Rapid free energy calculation of peptide self-assembly by REMD umbrella sampling.
We extend umbrella sampling with replica exchange steps to calculate free energies that are important in the self-assembly of peptides. This leads to a more than 10-fold speed up over conventional umbrella sampling, thereby providing a practical method to calculate these free-energy differences. This approach can also observe first-order phase transitions and pinpoint the location of the concomitant boundary. When conformational changes are involved, this method can handle peptides up to approximately 7 residues, providing a rapid and accurate assessment of the thermodynamic properties of model systems, and can thus be used to answer fundamental questions about peptide self-assembly. When no major conformational changes are involved, we expect the size limit to be equal to that of standard molecular dynamics.
Wolf
Maarten G
MG
Delft University of Technology, Julianalaan 136, 2628 BL Delft, Netherlands.
Jongejan
Jaap A
JA
Laman
Jon D
JD
de Leeuw
Simon W
SW
D000465:Algorithms; D001704:Biopolymers / Q000737:chemistry; D003198:Computer Simulation; D004735:Energy Transfer; D015233:Models, Statistical; D010455:Peptides / Q000138:chemical synthesis* / Q000737:chemistry*; D011487:Protein Conformation; D012984:Software
D001704:Biopolymers; D010455:Peptides