Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)


Agricultural and Biological Engineering

Committee Chair

Ganesan Narsimhan

Committee Member 1

Xiao Zhu

Committee Member 2

Arun Bhunia

Committee Member 3

Nathan Mosier

Committee Member 4

Osvaldo Campanella

Committee Member 5

Meng Deng


Antimicrobial peptides (AMPs) inactivate microbial cells through pore formation in cell membrane. Because of their different mode of action compared to antibiotics, AMPs can be effectively used to combat drug resistant bacteria in human health. AMPs can also be used to replace antibiotics in animal feed and immobilized on food packaging films. We developed a methodology based on mechanistic evaluation of peptide-lipid bilayer interaction to identify AMPs from soy protein. Production of AMPs from soy protein is an attractive, cost-saving alternative for commercial consideration, because soy protein is an abundant and common protein resource. This methodology is also applicable for identification of AMPs from any protein. Initial screening of peptide segments from soy protein was based on their hydrophobicity, hydrophobic moment and net charge. Delicate balance between hydrophilic and hydrophobic interactions is necessary for pore formation. High hydrophobicity decreases the peptide solubility in aqueous phase whereas high hydrophilicity limits binding of the peptide to the bilayer. Out of several candidates chosen from the initial screening, two peptides satisfied the criteria for antimicrobial activity, viz. (i) lipid-peptide binding in surface state and (ii) pore formation in transmembrane state of the aggregate. This method of identification of antimicrobial activity via MD simulation was shown to be robust in that it is insensitive to the number of peptides employed in the simulation, initial peptide structure and force field. Their antimicrobial activity against Gram positive Listeria monocytogenes and Gram negative Escherichia coli was further confirmed by spot-on-lawn test. The effects of (i) number of total and net charges, (ii) hydrophobicity (iii) hydrophobic moment and (iv) helicity of peptides from soy protein on their ability to bind to lipid bilayer and their transmembrane aggregates to form pores were investigated by explicit solvent MD simulation. Interaction of possible AMP segments from soy protein with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPC/POPG) bilayers, a mimic of bacterial cell membrane, was investigated. Pore formation was insensitive to helicity and occurred for hydrophobicity threshold in the range of -0.3 to 0 kcal/mol, hydrophobic moment threshold of 0.3 kcal/mol, net charge threshold of 2. Though low hydrophobicity and high number of charges help in the formation of water channel for transmembrane aggregates, insertion of peptides with these properties requires overcome of energy barrier, as shown by potential mean force calculations, thereby resulting in low antimicrobial activity. Experimental evaluation of antimicrobial activity of these peptides against Gram positive L. monocytogenes and Gram negative E. coli as obtained by spot-on-lawn assay was consistent with simulation results. These results should help in the development of guidelines for selection of peptides with antimicrobial activity based on their physicochemical properties. MD simulation was also employed to investigation interaction between amyloid β (Aβ) peptide and lipid bilayer. Some amyloid-related proteins/peptides are involved in aggregation and pore formation in phospholipid membranes (cell membranes), which result in a variety of neurological disorders such as Alzheimer disease (AD), Parkinson disease (PD), Huntington disease etc. We investigated the mechanism of pore formation by Aβ peptides using MD simulation by simulating the interaction of Aβ (11-42) peptide, with lipid membrane and evaluated the potential of mean force of interaction. 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane system with different cholesterol concentration was used to simulate mammalian cell membrane. The results indicated that Aβ (11-42) peptide oligomers with peptide number larger than two are more likely to lead to lipid deformation and water channel, and the free energy of penetration into membrane decreased with increasing number of peptides. Increasing concentration of cholesterol leads to higher energy barrier for penetration of peptide into lipid bilayer thereby protecting the membrane. The results of this research have potential application in the prevention of pore formation on lipid membrane by Aβ aggregates.