Research Themes

Amphiphilic peptides and biomimetic peptide amphiphiles

The term ‘‘peptide-amphiphile’’ can be used to describe amphiphilic peptides consisting only of amino acids that show segregation of charged and uncharged components within the primary or secondary structure. Alternatively they may be composed of hydrophilic peptides linked to hydrophobic alkyl chains or lipids, and peptide based copolymers. Such molecules are of significant biological importace due to the range of asymmetric boundaries that occur in nature such as those found at a membrane lipid interface. In addition to amphiphilic peptides possessing key biological functions amphiphiles are becoming of increasing interest in the creation of new biomaterials. Amphiphiles can self-assemble into a variety of different structures such as micelles, vesicles, monolayers, bilayers, nanofibers, nanotapes, ribbons, and twisted ribbons, to minimize unfavorable interactions with their surroundings.
The groups focus is on understanding structure function relationships in the creation of bioactive peptides and new biomaterials. Research utilizes two main groups of techniques:

peptidesExperimental Biophysics. Langmuir troughs, allow a highly flexible approach to the study of membrane interactive molecules in terms of model membrane composition, subphase pH, ionic strength and other factors. Monolayers have been used to mimic bacterial and tumour cell membranes to investigate the peptide lipid interactions. The group also applies patch clamp technology to study transient pore formation and uses a range of imaging techniques including Cd, nmr and X-ray diffraction to study peptide structures within biologically revenant environements.

  1. Dennison, S.R. and Phoenix, D.A. 2011. Influence of C-terminal amidation on efficacy of modelin-5. Biochemistry. 50(9) 1514-1523
  2. Dennison, S. R. Morton LHG and Phoenix D.A 2012. Role of molecular architecture on the relative efficacy of aurein 2.5 and modelin 5 Biochimica et Biophysica Acta (BBA) – Biomembranes, 1818(9) 2094-2102

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Computational Biophysics. Molecular dynamics (MD) simulations  have provided detailed information on the fluctuations and conformational changes of proteins and are now routinely used to investigate the structure, dynamics and thermodynamics of biological molecules and their complexes. The laboratory focuses on the role of physico chemical characteristics and sequence effects on the mechanism interfacial folding and membrane insertion. Impact of residue replacement on peptide stability etc

Mura, M., Dennison, S.R., Zvelindovsky,, A.V., and Phoenix, D.A. 2012. Aurein 2.3 functionality is supported by oblique orientated α-helical formation Biochimica et Biophysica Acta (BBA) – Biomembranes, 1828 (2013),  586–594

Current themes:

A. Antimicrobial peptide structure function relationships

Antimicrobial peptides are relatively small, amphipathic molecules of variable length, sequence and structure with activity against a wide range of microorganisms including bacteria, protozoa, yeast, fungi, viruses and can also show selectivity for tumor cells. Antimicrobial peptides, both synthetic and from natural sources, have raised interest as pathogens become resistant against conventional antibiotics due to broad spectrum activity and their ability to kill multidrug-resistant bacteria.
Given they tend to be short (<40 residues), have relatively simple structures and are easy to make by chemical synthesis, so peptides of this type, both natural and designed, have been subject to numerous structure/activity relationship studies, aimed at understanding and improving their activity and elucidating their mode of action.
They usually act through relatively non-specific mechanisms resulting in membranolytic activity but they can also stimulate the innate immune response with recent evidence indicating they can kill microbes in a more sophisticated fashion. Several peptides have already entered pre-clinical and clinical trials for the treatment of catheter site infections, cystic fibrosis, acne, wound healing and patients undergoing stem cell transplantation. The group draws on a range of specialisms, including computational modeling, biochemistry, biophysics, and microbiology to:

  • Investigate the mode of action of helical peptides, determine their mechanisms of membrane lysis and identify their molecular target(s)
  • Undertake structure-activity studies to improve the antimicrobial activity and target selectivity of helical peptides, develop sequence templates for de novo AMP design
  • Develop computational methods for analyzing AMP sequences and for the identification and assessment of key functional characteristics

Projects:

  1. Peptidomimetics. Mimetics of antimicrobial peptides can be used to provide antimicrobial design templates as part of de novo AMP design strategies but also to give insight into key structural features involved in AMP activity. Synthetic oligoureas of metaphenylenediamine have been used to mimic host defense peptides and investigate key structural features such as length and physicochemical properties in order to seek new lead compounds.
  2. Antimicrobial peptide structure function relationships. For all known α-AMPs, the mechanism of membrane interaction are believed to involve membrane invasion although in some cases this appears to lead to membrane translocation and attack upon intracellular targets. In general, the ability of α-AMPs to invade microbial membranes primarily depends upon their positive charge, which allows them to target and bind anionic components of these membranes, and their amphiphilicity, which facilitates partitioning into these membranes. Therefore, the main focus for the group’s interest is to investigate the structure function relationships underpinning the membrane interactions of known antimicrobial and anticancer peptides and the role of amphiphilicity in the activity of biomolecules. Comparisons are made between a range of AMPs such as cationic aureins and anionic AMPs such as H5. The use of molecular dynamic simulations coupled to synthesis and testing of peptide homologues has allowed key structural and sequence specific features to be assessed as a function of activity. Research has suggested, for example that Phe is a key driver of antibacterial activity in a range of aureins. The Phe penetrates the hydrophobic core orientating the peptide to enable deeper membrane penetration.
  3. Antimicrobial mechanisms of action. There are multiple mechanisms that have been postulated to underpin AMP activity. We are observing the ability of AMPs to form transient pores via use of patch clamp technology and by use of molecular dynamic simulations, structure analysis and biophysics are seeking to asses different modes of action and the dependency of mode on peptide structure and membrane composition. To date we have shown the importance of key features such as oblique orientation and in some cases have postulated that the AMPs may function by formation of amyloid like intermediates. Recent work has identified the importance of cooperative interactions between peptides for activity of some AMPs with, for example, some aurein peptides working most effectively as trimers enabling one of the chains to be forced deep into the membrane interior via such cooperative activity. In addition we have confirmed the importance of the membrane lipid composition with sterols providing a protective effect for eukaryotic cells and specific lipids enhancing efficacy or in some cases inhibiting activity highlighting the complexity of this field.

B Biomimetic peptide amphiphiles.

Peptide-amphiphiles are amphiphilic structures with a hydrophilic peptide headgroup that incorporates a bioactive sequence and has the potential to form distinct structures, and a hydrophobic tail that serves to align the headgroup, drive self-assembly, and induce secondary and tertiary conformations.

Projects:

  1. Development of membrane interactive peptides for self-assembly of biologically active nanoparticles. Recent work has identified the potential for appropriately modified synthetic analogues based on protein transmembrane domains to form nanoparticles with relevance to drug delivery. These particles can act as vehicles into which hydrophobic drugs can be entrapped and therefore have the potential for enhanced targeting of hydrophobic anticancer molecules. Furthermore such sequences are able to support cellular targeting and their spontaneous fusion with cell membranes supports the release of a cargo into the cell interior. The project aims to further investigate the characteristics of fusogenic peptides and their ability to support formation of biologically relevant nanoparticles.