Worch Remigiusz, Stolarski Ryszard
Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, Warsaw University, 02-089 Warszawa, Poland.
Proteins. 2008 Jun;71(4):2026-37. doi: 10.1002/prot.21882.
Recognition of the ribonucleic acid 5' termini (RNA 5' cap) by a wide class of cap-binding proteins is largely accomplished by cation-pi stacking that involves the positively charged 7-methylguanine ring and aromatic amino acid side chains. Quantum calculations of the stacking energy were performed by means of MP2 perturbation method for binary and ternary associates composed of the 7-methylguanine moiety and tryptophan, tyrosine, or phenylalanine, in their spatial orientations known from the crystalline cap-protein complexes. The results clearly pointed to an enhancement of the stacking energy due to a net positive charge in the cap guanine moiety and allowed analysis of a role of various amino acids in stabilization of the complexes. Conformational flexibility of the aromatic amino acids taking part in binding ligands to a wide class of RNA-recognizing proteins, including the cap-binding proteins, was determined by regional order neural network (RONN) algorithm that provides results close to those of the crystallographic B-factors analysis. Interestingly, some of the tyrosines that are classified in general as "rigid" showed high flexibility when engaged in binding the cap to nuclear cap-binding protein complex CBC and to viral methyltransferase VP39. Parallel analyses of the binding energy and flexibility of the protein fragments engaged in the binding leads to understanding differences in molecular mechanisms of the cap recognition by various proteins, CBC compared with the eukaryotic initiation factor eIF4E, and enzymes vs. other protein factors.
一类广泛的帽结合蛋白对核糖核酸5'末端（RNA 5'帽）的识别主要通过阳离子-π堆积来实现，这种堆积涉及带正电荷的7-甲基鸟嘌呤环和芳香族氨基酸侧链。利用MP2微扰方法对由7-甲基鸟嘌呤部分与色氨酸、酪氨酸或苯丙氨酸组成的二元和三元缔合体进行堆积能的量子计算，这些缔合体的空间取向取自晶体帽蛋白复合物。结果清楚地表明，帽鸟嘌呤部分的净正电荷导致堆积能增强，并有助于分析各种氨基酸在复合物稳定中的作用。参与将配体结合到包括帽结合蛋白在内的一类广泛的RNA识别蛋白上的芳香族氨基酸的构象灵活性，是通过区域有序神经网络（RONN）算法确定的，该算法提供的结果与晶体学B因子分析的结果相近。有趣的是，一些通常被归类为“刚性”的酪氨酸在与核帽结合蛋白复合物CBC以及病毒甲基转移酶VP39结合帽时表现出很高的灵活性。对参与结合的蛋白质片段的结合能和灵活性进行平行分析，有助于理解各种蛋白质识别帽的分子机制的差异，如CBC与真核起始因子eIF4E的差异，以及酶与其他蛋白质因子的差异。
