Bierzyński A, Pawłowski K
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa.
Acta Biochim Pol. 1997;44(3):423-32.
Principles of contemporary theoretical description of alpha-helix formation by polypeptide chains in water solution are shortly presented and critically discussed. The theory treats the unfolded state of a peptide as "random coil"--an ideal conformation quite distant from reality. We suggest that for this reason the helix propagation parameters of amino-acid residues, determined using series of model peptides with different sequential patterns, are not the same. Interpretation of the so called "nucleation parameter" is erroneous. In fact, it is not determined by the helix nucleation process but rather by a specific situation of residues at the helix N- and C-termini, and it strongly depends on solvation of their NH and CO groups, respectively. Consequently, helical segments with terminal sequences dominated by residues with strongly hydrophobic, bulky side chains can be very unstable. We postulate that an unexpectedly high stability of very short, pre-nucleated helices studied by us arises from a "helix end separation effect": separated helix termini are better solvated than when they overlap each other. Because of this effect, helix initiation may be much more difficult than predicted by the theoretical "helix nucleation parameters".
本文简要介绍并批判性地讨论了多肽链在水溶液中形成α-螺旋的当代理论描述原则。该理论将肽的未折叠状态视为“无规卷曲”——一种与现实相差甚远的理想构象。我们认为，因此，使用具有不同序列模式的一系列模型肽确定的氨基酸残基的螺旋延伸参数并不相同。对所谓“成核参数”的解释是错误的。事实上，它不是由螺旋成核过程决定的，而是由螺旋N端和C端残基的特定情况决定的，并且它分别强烈依赖于它们的NH和CO基团的溶剂化作用。因此，末端序列由具有强疏水性、大体积侧链的残基主导的螺旋片段可能非常不稳定。我们推测，我们研究的非常短的预成核螺旋具有出乎意料的高稳定性，这源于“螺旋末端分离效应”：分离的螺旋末端比它们相互重叠时具有更好的溶剂化作用。由于这种效应，螺旋起始可能比理论“螺旋成核参数”预测的要困难得多。
