FREE-ENERGY CALCULATIONS PREDICT SEQUENCE SPECIFICITY IN DNA-DRUG COMPLEXES

被引：4
作者：
HARD, T
NILSSON, L
机构：
[1] Department of Medical Biophysics, Karolinska Institutet, Stockholm
来源：
NUCLEOSIDES & NUCLEOTIDES | 1992年 / 11卷 / 01期
关键词：
D O I：
10.1080/07328319208021159
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
Molecular dynamics simulations of DNA-netropsin complexes in water were performed using the thermodynamic cycle-perturbation method to calculate the free energy difference between complexes with an adenine-containing binding site and corresponding complexes where adenines are replaced by 2,6-diaminopurines (dap). The calculations predict a free energy difference of 3.7 +/- 0.9 kcal/mol (at 300K) in favour of netropsin binding to an (AATT)2 DNA sequence compared to a (dapdapTT)2 sequence.
引用
收藏
页码：167 / 173
页数：7
相关论文
共 50 条
[41]   NONEQUILIBRIUM SOLVATION AND THERMODYNAMIC INTEGRATION FREE-ENERGY CALCULATIONS [J].
RAINERI, FO .
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 1995, 210 :260-PHYS
[42]   Free-energy calculations to guide bromodomain inhibitor optimization [J].
Bluck, Joseph ;
See, Larissa ;
Scorah, Amy ;
Reynolds, Jessica ;
Rianjongdee, Francesco ;
Morris, Garrett ;
Conway, Stuart ;
Biggin, Phil .
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2019, 257
[43]   CONVERGENCE PROPERTIES OF FREE-ENERGY CALCULATIONS - ALPHA-CYCLODEXTRIN COMPLEXES AS A CASE-STUDY [J].
MARK, AE ;
VANHELDEN, SP ;
SMITH, PE ;
JANSSEN, LHM ;
VANGUNSTEREN, WF .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1994, 116 (14) :6293-6302
[44]   Method for free-energy calculations using iterative techniques [J].
Kumar, S ;
Payne, PW ;
Vasquez, M .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1996, 17 (10) :1269-1275
[45]   Measuring the convergence of Monte Carlo free-energy calculations [J].
Hahn, Aljoscha M. ;
Then, Holger .
PHYSICAL REVIEW E, 2010, 81 (04)
[46]   Origin of Ion Specificity of Telomeric DNA G-Quadruplexes Investigated by Free-Energy Simulations [J].
Siebenmorgen, Till ;
Zacharias, Martin .
BIOPHYSICAL JOURNAL, 2017, 112 (11) :2280-2290
[47]   Enhanced configurational sampling in binding free-energy calculations [J].
Woods, CJ ;
Essex, JW ;
King, MA .
JOURNAL OF PHYSICAL CHEMISTRY B, 2003, 107 (49) :13711-13718
[48]   ON THE USE OF ACCEPTANCE RATIO METHODS IN FREE-ENERGY CALCULATIONS [J].
FERGUSON, DM .
JOURNAL OF CHEMICAL PHYSICS, 1993, 99 (12) :10086-10087
[49]   Free-energy calculations with multiple Gaussian modified ensembles [J].
Neuhaus, T. ;
Hager, J. S. .
PHYSICAL REVIEW E, 2006, 74 (03)
[50]   Guidelines for Free-Energy Calculations Involving Charge Changes [J].
Petrov, Drazen ;
Perthold, Jan Walther ;
Oostenbrink, Chris ;
de Groot, Bert L. ;
Gapsys, Vytautas .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2024, 20 (02) :914-925
12345