Simulation of Membrane Proteins and Lipids: Dynamic Behavior of a Small Antimicrobial Peptide Open Access

Reid, Keon (Spring 2018)

Permanent URL: https://etd.library.emory.edu/concern/etds/12579s263?locale=en
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Abstract

 

Antimicrobial peptides (AMPs) are ubiquitous across multicellular systems. These small peptides are highly functional and can be easily modified. In recent decades, AMPs have been on the frontier of therapeutic advances. Particularly, these small proteins have now been used in studies that target cancer. Namely, SVS-1 is an antimicrobial hairpin peptide that was engineered to preferentially bind, fold and disrupt cancer membranes. SVS-1 is of particular interest because of the relatively high efficacy in which the peptide disrupts cancer cells in vitro. This thesis expands the understanding of this novel peptide design to decipher the ingredients necessary for its mode of action. 

Atomistic molecular simulation conducted on the small peptide reveal the complex role electrostatics and lipid packing play on its mode of action. SVS-1 is a beta-hairpin AMP designed to selectively adsorb to cancer cells, fold at the surface and consequentially disrupt the cell membrane. In vitro studies conducted by Sinthuvanich et al. [JACS, 2012] demonstrate the selectivity of SVS-1 towards anionic cancerous cells versus normal mammalian cells. SVS-1 has 18 residues consisting of alternating Lys-Val sidechains on each arm and maintains a fairly rigid turn resulting from a LPro-DPro motif. These lysine residues dominate the initial contact and sustained binding atop charged surfaces. On the contrary, the AMP will only undergo transient binding in the presence of zwitterionic surfaces. Simulations reveal binding to the surface of the charged surface promotes folding at the surface and reorganization of the sidechains such that hydrophobic residues face solution and hydrophilic ones face the surface of the membrane. We found that at sufficiently long timescales or with an applied surface tension, SVS-1 can undergo a “flip and dip” mechanism via the turn or the tail of a folded structure. Provided with sufficient area to embed beneath the headgroups, the peptide rotates in a cascading motion to bury the valine residues below the headgroups. This buried state is possibly a precursor to a deeper insertion state that could lead to membrane disruption of charged membranes similar to that of cancer cells. It is also possible that a cooperative effect of multiple peptides could lead to insertion events that precedes subsequent break down of the membrane integrity. The dynamic behavior of this insertion mechanism elucidates the efficacy of AMPs and the need for further experimental and theoretical work. Future studies on sidechain modifications and free energy of insertion will provide more insight on improving peptide design and function.

 

Table of Contents

 

1         Introduction...............................................................................3                             

1.1  Overview.............................................................................3

           1.2  Protein and Lipid Interactions.................................................4

           1.3  Role of Peptides in Cancer Studies..........................................6

           1.4  Approaches for Studying Antimicrobial Peptides........................9

                  1.4.1  Membrane-Active Peptides...........................................9

                  1.4.2  Experimental Techniques............................................12

                  1.4.3  Simulation Methods...................................................14

           1.5  Thesis Outline....................................................................18

2         Investigating Binding and Folding of an Anti-cancer peptide............20  

2.1  Introduction.......................................................................21

           2.2  Computational Details.........................................................22       

           2.3  Results and Discussion........................................................25    

                  2.3.1  Effects of Electrostatics..............................................25

                  2.3.2  Folding Dynamics......................................................27      

           2.4  Conclusions.......................................................................30     

3         The Influence of Tension and a Novel Insertion Mechanism.............34

3.1  Introduction.......................................................................35

           3.2  Computational Details.........................................................36   

           3.3  Results and Discussion........................................................36    

                  3.3.1  Effects of Surface Tension..........................................36        

                  3.3.2  Lipid Tail Packing......................................................39        

           3.4  Conclusions.......................................................................42     

4          Concluding Remarks and Outlook...............................................46

 

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