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

被引：2
|
作者：
HARD, T
NILSSON, L
机构：
[1] Department of Medical Biophysics, Karolinska Institutet
来源：
NUCLEOSIDES & NUCLEOTIDES | 1991年 / 10卷 / 1-3期
关键词：
D O I：
10.1080/07328319108046577
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：701 / 709
页数：9
相关论文
共 50 条
  • [41] Free-energy calculations to guide bromodomain inhibitor optimization
    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
  • [42] CONVERGENCE PROPERTIES OF FREE-ENERGY CALCULATIONS - ALPHA-CYCLODEXTRIN COMPLEXES AS A CASE-STUDY
    MARK, AE
    VANHELDEN, SP
    SMITH, PE
    JANSSEN, LHM
    VANGUNSTEREN, WF
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1994, 116 (14) : 6293 - 6302
  • [43] Method for free-energy calculations using iterative techniques
    Kumar, S
    Payne, PW
    Vasquez, M
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 1996, 17 (10) : 1269 - 1275
  • [44] Measuring the convergence of Monte Carlo free-energy calculations
    Hahn, Aljoscha M.
    Then, Holger
    PHYSICAL REVIEW E, 2010, 81 (04):
  • [45] Origin of Ion Specificity of Telomeric DNA G-Quadruplexes Investigated by Free-Energy Simulations
    Siebenmorgen, Till
    Zacharias, Martin
    BIOPHYSICAL JOURNAL, 2017, 112 (11) : 2280 - 2290
  • [46] Guidelines for Free-Energy Calculations Involving Charge Changes
    Petrov, Drazen
    Perthold, Jan Walther
    Oostenbrink, Chris
    de Groot, Bert L.
    Gapsys, Vytautas
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2024, 20 (02) : 914 - 925
  • [47] Ab initio calculations of free-energy reaction barriers
    Bucko, T.
    JOURNAL OF PHYSICS-CONDENSED MATTER, 2008, 20 (06)
  • [48] Nonequilibrium free-energy calculations of fluids using LAMMPS
    Leite, Rodolfo Paula
    de Koning, Maurice
    COMPUTATIONAL MATERIALS SCIENCE, 2019, 159 : 316 - 326
  • [49] A method for free-energy calculations using iterative techniques
    Kumar, S
    Payne, PW
    Vasquez, M
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 1996, 211 : 9 - COMP
  • [50] Free-energy calculations of intrinsic point defects in silicon
    Al-Mushadani, OK
    Needs, RJ
    PHYSICAL REVIEW B, 2003, 68 (23)
12345