temperature profiles of the fractions of monomers and octamers showed a clear transition corresponding to aggregate dissociation. Low simulated transition temperatures were obtained for the peptides, which did not precipitate after incubation, as well as for the H-GNNQQNY-NH₂ prion–protein fragment, which forms small fibrils. A substantial amount of inter-strand β-sheets was found in most of the systems. The results suggest that UNRES simulations can be used to assess peptide aggregation except for glutamine- and asparagine-rich peptides, for which a revision of the UNRES sidechain–sidechain interaction potentials appears necessary.

Keywords: peptide aggregation; molecular dynamics; replica exchange; UNRES model

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MDPI and ACS Style

Biskupek, I.; Czaplewski, C.; Sawicka, J.; Iłowska, E.; Dzierżyńska, M.; Rodziewicz-Motowidło, S.; Liwo, A. Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model. Biomolecules 2022, 12, 1140. https://doi.org/10.3390/biom12081140

AMA Style

Biskupek I, Czaplewski C, Sawicka J, Iłowska E, Dzierżyńska M, Rodziewicz-Motowidło S, Liwo A. Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model. Biomolecules. 2022; 12(8):1140. https://doi.org/10.3390/biom12081140

Chicago/Turabian Style

Biskupek, Iga, Cezary Czaplewski, Justyna Sawicka, Emilia Iłowska, Maria Dzierżyńska, Sylwia Rodziewicz-Motowidło, and Adam Liwo. 2022. "Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model" Biomolecules 12, no. 8: 1140. https://doi.org/10.3390/biom12081140

APA Style

Biskupek, I., Czaplewski, C., Sawicka, J., Iłowska, E., Dzierżyńska, M., Rodziewicz-Motowidło, S., & Liwo, A. (2022). Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model. Biomolecules, 12(8), 1140. https://doi.org/10.3390/biom12081140

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Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model

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