Three-dimensional structure and dynamics of a de novo designed, amphiphilic, metallo-porphyrin-binding protein maquette at soft interfaces by molecular dynamics simulations.
The three-dimensional structure and dynamics of de novo designed, amphiphilic four-helix bundle peptides (or "maquettes"), capable of binding metallo-porphyrin cofactors at selected locations along the length of the core of the bundle, are investigated via molecular dynamics simulations. The rapid evolution of the initial design to stable three-dimensional structures in the absence (apo-form) and presence (holo-form) of bound cofactors is described for the maquettes at two different soft interfaces between polar and nonpolar media. This comparison of the apo- versus holo-forms allows the investigation of the effects of cofactor incorporation on the structure of the four-helix bundle. The simulation results are in qualitative agreement with available experimental data describing the structures at lower resolution and limited dimension.
Zou
Hongling
H
Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
Strzalka
Joseph
J
Xu
Ting
T
Tronin
Andrey
A
Blasie
J Kent
JK
D001665:Binding Sites; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008665:Metalloporphyrins / Q000737:chemistry*; D009795:Octanes / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D013997:Time Factors; D014867:Water / Q000737:chemistry
D008665:Metalloporphyrins; D009795:Octanes; D010455:Peptides; D011506:Proteins; D012997:Solvents; D014867:Water; C026728:octane