Search

This paper investigates the dynamic behavior of EthylChlorophyllide A (EChlideA) molecules in a methanol solution confined within a 4 nm silica nanoslit, using molecular dynamics simulations over a duration of 1 ms. Three systems, containing 1, 2, and 4 solutes, were studied at 298 K. The results demonstrate that EChlideA molecules predominantly adsorb onto the silica surfaces, driven by specific interactions between chlorin ring's methyl group and the hydroxyl groups of the silica. This adsorption leads to stable binding, particularly in less crowded environments, as indicated by the potential of mean force analysis. Higher molecular concentrations, such as those with four EChlideA molecules, introduce variation in binding strength due to molecular aggregation and complex interactions. The orientation analysis reveals that the chlorin ring tends to align parallel to the surface, requiring rotational adjustments during surface diffusion. In addition, solvent coordination around the Mg ion remains consistent under bulk conditions, although with some variation in higher concentrations. This study also highlights a decrease in linear diffusion and an increase in rotational relaxation times for EChlideA molecules within the confined nanoslit, reflecting the influence of molecular concentration and arrangement on their dynamics. These findings provide valuable insights into the role of surface interactions, molecular orientation, and solvent coordination in confined environments, offering implications for the design of nanoscale systems. [ABSTRACT FROM AUTHOR]

The compound 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) is a versatile fluorophore widely used in Förster resonance energy transfer (FRET) spectroscopy studies due to its remarkable sensitivity, enabling precise donor–acceptor distance measurements, even for short peptides. Integrating time-resolved and FRET spectroscopies with molecular dynamics simulations provides a robust approach to unravel the structure and dynamics of biopolymers in a solution. This study investigates the structural behavior of three octapeptide variants: Trp-(Gly-Ser)3-Dbo, Trp-(GlyGly)3-Dbo, and Trp-(SerSer)3-Dbo, where Dbo represents the DBO-containing modified aspartic acid, using molecular dynamics simulations. Glycine- and serine-rich amino acid fragments, common in flexible protein regions, play essential roles in functional properties. Results show excellent agreement between end-to-end distances, orientational factors from simulations, and the available experimental and theoretical data, validating the reliability of the GROMOS force field model. The end-to-end distribution, modeled using three Gaussian distributions, reveals a complex shape, confirmed by cluster analysis highlighting a limited number of significant conformations dominating the peptide landscape. All peptides predominantly adopt a disordered state in the solvent, yet exhibit a compact shape, aligning with the model of disordered polypeptide chains in poor solvents. Conformations show marginal dependence on chain composition, with Ser-only chains exhibiting slightly more elongation. This study enhances our understanding of peptide behavior, providing valuable insights into their structural dynamics in solution. [ABSTRACT FROM AUTHOR]

Peptides are versatile molecules with applications spanning from biotechnology to nanomedicine. They exhibit a good capability to unbundle carbon nanotubes (CNT) by improving their solubility in water. Furthermore, they are a powerful drug delivery system since they can easily be uptaken by living cells, and their high surface-to-volume ratio facilitates the adsorption of molecules of different natures. Therefore, understanding the interaction mechanism between peptides and CNT is important for designing novel therapeutical agents. In this paper, the mechanisms of the adsorption of antimicrobial peptide Cecropin A-Magainin 2 (CA-MA) on a graphene nanosheet (GNS) and on an ultra-short single-walled CNT are characterized using molecular dynamics simulations. The results show that the peptide coats both GNS and CNT surfaces through preferential contacts with aromatic side chains. The peptide packs compactly on the carbon surfaces where the polar and functionalizable Lys side chains protrude into the bulk solvent. It is shown that the adsorption is strongly correlated to the loss of the peptide helical structure. In the case of the CNT, the outer surface is significantly more accessible for adsorption. Nevertheless when the outer surface is already covered by other peptides, a spontaneous diffusion, via the amidated C-terminus into the interior of the CNT, was observed within 150 ns of simulation time. We found that this spontaneous insertion into the CNT interior can be controlled by the polarity of the entrance rim. For the positively charged CA-MA peptide studied, hydrogenated and fluorinated rims, respectively, hinder and promote the insertion. [ABSTRACT FROM AUTHOR]

1,1,1-trifluoropropan-2-ol (TFIP) alcohol is used to study the influence of trifluoromethyl groups (CF3) on the physicochemical properties of fluorinated organic molecules. The difference in organization of hydration shell around the CF3 and CH3 groups helped in determining the trifluoromethanol and 1,1,1,3,3,3-hexafluropropano-2-ol.

A new model of 2,2,2-trifluoroethanol (TFE) suitable for condensed phase simulations is presented. The properties of the new model was compared with the available experimental data over a range of temperatures and the results indicate that the model reproduces the experimental properties of the neat liquid and of the mixtures with water.

In this paper, the conformation and dynamics properties of polyethylene oxide (PEO) and polypropylene oxide (PPO) polymer chains at 298 K have been studied in the melt and at infinite dilution condition in water, methanol, chloroform, carbon tetrachloride, and n-heptane using molecular dynamics simulations. The calculated density of PEO melt with chain lengths of n = 2, 3, 4, 5 and, for PPO, n = 7 are in good agreement with the available experimental data. The conformational properties of PEO and PPO show an increasing gauche preference for the O-C-C-O dihedral in the following order water>methanol>chloroform>carbon tetrachloride = n-heptane. On the contrary, the preference for trans conformation has a maximum in carbon tetrachloride and n-heptane followed in the order by chloroform, methanol, and water. The PEO conformational preferences are in qualitative agreement with results of NMR studies. PEO chains formed different types of hydrogen bonds with polar solvent molecules. In particular, the occurrence of bifurcated hydrogen bonding in chloroform was also observed. Radii of gyration of PEO chains of length larger than n = 9 monomers showed a good agreement with light scattering data in water and in methanol. For the shorter chains the observed deviations are probably due to the enhanced hydrophobic effects caused by the terminal methyl groups. For PEO the fitting of end-to-end distance distributions with the semi-flexible chain model at 298 K provided persistence lengths of 0.375 and 0.387 nm in water and methanol, respectively. Finally, the radius of gyration of Pluronic P85 turned out to be 2.25 ± 0.4 nm at 293 K in water in agreement with experimental data. [ABSTRACT FROM AUTHOR]

Herein, we report a comparative modelling study of 1,2-dimethoxyethane (DME) and 1,2-dimethoxypropane (DMP) at 298 K and 318 K in the liquid state, water mixtures, and at infinite dilution condition in water, methanol, carbon tetrachloride, and n-heptane. Both DME and DMP are united-atom models compatible with GROMOS/OPLS force fields. Calculated thermodynamic and structural properties of the pure DME and DMP liquids resulted in excellent agreement with the experimental data. In aqueous solutions, densities, diffusion coefficients, and concentration dependent conformers of DME, were in agreement with experimental data. The calculated free energy of solvation (ΔGhyd) at 298 K is equal to -22.1 ± 0.8 kJ mol-1 in good agreement with the experimental value of 20.2 kJ mol-1. In addition, the free energy of solvation of DME in non-aqueous solvents follows the trend methanol ≈ water < carbon tetrachloride < n-heptane, consistently with the dielectric constant of the solvents. On contrary, the presence of an extra methyl group on chiral carbon makes DMP less soluble than DME in water (ΔGhyd = -16.0 ± 1.1 kJ mol-1) but more soluble in non-polar solvents as n-heptane. Finally, for the DMP the chiral discrimination of the two enantiomers was calculated as solvation free energy difference of one DMP isomer in the solution of the other. The obtained value of ΔΔGRS = -3.7 ± 1.4 kJ mol-1 indicates a net chiral discrimination of the two enantiomers. [ABSTRACT FROM AUTHOR]

Steady-state and time-resolved fluorescence is used for investigating fluorescence resonance energy transfer (FRET) from the amino acid tryptophan (Trp) as donor and a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) as acceptor in peptides. The obtained 10-Angstrom spectroscopic ruler can be used for studying supramolecular conformational changes, allosteric effects, induced-fit binding phenomena, protein folding events and domain motions in proteins and short polyprolines.

The temperature-dependent looping rates of the Dbo-AlaGlyGln-Trp-N[H.sub.2] peptide (where Dbo = 2,3-diazabicyclo-[2.2.2]oct-2-ene-labeled asparagine) is investigated by using a mix of time-resolved spectroscopy and molecular dynamics (MD) simulations techniques. It is observed that the diffusion-limited rate and associated activation energy of any initial protein folding step depends on the amino acid sequence.

Molecular dynamics (MD) and steered molecular dynamics (SMD) simulations are used to investigate the structural and dynamical properties of poly(ethylene oxide) (PEO) at the dimyristoylphospatidylcholine (DMPC) bilayer/water interface. The results have indicated the presence of a barrier for the PEO penetration of the DMPC bilayer, where the calculated barrier is connected to an entropic penalty due to a restriction of polymer conformational freedom inside the bilayer.

The use of 2,3-diazabicylo[2.2.2]oct-2-ene as an acceptor which in combination with the intrinsic fluorescence of tryptophan constitutes a convenient donor/acceptor pair with an [R.sub.0] value of 10 Angstrom is introduced. These constitute benchmarks for the refinement of force fields and modeling of larger proteins and apart from affording absolute distances, the fluorescence resonance energy transfer pair has similar potential for probing relative proximity relationships and structural transitions in the 10 Angstrom domain.

The framework of the quasi-Gaussian entropy (QGE) theory was used to formulate a general model for the description of the thermodynamic properties of the folding/unfolding of single-domain proteins. This theory provides models for homogeneous fluids, solids, and recently for the thermodynamics of flexible organic molecules in vacuo and solutes.

Generally, the high diversity of protein properties necessitates the development of unique nanoparticle bio-conjugation methods, optimized for each different protein. Here we describe a universal bio-conjugation approach which makes use of a new recombinant fusion protein combining two distinct domains. The N-terminal part is Glutathione S-Transferase (GST) from Schistosoma japonicum, for which we identify and characterize the remarkable ability to bind gold nanoparticles (GNPs) by forming gold–sulfur bonds (Au–S). The C-terminal part of this multi-domain construct is the SpyCatcher from Streptococcus pyogenes, which provides the ability to capture recombinant proteins encoding a SpyTag. Here we show that SpyCatcher can be immobilized covalently on GNPs through GST without the loss of its full functionality. We then show that GST-SpyCatcher activated particles are able to covalently bind a SpyTag modified protein by simple mixing, through the spontaneous formation of an unusual isopeptide bond. [ABSTRACT FROM AUTHOR]

The crystal structures of cytochrome P450 BM-3 (BM3) heme domain (BMP) cocrystallized with 14% and 28% dimethylsulfoxide (DMSO) are reported. The analysis will help in understanding the cosolvent effect and to tailor BM3 for industrially relevant catalysis in nonaqueous medium.