Date of Award


Degree Type


Degree Name

Doctor of Philosophy in Chemical Engineering


Chemical Engineering

First Advisor

Michael L. Greenfield


Interest in studying anti-microbial peptides (AMPs) has increased becasue of their potential as future applicable antibiotic drugs. In my research under supervision of Professor Michael L. Greenfield, we attempt to understand the structure and dynamics of a novel hybrid AMP LM7-2, which was designed previously in Professor Lenore M. Martin’s research group (Cell and Molecular Biology Department at URI). Several experimental studies have successfully investigated mechanisms of AMPs against bacteria and shown that AMPs attack the membrane of bacteria and induce bacteria death. However, there is still much uncertainty in the exact mechanisms because of experimental restrictions. Hence, studying the structure and dynamics of lipid bilayers are as important as AMPs. Since molecular modeling provides atomistic details and 3D structure of a system, it can significantly contribute to investigating these mechanisms in more detail. In this work, it is shown how molecular modeling helps in understanding biological systems such as an α-helix LM7-2 in solution and the S. aureus lipid bilayer and deciphering biochemical and biophysical information, which is challenging to obtain by experiments. And since the precision of biomolecular modeling results is significantly based on force field (FF) parameters, the importance of developing FFs is demonstrated in this research.

Force Field Development. Simulation results on the basis of CHARMM36 (C36) FF showed that the structures of two aromatic amino acids, Tryptophan (Trp) and Tyrosine (Tyr), deviate from planarity. Hence, the geometry, dynamics, and out-of-plane vibrations of atoms in these rings were investigated by imposing improper torsion and changing torsion angle force constants. To that end, molecular dynamics (MD) simulation and allatom normal mode analysis (NMA) were implemented. The pattern and frequencies of out-of-plane vibrations of these rings matched with Raman and infrared spectra, and the extent of out-of-plane vibrations for atoms in these rings decreased.

A Helical Peptide in Water. AMPs usually have a helical structure on the membraneof bacteria. Some studies have stated that the flexible loop at the middle of helical AMPs, which leads a peptide to bend and snap the lipid bilayer, has a direct effect on AMPs activity against bacteria. Dynamics and vibrations of a helical and α helix-hingedhelix structure of an a-helix LM7-2 were studied computationally in solution. Although some vibrational experimental studies have been done on proteins or peptides, we show extended and interesting details about peptide vibrations by our study. Instantaneous NMA and Fourier transformation method were applied to understand how a change in the structure of a peptide will affect peptide fluctuations especially amide band vibrations. These computational methods could complement experimental vibrational studies to interpret spectra for similar systems and assign a marker for helix-hinge-helix structure of helical peptides.

A Complex Lipid Membrane. Lipid bilayers play a crucial role in a peptidemembrane interactions. Therefore, more realistic system of lipids will provide more detail of this interaction. To that end, we have designed a realistic S. aureus membrane by including 19 different types of lipids that are more consistent with experimental data than using a single lipid. Reverse Monte Carlo method was applied to match lipid bilayer composition to experimental results in the literature. Dynamics and membrane characteristics of this complex system were studied. Density profiles of atoms P, N, C, and H were used to compare the location of diverse headgroup types and study tail-tail interactions within both leaflets. Density profile of water molecules confirmed that small number of water molecules could penetrate to the center of membrane. The order parameter results were used to study how the range of chain reorientation motions differed for different lipids. Mean square displacement of each lipid showed diverse diffusion patterns for lipids even with the same type. (268609 kB)
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