Analysis of Melittin Structures Using HyperChem® and CHARMM®
Elizabeth J. Denning
Department of Chemistry,JuniataCollege, Huntingdon, PA16652
Melittin is a 26 amino acid peptide that makes up about fifty percent of the weight of raw venom from the common honeybee, Apis mellifera. It is a biologically active molecule with both lytic and antibacterial activities. The secondary structure of melittin has been studied by x-ray crystallography, and it contains two distinct alpha helical stretches in regions 1-13 and 15-26, separated by a proline kink at residue number 14. Overall, the distribution of amino acids aide chains about the surfaces of these two helical segments results in clearly defined polar and non-polar sides that run the length of both segments. The 20-residue N-terminal segment of the peptide is hydrophobic, while the six-residue C-terminal segment is highly cationic with two lysine and two arginines followed by two glutamines. The cationic regionis believed to be associated with the lytic activity of the peptide because previous research has shown that the degree of lysis is dependent on the stability of the -helical regions of the peptide. Therefore understanding melittin’s helicity may lead to the design of peptides that have enhanced the beneficial activities while lowering their toxicities.
To show a reduction in the lytic properties of melittin, the change in helical content using computational modeling was examined. Melittin is a good candidate for computational analysis due to its smaller size, even when in tetrameric form. Preliminary experimentation was performed using HyperChem® in an AMBER force field to record the changes in hydrogen bond lengths and the root mean square deviations of the -carbon position for each amino acid residue. Upon becoming more experienced with HyperChem®, the CHARMM® software and Visual Molecular Dynamics® visualization program were used because CHARMM® is a more sophisticated computational system. CHARMM® is also designed specifically for protein computation in comparison to HyperChem®.
In HyperChem®, the tetrameric forms of the two dielectric constants both resembled Figure 1 (a).
(a) (b)
Figure 1: Shows the melittin tetramer runin CHARMM® for a total of 10 ps at dielectric constant 4 (a) and dielectric constant 80 (b) to simulate different environmental conditions.
By contrast, CHARMM® conformation results were as expected: a decrease in the tightness of the helical coils with dielectric constant 80 due to the attractive forces of implicit solvent present (see Figure 1). Due to the presence of significant conformational differences, future computational experimentation will be performed with explicit waters and explicit waters with lipid molecules simulations to determine how tetrameric melittin might change structure to cause cell lysis. These types of simulations may allow researchers to determine ways to isolate and eliminate the lytic properties of melittin, thus lowering its toxicity and enhancing its beneficial activities.
Short simulations of about 7 picosecond (ps) as well as longer simulations of 30 ps and greater were performed to determine the necessary run time to acquire the most stable and energetically favorable tetrameric conformation using CHARMM® (see Figure 2).
Figure 2: Shows the simulation energy graphs of the different dielectric constants for simulations of 7 ps. The energy for longer simulations remained constant after 7 ps for temperatures 298 K and 310 K.