MONTE-CARLO SIMULATIONS YIELD ABSOLUTE FREE-ENERGIES OF BINDING FOR GUANINE CYTOSINE AND ADENINE URACIL BASE-PAIRS IN CHLOROFORM

被引:30
作者
PRANATA, J [1 ]
JORGENSEN, WL [1 ]
机构
[1] YALE UNIV,DEPT CHEM,NEW HAVEN,CT 06511
基金
美国国家卫生研究院;
关键词
D O I
10.1016/S0040-4020(01)81783-X
中图分类号
O62 [有机化学];
学科分类号
070303 ; 081704 ;
摘要
Monte Carlo simulations with statistical perturbation theory and the OPLS potential functions were employed to calculate the absolute free energies of binding between 9-methyladenine (A) and 1-methyluracil (U) and between 9-methylguanine (G) and 1-methylcytosine (C). The results for both A-U (ca. -3.6 kcal/mol) and G-C (ca. -7.9 kcal/mol) compare well with the values from experimentally determined association constants for these systems. Several thermodynamic cycles were also considered that demonstrated the high precision of the methodology.
引用
收藏
页码:2491 / 2501
页数:11
相关论文
共 71 条
  • [2] [Anonymous], 1987, DYNAMICS PROTEINS NU
  • [3] STATISTICAL EFFECTS AND EVALUATION OF ENTROPY DIFFERENCES IN EQUILIBRIUM PROCESSES - SYMMETRY CORRECTIONS AND ENTROPY OF MIXING
    BAILEY, WF
    MONAHAN, AS
    [J]. JOURNAL OF CHEMICAL EDUCATION, 1978, 55 (08) : 489 - 493
  • [4] FREE-ENERGY CALCULATIONS BY COMPUTER-SIMULATION
    BASH, PA
    SINGH, UC
    LANGRIDGE, R
    KOLLMAN, PA
    [J]. SCIENCE, 1987, 236 (4801) : 564 - 568
  • [5] CALCULATION OF THE RELATIVE CHANGE IN BINDING FREE-ENERGY OF A PROTEIN-INHIBITOR COMPLEX
    BASH, PA
    SINGH, UC
    BROWN, FK
    LANGRIDGE, R
    KOLLMAN, PA
    [J]. SCIENCE, 1987, 235 (4788) : 574 - 576
  • [6] SODIUM-CHLORIDE ION-PAIR INTERACTION IN WATER - COMPUTER-SIMULATION
    BERKOWITZ, M
    KARIM, OA
    MCCAMMON, JA
    ROSSKY, PJ
    [J]. CHEMICAL PHYSICS LETTERS, 1984, 105 (06) : 577 - 580
  • [7] BEVERIDGE DL, 1989, ANNU REV BIOPHYS BIO, V18, P431, DOI 10.1146/annurev.biophys.18.1.431
  • [8] BLAKE JF, IN PRESS J AM CHEM S
  • [9] MONTE-CARLO SIMULATIONS ON THE LIKE-CHARGED GUANIDINIUM GUANIDINIUM ION-PAIR IN WATER
    BOUDON, S
    WIPFF, G
    MAIGRET, B
    [J]. JOURNAL OF PHYSICAL CHEMISTRY, 1990, 94 (15) : 6056 - 6061
  • [10] ENERGETICS AND HYDRATION OF THE CONSTITUENT ION-PAIRS OF TETRAMETHYLAMMONIUM CHLORIDE
    BUCKNER, JK
    JORGENSEN, WL
    [J]. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1989, 111 (07) : 2507 - 2516