Interaction of Scots Pine Defensin with Model Membrane by Coarse-Grained Molecular Dynamics

Interaction of Uperin Peptides with Model Membranes: Molecular Dynamics Study

The interaction of antimicrobial and amyloid peptides with cell membranes is a critical step in their activities. Peptides of the uperin family obtained from the skin secretion of Australian amphibians demonstrate antimicrobial and amyloidogenic properties. All-atomic molecular dynamics and an umbrella sampling approach were used to study the interaction of uperins with model bacterial membrane. Two stable configurations of peptides were found. In the bound state, the peptides in helical form were located right under the head group region in parallel orientation with respect to the bilayer surface. Stable transmembrane configuration was observed for wild-type uperin and its alanine mutant in both alpha-helical and extended unstructured forms. The potential of mean force characterized the process of peptide binding from water to the lipid bilayer and its insertion into the membrane, and revealed that the transition of uperins from the bound state to the transmembrane position was accompanied by the rotation of peptides and passes through the energy barrier of 4-5 kcal/mol. Uperins have a weak effect on membrane properties.

Enhanced antifouling properties of marine antimicrobial peptides by PEGylation

Covalent immobilisation of antimicrobial peptides (AMPs) on underwater surfaces to combat marine biofouling is of great interest as it is an efficient, broad-spectrum and environmentally friendly strategy. Similar to post-translational modifications of natural proteins, artificial modifications of antimicrobial peptides can introduce important impacts on their properties and functions. The present work revealed the enhanced effect of PEGylation on the antifouling properties of marine antimicrobial peptides (LWFYTMWH) through grafting the modified peptides on aluminium surfaces. PEG was coupled to the peptide by solid-phase peptide synthesis, and the PEGylated peptides were bioconjugated to the aluminium surfaces which was pre-treated by aryldiazonium salts to introduce carboxyl groups. The carboxy group has been activated through the reaction with 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride and N-hydroxysuccinimide. The successful modification was confirmed via FT-IR and XPS. Interestingly, the PEGylated peptides modified surfaces could kill 90.0% Escherichia coli (Gram-negative) and 76.1% Bacillus sp. (Gram-positive), and showed better antifouling performance than the original peptides modified surfaces. Furthermore, molecular dynamics simulations showed PEGylation could enhance the ability of peptides to destroy membrane. The PEGylated peptides inserted into the membrane and induced the change in local curvature of membrane, leading to the rupture of membrane. The presence of PEG changed the antimicrobial peptides into more flexible conformations and the high hydrophilicity of PEG hindered the settlement of bacteria. These might be the two main working mechanisms for the increased antifouling efficiency of PEGylated peptides modified surface. This study provided a feasible modification strategy of antimicrobial peptides to enhance their antifouling properties.

Pore-forming proteins: From defense factors to endogenous executors of cell death

Pore-forming proteins (PFPs) and small antimicrobial peptides (AMPs) represent a large family of molecules with the common ability to punch holes in cell membranes to alter their permeability. They play a fundamental role as infectious bacteria's defensive tools against host's immune system and as executors of endogenous machineries of regulated cell death in eukaryotic cells. Despite being highly divergent in primary sequence and 3D structure, specific folds of pore-forming domains have been conserved. In fact, pore formation is considered an ancient mechanism that takes place through a general multistep process involving: membrane partitioning and insertion, oligomerization and pore formation. However, different PFPs and AMPs assemble and form pores following different mechanisms that could end up either in the formation of protein-lined or protein-lipid pores. In this review, we analyze the current findings in the mechanism of action of different PFPs and AMPs that support a wide role of membrane pore formation in nature. We also provide the newest insights into the development of state-of-art techniques that have facilitated the characterization of membrane pores. To understand the physiological role of these peptides/proteins or develop clinical applications, it is essential to uncover the molecular mechanism of how they perforate membranes.

Plant Defensins from a Structural Perspective

Plant defensins form a family of proteins with a broad spectrum of protective activities against fungi, bacteria, and insects. Furthermore, some plant defensins have revealed anticancer activity. In general, plant defensins are non-toxic to plant and mammalian cells, and interest in using them for biotechnological and medicinal purposes is growing. Recent studies provided significant insights into the mechanisms of action of plant defensins. In this review, we focus on structural and dynamics aspects and discuss structure-dynamics-function relations of plant defensins.

Disulfide Bonds Affect the Binding Sites of Human β Defensin Type 3 on Negatively Charged Lipid Membranes

Human β defensin type 3 (hBD-3) is a small natural antimicrobiotic. It is strongly cationic and has six cysteine residues which can form three pairs of intramolecular disulfide bonds under oxidized condition. Those disulfide bonds can break under reducing condition. However, the antibacterial activities of hBD-3 in its wild-type and analog forms are similar. In this project, the structure and dynamics of hBD-3 were investigated by running simulations on hBD-3 in its wild-type and analog forms in solvent, binding to negatively charged lipid bilayers, and self-assembly with POPG lipids. It was found that the RMSFs of hBD-3 in both its wild-type and analog forms are similar in solvent, while they are very diverse depending on the binding sites of hBD-3 with negatively charged bilayers. Calculating both the distance map and insertion depths for 18 hBD-3 molecules binding on the POPG bilayer, hBD-3 in its analog form binds stably with the POPG bilayer through the head and loop regions, while hBD-3 wild-type binds with the POPG bilayer on the two loop regions stably. hBD-3 analog caused membrane thinning and disrupted the POPG lipids more significantly than the wildtype. Based on the self-assembly simulations, hBD-3 monomer can bind with and embed inside the negatively charged POPG lipid membrane and have more contacts with the POPG lipid heads than with tails. The current work emphasized the structural diversity of hBD-3 interacting with negatively charged lipid membrane affected by the disulfide bonding states.

Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.