Bordo D, Argos P
Unita' Biostrutture-Centro Biotecnologie Avanzate IST, Genova, Italy.
J Mol Biol. 1994 Oct 28;243(3):504-19. doi: 10.1006/jmbi.1994.1676.
Intra-molecular side-chain:main-chain (sch:mch) and side-chain (sch:sch) hydrogen bonds observed in 44 well refined crystallographic protein structures with non-homologous sequences have been identified, classified and analysed to detect recurring structural patterns. Each observed bond was characterized by the position of its acceptor and donor groups relative to the N and C termini of the particular secondary structure in which they occur and according to their appearance within the same of sequentially separated secondary structures. The role of short-range hydrogen bonds in the formation and stabilization of a secondary structure and the importance of long-range hydrogen bonds as a cohesive force for different structural segments were also examined. It was found that the N terminus of alpha-helices is characterized by recurring sch:mch and sch:sch bonds with elements of the preceding coil segment, while at the C terminus a frequent intra-helix sch:mch hydrogen bond was frequently observed. The residues at or near the beta-strand termini often cross-linked, through hydrogen-bonding, non-sequential coil segments. Coil structures were characterized by recurring, internal sch:mch hydrogen bonding involving small polar side-chain groups situated at or near their N termini (coil N-capping). The significance of hydrogen bonds as formers and stabilizers of a protein fold and the association of its secondary structural units was also considered through an examination of bond density and distribution throughout the protein tertiary structure.
在44个具有非同源序列且结构精修的晶体学蛋白质结构中观察到的分子内侧链：主链（sch:mch）和侧链（sch:sch）氢键已被识别、分类和分析，以检测重复出现的结构模式。每个观察到的氢键的特征在于其受体和供体基团相对于它们所在特定二级结构的N端和C端的位置，并根据它们在相同或顺序分离的二级结构中的出现情况来确定。还研究了短程氢键在二级结构形成和稳定中的作用以及长程氢键作为不同结构片段内聚作用力的重要性。结果发现，α螺旋的N端的特征是与前一个卷曲片段的元素反复形成sch:mch和sch:sch键，而在C端，经常观察到频繁的螺旋内sch:mch氢键。β链末端或其附近的残基经常通过氢键与非连续的卷曲片段交联。卷曲结构的特征是反复出现内部sch:mch氢键，涉及位于其N端或附近的小极性侧链基团（卷曲N端封端）。还通过检查整个蛋白质三级结构中的键密度和分布，考虑了氢键作为蛋白质折叠的形成者和稳定剂及其二级结构单元关联的重要性。
