OPTICAL PROPERTIES OF BIOLOGICAL MACROMOLECULES

本项目的目的是扩大光学光谱学，特别是圆二色谱(CD)在大分子结构和功能研究中的应用。在过去的十年中，CD光谱学经历了一次重大的复兴。CD越来越受欢迎，因为它对蛋白质和核酸构象以及配体结合高度敏感；它对样本量的要求不高；它适合于测量广泛的溶液条件和温度。圆二色谱和核磁共振是研究DNA和RNA中蛋白质折叠和构象转变的最广泛的技术。CD在蛋白质-DNA相互作用的研究中也具有重要的价值。建议在两个基本领域进行研究：(1)蛋白质的内在CD，同时考虑主链和侧链的贡献；(2)血红素在血红素蛋白质中的外在CD贡献。基于从头算波函数的新参数将被开发出来，并被纳入到α-螺旋、β-折叠和聚(Pro)II构象以及已知结构的蛋白质的CD的计算中。计算中还将引入高能跃迁的通键耦合和可极化群模型。小肽的CD谱--封闭的α-氨基酸--α-二肽和三肽，以及β-六肽和七肽--将从分子动力学轨迹计算出来。改进的基于从头算的参数将被开发用于侧链基团，特别是二硫化物。分子动力学模拟将与几个小蛋白质的改进的CD计算相结合。使用改进的参数将详细研究几种蛋白质的芳香族侧链对CD的贡献。一个平行的β-螺旋蛋白，野生型和突变型的折叠和去折叠的平衡和动力学将用CD和荧光来研究。我们将研究血红素的非平面性对血红素蛋白的可见光和近紫外光CD的贡献。对于已知结构的广泛的血红素蛋白质，将评估固有的血红素-芳香作用和血红素-多肽相互作用的相对重要性。将计算多个血红素蛋白的血红素-血红素相互作用。细胞色素b5中的血红素异构性将通过实验和MD-CD计算进行研究。通过对由随机动力学模拟得到的结构进行CD计算，研究了双卟啉类化合物中的激子耦合。将从实验和理论上研究通过蛋白质设计(模板)获得的多个血红素蛋白质模型。

The objective of this project is to extend the applications of optical spectroscopy, especially circular dichroism (CD), in the study of macromolecular structure and function. CD spectroscopy has undergone a major renaissance during the past decade. CD is increasingly popular because it is highly sensitive to protein and nucleic acid conformations and to ligand binding; its demands in quantity of sample are modest; and it lends itself well to surveying a broad range of solution conditions and temperature. CD and NMR are the most widely used techniques for studying protein folding and conformational transitions in DNA and RNA. CD is also of great value in studies of protein-DNA interactions. Studies in two basic areas are proposed: (1) the intrinsic CD of proteins, considering both backbone and side-chain contributions; (2) extrinsic CD contributions of hemes in heme proteins. New parameters, based upon ab initio wave functions for the peptide group will be developed and incorporated in calculations of the CD of alpha-helix, beta-sheet and poly(Pro)II conformations, as well as proteins of known structure. Through-bond coupling and polarizable group models for high energy transitions will also be introduced in the calculations. The CD spectra of small peptides - blocked alpha-amino acids alpha-di- and tripeptides, and beta-hexa- and heptapeptides- will be calculated from MD trajectories. Improved ab initio- based parameters will be developed for side chains groups , especially disulfides. Molecular dynamic simulations will be coupled with the improved CD calculations for several small proteins. Aromatic side- chain contributions to the CD of several proteins will be investigated in detail using improved parameters. The equilibrium and kinetics of folding and unfolding of a parallel beta-helix protein, wild-type and mutants, will be investigated by CD and fluorescence. The contribution of heme nonplanarity to the visible and near-uv CD of heme proteins will be investigated. The relative importance of intrinsic heme-aromatic, and heme-peptide interactions will be assessed for a wide range of heme proteins of known structure. Heme-heme interactions will be calculated for multi-heme proteins. Heme isomerism in cytochrome b5 will be studied experimentally and by MD-CD calculations. Exciton coupling of porphyrins in bisporphyrin steroids will be studied by calculations of CD for structures obtained by a stochastic dynamics simulation. Models of multi-heme proteins obtained by protein design (maquettes) will be studied experimentally and theoretically.