OPTICAL PROPERTIES OF BIOLOGICAL MACROMOLECULES

本项目旨在拓展光谱学，特别是圆二色性（CD）在大分子结构和功能研究中的应用。CD光谱学在过去十年中经历了一次重大的复兴。乳糜泻越来越受欢迎，因为它对蛋白质和核酸构象以及配体结合高度敏感；其对样品数量的需求不大；而且它还能很好地测量各种溶液条件和温度。CD和NMR是研究DNA和RNA中蛋白质折叠和构象转变最广泛使用的技术。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)考虑主链和侧链贡献的蛋白质的内在CD；(2)血红素在血红素蛋白中的外源性CD贡献。新的参数，基于从头算波函数的肽组将开发和纳入计算的CD α -螺旋，β -片和聚（Pro）II构象，以及已知结构的蛋白质。在计算中还将引入高能跃迁的通键耦合和极化基团模型。小肽-阻断α -氨基酸-二肽和三肽，以及-六肽和七肽-的CD光谱将从MD轨迹计算。改进的基于从头算的参数将用于侧链基团，特别是二硫化物。分子动力学模拟将与改进的CD计算相结合，用于几种小蛋白质。芳香侧链对几种蛋白质CD的贡献将使用改进的参数进行详细的研究。平行β -螺旋蛋白折叠和展开的平衡和动力学，野生型和突变型，将通过CD和荧光进行研究。血红素非平面性对血红素蛋白可见光和近紫外CD的影响将被研究。内在血红素-芳香和血红素-肽相互作用的相对重要性将被评估为广泛的已知结构的血红素蛋白。对于多血红素蛋白，将计算血红素-血红素相互作用。细胞色素b5中的血红素同分异构体将通过实验和MD-CD计算进行研究。双卟啉类固醇中卟啉的激子耦合将通过随机动力学模拟得到的结构的CD计算来研究。通过蛋白质设计（模型）获得的多血红素蛋白模型将进行实验和理论研究。

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.