Team:Aalto-Helsinki/Model
Modeling Overview
Lorem Ipsum is simply dummy text of the printing and typesetting industry. Lorem Ipsum has been the industry's standard dummy text ever since the 1500s, when an unknown printer took a galley of type and scrambled it to make a type specimen book [1]. It has survived not only five centuries, but also the leap into electronic typesetting, remaining essentially unchanged. It was popularised in the 1960s with the release of Letraset sheets containing Lorem Ipsum passages, and more recently with desktop publishing software like Aldus PageMaker including versions of Lorem Ipsum.
Many dermcidin derivatives exhibit broad-spectrum anti microbial properties, with the most abundant species exhibiting antimicrobial activity in the human sweat being DCD-1 and DCD-1L. Both DCD-1L and DCD-1 have been shown to exhibit antimicrobial activity against gram positive bacteria and gram negative bacteria. Notably different from the typical behavior of most AMPs, both DCD-1 and DCD-1L embody a negative net charge and their antimicrobial activity has been reported to be maintained over a wide pH and salt concentration range. These discrepancies in the behavior of dermcidin derivatives give merit to the assumption that the mechanism of action of DCD-1L may differ from other charged, mostly cationic, AMPs. While the main suggested mechanism of action for the DCD-1L peptide appears to be insertion into the bacterial phospholipid membrane and pore formation, studies have indicated that dermcidin effectively disturbs bacterial macromolecular synthesis.
Contrary to popular belief, Lorem Ipsum is not simply random text. It has roots in a piece of classical Latin literature from 45 BC, making it over 2000 years old. Richard McClintock, a Latin professor at Hampden-Sydney College in Virginia, looked up one of the more obscure Latin words, consectetur, from a Lorem Ipsum passage, and going through the cites of the word in classical literature, discovered the undoubtable source. Lorem Ipsum comes from sections 1.10.32 and 1.10.33 of "de Finibus Bonorum et Malorum" (The Extremes of Good and Evil) by Cicero, written in 45 BC. This book is a treatise on the theory of ethics, very popular during the Renaissance. The first line of Lorem Ipsum, "Lorem ipsum dolor sit amet..", comes from a line in section 1.10.32.
It is widely acknowledged that protein three dimensional conformation largely dictates its activity. Previously, there have been some conformational studies of dermcidin and its derivative peptides. However, these have been largely limited to protein secondary structure promoting solvent environments, such as trifluoroethanol (TFE), and environments aiming to mimic the bacterial cell membrane.
Here, we examine the behavior of DCD-1L in aqueous, low salt solvent environments through the application of molecular dynamics simulation. We use a well documented and widely used united atom force-field to describe the structure and interactions of the molecules. Based on the calculated trajectories characterize the behavior of DCD-1L in range of varying salt concentrations and temperatures. We characterize the evolution of the peptide three dimensional conformation as a function of simulation time, slat concentration and temperature, emphasizing the development of secondary structure in terms of retention of antimicrobial functionality.
Based on our results, we find that the helicity of DCD-1L is mostly lost in favour of a random coil conformation. In the cases where helicity is retained, we find that the first half of the peptide assumes a rare 5-helical secondary structure that is often incorrectly characterized using experimental methods. We postulate that the retention of helicity in the cationic half of DCD-1L could in part explain retention of the peptide's antimicrobial activity as said region of the peptide has been hypothesized to play an important part in the initial interaction between DCD-1L and the negatively charged bacterial cell membrane.
