Experimental and Computational Characterization of Oxidized and Reduced Protegrin Pores in Lipid Bilayers

Rodnin, Mykola V.; Vasquez‐Montes, Victor; Nepal, Binod; Ladokhin, Alexey S.; Lazaridis, Themis

doi:10.1007/s00232-020-00124-3

Cited by 7 publications

(4 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Further, molecular dynamics (MD) simulation studies of hBD-3 analogues lacking SS-linkages induce significant disruption of negatively charged lipid bilayers, compared to their native counter-part (Zhang 2020 ). Similarly, the antimicrobial activity of other disulphide-rich peptides has been known to be regulated by presence / absence of SS-bonds (Doherty et al 2006 ; Lipkin & Lazaridis 2015 ; Rodnin et al 2020 ; Shi et al 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Role of Disulphide Bonds in Membrane Partitioning of a Viral Peptide

2022

View full text Add to dashboard Cite

The importance of disulphide bond in mediating viral peptide entry into host cells is well known. In the present work, we elucidate the role of disulphide (SS) bond in partitioning mechanism of membrane-active Hepatitis A Virus-2B (HAV-2B) peptide, which harbours three cysteine residues promoting formation of multiple SS-bonded states. The inclusion of SS-bond not only results in a compact conformation but also induces distorted α-helical hairpin geometry in comparison to SS-free state. Owing to these, the hydrophobic residues get buried, restricting the insertion of SS-bonded HAV-2B peptide into lipid packing defects and thus the partitioning of the peptide is completely or partly abolished. In this way, the disulphide bond can potentially regulate the partitioning of HAV-2B peptide such that the membrane remodelling effects of this viral peptide are significantly reduced. The current findings may have potential implications in drug designing, targeting the HAV-2B protein by promoting disulphide bond formation within its membrane-active region. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s00232-022-00218-0

show abstract

Section: Introductionmentioning

confidence: 99%

Role of Disulphide Bonds in Membrane Partitioning of a Viral Peptide

2022

View full text Add to dashboard Cite

show abstract

“…Our study is just a first attempt to design membrane-selective peptides via a joint match between experimental library screening and MD simulation poration prediction. The ultimate goal is computer-guided antibiotics design (Torres and de la Fuente-Nunez 2019; Chen et al 2019;Wu et al 2019;Yang et al 2019;Rodnin et al 2020), developing potent antimicrobial peptides that have effective membrane selectivity to distinguish between human red blood cells and bacterial membranes, and even between different bacterial species. The key advantage of in-silico techniques is the vastly larger combinatorial space that can be explored in comparison to experimental library screening.…”

Section: A U T H O R Accepted Manuscriptmentioning

confidence: 99%

Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition

et al. 2021

View full text Add to dashboard Cite

The use of designed antimicrobial peptides as drugs has been impeded by the absence of simple sequence-structure-function relationships and design rules. The likely cause is that many of these peptides permeabilize membranes via highly disordered, heterogeneous mechanisms, forming aggregates without well-defined tertiary or secondary structure. We suggest that the combination of high-throughput library screening with atomistic computer simulations can successfully address this challenge by tuning a previously developed general pore forming peptide into a selective pore former for different lipid types. A library of 2,916 peptides was designed based on the LDKA template. The library peptides were synthesized and screened using a high-throughput orthogonal vesicle leakage assay. Dyes of different sizes were entrapped inside vesicles with varying lipid composition to simultaneously screen for both pore size and affinity for negatively charged and neutral lipid membranes. From this screen, nine different LDKA variants that have unique activity were selected, sequenced, synthesized, and characterized. Despite the minor sequence changes, each of these peptides has unique functional properties, forming either small or large pores and being selective for either neutral or anionic lipid bilayers. Long-scale, unbiased atomistic molecular dynamics (MD) simulations directly reveal that rather than rigid, well-defined pores, these peptides can form a large repertoire of functional dynamic and heterogeneous aggregates, strongly affected by single mutations. Predicting the propensity to aggregate and assemble in a given environment from sequence alone holds the key to functional prediction of membrane permeabilization.

show abstract

“…These studies include simulations using both coarse grained [25,26], atomistic [27][28][29][30][31] or a combination of both methods [32]. Vesicle leakage assays in combination with MD simulations have also been used to determine aggregation states and develop a molecular understanding for the AMP activity [33,34]. Additionally vesicle based experiments allow the determination of the partitioning coefficients and associated free energies of insertion [35].…”

Section: Introductionmentioning

confidence: 99%

A molecular dynamics study of antimicrobial peptide translocation across the outer membrane of Gram-negative bacteria

Sharma

Ayappa

2022

Preprint

View full text Add to dashboard Cite

With rising bacterial resistance, antimicrobial peptides (AMPs) have been widely investigated as potential antibacterial molecules to replace conventional antibiotics. Our understanding of the molecular mechanism for membrane disruption are largely based on AMP interactions with the inner phospholipid bilayers of both Gram-negative and Gram-positive bacteria. Mechanisms for AMP translocation across the outer membrane of Gram-negative bacteria composed of lipopolysaccharides and the asymmetric lipid bilayer are incompletely understood. In the current study, we have employed atomistic molecular dynamics and umbrella sampling simulations with an aggregate duration of ~ 8 microseconds to understand the free energy landscape of CM15 peptide within the OM of Gram-negative bacteria, E. coli. The peptide has a favourable binding free energy (-130 kJ mol-1) in the O-antigen region with a large barrier (150 kJ mol-1) at the interface between the anionic core-saccharides and upper bilayer leaflet made up of lipid A molecules. We have analyzed the peptide and membrane properties at each of the 100 ns duration umbrella sampling windows to study variations in the membrane and the peptide structure during the translocation through the OM. Interestingly the peptide is seen to elongate, adopting a membrane perpendicular orientation in the phospholipid region resulting in the formation of a transient water channel during it's translocation through the bilayer. The presence of the peptide at the lipid A and core-saccharide interface results in a 11% increase in the membrane area with the peptide adopting a predominantly membrane parallel orientation in this cation rich region. Additionally, the lateral displacement of the peptide is significantly reduced in this region, and increases toward the inner phospholipid leaflet and the outer O-antigen regions of the membrane. The peptide is found to be sufficiently hydrated across both the hydrophilic as well as hydrophobic regions of the membrane and remains unstructured without any gain in helical content. Our study unravels the complex free energy landscape for the translocation of the AMP CM15 across the outer membrane of Gram-negative bacteria and we discuss the implications of our findings with the broader question of how AMPs overcome this barrier during antimicrobial activity.

show abstract

Experimental and Computational Characterization of Oxidized and Reduced Protegrin Pores in Lipid Bilayers

Cited by 7 publications

References 49 publications

Role of Disulphide Bonds in Membrane Partitioning of a Viral Peptide

Role of Disulphide Bonds in Membrane Partitioning of a Viral Peptide

Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition

A molecular dynamics study of antimicrobial peptide translocation across the outer membrane of Gram-negative bacteria

Contact Info

Product

Resources

About