Predicted Hotspot Residues Involved in Allosteric Signal Transmission in Pro-Apoptotic Peptide-Mcl1 Complexes

Mcl1 is a primary member of the Bcl-2 family-anti-apoptotic proteins (AAP)-that is overexpressed in several cancer pathologies. The apoptotic regulation is mediated through the binding of pro-apoptotic peptides (PAPs) (e.g., Bak and Bid) at the canonical hydrophobic binding groove (CBG) of Mcl1. Although all PAPs form amphipathic alpha-helices, their amino acid sequences vary to different degree. This sequence variation exhibits a central role in the binding partner selectivity towards different AAPs. Thus, constructing a novel peptide or small organic molecule with the ability to mimic the natural regulatory process of PAP is essential to inhibit various AAPs. Previously reported experimental binding free energies (BFEs) were utilized in the current investigation aimed to understand the mechanistic basis of different PAPs targeted to mMcl1. Molecular dynamics (MD) simulations used to estimate BFEs between mMcl1-PAP complexes using Molecular Mechanics-Generalized Born Solvent Accessible (MMGBSA) approach with multiple parameters. Predicted BFE values showed an excellent agreement with the experiment (R-2= 0.92). The van-der Waals (Delta G(vdw)) and electrostatic (Delta G(ele)) energy terms found to be the main energy components that drive heterodimerization of mMcl1-PAP complexes. Finally, the dynamic network analysis predicted the allosteric signal transmission pathway involves more favorable energy contributing residues. In total, the results obtained from the current investigation may provide valuable insights for the synthesis of a novel peptide or small organic inhibitor targeting Mcl1

Structural and thermal analyses in semiconducting and metallic zigzag single-walled carbon nanotubes using molecular dynamics simulations

© 2024 The Author(s). This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY), https://creativecommons.org/licenses/by/4.0/Equilibrium molecular dynamics (EMD) simulations have been performed to investigate the structural analysis and thermal conductivity (λ) of semiconducting (8,0) and metallic (12,0) zigzag single-walled carbon nanotubes (SWCNTs) for varying ±γ(%) strains. For the first time, the present outcomes provide valuable insights into the relationship between the structural properties of zigzag SWCNTs and corresponding thermal behavior, which is essential for the development of high-performance nanocomposites. The radial distribution function (RDF) has been employed to assess the buckling and deformation understandings of the (8,0) and (12,0) SWCNTs for a wide range of temperature T(K) and varying ±γ(%) strains. The visualization of SWCNTs shows that the earlier buckling and deformation processes are observed for semiconducting SWCNTs as compared to metallic SWCNTs for high T(K) and it also evident through an abrupt increase in RDF peaks. The RDF and visualization analyses demonstrate that the (8,0) SWCNTs can more tunable under compressive than tensile strains, however, the (12,0) zigzag SWCNTs indicate an opposite trend and may tolerate more tensile than compressive strains. Investigations show that the tunable domain of ±γ(%) strains decreases from (-10%≤ γ ≤+19%) to (-5%≤ γ ≤+10%) for (8,0) SWCNTs and the buckling process shifts to lower ±γ(%) for (12,0) SWCNTs with increasing T(K). For intermediate-high T(K), the λ(T) of (12,0) SWCNTs is high but the (8,0) SWCNTs show certainly high λ(T) for low T(K). The present λ(T, ±γ) data are in reasonable agreement with parts of previous NEMD, GK-HNEMD data and experimental investigations with simulation results generally under predicting the λ(T, ±γ) by the ∼1% to ∼20%, regardless of the ±γ(%) strains, depending on T(K). Our simulation data significantly expand the strain range to -10% ≤ γ ≤ +19% for both zigzag SWCNTs, depending on temperature T(K). This extension of the range aims to establish a tunable regime and delve into the intrinsic characteristics of zigzag SWCNTs, building upon previous work.Peer reviewe

Bias-force guided simulations combined with experimental validations towards GPR17 modulators identification

Glioblastoma Multiforme (GBM) is known to be by far the most aggressive brain tumor to affect adults. The median survival rate of GBM patient's is < 15 months, while the GBM cells aggressively develop resistance to chemo- and radiotherapy with their self-renewal capacity which suggests the pressing need to develop novel preventative measures. We have recently proved that GPR17 —an orphan G protein-coupled receptor— is highly expressed on the GBM cell surface and it has a vital role to play in the disease progression. Despite the progress made on GBM downregulation, there still remain difficulties in developing a promising modulator for GPR17, till date. Here, we have performed robust virtual screening combined with biased-force pulling molecular dynamic (MD) simulations to predict high-affinity GPR17 modulators followed by experimental validation. Initially, the database containing 1379 FDA-approved drugs were screened against the orthosteric binding pocket of the GPR17. The external bias-potentials were then applied to the screened hits during the MD simulations which enabled to predict a spectrum of rupture peak force values that were used to select four approved drugs –ZINC000003792417 (Sacubitril), ZINC000014210457 (Victrelis), ZINC000001536109 (Pralatrexate) and ZINC000003925861 (Vorapaxar)– as top hits. The hits selected turns out to demonstrate unique dissociation pathways, interaction pattern, and change in polar network over time. Subsequently the selected hits with GPR17 were measured by inhibiting the forskolin-stimulated cAMP accumulation in GBM cell lines, LN229 and SNB19. The ex vivo validations shows that Sacubitril drug can act as a full agonist, while Vorapaxar functions as a partial agonist for GPR17. The pEC50 of Sacubitril was identified as 4.841 and 4.661 for LN229 and SNB19, respectively. Small interference of the RNA (siRNA)– silenced the GPR17 to further validate the targeted binding of Sacubitril with GPR17. In the current investigation, we have identified new repurposable GPR17 specific drugs which are likely to increase the opportunity to treat orphan deadly diseases.publishedVersionPeer reviewe

Possible Mechanism of Glucose Uptake Enhanced by Cold Atmospheric Plasma: Atomic Scale Simulations

Cold atmospheric plasma (CAP) has shown its potential in biomedical applications, such as wound healing, cancer treatment and bacterial disinfection. Recent experiments have provided evidence that CAP can also enhance the intracellular uptake of glucose molecules which is important in diabetes therapy. In this respect, it is essential to understand the underlying mechanisms of intracellular glucose uptake induced by CAP, which is still unclear. Hence, in this study we try to elucidate the possible mechanism of glucose uptake by cells by performing computer simulations. Specifically, we study the transport of glucose molecules through native and oxidized membranes. Our simulation results show that the free energy barrier for the permeation of glucose molecules across the membrane decreases upon increasing the degree of oxidized lipids in the membrane. This indicates that the glucose permeation rate into cells increases when the CAP oxidation level in the cell membrane is increased

Oxidation destabilizes toxic amyloid beta peptide aggregation

Abstract The aggregation of insoluble amyloid beta (Aβ) peptides in the brain is known to trigger the onset of neurodegenerative diseases, such as Alzheimer’s disease. In spite of the massive number of investigations, the underlying mechanisms to destabilize the Aβ aggregates are still poorly understood. Some studies indicate the importance of oxidation to destabilize the Aβ aggregates. In particular, oxidation induced by cold atmospheric plasma (CAP) has demonstrated promising results in eliminating these toxic aggregates. In this paper, we investigate the effect of oxidation on the stability of an Aβ pentamer. By means of molecular dynamics simulations and umbrella sampling, we elucidate the conformational changes of Aβ pentamer in the presence of oxidized residues, and we estimate the dissociation free energy of the terminal peptide out of the pentamer form. The calculated dissociation free energy of the terminal peptide is also found to decrease with increasing oxidation. This indicates that Aβ pentamer aggregation becomes less favorable upon oxidation. Our study contributes to a better insight in one of the potential mechanisms for inhibition of toxic Aβ peptide aggregation, which is considered to be the main culprit to Alzheimer’s disease

Nanoscale insight into silk-like protein self-assembly : Effect of design and number of repeat units

By means of replica exchange molecular dynamics simulations we investigate how the length of a silk-like, alternating diblock oligopeptide influences its secondary and quaternary structure. We carry out simulations for two protein sizes consisting of three and five blocks, and study the stability of a single protein, a dimer, a trimer and a tetramer. Initial configurations of our simulations are β-roll and β-sheet structures. We find that for the triblock the secondary and quaternary structures upto and including the tetramer are unstable: the proteins melt into random coil structures and the aggregates disassemble either completely or partially. We attribute this to the competition between conformational entropy of the proteins and the formation of hydrogen bonds and hydrophobic interactions between proteins. This is confirmed by our simulations on the pentablock proteins, where we find that, as the number of monomers in the aggregate increases, individual monomers form more hydrogen bonds whereas their solvent accessible surface area decreases. For the pentablock β-sheet protein, the monomer and the dimer melt as well, although for the β-roll protein only the monomer melts. For both trimers and tetramers remain stable. Apparently, for these the entropy loss of forming β-rolls and β-sheets is compensated for in the free-energy gain due to the hydrogen-bonding and hydrophobic interactions. We also find that the middle monomers in the trimers and tetramers are conformationally much more stable than the ones on the top and the bottom. Interestingly, the latter are more stable on the tetramer than on the trimer, suggesting that as the number of monomers increases protein-protein interactions cooperatively stabilize the assembly. According to our simulations, the β-roll and β-sheet aggregates must be approximately equally stable

Prediction of the structure of a silk-like protein in oligomeric states using explicit and implicit solvent models

We perform Replica Exchange Molecular Dynamics (REMD) simulations on a silk-like protein design with amino-acid sequence [(Gly-Ala)3-Gly- Glu]5 to investigate the stability of a single protein, a dimer, a trimer and a tetramer made up of these proteins starting from β-roll and β-sheet structures in both explicit (TIP3P) and implicit (GBSA) solvent models. Our simulation results for the implicit solvent model agree with those for the explicit solvent model for simulation times up to the longest tested, being 30 ns per replica. From this we infer that the implicit solvent model that we use is reliable, allowing us to reach much longer time scales (up to 200 ns per replica). We find that the self-assembly of fibers of these proteins in solution must be a nucleated process, involving nuclei made up of at least three monomers. We also find that the conformation of the protein changes upon assembly, i.e., there is a transition from a disordered globular state to an ordered β-sheet structure in the self-assembled state of aggregates containing more than two monomers. This indicates that autosteric effects must be important in the polymerization of this protein, reminiscent of what is observed for β-amyloids. Our findings are consistent with recent experimental results on a protein with an amino acid sequence similar to that of the protein we study. This journal i