Gandini D, Gogioso L, Bolognesi M, Bordo D
Centro Biotecnologie Avanzate-IST, Universita di Genova, Italy.
Proteins. 1996 Apr;24(4):439-49. doi: 10.1002/(SICI)1097-0134(199604)24:4<439::AID-PROT4>3.0.CO;2-9.
In a selected set of 44 high-resolution, non-homologous protein structures, the intramolecular hydrogen bonds or salt bridges formed by ionizable amino acid side chains were identified and analyzed. The analysis was based on the investigation of several properties of the involved residues such as their solvent exposure, their belonging to a certain secondary structural element, and their position relative to the N- and C-termini of their respective structural element. It was observed that two-thirds of the interactions made by basic or acidic side chains are hydrogen bonds to polar uncharged groups. In particular, the majority (78%) of the hydrogen bonds between ionizable side chains and main chain polar groups (sch:mch bonds) involved at least one buried atom, and in 42% of the cases both interacting atoms were buried. In alpha-helices, the sch:mch bonds observed in the proximity of the C- and N-termini show a clear preference for acidic and basic side chains, respectively. This appears to be due to the partial charges of peptide group atoms at the termini of alpha-helices, which establish energetically favorable electrostatic interactions with side chain carrying opposite charge, at distances even greater than 4.5 angstrom. The sch:mch interactions involving ionizable side chains that belong either to beta-strands or to the central part of alpha-helices are based almost exclusively on basic residues. This results from the presence of main chain carbonyl oxygen atoms in the protein core which have unsatisfied hydrogen bonding capabilities.
在一组选定的44个高分辨率、非同源蛋白质结构中，对可电离氨基酸侧链形成的分子内氢键或盐桥进行了识别和分析。该分析基于对所涉及残基的若干性质的研究，如它们的溶剂可及性、它们属于某种二级结构元件以及它们相对于各自结构元件的N端和C端的位置。据观察，碱性或酸性侧链形成的相互作用中有三分之二是与极性不带电基团形成的氢键。特别是，可电离侧链与主链极性基团之间的氢键（sch:mch键）中的大多数（78%）涉及至少一个埋藏原子，在42%的情况下，两个相互作用的原子都是埋藏的。在α-螺旋中，在C端和N端附近观察到的sch:mch键分别对酸性和碱性侧链表现出明显的偏好。这似乎是由于α-螺旋末端肽基团原子的部分电荷，它们在距离甚至大于4.5埃时与携带相反电荷的侧链建立了能量上有利的静电相互作用。涉及属于β-链或α-螺旋中心部分的可电离侧链的sch:mch相互作用几乎完全基于碱性残基。这是由于蛋白质核心中存在氢键能力未满足的主链羰基氧原子。
