蛋白质的三维结构,蛋白质三维结构是由其氨基酸序列决定的； 蛋白质功能依赖其结构，或结构决定功能； 一般来讲，蛋白质具有（接近）唯一确定的结构； 非共价相互作用是稳定蛋白结构的最主要因素； (疏水作用；氢键；离子键；VDW范德华) 在众多蛋白质结构中，其折叠类型（fold）是有限的（2000个？）； 研究蛋白结构的方法 （X光晶体学及核磁共振）； 一些结构与功能关系的例子,本章要点,尽管蛋白质结构比较复杂，但仍然有许多规律。蛋白质结构研究得出的第一个基本规律是：,亲水表面,疏水内核,水溶性球蛋白的折叠是将其疏水侧链置于分子的内部，产生一个“疏水内核”和一个“亲水表面”。,氨基酸残基序列,二级结构,超二级结构,结构域与三级结构,多亚基结构与分子聚合体,蛋白质分子的结构层次,蛋白质分子的超二级结构(花样,motif),若干二级结构单元 (secondary structure element) 可以形成特殊的几何组合出现在蛋白质结构中。这些由二级结构依据特殊的几何关系组合起来的结构称为超二级结构 (super-secondary structure) 或花样 (motif)。 超二级结构（花样）的存在，既可能与某些特殊的生物功能相关联，也可能仅仅作为蛋白质结构的组装模块。,蛋白质结构中的若干个二级结构和/或结构花样（motif）通常会依据特定的几何位置排列形成较为致密的称为“结构域(domain)”的球形结构。 三级结构（tertiary structure）作为常用的术语有两重含义： 其一，单条多肽链折叠形成的由一个或者多个结构域组成的全部结构； 其二，二级结构和/或结构花样排列形成的结构域。,蛋白质分子的结构域与三级结构,From Science. 2003 Apr 18;300(5618):445-52,a/b structures,SCOP statistics,Graphical representation of protein structures,Some crystals from Su Lab, Peking University,Some structures solved,AK6 (AD-004),NCC27,Human LMW PTP-B,OXY-1A -lactamase,Bs803(YjbK),Bs YflL,Bs47(HutI),Bs99 (YjcG),LC1,WRKY1-C,Sm35,Sm32,B.s. YwlE,Sm23,BsTim344,Kurt Wthrich 1938 Nobelpris 2002,Utvecklade metoder att studera struktur och dynamik av proteiner i lsning med NMR,Ett prion proteinet som ger galna ko-sjukan,Beijing NMR Center,Protein Folding,?,a-helix local interaction b-sheet long range interaction Hydrophoic residues protein core,Protein Folding,About equilibrium of any process or reaction. What direction will process proceed toward equilibrium? How far will it go toward completion before it reaches equilibrium? Not about how it gets there. (e.g. how fast or what path it takes) First Law: Energy is conserved. Second Law: Disorder increases.,Thermodynamics,DG = DH T DS DG is change in Gibbs Free Energy. If the ending state is lower in free energy than the starting state, reaction will proceed spontaneously. DH is change in Enthalpy. Enthalpy is the energy from bonds and attractive interactions. Negative DH is favorable. (e.g. forming more bonds.) DS is change in Entropy. Entropy is disorder. Positive DS is favorable. (e.g. increasing the amount of disorder.),Direction of Biochemical Processes,Studies of the RNase A,Small protein with 4 disulfide bonds.,Fact 1: Urea Unfolds Proteins,Fact 2: b-mercaptoethanol breaks disulfide bonds,Studies of the RNase A,Studies of the RNase A,Inactive RNase had formed “wrong” disulfide bonds while unfolded. The wrong links prevented the polypeptide chain from attaining the active configuration when urea was removed. The active ribonuclease had formed the correct disulfide bonds when bME was removed. The backbone had refolded correctly, prior to reoxidation If “wrong” disulfides could be fixed, the activity of inactive RNase could be restored?,Studies of the RNase A,Trace of b-ME present with the “scrambled“ RNase permitted disulfide bonds to re-reduce and then reoxidize, so native active structure could form. When right combinations of S-S bonds formed, they remained, because native structure was the thermodynamically most stable (favored) state.,Studies of the RNase A,The sequence determines the structure! The information necessary to specify the structure is present in the sequence.,Proteins do not sample all possible conformations- rather, “partially folded” states (“folding intermediates”) with some but not all possible bonds and interactions occur during the folding process. The sequence also specifies the folding pathway. As more interactions form, the structure gets closer and closer to the final folded state. Typical times for protein folding are 10-6 sec to 102 sec.,Protein Folding Pathways,Protein Folding Pathways,Free Energy Landscape,The central dogma 中心法则 Flow of information in gene expression,The genetic code The mRNA consists of four nucleotides A, G, C and U. Three consecutive nucleotides form a “codon” The 64 codons encode 20 aminoacids, “Start” and “Stop”,SGs first task: Sequence the domains (or families),From Science. 2003 Apr 18;300(5618):445-52,SCOP statistics,生物大分子结构与功能的关系： 功能=运动着的结构 生命是由蛋白复合物纳米机器运转着,Some say: Function is structure! Others say: Structure is function! I say: Functions are structures in motion!,The ribosome translates the mRNA sequence into protein sequence,Ramakrishnan (2002), Cell 108, 557-572,The structure of the large and small ribosomal subunit Schematic surface representation with animation 23S RNA: orange 5S RNA: yellow proteins: blue Active site: green Ban, Nissen, Hansen, Moore & Steitz (2000) Nissen, Hansen, Ban, Moore & Steitz (2000),The Elongation Cycle studied by Cryo-EM,1,3,4,5,2,E P A R,How do 100 RNA helices in 6 RNA domains pack together and form a compact structure?,The large ribosomal subunit contains a 100 long tunnel for product release - the polypeptide exit tunnel. Non-stick surface - “teflon” mixed surface of hydrophobic and polar patches,谢谢大家!,