Volumetric properties of human islet amyloid polypeptide in liquid water

Brovchenko, Ivan; Andrews, Maximilian N.; Oleinikova, Alla

doi:10.1039/b918706e

Cited by 15 publications

(18 citation statements)

References 26 publications

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“…It is worth noting that within our knowledge, only a few theoretical-computational studies on protein partial molecular volumes based on atomistic simulations have been attempted. [15][16][17][18][19] Such computational studies were based on isobaric-isothermal simulations (i.e. NpT ensemble) thus making hopeless 15 any reliable direct measure of the protein partial molecular volume.…”

Section: Introductionmentioning

confidence: 99%

In silico characterization of protein partial molecular volumes and hydration shells

Galdo

Marracino

D’Abramo

et al. 2015

Phys. Chem. Chem. Phys.

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In this paper we present a computational approach, based on NVT molecular dynamics trajectories, that allows the direct evaluation of the protein partial molecular volume. The results obtained for five different globular proteins demonstrate the accuracy of this computational procedure in reproducing protein partial molecular volumes, providing quantitative characterization of the hydration shell in terms of the protein excluded volume, hydration shell ellipsoidal volume and related solvent density. Remarkably, our data indicate for the hydration shell a ≈10% solvent density increase with respect to the liquid water bulk density, in excellent agreement with the available experimental data.

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Section: Introductionmentioning

confidence: 99%

In silico characterization of protein partial molecular volumes and hydration shells

Galdo

Marracino

D’Abramo

et al. 2015

Phys. Chem. Chem. Phys.

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“…Petrache et al [34] considered the volume of the peptide side chain a suitable parameter to understand the peptide-bilayer interaction and they showed the dependence of side chain volumes on the peptides location. Additionally, Brovchenko et al [41] demonstrated a direct correlation between the intrinsic peptide volumes and the number of intrapeptide hydrogen bonds (secondary structure content). They showed that the formation of these hydrogen bonds produces voids non-accessible for water, which contribute to an increased peptide volume.…”

Section: Discussionmentioning

confidence: 99%

MD simulations and multivariate studies for modeling the antileishmanial activity of peptides

Guerra

Fadel

Baldissera³

et al. 2017

Chem Biol Drug Des

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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.

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“…The apparent volume of a solute in solution from a molecular dynamics model can be calculated, by definition, as the difference between the volume of the model box containing the solution, and the volume of the model box containing the same amount of the pure solvent: 53,59,60…”

Section: Volumetric Characteristicsmentioning

confidence: 99%

Exploring volume, compressibility and hydration changes of folded proteins upon compression

Voloshin

Medvedev

Smolin

et al. 2015

Phys. Chem. Chem. Phys.

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Understanding the physical basis of the structure, stability and function of proteins in solution, including extreme environmental conditions, requires knowledge of their temperature and pressure dependent volumetric properties. One physical-chemical property of proteins that is still little understood is their partial molar volume and its dependence on temperature and pressure. We used molecular dynamics simulations of aqueous solutions of a typical monomeric folded protein, staphylococcal nuclease (SNase), to study and analyze the pressure dependence of the apparent volume, Vapp, and its components by the Voronoi-Delaunay method. We show that the strong decrease of Vapp with pressure (βT = 0.95 × 10(-5) bar(-1), in very good agreement with the experimental value) is essentially due to the compression of the molecular volume, VM, ultimately, of its internal voids, V. Changes of the intrinsic volume (defined as the Voronoi volume of the molecule), the contribution of the solvent to the apparent volume, and of the contribution of the boundary voids between the protein and the solvent have also been studied and quantified in detail. The pressure dependences of the volumetric characteristics obtained are compared with the temperature dependent behavior of these quantities and with corresponding results for a natively unfolded polypeptide.

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Volumetric properties of human islet amyloid polypeptide in liquid water

Cited by 15 publications

References 26 publications

In silico characterization of protein partial molecular volumes and hydration shells

In silico characterization of protein partial molecular volumes and hydration shells

MD simulations and multivariate studies for modeling the antileishmanial activity of peptides

Exploring volume, compressibility and hydration changes of folded proteins upon compression

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