Type IV pili (T4P) are long protein filaments which protrude from the surface of bacterial cells and are assembled from monomers called “pilins.” T4P serve many functions for bacteria, including the uptake of DNA from their environment. DNA uptake is enabled by a “minor” type IV pilin called ComP, which can be incorporated into T4P filaments. ComP aids in the recognition of double stranded helical DNA by binding to a specific DNA uptake sequence (DUS). A recent computational model of the ComP/DNA complex from <i>Neisseria subflava</i> has provided insights into which amino acids of ComP are most important for stabilizing the protein/DNA interface. However, the static docked model does not provide any information into the dynamic motions of the ComP/DNA complex.<br/>            In this work, all-atom molecular dynamics simulations using the AMBER16 software on GPUs is used to study the ComP/DNA complex. These simulations help to unveil which interactions between ComP and DNA are most critical for DNA binding stability. In particular, the ComP protein includes two disulfide bonds which help to hold together the “DD” region of the protein. This region’s importance for DNA recognition and binding has been previously reported. Consequently, it has been proposed that both disulfide bonds are essential for ComP to remain stably bound to DNA. This hypothesis is evaluated by carrying out molecular simulations of the wild-type ComP/DNA complex and comparing them to simulations in which the disulfide bonds have been removed. Several properties of the complex were measured, such as backbone root mean square deviations, amino acid and nucleotide root mean square fluctuations, and distances between DNA and critical amino acids in the DD region of ComP. Interaction energies and hydrogen bonding interactions between ComP and DNA are also calculated. The MM-PBSA method is used to investigate how cysteine to alanine mutations impact the binding free energy between ComP and DNA. From these analyses, it was determined that removing the disulfide bonds has a dramatic effect on the stability of the ComP/DNA complex compared to the wild-type system.

Investigating the role of disulfide bonds in stabilizing the interactions between DNA and the type IV pilin ComP using molecular simulation

256th National Meeting (2018)

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