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.
Delft University of Technology, Julianalaan 136, 2628 BL Delft, Netherlands.
Maarten G
MG
Wolf
Jaap A
JA
Jongejan
Jon D
JD
Laman
Simon W
SW
de Leeuw
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