摘要 本文选用经过实验验证的碱基序列，用简化的方式，构建了被水分子和镁离子修饰的 核酸序列的分子模型，应用分子力学模拟方法对序列进行能量优化，对优化后序列的构象参 数、成键状况和能量数据等进行了分析。对tRNAH^His/GUG的识别特性作了初步的探索 ，得到 了和实验结果相近的结论。此外，还从能力学的角度讨论了溶剂－溶质－溶剂相互作用形成 的网状氢键网络对核酸结构稳定性的影响，探讨了非Crick-Watson G U、U U配对的能力学 特征并存在于被水分子和镁离子修饰的核酸序列中的G U、U U配对情况。

中图号P969.1文献标识码:A文章编号:1006-8783(2000)01-0001-06

Molecular Mechanics Simulation of Recognition

Identity of tRNA^{His/ GUG}

YAO Li-xin

（Institute of Materia Medica, Guangdong College of Pharmacy, Guangzhou，510 240）

CAO Huai

（Modern Biological Research Center, Yunnan University）

LIU Ci-quan

（Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zo ology, Chinese Academy of Sciences）

Abstract A group of nucleic acid sequences retrieved from experiment was analyzed based o n molecular mechanics simulation method to prove tRNA recognition identity that was derived from parts of tRNA^His/GUG sequence. A simplified molecular mod el of nucleic acid sequences with cage-like water molecules and Mg²⁺ ions was co nstruc ted. Based upon the primary analyses of the optimized molecular models, such as conformation parameters, bonding propensities, and energies of optimized models, etc., the recognition identity of tRNA^His/GUG was probed and the result w as s imilar to experiment-determined ones. Some problems, such as stem-loop structure (hair-pin structure), the impacts of charged metal ions (Mg²⁺) and H₂O molecule s on the stability of nucleic acid sequences, non-Watson-Crick base pairing (i.e . U·U/G·U base pairing), and stabilizing influence of the ″cage-like″ solven t-solvent and solvent-solute bonds were also discussed.

Key Wordscomputer-aided molecular modeling (CAMM), tRNA^His/GUG , recognition identity, molecular mechanics, hydrogen-bond network

CLC numberR 969.1Document co de:AArticle ID:1006-8783(2000)01-0001-06

1Introduction

The interaction of mRNA with tRNA charged with amino acid takes part in the determination of collinear genetic code. The charging of amino acids with tRNAs is catalyzed by aminoacyl-tRNA synthetases (aaRs)^［1］.The nucleic acid sequences of tRNAs and minor variations both in nucleic sequ ences and the conformations are concerned with the interaction of tRNAs with ami noacyl-tRNA synthetases, both structurally and functionally^［2］.So far, 20 kinds of aminoacyl-tRNA synthetases have been reported,each of them responsible for the relevant amino acid and the special tRNA. Usually, each enzym e can be charged with various iso-acceptors of different tRNA molecules^{［1 ］}. Analogous to RNA replicase that has been considered as the first ribosome in the evolution ^［2］, the occurrence of aminoacyl-tRNA synthetases in early protein evolution seems i mproving fidelity of protein synthesis by the special charging with tRNA. Due to the universal conservation of aminoacyl-tRNA synthetases, it has been considere d that the enzymes had come into being in the early evolution, playing the same important role as the catalysis effect that RNAs did in the soup of early organi sm system, the recognition identity between aminoacyl-tRNA and tRNA led to the s peedy evolution of genetic code. This recognition system was called second genet ic code or paracoden^［3］.

The recognition of tRNA is so complex that it is not enough to be determined onl y based on clove structure of tRNA^4,5. The explication of recognition identity of tRNAs lies i n the comprehensive studies of tertiary structures of tRNAs and various recognit ion elements in various levels, particularly the involved regions for the recogn ition of aminoacyl-tRNA synthetases and tRNAs. Aminoacyl-tRNA synthetases bind t he inner side of L-shaped tRNAs, the binding locus include accepting arm, DHU-ar m and anticodon arm^［6］. Traditional codon-anticodon interactions in ribo somes ar e involved with up-stream factors, down-stream factors and RFs (releasing factor s), while translation process in ribosomes is related with interactions in A-si te, P-site and E-site, etc^［7］. While keeping the nucleic acids the same in the a nticodon, mutagenesis of 12 nucleic acids in other regions had changed tRNA^{l eu} t o tRNA^Ser［8］. The 0.29nm crystal structure of T. Thermophilus Seryl-tRNA synthetas es complexed with tRNA^Ser showed that, the anti-parallel super-coiling dom ain in one sub-unit of the aminoacyl-tRNA synthetase contacted with TψC loop and vari able pocket and lead accepting arm of tRNA to the active site of the enzyme ^［9］. T he recognition identity mainly lay in the contact of backbone of tRNA rather tha n in the sequence identity of tRNA^［9］. In vitro nucleic synthesis experi ment als o showed that the changing of charging identity only happened in the mutation of G3·U70 base pair in various mutants of inhibitory E. Coli. tRNAs and relat ive a minoacyl-tRNA synthetases carrying tRNA^{Ala/Glu［10］}. Evolutionarily , this nondeg enerate paracodon may be more ancient and more decisive, the charging of amino a cids with tRNAs catalyzed by aminoacyl-tRNA synthetases can be considered as the interactive and indirect charging of two different kinds of genetic languages, and ″entries of genetic″ dictionary are carried by tRNAs and aminoacyl-tRNA sy nt hetases^［3］. However, for most tRNAs, the recognition identities are main ly relat ed with nucleic acid sequence of anticodons^{［2、6、11、12］}, the clarific ation of this paracodon will contribute to further understanding of the evolution of tran slation process in the transmission of genetic information^［6］.

CPK (Corey-Pauling-Koltum) modeling and lock-key relationship has been employe d in the stacking structure of tRNA^［13］, however, it seems inappropriate to use rigid lock-key relationship to describe the flexible interaction of nuc leic acid with proteins. Various methods have been employed in the simulation or theoretical calculation of the recognition identity of tRNA^{［14、15］}.Us ing simp lified method to analyze may be possible, such as energy minimization and normal mode methods^{［16、17］}. Based on four sequence retrieved from the concern ed experi ment^［18］, computer-aided molecular modeling, molecular mechanics methods were performed in this study by using simplified methods.

2Computational Methods

All the modeling, visualization, simulation, and analyses in this study were done using Biosym/Molecular Simulation Insight-Ⅱ software in SiliconGr aphics Indigo² workstation (Mountain View, CA 94043-1389). The measuremen t of dihedral angles of the sequences was conducted with Tripos Sybyl molecular modeling software.

3Molecular Modeling

The stem region of the retrieved^［18］sequences was constructed as A-RNA d uplex, and the loop region was constructed as single A-RNA helix. Conside