Molecular Dynamics and Spin-Lattice NMR Relaxation in $$\alpha$$- and $$\varepsilon$$-Polylysine

Bezrodnyi, Valeriy V; Shavykin, Oleg V.; Mikhtaniuk, Sofia E.; Neelov, Igor M.; Markelov, Denis A.

doi:10.1007/s00723-020-01260-8

Cited by 3 publications

(1 citation statement)

References 43 publications

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“…Other proteins become unstable to changes of pH due to ionizable side chains and Coulomb repulsion between the polar groups of the charged heads of amino acids ( e.g. , Asp, Glu, His, Lys, and Arg) [ 66 - 68 ]. Analysis of the amino acid composition of PilV of A. thiooxidans indicates a significant decrease in charged amino acids, which most likely confers acid stability.…”

Section: Discussionmentioning

confidence: 99%

Understanding a Core Pilin of the Type IVa Pili of Acidithiobacillus thiooxidans, PilV

Hernández-Sánchez,

Páez-Pérez,

Alfaro-Saldaña

et al. 2024

J. Microbiol. Biotechnol.

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Pilins are protein subunits of pili. The pilins of type IV pili (T4P) in pathogenic bacteria are well characterized, but anything is known about the T4P proteins in acidophilic chemolithoautotrophic microorganisms such as the genus Acidithiobacillus . The interest in T4P of A. thiooxidans is because of their possible role in cell recruitment and bacterial aggregation on the surface of minerals during biooxidation of sulfide minerals. In this study we present a successful ad hoc methodology for the heterologous expression and purification of extracellular proteins such as the minor pilin PilV of the T4P of A. thiooxidans , a pilin exposed to extreme conditions of acidity and high oxidation-reduction potentials, and that interact with metal sulfides in an environment rich in dissolved minerals. Once obtained, the model structure of A. thiooxidans PilV revealed the core basic architecture of T4P pilins. Because of the acidophilic condition, we carried out in silico characterization of the protonation status of acidic and basic residues of PilV in order to calculate the ionization state at specific pH values and evaluated their pH stability. Further biophysical characterization was done using UV-visible and fluorescence spectroscopy and the results showed that PilV remains soluble and stable even after exposure to significant changes of pH. PilV has a unique amino acid composition that exhibits acid stability, with significant biotechnology implications such as biooxidation of sulfide minerals. The biophysics profiles of PilV open new paradigms about resilient proteins and stimulate the study of other pilins from extremophiles.

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Section: Discussionmentioning

confidence: 99%

Understanding a Core Pilin of the Type IVa Pili of Acidithiobacillus thiooxidans, PilV

Hernández-Sánchez,

Páez-Pérez,

Alfaro-Saldaña

et al. 2024

J. Microbiol. Biotechnol.

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Computational driven molecular dynamics simulation of keratinocyte growth factor behavior at different pH conditions

Boroujeni

Dastjerdeh

Shokrgozar

et al. 2021

Informatics in Medicine Unlocked

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MD Simulation of AEDG Peptide Complexes with New K2R Dendrimer and Dendrigraft

Fatullaev

Bezrodnyi

Neelov

2022

International Journal of Biology and Biomedical Engineering

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Biocompatible peptide dendrimers and dendrigrafts have useful properties for application in biomedicine. In previous papers the computational approach for study lysine dendrimers and dendrigrafts as well as their complexes with various medical peptides was used. In this paper the comparison of complex formation between molecules of therapeutic AEDG tetrapeptide and novel K2R peptide dendrimer or DG2 dendrigraft of near the same size and charge was fulfilled. The systems consisting of 16 therapeutic AEDG tetrapeptide molecules and one dendrimer or one dendrigraft were studied by molecular dynamics simulation. Full atomic models of these molecules in water with explicit counterions were used for this goal. First of all, the process of complex formation was studied. It was obtained that peptide molecules were attracted by both branched molecules and were quickly adsorbed by them. Times of complexes formation as well as size, anisotropy and structure of each complex were calculated. It was demonstrated that both K2R dendrimer and DG2 dendrigraft are effective for complexation of these peptide molecules but new dendrimer complex is more stable than dendrigraft complex because it has almost twice more hydrogen bonds with peptide molecules and 33% more ion pairs with their charged groups.

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Molecular Dynamics and Spin-Lattice NMR Relaxation in $$\alpha$$- and $$\varepsilon$$-Polylysine

Cited by 3 publications

References 43 publications

Understanding a Core Pilin of the Type IVa Pili of Acidithiobacillus thiooxidans, PilV

Understanding a Core Pilin of the Type IVa Pili of Acidithiobacillus thiooxidans, PilV

Computational driven molecular dynamics simulation of keratinocyte growth factor behavior at different pH conditions

MD Simulation of AEDG Peptide Complexes with New K2R Dendrimer and Dendrigraft

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