Mirny L A, Abkevich V I, Shakhnovich E I
Harvard University, Department of Chemistry and Chemical Biology, 12 Oxford Street, Cambridge MA 02138, USA.
Proc Natl Acad Sci U S A. 1998 Apr 28;95(9):4976-81. doi: 10.1073/pnas.95.9.4976.
Sequences of fast-folding model proteins (48 residues long on a cubic lattice) were generated by an evolution-like selection toward fast folding. We find that fast-folding proteins exhibit a specific folding mechanism in which all transition state conformations share a smaller subset of common contacts (folding nucleus). Acceleration of folding was accompanied by dramatic strengthening of interactions in the folding nucleus whereas average energy of nonnucleus interactions remained largely unchanged. Furthermore, the residues involved in the nucleus are the most conserved ones within families of evolved sequences. Our results imply that for each protein structure there is a small number of conserved positions that are key determinants of fast folding into that structure. This conjecture was tested on two protein superfamilies: the first having the classical monophosphate binding fold (CMBF; 98 families) and the second having type-III repeat fold (47 families). For each superfamily, we discovered a few positions that exhibit very strong and statistically significant "conservatism of conservatism"-amino acids in those positions are conserved within every family whereas the actual types of amino acids varied from family to family. Those amino acids are in spatial contact with each other. The experimental data of Serrano and coworkers [Lopez-Hernandez, E. & Serrano, L. (1996) Fold. Des. (London) 1, 43-55]. for one of the proteins of the CMBF superfamily (CheY) show that residues identified this way indeed belong to the folding nucleus. Further analysis revealed deep connections between nucleation in CMBF proteins and their function.
通过向快速折叠的类似进化选择生成了快速折叠模型蛋白（在立方晶格上长度为48个残基）的序列。我们发现快速折叠蛋白展现出一种特定的折叠机制，其中所有过渡态构象共享一个较小的共同接触子集（折叠核）。折叠加速伴随着折叠核内相互作用的显著增强，而非核相互作用的平均能量基本保持不变。此外，参与核的残基是进化序列家族中最保守的残基。我们的结果表明，对于每种蛋白质结构，都有少量保守位置是快速折叠成该结构的关键决定因素。这个猜想在两个蛋白质超家族上进行了测试：第一个具有经典单磷酸结合折叠（CMBF；98个家族），第二个具有III型重复折叠（47个家族）。对于每个超家族，我们发现了一些位置表现出非常强且具有统计学意义的“保守性的保守性”——这些位置的氨基酸在每个家族中都是保守的，而氨基酸的实际类型因家族而异。这些氨基酸彼此在空间上相互接触。Serrano及其同事的实验数据[Lopez-Hernandez, E. & Serrano, L. (1996) Fold. Des. (London) 1, 43 - 55]。对于CMBF超家族的一种蛋白质（CheY）表明，以这种方式鉴定出的残基确实属于折叠核。进一步分析揭示了CMBF蛋白中的成核与其功能之间的深层联系。
