MONTE-CARLO SIMULATION OF THE HYDRATION SHELL OF DOUBLE-HELICAL AMYLOSE - A LEFT-HANDED ANTIPARALLEL DOUBLE HELIX FITS BEST INTO LIQUID WATER-STRUCTURE
MONTE-CARLO SIMULATION OF THE HYDRATION SHELL OF DOUBLE-HELICAL AMYLOSE - A LEFT-HANDED ANTIPARALLEL DOUBLE HELIX FITS BEST INTO LIQUID WATER-STRUCTURE
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DOI：
10.1002/bip.360321207
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发表时间：
1992-12-01
期刊：
影响因子：
2.9
通讯作者：
SCHULZ, W
中科院分区：
文献类型：
--
作者：
EISENHABER, F;SCHULZ, W
双螺旋直链淀粉的构象受其水环境的影响[A. Imberty，H. Chanzy，S. Perez，A. Buleon和V. Tran（1988）Journal of Molecular Biology，第201卷，第201页。365-378; A. Imberty和S. Perez（1988）Biopolymers，第27卷，1205-12211。对于几个低能量构象的左手直链淀粉双螺旋，我们进行了Monte Carlo模拟的（N，V，T）-系综周围的一个单一的双链体的水分子的配置。这种模拟的关键点是使用圆柱形周期性边界条件与一个相对较小的非对称单元，包括有限数量的水分子。输出数据包括大分子附近空间水密度的局部最大值、直链淀粉极性基团之间的一元和二元水桥信息以及所研究系统的能量特征。（每葡萄糖单位的上升和扭曲为0.343 nm和-58.1度）对应于双链体内势能的全局最小值[W. Schulz和H. Sklenar（1993）生物聚合物，提交; W.舒尔茨，H. Sklenar，W. Hinrichs和W. Saenger（1993）Biopolymers，待出版]。我们发现，这种构象是有利的，也通过其水化壳的特性相比，平行链结构。三个水合位点，每个葡萄糖单位在附近的HO 6，O 6和O3可以确定。观察到在双链体周围形成网络的规则水桥。左旋反平行结构家族中螺旋参数的适度变化（每葡萄糖单位上升和扭曲0.233 nm和-45度）对水合壳的特性没有显著影响。水合位点相对于直链淀粉极性基团的位置和观察到的水桥与高分辨率晶体研究中描述的对硝基苯基α-麦芽己糖的高度水合反平行链左手双螺旋的水合几何形状非常一致[W. Hinrichs，G. Buttner，M. Steifar，Ch. Betzel，V. Zabel，B. Pfannemuller和W. Saenger（1987）Science，Vol. 238，pp. 205-208; W. Hinrichs和W. Saenger（1990）Journal of the American Chemical Society，Vol. 112，pp. 2789-2796]。在平行链（非对称或对称）双螺旋的情况下，仅可鉴定出靠近（H）O3基团的一个水合位点。没有观察到具有足够高概率的系统性水桥。直链淀粉-水和水-水相互作用的平均势能的总和与反平行链双螺旋的能量相比是不利的。水-水相互作用高，即，平行链的直链淀粉破坏了液态水的结构。这种效应可以解释天然直链淀粉在冷水中的不溶性，并支持在淀粉颗粒的微晶和仅具有低含水量的直链淀粉微晶中平行链双螺旋的存在[参见上文Imberty等人（1988）和Imberty和Perez（1988）]。对称的平行链双螺旋具有非常充分暴露的极性基团，并且它们的构象在晶体中应该通过直接或经由单个水分子形成广泛的双链体间氢键的能力而有利。将单个水分子掺入到晶体中可以弥补对称平行双螺旋表面上氢键供体的不足。实际上，根据衍射数据[参见上文的Imberty和Perez（1988）;以及A. Imberty，H. Chanzy，S. Perez，A. Buleon，V. Tran（1987）Macromolecules，Vol. 20，pp. 2636-2638]临界量的水增加了直链淀粉的结晶度，并且只有对称的平行链双螺旋适合于c = 1.05 nm的晶体学晶胞。平行链双螺旋直链淀粉的不利水合将增加天然淀粉颗粒的稳定性（例如，在种子中），因此，在生物学上是合理的。
The conformation of double-helical amylose is influenced by its water environment [A. Imberty, H. Chanzy, S. Perez, A. Buleon, and V. Tran (1988) Journal of Molecular Biology, Vol. 201, pp. 365-378; A. Imberty and S. Perez (1988) Biopolymers, Vol. 27, 1205-12211. For several low-energy conformations of left-handed amylose double helices, we performed Monte Carlo simulations of the (N, V, T) -ensemble of configurations of water molecules surrounding a single duplex. The crucial point of this simulation is the use of cylindrical periodical boundary conditions with a relatively small asymmetric unit comprising a limited number of water molecules. The output data consists of local maxima of water density in the space near the macromolecule and information on one- and two-membered water bridges between polar groups of amylose as well as energetic characteristics of the system under study.A left-handed antiparallel-stranded conformation of the amylose double helix (rise and twist per glucose unit are 0.343 nm and -58.1-degrees) corresponds to the global minimum of intraduplex potential energy [W. Schulz and H. Sklenar (1993) Biopolymers, submitted; W. Schulz, H. Sklenar, W. Hinrichs, and W. Saenger (1993) Biopolymers, to be published]. We found that this conformation is favored also by its hydration shell characteristics in comparison to parallel-stranded structures. Three hydration sites per glucose unit in the vicinity of HO6, O6, and O3 could be identified. Regular water bridges forming a network around the duplex were observed. A moderate change of the helical parameters within the family of left-handed antiparallel structures (to a rise and twist per glucose unit of 0.233 nm and -45-degrees) does not have noteworthy consequences for the characteristics of the hydration shell. The location of the hydration sites with respect to the polar groups of amylose and the observed water bridges are in excellent agreement with the hydration geometry of the heavily hydrated antiparallel-stranded left-handed double helix of p-nitrophenyl alpha-maltohexose described in a high-resolution crystal study [W. Hinrichs, G. Buttner, M. Steifar, Ch. Betzel, V. Zabel, B. Pfannemuller, and W. Saenger (1987) Science, Vol. 238, pp. 205-208; W. Hinrichs and W. Saenger (1990) Journal of the American Chemical Society, Vol. 112, pp. 2789-2796].In the case of parallel-stranded (nonsymmetric or symmetric) double helices, only one hydration site near the (H) O3 group could be identified. No systematic water bridges with sufficient high probability were observed. The sum of the average potential energies of the amylose-water and water-water interactions is not favourable in comparison with the energy for antiparallel-stranded double helices. The water-water interaction is high, i.e., parallel-stranded amylose breaks the structure of liquid water. This effect would explain the insolubility of natural amylose in cold water and support the occurrence of parallel-stranded double helices in crystallites of starch granules and in amylose microcrystals having only low water content [see Imberty et al. (1988) and Imberty and Perez (1988) above]. Symmetric parallel-stranded double helices have very well-exposed polar groups and their conformation should be favored in crystals by the ability to form extensively interduplex hydrogen bonds directly or via single water molecules. Single water molecules incorporated into the crystal would compensate for the shortage of donors of hydrogen bonds on the surface of the symmetric parallel-stranded double helix. Indeed, in accordance with diffraction data [see Imberty and Perez (1988) above; also A. Imberty, H. Chanzy, S. Perez, A. Buleon, V. Tran (1987) Macromolecules, Vol. 20, pp. 2636-2638] a critical amount of water increases the crystallinity of amylose and only symmetric parallel-stranded double helices would fit into a crystallographic unit cell with c = 1.05 nm. The unfavorable hydration of parallel-stranded double-helical amylose would increase the stability of natural starch granules (e.g., in seeds) and, therefore, be biologically sensible.