Widmalm G, Venable R M
Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Sweden.
Biopolymers. 1994 Aug;34(8):1079-88. doi: 10.1002/bip.360340811.
Molecular dynamics simulations in vacuum and solution have been carried out on 2'-alpha-L-fucosyl-lactitol, a model for blood group H in conjunction with two-dimensional nmr measurements on the same compound. Three independent starting conformations for the dynamics were chosen from low energy conformations obtained by a phi/psi grid search. Nine 5 ns vacuum simulations of the trisaccharide were performed, employing three different ways to treat electrostatic interactions for each starting conformation: distance-dependent dielectric with epsilon = r, constant dielectric with epsilon = 1, or constant dielectric with epsilon = 80. In vacuum, transitions of phi and psi for the alpha-L-Fuc-(1-->2)-beta-D-Gal element occur in a cooperative manner. The virtual distance obtained for H1 in fucose to H2 in galactose from nuclear Overhauser effect spectroscopy experiments agree with one of the conformations of the trisaccharide in one of the three 100 ps aqueous simulations (phi/psi ca. -100 degrees/150 degrees), indicating this may be a dominant solution conformation. The rms fluctuations of the phi- and psi-dihedral angles were approximately 10 degrees for a conformational state, both in the vacuum and the aqueous simulations. For the simulations in vacuum, the agreement with experimental NOE data is reasonable when a constant dielectric of 1 is used (major conformers having phi/psi ca. -100 degrees/150 degrees and -140 degrees/100 degrees), whereas the agreement was poor with a constant dielectric of 80. Translational diffusion coefficients calculated from the simulation of the oligosaccharides were 0.12-0.18 x 10(-5) cm2/s and from nmr measurements 0.27 x 10(-5) cm2/s.
已对2'-α-L-岩藻糖基乳糖醇进行了真空和溶液中的分子动力学模拟，该化合物是血型H的模型，并结合了对同一化合物的二维核磁共振测量。动力学的三个独立起始构象是从通过φ/ψ网格搜索获得的低能构象中选择的。对三糖进行了九次5纳秒的真空模拟，针对每个起始构象采用三种不同的方法处理静电相互作用：ε = r的距离相关介电常数、ε = 1的恒定介电常数或ε = 80的恒定介电常数。在真空中，α-L-岩藻糖-(1→2)-β-D-半乳糖单元的φ和ψ发生协同转变。从核Overhauser效应光谱实验中获得的岩藻糖中H1到半乳糖中H2的虚拟距离与三次100皮秒水模拟之一中三糖的一种构象相符（φ/ψ约为-100°/150°），表明这可能是主要的溶液构象。在真空和水模拟中，对于一种构象状态，φ和ψ二面角的均方根波动约为10°。对于真空模拟，当使用1的恒定介电常数时（主要构象体的φ/ψ约为-100°/150°和-140°/100°），与实验NOE数据的一致性是合理的，而使用80的恒定介电常数时一致性较差。从寡糖模拟计算得到的平移扩散系数为0.12 - 0.18×10⁻⁵ cm²/s，从核磁共振测量得到的为0.27×10⁻⁵ cm²/s。
