Comparative estimation of vibrational entropy changes in proteins through normal modes analysis.
We compare the vibrational entropy changes of proteins calculated using a full and a number of approximate normal modes analysis methods. The vibrational entropy differences for three conformational changes and three protein binding interactions were computed. In general, the approximate methods yield good estimates of the vibrational entropy change in a fraction of the time required by full normal modes analysis. The absolute entropies are either overestimated or greatly underestimated, but the difference is sufficiently accurate for some methods. This indicates that some of the approximate methods can give reasonable estimates of the associated vibrational entropy changes, making them suitable for inclusion in free energy calculations.
Carrington
Benjamin J
BJ
Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK.
Mancera
Ricardo L
RL
D000818:Animals; D019277:Entropy; D066298:In Vitro Techniques; D046912:Multiprotein Complexes; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D046912:Multiprotein Complexes; D011506:Proteins