The effects of amino acid sequence and solvent polarity on the self-assembling of cyclic peptide nanotubes and molecular channel formation inside the lipid bilayer

Hydrogen-Bond-Driven Peptide Nanotube Formation: A DFT Study

DFT calculations were carried out to examine geometries and binding energies of H-bond-driven peptide nanotubes. A bolaamphiphile molecule, consisting of two N-α amido glycylglycine head groups linked by either one CH2 group or seven CH2 groups, is used as a building block for nanotube self-assembly. In addition to hydrogen bonds between adjacent carboxy or amide groups, nanotube formation is also driven by weak C-H· · ·O hydrogen bonds between a methylene group and the carboxy OH group, and between a methylene group and an amide O=C group. The intratubular O-H· · ·O=C hydrogen bonds account for approximately a third of the binding energies. Binding energies calculated with the wB97XD/DGDZVP method show that the hydrocarbon chains play a stabilizing role in nanotube self-assembly. The shortest nanotube has the length of a single monomer and a diameter than increases with the number of monomers. Lengthening of the tubular structure occurs through intertubular O-H· · ·O=C hydrogen bonds. The average intertubular O-H· · ·O=C hydrogen bond binding energy is estimated to change with the size of the nanotubes, decreasing slightly towards some plateau value near 15 kcal/mol according to the wB97XD/DGDZVP method.

On the potentials of sialic acid derivatives as inhibitors for the mumps virus: A molecular dynamics and quantum chemistry investigation

Mumps virus is an infectious pathogen causing major health problems for humans such as encephalitis, orchitis, and parotitis. Therefore, designing an inhibitor for this virus is of great medical and public health importance. With this goal in mind, we investigate the affinity of different sialic acid-based compounds (ligands) against the hemagglutinin-neuraminidase (HN) protein of the mumps virus, using a combination of molecular dynamics (MD) simulations and quantum chemistry calculations. Our MD simulation results indicate that the ligands form stable complexes with the HN protein through a combination of electrostatic, van der Waals (vdW), and hydrogen bond (H-bond) interactions, which the electrostatic interactions play a more important role in the complexation process. Based on the obtained results from the structural analysis Arg381, Arg291, and Arg49 play a key role in the binding site interactions with the different ligands, in comparison with other residues. There are some candidates such as Neu5Acα2-6Galβ1-4GlcNAcβ, Neu5Acα2-3Galβ1-3GlcNacβ1-3Galβ1-4Glc, and Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4Glc that form more stable complexes with the HN than the α2-3-Sialyllactose confirmed by the calculated Gibbs binding energies (-39.65, -46.93, and -36.49 kcal.mol^-1, respectively). To investigate the relationship between the molecular properties of the selected compounds and their affinity to the HN receptor, density functional theory dispersion corrected (DFT-D3) calculations were employed. According to our DFT-D3 results, neutral sialic acid-based compounds have lower reactivity to the mumps virus than the negativity charge structures. Moreover, by increasing the electronic chemical potential (μ) the vdW and H-bond interactions between drugs and the HN protein increase. In other words, by elevating the electron tendency of the selected ligands their affinity to the mumps virus increases. Our quantum chemistry calculations reveal that in addition to the structural features the molecular properties of the drugs can play important roles in their affinity and reactivity against the virus. The results of this study can provide useful details to design new compounds or improve their properties against the mumps virus.

On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study

The novel coronavirus disease and its complications have motivated the design of new sensors with the highest sensitivity, and affinity for the detection of the SARS-CoV-2 virus is considered in many research studies. In this research article, we employ full atomistic molecular dynamics (MD) models to study the interactions between the receptor binding domain (RBD) and spike protein of the coronavirus and different metals such as gold (Au), platinum (Pt), and silver (Ag) to analyze their sensitivity against this virus. The comparison between the RBD interactions with ACE2 (angiotensin-converting enzyme 2) and different metals indicates that metals have remarkable effects on the structural features and dynamical properties of the RBD. The binding site of the RBD has more affinity to the surfaces of gold, platinum, and silver than to the other parts of the protein. Moreover, the initial configuration of the RBD relative to the metal surface plays an important role in the stability of metal complexes with the RBD. The binding face of the protein to the metal surface has been changed in the presence of different metals. In other words, the residues of the RBD that participate in RBD interactions with the metals are different irrespective of the initial configurations in which the [Asn, Thr, Tyr], [Ser, Thr, Tyr], and [Asn, Asp, Tyr] residues of the protein have a greater affinity to Ag, Au, and Pt, respectively. The corresponding metals have a considerable affinity to the RBD, which due to strong interactions with the protein can change the secondary structure and structural features. Based on the obtained results during the complexation process between the protein and metals, the helical structure of the protein changes to the bend and antiparallel β-sheets. The calculated binding energies for the RBD complexes with silver, gold, and platinum are -95.03, -138.03, and -133.96 kcal·mol-1, respectively. The adsorption process of the spike protein on the surfaces of different metals represents similar results and indicates that the entire spike protein of the coronavirus forms a more stable complex with the gold surface compared with other metals. Moreover, the RBD of the spike protein has more interactions with the surfaces than with the other parts of the protein. Therefore, it is possible to predict the properties of the coronavirus on the metal surface based on the dynamical behavior of the RBD. Overall, our computational results confirm that the gold surface can be considered as an outstanding substrate for developing new sensors with the highest sensitivity against SARS-CoV-2.

Influence of salt and temperature on the self-assembly of cyclic peptides in water: a molecular dynamics study

It is found in the literature that cyclic peptides (CPs) are able to self-assemble in water to form cyclic peptide nanotubes (CPNTs) and are used extensively in the field of nanotechnology. Several factors influence the formation and stability of these nanotubes in water. However, an extensive study of the contribution of several important factors is still lacking. The purpose of this study is to explore the effect of temperature and salt (NaCl) on the association tendency of CPs. Furthermore, the self-association behavior of CPs in aqueous solutions at various temperatures is also thoroughly discussed. Cyclo-[(Asp-D-Leu-Lys-D-Leu)₂] is considered for this study and a series of classical molecular dynamics (MD) simulations at three different temperatures, viz. 280 K, 300 K, and 320 K, both in pure water and in NaCl solutions of different concentrations are carried out. The calculations of radial distribution functions, preferential interaction parameters, cluster formation and hydrogen bonding properties suggest a strong influence of NaCl concentration on the association propensity of CPs. Low NaCl concentration hinders CP association while high NaCl concentration facilitates the association of CPs. Besides this, the association of CPs is found to be enhanced at low temperature. Furthermore, the thermodynamics of CP association is predominantly found to be enthalpy driven in both the presence and absence of salt. No crossover between enthalpy and entropy in CP association is observed. In addition, the MM-GBSA method is used to investigate the binding free energies of the CP rings that self-assembled to form nanotube like structures at all three temperatures.

Effects of Ionic Liquids on the Stabilization Process of Gold Nanoparticles

Improving the stability of the gold nanoparticles (AuNPs) is an important challenge in nanoscience, given that the activity and ubiquitous application of the AuNPs in different fields depend largely on their stability in the solution phase. Ionic liquids (ILs) can be used as new alternatives in comparison to water and organic solvents due to their considerable properties to elevate the stability and resistance of the AuNPs against aggregation for a long period of storage. In this study, we employ molecular dynamics simulation and quantum chemistry calculations to investigate the effects of amino acid ILs ([BMIM][Gly], [BMIM][Leu], [BMIM][Pro], [BMIM][Val], and [BMIM][Ala]) on the stability and aggregation process of the AuNPs from the molecular viewpoint. Our results suggest that ILs can prevent AuNP aggregation. These ILs penetrate the solvation shell of the nanoparticles and by increasing the electrostatic repulsions on the surface of the AuNPs improve their stability against aggregation. Moreover, the [BMIM]⁺ cation is more effective on the stability of the AuNPs in comparison with the corresponding anions. The ring of the cation, due to the stronger interaction with the AuNPs compared to the side chain, contributes predominantly to the stability of the nanostructures. Our quantum chemistry calculations confirm that dispersion interactions between the cation and anions of the ILs and the surface of gold play a key role in the stability of the IL-AuNP complexes. [Leu]^- anion has the strongest dispersion interactions with the metal surface and forms the most stable complex with the AuNPs. Overall, the results of this study offer new insights into the properties of amino acid ILs as effective agents to improve the stability of AuNPs for long-term storage.

Application of amino acid ionic liquids for increasing the stability of DNA in long term storage

The structural stability of DNA is important because of its biological activity. DNAs due to their inherent chemical properties are not stable in an aqueous solution, therefore, a long period of storage of DNA at the ambient condition in bioscience is of importance. Ionic liquids (ILs) as interesting alternatives compared to organic solvents and water due to their considerable properties can be used as new agents to increase the stability of DNA for a long period of storage. In this article, molecular dynamics (MD) simulations and quantum chemistry calculations were applied to investigate the effects of amino acid ionic liquids ([BMIM][Ala], [BMIM][Gly], [BMIM][Val], [BMIM][Pro] and [BMIM][Leu]) on the dynamical behavior and the structural stability of calf thymus DNA. Based on the obtained MD results ILs enter into the solvation shell of the DNA and push away the water molecules from the DNA surface. Structural analysis shows that [BMIM]⁺ cations can occupy the DNA minor groove without disturbing the double-helical structure of DNA. ILs due to strong electrostatic and van der Waals (vdW) interactions with the DNA structure contribute to the stability of the double-helical structure. Quantum chemistry calculations indicate that the interactions between the [BMIM]⁺ cation and DNA structure has an electrostatic character. Moreover, this cation forms a more stable complex with the CGCG region of the DNA in comparison with AATT base pairs. Overall, the results of this study can provide new insight into the application of ILs for maintaining DNA stability during long-term storage.Communicated by Ramaswamy H. Sarma.

Structural and photoactive properties of self-assembled peptide-based nanostructures and their optical bioapplication in food analysis

BACKGROUND

Food processing plays an important role in the modern industry because food quality and security directly affect human health, life safety, and social and economic development. Accurate, efficient, and sensitive detection technology is the basis for ensuring food quality and security. Optosensor-based technology with the advantage of fast and visual real-time detection can be used to detect pesticides, metal ions, antibiotics, and nutrients in food. As excellent optical centres, self-assembled peptide-based nanostructures possess attractive advantages, such as simple preparation methods, controllable morphology, tunable functionality, and inherent biocompatibility.

AIM OF REVIEW

Self-assembled peptide nanostructures with good fabrication yield, stability, dispersity in a complex sample matrix, biocompatibility, and environmental friendliness are ideal development goals in the future. Owing to its flexible and unique optical properties, some short peptide self-assemblies can possibly be used to achieve the purpose of rapid and sensitive detection of composition in food, agriculture, and the environment, expanding the understanding and application of peptide-based optics in analytical chemistry.

KEY SCIENTIFIC CONCEPT OF REVIEW

The self-assembly process of peptides is driven by noncovalent interactions, including hydrogen bonding, electrostatic interactions, hydrophobic interactions, and π-π stacking, which are the key factors for obtaining stable self-assembled peptide nanostructures with peptides serving as assembly units. Controllable morphology of self-assembled peptide nanostructures can be achieved through adjustment in the type, concentration, and pH of organic solvents and peptides. The highly ordered nanostructures formed by the self-assembly of peptides have been proven to be novel biological structures and can be used for the construction of optosensing platforms in biological or other systems. Optosensing platforms make use of signal changes, including optical signals and electrical signals caused by specific reactions between analytes and active substances, to determine the content or concentration of an analyte.

A molecular dynamic study on the ability of phosphorene for designing new sensor for SARS-CoV-2 detection

Due to the dramatic increase in the number of patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), designing new selective and sensitive sensors for the detection of this virus is of importance. In this research, by employing full atomistic molecular dynamics (MD) simulations, the interactions of the receptor-binding domain (RBD) of the SARS-CoV-2 with phosphorene and graphene nanosheets were analyzed to investigate their sensing ability against this protein. Based on the obtained results, the RBD interactions with the surface of graphene and phosphorene nanosheets do not have important effects on the folding properties of the RBD but this protein has unique dynamical behavior against each nanostructure. In the presence of graphene and phosphorene, the RBD has lower stability because due to the strong interactions between RBD and these nanostructures. This protein spreads on the surface and has lower structural compaction, but in comparison with graphene, RBD shows greater stability on the surface of the phosphorene nanosheet. Moreover, RBD forms a more stable complex with phosphorene nanosheet in comparison with graphene due to greater electrostatic and van der Waals interactions. The calculated Gibbs binding energy for the RBD complexation process with phosphorene and graphene are −200.37 and −83.65 kcal mol⁻¹, respectively confirming that phosphorene has higher affinity and sensitivity against this protein than graphene. Overall, the obtained results confirm that phosphorene can be a good candidate for designing new nanomaterials for selective detection of SARS-CoV-2.