Soumpasis D M, Tung C S
Theoretical Biology and Biophysics Theoretical Division, Los Alamos National Laboratory, NM 87545.
J Biomol Struct Dyn. 1988 Dec;6(3):397-420. doi: 10.1080/07391102.1988.10506497.
We propose new, rigorous definitions for (i) basepair fixed coordinate systems and (ii) the twist, tilt, and roll angles (called tau, t, rho) describing the relative orientation of adjacent basepairs and bases in a pair, in arbitrary DNA structures obtained from x-ray diffraction, 2D NMR, or energy calculations. In contrast to the corresponding angular parameters (tg, theta T, theta R) and coordinate systems introduced by Dickerson and co-workers and currently in use, our angular parameters and coordinate systems, together with a set of three displacement parameters, dx, dy, dz, provide a mathematically correct and general description of DNA conformations at the basepairs and/or base level. For instance, our description is applicable when the DNA structure considered is inherently curved, irregular, and/or does not possess dyad (or pseudodyad) axes. We develop a computationally convenient algorithm for rigorous DNA conformational analysis and apply it to some of the known crystal structures. We establish the connection to the currently used parameters and test the consistency and efficiency of our methodology by reconstructing the Dickerson B dodecamer using only the sequence and the set of parameters obtained from the atomic coordinates. The six parameter (tau, t, rho, dx, dy, dz) basepair level reconstruction is good but not perfect. Perfect reconstruction is obtained when one also considers each base in a basepair (consideration of propeller twist alone is not sufficient). The variation of the rigorous parameters proposed along the sequence is much larger, but their average values agree with fiber and solution data much better than in the case of the currently used set. The results of our analysis do not support Trifonov's AA.TT wedge model for DNA curvature but provide some evidence in favor of the Crothers junction-bend model. We point out some of the limitations of basepair level approaches when applied to DNA structure prediction and quantitative understanding of sequence-dependent variations in structure.
我们针对（i）碱基对固定坐标系以及（ii）用于描述任意DNA结构中相邻碱基对和碱基对中碱基相对取向的扭转角、倾斜角和滚动角（分别称为τ、t、ρ）提出了新的、严格的定义，这些DNA结构是通过X射线衍射、二维核磁共振或能量计算获得的。与Dickerson及其同事引入并目前仍在使用的相应角度参数（tg、θT、θR）和坐标系不同，我们的角度参数和坐标系，连同一组三个位移参数dx、dy、dz，在碱基对和/或碱基水平上对DNA构象提供了数学上正确且通用的描述。例如，当所考虑的DNA结构本质上是弯曲的、不规则的和/或不具有二重对称轴（或假二重对称轴）时，我们的描述仍然适用。我们开发了一种计算方便的算法用于严格的DNA构象分析，并将其应用于一些已知的晶体结构。我们建立了与当前使用参数的联系，并通过仅使用序列和从原子坐标获得的参数集重建Dickerson B型十二聚体来测试我们方法的一致性和效率。六参数（τ、t、ρ、dx、dy、dz）的碱基对水平重建效果较好但并不完美。当同时考虑碱基对中的每个碱基时（仅考虑螺旋桨扭转是不够的），可以获得完美的重建。所提出的严格参数沿序列的变化要大得多，但它们的平均值与纤维和溶液数据的吻合程度比当前使用的参数集要好得多。我们的分析结果不支持Trifonov的DNA曲率AA.TT楔形模型，但为Crothers连接弯曲模型提供了一些证据。我们指出了碱基对水平方法在应用于DNA结构预测以及对序列依赖性结构变化进行定量理解时的一些局限性。
