Mooren M M, Wijmenga S S, van der Marel G A, van Boom J H, Hilbers C W
NSR Centre for Molecular Structure, Design, and Synthesis, University of Nijmegen, The Netherlands.
Nucleic Acids Res. 1994 Jul 11;22(13):2658-66. doi: 10.1093/nar/22.13.2658.
The 3'-5' circular trinucleotide cr(GpGpGp) was studied by means of 1D and 2D high resolution NMR techniques and molecular mechanics calculations. Analysis of the J-couplings, obtained from the 1H and 13C-NMR spectra, allowed the determination of the conformation of the sugar rings and of the 'circular' phosphate backbone. In the course of the investigations it was found that the Karplus-equation most recently parametrized for the CCOP J-coupling constants could not account for the measured J(C4'P) of 11.1 Hz and a new parametrization for both HCOP and CCOP coupling constants is therefore presented. Subsequent analysis of the coupling constants yielded 'fixed' values for the torsion angles beta and delta (with beta = 178 degrees and delta = 139 degrees). The value of the latter angle corresponds to an S-type sugar conformation. The torsion angles gamma and epsilon are involved in a rapid equilibrium in which they are converted between the gauche(+) and trans and between the trans and gauche(-) domain respectively. We show that the occurrence of epsilon in the gauche(-) domain necessitates S-type sugar conformations. Given the aforementioned values for beta, gamma, delta and epsilon the ring closure constraints for the ring, formed by the phosphate backbone can only be fulfilled if alpha and zeta adopt some special values. After energy minimization with the CHARMm force field only two combinations of alpha and zeta result in energetically favourable structures, i.e. the combination alpha (t)/zeta(g-) in case gamma is in a gauche(+) and epsilon is in a trans conformation, and the combination alpha (t)/zeta (g+) for the combination gamma (t)/epsilon (g-). The results are discussed in relation to earlier findings obtained for cd(ApAp) and cr(GpGp), the latter molecule being a regulator of the synthesis of cellulose in Acetobacter xylinum.
通过一维和二维高分辨率核磁共振技术以及分子力学计算对3'-5'环状三核苷酸cr(GpGpGp)进行了研究。对从1H和13C-NMR谱获得的J-耦合进行分析，从而确定糖环和“环状”磷酸主链的构象。在研究过程中发现，最近针对CCOP J-耦合常数参数化的Karplus方程无法解释测得的11.1 Hz的J(C4'P)，因此提出了针对HCOP和CCOP耦合常数的新参数化。随后对耦合常数的分析得出了扭转角β和δ的“固定”值（β = 178°，δ = 139°）。后一个角度的值对应于S型糖构象。扭转角γ和ε参与快速平衡，在该平衡中它们分别在gauche(+)和反式之间以及反式和gauche(-)域之间转换。我们表明，ε出现在gauche(-)域中需要S型糖构象。鉴于上述β、γ、δ和ε的值，只有当α和ζ采用一些特殊值时，由磷酸主链形成的环的闭环约束才能得到满足。使用CHARMm力场进行能量最小化后，只有α和ζ的两种组合会产生能量有利的结构，即当γ处于gauche(+)且ε处于反式构象时的α(t)/ζ(g-)组合，以及γ(t)/ε(g-)组合的α(t)/ζ(g+)。结合之前对cd(ApAp)和cr(GpGp)的研究结果对这些结果进行了讨论，后者是木醋杆菌中纤维素合成的调节剂。
