氢键对涉及核糖核苷酸碱基和精氨酸，谷氨酸或谷氨酰胺残基的结构模式和稳定性的量子力学计算。,ACS Omega

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氢键对涉及核糖核苷酸碱基和精氨酸，谷氨酸或谷氨酰胺残基的结构模式和稳定性的量子力学计算。
ACS Omega ( IF 3.7 ) Pub Date : 2020-02-12 , DOI: 10.1021/acsomega.9b04083
Deepika Kagra ₁ , Preethi Seelam Prabhakar ₂ , Karan Deep Sharma ₁ , Purshotam Sharma ₁

Affiliation

核糖核苷酸：蛋白质相互作用在许多生物学过程中起着至关重要的作用。与范德华接触普遍存在的RNA：蛋白质界面不同，蛋白质对单个核糖核苷酸（如ATP）的识别主要通过氢键相互作用进行。作为了解氢键在核糖核苷酸：蛋白质识别中的作用的第一步，本研究采用密度泛函理论对涉及核碱基/核苷的18个独特氢键对的结构和能量特征进行了详细的量子力学分析。四个典型核糖核苷酸的组成部分和蛋白质的三个极性氨基酸残基（精氨酸，谷氨酰胺和谷氨酸）的侧链。此外，我们建立了五对新的模型，这些晶体迄今为止在结晶学上鉴定的核糖核苷酸：蛋白质复合物中还没有观察到，但将来可能在结晶的复合物中被鉴定出来。我们批判性地检查了每一对核糖核苷酸的特征：蛋白质晶体结构的出现和（气相和水相）优化的固有结构。我们进一步评估了每对的相互作用能，并使用了许多基于量子力学的关系，包括自然键轨道分析，分子分析中的量子理论原子，Iogansen关系，Nikolaienko-Bulavin-Hovorun关系和非共价相互作用，对相关的氢键进行了表征。降低密度梯度分析。我们的分析揭示了晶体对中氢键的丰富变异以及每对氢键的固有结构，包括常规的O / NH···N / O和CH···O氢键以及供体/受体分叉的氢键。此外，我们确定了核碱基和氨基酸部分的五种组合。每个具有至少两个通过相同核碱基边缘相互作用的交替（即多峰）结构。实际上，一对这样的对具有四个多峰结构。其中一个具有非常规的“氨基受体”氢键，其强度与相应的常规（即氨基：供体）结构（-9.2 kcal mol-1）相当（-9.4 kcal mol-1）。这表明了RNA中氨基受体氢键的重要性：蛋白质相互作用，并建议在将来在分子识别的背景下研究动力学时必须考虑这种相互作用。总的来说，我们的研究为核糖核苷酸：氨基酸相互作用的内在特征提供了初步的见识，这可能有助于对RNA：蛋白质识别的分子基础有更清晰的了解，并进一步了解这种接触在生物学中的作用。

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Structural Patterns and Stabilities of Hydrogen-Bonded Pairs Involving Ribonucleotide Bases and Arginine, Glutamic Acid, or Glutamine Residues of Proteins from Quantum Mechanical Calculations.

Ribonucleotide:protein interactions play crucial roles in a number of biological processes. Unlike the RNA:protein interface where van der Waals contacts are prevalent, the recognition of a single ribonucleotide such as ATP by a protein occurs predominantly through hydrogen-bonding interactions. As a first step toward understanding the role of hydrogen bonding in ribonucleotide:protein recognition, the present work employs density functional theory to provide a detailed quantum-mechanical analysis of the structural and energetic characteristics of 18 unique hydrogen-bonded pairs involving the nucleobase/nucleoside moiety of four canonical ribonucleotides and the side chains of three polar amino-acid residues (arginine, glutamine, and glutamic acid) of proteins. In addition, we model five new pairs that are till now not observed in crystallographically identified ribonucleotide:protein complexes but may be identified in complexes crystallized in the future. We critically examine the characteristics of each pair in its ribonucleotide:protein crystal structure occurrence and (gas phase and water phase) optimized intrinsic structure. We further evaluated the interaction energy of each pair and characterized the associated hydrogen bonds using a number of quantum mechanics-based relationships including natural bond orbital analysis, quantum theory atoms in molecules analysis, Iogansen relationships, Nikolaienko-Bulavin-Hovorun relationships, and noncovalent interaction-reduced density gradient analysis. Our analyses reveal rich variability in hydrogen bonds in the crystallographic as well as intrinsic structure of each pair, which includes conventional O/N-H···N/O and C-H···O hydrogen bonds as well as donor/acceptor-bifurcated hydrogen bonds. Further, we identify five combinations of nucleobase and amino acid moieties; each of which exhibits at least two alternate (i.e., multimodal) structures that interact through the same nucleobase edge. In fact, one such pair exhibits four multimodal structures; one of which possesses unconventional "amino-acceptor" hydrogen bonding with comparable (-9.4 kcal mol-1) strength to the corresponding conventional (i.e., amino:donor) structure (-9.2 kcal mol-1). This points to the importance of amino-acceptor hydrogen bonds in RNA:protein interactions and suggests that such interactions must be considered in the future while studying the dynamics in the context of molecular recognition. Overall, our study provides preliminary insights into the intrinsic features of ribonucleotide:amino acid interactions, which may help frame a clearer picture of the molecular basis of RNA:protein recognition and further appreciate the role of such contacts in biology.

更新日期：2020-02-25

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