Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding.

Abstract:

:Binding of a small molecule to a macromolecular target reduces its conformational freedom, resulting in a negative entropy change that opposes the binding. The goal of this study is to estimate the configurational entropy change of two minor-groove-binding ligands, netropsin and distamycin, upon binding to the DNA duplex d(CGCGAAAAACGCG).d(CGCGTTTTTCGCG). Configurational entropy upper bounds based on 10-ns molecular dynamics simulations of netropsin and distamycin in solution and in complex with DNA in solution were estimated using the covariance matrix of atom-positional fluctuations. The results suggest that netropsin and distamycin lose a significant amount of configurational entropy upon binding to the DNA minor groove. The estimated changes in configurational entropy for netropsin and distamycin are -127 J K(-1) mol(-1) and -104 J K(-1) mol(-1), respectively. Estimates of the configurational entropy contributions of parts of the ligands are presented, showing that the loss of configurational entropy is comparatively more pronounced for the flexible tails than for the relatively rigid central body.

journal_name

Biophys J

journal_title

Biophysical journal

authors

Dolenc J,Baron R,Oostenbrink C,Koller J,van Gunsteren WF

doi

10.1529/biophysj.105.074617

subject

Has Abstract

pub_date

2006-08-15 00:00:00

pages

1460-70

issue

4

eissn

0006-3495

issn

1542-0086

pii

S0006-3495(06)71857-4

journal_volume

91

pub_type

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