核酸基对与结合的精确相互作用能量
Jirí Sponer1, Petr Jurecka, Pavel Hobza
1Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic. sponer@ncbr.chemi.muni.cz
Journal of the American Chemical Society
|August 12, 2004
概括
这项研究为结核酸基对提供了准确的初始结构和相互作用能量. 像PW91这样的密度函数理论 (DFT) 方法与基础配对稳定性的高级计算有很好的一致性.
科学领域:
- 计算化学计算化学
- 生物物理学的生物物理.
- 分子生物学分子生物学
背景情况:
- 与结合的核酸基对对于DNA/RNA结构和稳定性至关重要.
- 需要准确的计算模型来理解基配对相互作用.
研究的目的:
- 为所选的核酸基对建立起初的参考结构和相互作用能量.
- 评估各种计算方法的准确性,以预测基配对的能量.
主要方法:
- 高层次的初始计算使用识别MøllerPlesset扰动理论 (RI-MP2) 与cc-pVTZ基础集.
- 完整的基础集 (CBS) 对相互作用能量的推断.
- 对于选定的案例,结合集群 (CCSD(T)) 纠正.
- 与密度函数理论 (DFT) 函数 (PW91,Becke3LYP) 和分子力学力场 (Cornell等) 的比较. ) 的情况.
主要成果:
- 基对的参考相互作用能量范围从-5到-47kcal/mol.
- RI-MP2/CBS计算提供了非常准确的相互作用能量.
- 具有特定几何形状的PW91 DFT功能非常接近RI-MP2/CBS的结果.
- 贝克3LYP DFT 函数显示了对相互作用能量的轻微低估.
- 康奈尔大学和其他人. 强力场表现出良好的性能,支持基础配对的静电性质.
结论:
- 高级ab initio方法为基对相互作用提供可靠的参考数据.
- DFT方法,特别是PW91,为研究基配对提供了一个计算效率高的替代方案.
- 静电相互作用是结基对稳定的主要驱动因素.
相关概念视频
Arrhenius Plots
The Arrhenius equation relates the activation energy and the rate constant, k, for chemical reactions. In the Arrhenius equation, k = Ae−Ea/RT, R is the ideal gas constant, which has a value of 8.314 J/mol·K, T is the temperature on the kelvin scale, Ea is the activation energy in J/mole, e is the constant 2.7183, and A is a constant called the frequency factor, which is related to the frequency of collisions and the orientation of the reacting molecules.
The Arrhenius equation can be used to...
The Arrhenius equation can be used to...
Relative Strengths of Conjugate Acid-Base Pairs
Brønsted-Lowry acid-base chemistry is the transfer of protons; thus, logic suggests a relation between the relative strengths of conjugate acid-base pairs. The strength of an acid or base is quantified in its ionization constant, Ka or Kb, which represents the extent of the acid or base ionization reaction. For the conjugate acid-base pair HA / A−, the ionization equilibrium equations and ionization constant expressions are
Noncovalent Attractions in Biomolecules
Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
Chemical Bonds
Atoms participate in a chemical bond formation to acquire a completed valence-shell electron configuration similar to that of the noble gas nearest to it in atomic number. Ionic, covalent, and metallic bonds are some of the important types of chemical bonds. Bond energy and bond length determine the strength of a chemical bond.
Types of Chemical Bonds
An ionic bond is formed due to electrostatic attraction between cations and anions. Often, the ions are formed by the transfer of electrons from...
Noncovalent Attractions in Biomolecules
Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
Drug-Receptor Bonds
Drug-receptor bonds are formed through various chemical forces when drugs interact with target cells. Covalent bonds, strong and irreversible, are exemplified by DNA-alkylating anticancer agents that inhibit cell division. However, such irreversible drug binding lacks selectivity and can modify the DNA of the surrounding healthy cells. Covalent binding often contributes to tissue toxicity, as seen with chloroform and paracetamol metabolites binding to the liver, causing hepatotoxicity.
In...
In...


