Difference between revisions of "Team:Aalto-Helsinki/Model Results"
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| − | + | DCD-1L consists of 48 amino residues and is processed proteolytically from a 110 amino acid precursor peptide. Contrary to many common AMPs, DCD-1L has a net negative charge at physiological pH. [10] The expected pI of DCD-1L is 5.07 and the expected molecular weight of the peptide is 4818.50 g/mol. Using a web-based tool Composition Profiler[16] we attempted to identify differences in amino acid residue expression in the sequence of DCD-1L when compared to the distribution of the 20 natural amino acids commonly found in nature. A p-value of 0.05 was used as a threshold and Swissprot51 dataset[1], which closely mirrors the amino acid distribution found in nature, was used for background screening. Figure 1 shows the results of the amino acid expression screening with the amino acids being color coded according to how often they are commonly found in β-helical structures. We find that especially the amino acids Aspartate, Glycine, Valine and Lysine are over-expressed when compared to the frequency of these amino acids commonly found in nature. Of the afore mentioned amino acids, Aspartate exhibits a negatively charged side chain, while Glycine, Valine are considered hydrophobic and Lysine polar amino acids. According to figure 1 Lysine is an amino acid commonly found in alpha helical structures, which are common for many AMPs[10][2]. The over-expression of negatively charged Aspartate residues is expected considering the overall negative net charge of DCD-1L. Additionally, in figure 1 we have included the amino acid sequence of DCD-1L in color differentiating between polar and hydrophobic residues. Unsurprisingly, DCD-1L appears to have alternating clusters of polar and hydrophobic amino acids, with such amphipathic regions being common for AMPs as previously discussed. | |
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| − | DCD-1L consists of 48 amino residues and is processed proteolytically from a 110 amino acid precursor peptide. Contrary to many common AMPs, DCD-1L has a net negative charge at physiological pH. | + | |
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Revision as of 00:09, 30 October 2017
Results and Discussion
Based on molecular dynamics simulations of DCD-1L at different salt concentrations and temperatures, we evaluated occurring changes in protein secondary structure through secondary structure assignment using DSSP and observed Ramachandran plot representations. Additionally we characterized the structure of the simulated peptide by scrutinizing the radius of gyration, solvent accessible surface area and hydrogen bonding.
Characterization of the amino acid sequence
Despite the great diversity of antimicrobial peptides, they exhibit many commonly shared characteristics. Such characteristics include the presence of multiple basic amino acids and amphipathic structures consisting of clusters of hydrophobic and hydrophilic amino acids. Commonly, AMPs have a positive net charge which has been shown to contribute to their initial binding to the often negatively charged bacterial cell membrane. The amphipathic structures found in AMPs have been found to enhance interactions with the phospholipids of the bacterial cell membrane, especially at the water-lipid interface.
DCD-1L consists of 48 amino residues and is processed proteolytically from a 110 amino acid precursor peptide. Contrary to many common AMPs, DCD-1L has a net negative charge at physiological pH. [10] The expected pI of DCD-1L is 5.07 and the expected molecular weight of the peptide is 4818.50 g/mol. Using a web-based tool Composition Profiler[16] we attempted to identify differences in amino acid residue expression in the sequence of DCD-1L when compared to the distribution of the 20 natural amino acids commonly found in nature. A p-value of 0.05 was used as a threshold and Swissprot51 dataset[1], which closely mirrors the amino acid distribution found in nature, was used for background screening. Figure 1 shows the results of the amino acid expression screening with the amino acids being color coded according to how often they are commonly found in β-helical structures. We find that especially the amino acids Aspartate, Glycine, Valine and Lysine are over-expressed when compared to the frequency of these amino acids commonly found in nature. Of the afore mentioned amino acids, Aspartate exhibits a negatively charged side chain, while Glycine, Valine are considered hydrophobic and Lysine polar amino acids. According to figure 1 Lysine is an amino acid commonly found in alpha helical structures, which are common for many AMPs[10][2]. The over-expression of negatively charged Aspartate residues is expected considering the overall negative net charge of DCD-1L. Additionally, in figure 1 we have included the amino acid sequence of DCD-1L in color differentiating between polar and hydrophobic residues. Unsurprisingly, DCD-1L appears to have alternating clusters of polar and hydrophobic amino acids, with such amphipathic regions being common for AMPs as previously discussed.
References
[1] Writers, YEAR. Name of article / book. Publication. Accessible at: [url here].
[2] Writers, YEAR. Name of article / book. Publication. Accessible at: [url here].
[3] Writers, YEAR. Name of article / book. Publication. Accessible at: [url here].
[4] Writers, YEAR. Name of article / book. Publication. Accessible at: [url here].
[5] Writers, YEAR. Name of article / book. Publication. Accessible at: [url here].
