Antibacterial peptides:vStructural parameters and activity relationship

1. Antibacterial peptides:
Structural parameters and
activity relationship

2. Antibacterial peptides
• Amphipathic peptides with membrane lytic activity are
ubiquitous in nature, constituting a defence systems
against invading microorganism in many organism
• Around 256 available in nature
• Widely available and studied peptides are
1 Mellitin from honey bee (26 Amino acids)
GLY-ILE-GLY-ALA-VAL-LEU-LYS-VAL-LEU-THR-THR-GLY-LEU-PRO-ALA-LEU-ILE-SER-TRP-ILE-LYS-
ARG-LYS-ARG-GLN-NH2
2 Magainins from frog skin (23 Amino acids)
GLY-ILE-GLY-LYS-PHE-LEU-HIS-SER-ALA-LYS-LYS-PHE-GLY-LYS-ALA-PHE-VAL-GLY-GLU-ILE-MET-
ASN-SER-NH2
3 Cecropin from pig intestine (31 Amino acids)
SER-TRP-LEU-SER-LYS-THR-ALA-LYS-LYS-LEU-GLU-ASN-SER-ALA-LYS-LYS-ARG-ILE-SER-GLY-ILE-
ALA-ILE-ALA-ILE-GLN-GLY-GLY-PRO-ARG
4 Synthetic KLAL(LYS-LEU-ALA-LEU)-model peptides

3. Origin and properties of representative
cytolytic peptides

4. Amino acid & peptide bond formation
General structure of an
amino acid
Depepnding of the nature of -R-,
there are 20 different amino
acids which act as the
building block of
peptides/proteins
Amide bond formation
Di-Peptide

5. Protein Secondary Structure
α-helix β-sheet

6. Structure of antibacterial peptides
• Linear peptide
• Largely unstructured in solution
• Folds into an amphipathic α-helix upon binding target
membrane
• Amphiphatic helix is a membrane-binding motif in many
proteins & Peptides formed by linear amino acid chains
with a periodicity of polar & nonpolar residues of about
three to four.

7. The different structural features of the amphipathic helices of the
peptides(Helical wheel projections and schematic drawings)
The one letter code for amino acids is used
Hydrophobic residues are shown in white
Polar residues in gray and cationic residues in black
circles.
N =number of residues.
Q =The total charge
H = mean residue hydrophobicity.
Φ = angle subtended by the charged residues on the helix
surface.
Hh = hydrophobicity of the non-charged domain (360°-
Φ).
µ=hydrophobic moment calculated as the vector sum of
the hydrophobicities of all residues, assuming an ideal α
-helix.
H and µ of melittin were calculated for the α-helical
region only

8. Antibacterial peptide
Mode of action/mechanism
Two steps process
• Binding to membrane surface and destabilization
of membrane structure (antibacterial activity).
• Membrane permeabilization Leads to
cell death (hemolytic activity).

9. Peptide structural parameters/motifs
• Helicity
• Hydrophobic moment
• Hydrophobicity
• Size of polar/apolar helix domain
• Charge

10. Helicity
• Amphiphatic helix is a membrane-binding motif in many
proteins & Peptides formed by linear amino acid chains
with a periodicity of polar & nonpolar residues of about
three to four
• In this structure, the polar side chains aligned along one
side and the hydrophobic resudues along the opposite side
of the helical coat.
• Exterior hydrophobic helical coat allows an optomal
interaction of the peptides with amphiphilic structure of
biological membranes.
• Helicity is the measure of helix content in a
protein/peptide containing other secondary structures (β-
sheet, unordered).

11. Helicity-amino acid substitution
• Substitution of an amino acid which increase helicity
produced enhanced hemolytic and antibacterial activity.
• Conversely substitution which prevent folding into a
helical conformation resulted in loss of both hemolytic and
antibacterial activity.
• Substitution of L-amino acid with its enatiomers (D-amino
acid) locally disturb helix formation as a result of which,
the hemolytic activity of linear peptide reduced.
• Substitution of two neighboring amino acid by their D-
enantiomers results in decreased helicity and distinctly
reduced hemolytic activity against neutral & charged
memmbranes.

12. Helicity
Helix inducing organic solvents
• Trifluoroethanol (TFE) act as helix inducing solvent,
which is frequently referred to as ‘membrane mimicking.
• Hydrophobic peptide in TFE adopt helical conformation β-
sheet structure is favored in sodium dodecyl sulphate
(SDS) solution.
• Addition peptide from TFE exhibit more hemolytic
activity than from SDS.

13. Hydrophobic moment
• Quantitative measure of peptide hydrophobicity
• Defined as the vector sum of the hydrophobicities of the
individual amino acids.
• Initially used for the study of protein folding.
• The more general definitions applicable to membrane
related proteins and peptide structures.
• Hydrophobic moment plot (dependence of the
hydrophobic moments per residue hydrophobicity) used to
predict the membrane activity of peptide helices.

14. Hydrophobic moment-peptide activity
• Play very important role in modulation of peptide
antibacterial and hemolytic activity.
• Correlation difficult-change in hydrophobic moments most
often leads to alteration in other parameters.
• Group of amino acid substitution having different HM, but
keeping other parameters almost unchanged.
• Increase in hydrophobic moment resulted in enhancement
in antibacterial and hemolytic activity.

15. Hydrophobicity
• Measure of the intrinsic capability of a peptide to
move from an aqueous into a hydrophobic phase.
• Peptide should be soluble in water for rapid
transfer to target and simultaneously it should be
able to interact with the hydrophobic region of
membrane to disturb membrane structure and
enhance permeability.
• Existence of optimal hydrophobicity.

16. Hydrophobicity-peptide activity
• Substitution by more hydrophobic amino acids
produced enhanced antibacterial and hemolytic
activity.
• The change in other parameters due to substitution
could be overcome by using model peptide having
varied hydrophobicity but with other structural
parameters unchanged.
• Peptides with higher hydrophobicity exhibit
higher antibacterial and hemolytic activity.

17. Angle subtended by the polar/apolar
helix domains/surfaces (Φ)
• Structural motif used to express the
hydrophobic/hydrophilic residue distribution within
amphopathic helical peptides.
• Estimated by the angle subtended by the hydrophobic or
hydrophilic helix face.
• Determine the location of membrane binding peptides
– Small hydrophilic angle and high hydrophobicity favor
transmembrane pore formation.
– Equivalent hydrophilic and hydrophobic surfaces favor parallel
orientation to the membrane surface.

18. The polar/apolar helix surfaces angles
-peptide activity
• Small polar angle and larger hydrophobic area favor
hemolytic activity.
• Peptide with higher polar angle and lower hydrophobic
face only able to interact with membrane surface.
• Increased polar angle
– reduced curvature strain-lower hemolytic activity

19. Charge of the peptide
• Most natural antibacterial and hemolytic peptides are
positively charged.
• Controlling parameters for binding of peptide to membrane
surface.

20. Charge of the peptide-peptide activity
• Natural peptide having more positive charge exhibit higher
binding activity.
• Substitution of non-polar amino acids by polar amin acids
– enhanced binding affinity.
• Presence of negatively charged lipids in membrane surface
produced higher binding affinity.
• Though one of the important structural motifs, no proper
correlation exist.

21. Synthesis/design of antibacterial
peptides with optimal activity
Different strategies
 Analysis of sequences of naturally occurring antimicrobial and
hemolytic peptides and extraction of sequence regions that
contribute activity
– Synthesis of peptides analogous to naturally
occuring patterns.
 Development of helical peptide from combinatorial library
 Systematic study of the role of structural properties on the peptide-
lipid interaction and design of antibacterial peptide having optimal
activity.

22. References
• Curr. Opin. Immunol, 1998, 10: 41-44
• J. Immunol. 1998, 48: 15-25
• Biopolymers 1998, 47: 435-450
• BBA 1999, 1462: 71-87