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Human β-defensins present in saliva have a broad spectrum of antimicrobial activities that work against infections in oral cavity. To provide a better understanding of these molecules' properties and functions at the molecular level, we have investigated and compared the important structural properties of human β-defensin-1, -2 and -3 using molecular dynamics simulations. Our results have shown that human β-defensin-3 has a more flexible structure in water than the other two because of its high hydrophilicity, low β-sheet content and high repulsive forces between its charged residues. Moreover, we found that the location of the salt bridges is important in protein's stability in water. Molecular dynamics simulations of human β-defensins 1, 2 and 3 revealed that the hbd-3 is more flexible in water than hbd-1 and hbd-2. [ABSTRACT FROM AUTHOR]

[Display omitted] • The Spike glycoprotein is decorated with N -linked Glycans (NAGs). • The precursor of nearly all eukaryotic glycans is N -Acetylglucosamine (GlcNAc) moiety. • United-atom Molecular Dynamics simulations were carried out. • GlcNAc molecules increase the local stability in their vicinity on the Spike Protein. A lot of effort has been made in developing vaccine and therapeutic agents against the SARS-CoV-2, concentrating on the Spike protein that binds angiotensin-converting enzyme 2 on human cells. Nowadays, some researches study the role of the N -linked glycans as potential targets for vaccines and new agents. Due to the flexibility and diversity of the N -linked glycans, in this work, we focus on the N -Acetylglucosamine moiety, which is the precursor of nearly all eukaryotic glycans. We performed molecular dynamics simulations to study the effects of the N -Acetylglucosamine on the stability of the spike glycoprotein in SARS-CoV-2. After a 100 ns of simulation on the spike proteins without and with the N -Acetylglucosamine molecules, we found that the presence of N -Acetylglucosamine increases the local stability in their vicinity; even though their effect on the full structure is negligible. Thus; it can be inferred that the N -Acetylglucosamine moieties can potentially affect the interaction of the S protein with the ACE2 receptor. We also found that the S1 domain is more flexible than the S2 domain. We propose which of the experimentally observed glycans found on the spike may be more functional than the others. Detailed understanding of glycans is key for the development of new therapeutic strategies. [ABSTRACT FROM AUTHOR]

The coenzyme Q (CoQ) molecule plays a critical role in the biochemical generation of energy in the form of adenosine triphosphate. Various types of CoQ can be classified according to their number of isoprenoid units in the tail. In human beings, CoQ10 is produced and is necessary for the basic functioning of cells. CoQ10 exists in two forms, as ubiquinone (UQ) and as ubiquinol (UQH2), which have different roles in the body. Molecular dynamics (MD) simulations for the analysis of the effects of solvents on the structure of the UQ molecule are presented. Besides, semi-empirical molecular orbital PM3 calculation is applied to obtain structural and electronic properties of both the UQ and the UQH2 molecules. According to the MD simulation, the UQ molecule seems to be flexible both in vacuum and in water. On the other hand, the molecule stays more rigid in methanol. PM3 calculations show that both molecules are quite hydrophobic. Furthermore, UQ is chemically more reactive than UQH2, but the latter is kinetically more stable than the former. [ABSTRACT FROM AUTHOR]

Amyloid peptides are important components in many degenerativediseases as well as in maintaining cellular metabolism. Their uniquestable structure provides new insights in developing new materials.Designing bioinspired self-assembling peptides is essential to generatenew forms of hierarchical nanostructures. Here we present oppositelycharged amyloid inspired peptides (AIPs), which rapidly self-assembleinto nanofibers at pH 7 upon mixing in water caused by noncovalentinteractions. Mechanical properties of the gels formed by self-assembledAIP nanofibers were analyzed with oscillatory rheology. AIP gels exhibitedstrong mechanical characteristics superior to gels formed by self-assemblyof previously reported synthetic short peptides. Rheological studiesof gels composed of oppositely charged mixed AIP molecules (AIP-1 2) revealed superior mechanical stability compared to individualpeptide networks (AIP-1 and AIP-2) formed by neutralization of netcharges through pH change. Adhesion and elasticity properties of AIPmixed nanofibers and charge neutralized AIP-1, AIP-2 nanofibers wereanalyzed by high resolution force–distance mapping using atomicforce microscopy (AFM). Nanomechanical characterization of self-assembledAIP-1 2, AIP-1, and AIP-2 nanofibers also confirmed macroscopicrheology results, and mechanical stability of AIP mixed nanofiberswas higher compared to individual AIP-1 and AIP-2 nanofibers self-assembledat acidic and basic pH, respectively. Experimental results were supportedwith molecular dynamics simulations by considering potential noncovalentinteractions between the amino acid residues and possible aggregateforms. In addition, HUVEC cells were cultured on AIP mixed nanofibersat pH 7 and biocompatibility and collagen mimetic scaffold propertiesof the nanofibrous system were observed. Encapsulation of a zwitterionicdye (rhodamine B) within AIP nanofiber network was accomplished atphysiological conditions to demonstrate that this network can be utilizedfor inclusion of soluble factors as a scaffold for cell culture studies. [ABSTRACT FROM AUTHOR]