Polar Zipper on a Peptide Nanomembrane: A Characterization by Potential of Mean Force

In this work, nanomembranes formed by the I₃XGK (X = Q, S, or N) polar peptides are studied to characterize the average force and energy required to separate two neighboring β-sheets laterally joined by polar zippers. The results presented are obtained using a methodology (state of the art) involving the pulling umbrella method to generate the samples (umbrella sampling) and the potential of mean force (PMF) to evaluate the energetic variation evolved in the process of separating the polar zipper. It was observed that the maximum force required to separate the regions linked by polar zippers is 1.48 kJ/mol nm for the I₃NGK nanomembrane and 1.22 kJ/mol nm [1.30 kJ/mol nm] for the I₃QGK [I₃SGK] nanomembranes, emphasizing that polar zippers play an important role in the interaction that interconnects β-sheets in broad and robust two-dimensional structures (tapes and membranes), offering an agile route to the construction of distinct nanomaterials from β-sheets. Also, negative values were obtained for energy as a function of the reaction coordinate for the regions where the formation of polar zippers occurs, showing that the lateral union of neighboring β-sheets is energetically favorable, with a value up to -3.0 kJ/mol, in the case of I₃NGK nanomembranes.

Effects of the structure of lipid-based agents in their complexation with a single stranded mRNA fragment: a computational study

In this work we employed fully atomistic molecular dynamics simulations, aiming towards a better understanding of the mechanisms associated with the formation and the stability of lipid-based RNA nanoassemblies, in an aqueous environment. We examined two groups of lipid-based complexation agents, differing in the degree of hydrophobicity and in the overall charge. The first group was comprised of cationic ionizable agents while the second included electrically neutral amphoteric phosphatidylcholine lipids. It was found that the overall charge of the complexation agents played the most decisive role in the energetics of the lipid/RNA association, while their degree of hydrophobicity affected their self-assembly and their complexation kinetics. The latter also affected the structural stability of the formed complexes since the water entrapped within the clusters of the less hydrophobic agents appeared to reduce the coherence of the lipid-RNA nanoassemblies. The combined effects of the aforementioned attributes dictated also the RNA conformation after complexation. The results from the present study provide thus new insight towards controlling the morphology, the energetic stability and the structural integrity of the formed complexes.

Functional Peptides from SARS-CoV-2 Binding with Cell Membrane: From Molecular Dynamics Simulations to Cell Demonstration

Herein, we have verified the interaction between the functional peptides from the SARS-CoV-2 and cell membrane, and we further proved that peptides exhibit little membrane disruption. The specific amino acids (Lys, Ile, Glu, Asn, Gln, etc.) with charge or hydrophobic residues play a significant role during the functional-peptide binding to membrane. The findings could provide the hints related to viral infection and also might pave the way for development of new materials based on peptides with membrane-binding activity, which would enable functional peptides further as peptide adjuvants, in order to help deliver the cancer drug into tumor cells for the efficient tumor therapy.

Surfactants: physicochemical interactions with biological macromolecules

Macromolecules are essential cellular components in biological systems responsible for performing a large number of functions that are necessary for growth and perseverance of living organisms. Proteins, lipids and carbohydrates are three major classes of biological macromolecules. To predict the structure, function, and behaviour of any cluster of macromolecules, it is necessary to understand the interaction between them and other components through basic principles of chemistry and physics. An important number of macromolecules are present in mixtures with surfactants, where a combination of hydrophobic and electrostatic interactions is responsible for the specific properties of any solution. It has been demonstrated that surfactants can help the formation of helices in some proteins thereby promoting protein structure formation. On the other hand, there is extensive research towards the use of surfactants to solubilize drugs and pharmaceuticals; therefore, it is evident that the interaction between surfactants with macromolecules is important for many applications which includes environmental processes and the pharmaceutical industry. In this review, we describe the properties of different types of surfactants that are relevant for their physicochemical interactions with biological macromolecules, from macromolecules–surfactant complexes to hydrophobic and electrostatic interactions.

Complexation of single stranded RNA with an ionizable lipid: an all-atom molecular dynamics simulation study

Complexation of a lipid-based ionizable cationic molecule (referred to as DML: see main text) with RNA in an aqueous medium was examined in detail by means of fully atomistic molecular dynamics simulations. The different stages of the DML-RNA association process were explored, while the structural characteristics of the final complex were described. The self-assembly process of the DML molecules was examined in the absence and in the presence of nucleotide sequences of different lengths. The formed DML clusters were described in detail in terms of their size and composition and were found to share common features in all the examined systems. Different timescales related to their self-assembly and their association with RNA were identified. It was found that beyond a time period of a few tens of ns, a conformationally stable DML-RNA complex was formed, characterized by DML clusters covering the entire contour of RNA. In a system with a 642-nucleotide sequence, the average size of the complex in the longest dimension was found to be close to 40 nm. The DML clusters were characterized by a rather low surface charge, while a propensity for the formation of larger size clusters close to RNA was noted. Apart from hydrophobic and electrostatic interactions, hydrogen bonding was found to play a key-role in the DML-DML and in the DML-RNA association. The information obtained regarding the structural features of the final complex, the timescales and the driving forces associated with the complexation and the self-assembly processes provide new insight towards a rational design of optimized lipid-based ionizable cationic gene delivery vectors.

Molecular dynamics of the membrane interaction and localisation of prodigiosin

The tripyrrolic antibiotic prodigiosin causes diverse reactions on its targets like energy spilling, membrane leakage, loss of motility and phototoxicity. It has bacteriostatic, bactericidal, anti-fungal, anti-cancer and immunosuppressive properties. Most of the functions suggest the role of prodigiosin in membrane disruption but the exact mechanism remains unknown. A molecular dynamics study was performed to understand the interactions of prodigiosin with the membrane. It was seen that prodigiosin from the solvent enters the membrane immediately either individually or as small clusters. Prodigiosin clusters with more than eight molecules do not appear to enter the membrane. Upon entry, the molecules orient themselves along the membrane-water interface with the pyrrole rings interacting with lipid head groups and with water. This orientation is stabilised by hydrogen bonding and hydrophobic interactions. The presence of prodigiosin molecules in the membrane changes the local lipid architecture and reduces the solvent accessibility of the membrane. The membrane fluidity, thickness or area per lipid head are largely unaffected. This suggests that prodigiosin could cause most damage in the vicinity of a membrane protein and thus could also explain the reason for varied effects on the targets.

Spectroscopic properties and solute–solvent structural analyses for ANR polypeptides in water solution: a sequential Monte Carlo/quantum mechanics (S-MC/QM) theoretical study

We present a theoretical study of the solvent influence on A_NR polypeptides, with N = 1, 2, 3, 4 and 5, in the gas phase and in water solution using the sequential MC/QM methodology combined with GIAO-DFT calculations.