Using computer simulation techniques to determine the structure and properties of a synthetic 4-helix bundle
Alissa Beth Woska · Scholarly Commons (University of Pennsylvania) · 1998
This work focused on using computer simulation techniques to determine the structure of a biologically-relevant macromolecule for the situation where an experimental determination is either inconvenient or impossible. The molecule of interest is the synthetic 4-helix bundle H10H24-L6I,L13F for which an NMR structure later became available. A direct comparison of these independently derived structures reveals striking similarities and further supports the use of computational methods in cases of minimal experimental data. The 4-helix bundle is a recurrent structural motif in proteins. They take on a myriad of functions in a variety of species. Gaining in- depth insight into how these bundles associate and fluctuate can lead to better synthetic protein design. A series of model bundles, referred to as maquettes, have been synthesized, based on the same sequence with minor variations. By computationally deriving an equilibrium structure for one of these bundles, the effects that various residues have on the shape and relative stabilities can be predicted through point mutations to the amino acid sequence. The structure for H10H24-L6I,L13F, a parallel homotetramer with 31 residues per helix, was determined through molecular dynamics calculations that provided a trajectory for the equilibrated system at 298 K. Found to be predominantly α-helical, the helices in the bundle move in pairs that adopt an X- shaped orientation. This tilt angle of 18° is evident in the divergence of the pairs at both the N- and C-termini and in a comparison of the helix dipoles. The presence of 2-fold symmetry is confirmed by the positions of the residues on the individual helices and in the association distances. These characteristics are all consistent with properties of bundles whose structures were experimentally determined. Recently, a solution state NMR structure has been solved. The computational result compares favorably to it. The basic structural characteristics including relative positions of the side chains and the secondary structure display a high level of similarity. Minor differences observed may be due to the fact that the simulated system is in pure water and the fact that in both cases average structural properties are being compared. Using computer simulation technique, an equilibrium structure for the synthetic bundle H10H24-L6I,L13F has been determined. Its favorable comparison with the NMR structure lends support for using computationally derived structures when experimental information is not available. In addition, the computer model has the advantage of providing detailed information at the atomic level.