蛋白质起源的小分子诱导/选择模型的实验验证
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摘要
“生命是如何起源的”是自然科学要解决的三大核心问题之一。由于蛋白质既是一种重要的生物大分子，同时又是生命结构和生物功能的执行者，因此原始蛋白质的起源是生命起源的重要研究内容之一。尽管没有原始蛋白的化石遗迹可供参考，但是近些年飞速发展的各种“组学”却使人们能够通过借助各种“分子化石”来推测原始蛋白质的结构和功能特征。我们在分析小分子配体在蛋白质空间中的分布模式时发现配体与蛋白（结构域、折叠类型层次）之间的映射存在幂律关系，该现象被证明可以用“优先添加原则”予以解释，据此可以推断出配体与原始蛋白的结合顺序及所结合蛋白的折叠类型。由于该研究得出的配体与蛋白的结合顺序与公认的蛋白质结构起源顺序基本一致，我们提出一个大胆的猜想，即原始蛋白的产生是小分子配体诱导、选择的结果。本文旨在通过对早起源氨基酸组成蛋白质的结构和性质及辅因子对早起源氨基酸组成的随机肽构象转变的诱导作用研究，为小分子配体对原始蛋白质起源的诱导/选择模型提供初步的实验验证。
研究目的：明确起源较早的氧化还原蛋白能否仅由早起源氨基酸构成；明确由四种早起源氨基酸组成的随机聚肽的二级结构特征；明确由VNM编码的早起源氨基酸子集组成随机多肽的二级结构特征；明确辅因子能否诱导早起源氨基酸组成的随机多肽产生构象转变。
研究方法：采用理性设计方法将起源较早的黄素氧化还原蛋白2FZ5中的晚起源氨基酸用早起源氨基酸进行替换，据此构建了突变型黄素氧化还原蛋白原核表达载体，并对其进行了原核表达、纯化及相关氧化还原性质测定。通过N-内羧酸酐开环聚合反应合成了（Val~x/Glu~y/Lys~z/Ser~Z）n随机共聚肽，采用圆二色性光谱研究了随机共聚肽的二级结构特点及三种有机辅因子对随机共聚肽构象转变的影响。采用两轮组装的小盒式DNA编码文库经体外翻译生成由VNM编码的15种氨基酸组成的随机多肽，采用圆二色性光谱和bis-ANS荧光结合实验研究了随机多肽的二级结构和疏水结构域的特征，研究了五种辅因子对随机多肽构象转变和疏水结构域的影响。
研究结论：实验结果表明突变型黄素氧化还原蛋白具有与野生型相似的结构特征，半醌型和氢醌型黄素氧化还原蛋白突变体较野生型的稳定性低，双电子氧化还原电位（E_(ox/hq)）达到-360mV，表明仅由早起源氨基酸和有机辅因子构成的突变型黄素氧化还原蛋白具有氧化还原蛋白活性。（Val~x/Glu~y/Lys~z/Ser~Z）n随机共聚肽的二级结构包括无规则卷曲和α螺旋，添加ATP、NAD或NADH均未诱导产生β片层结构；低浓度的有机辅因子诱导β转角的产生，高浓度的有机辅因子倾向于使β转角转变为无规则卷曲或α螺旋。由VNM编码的15种早起源氨基酸子集组成的随机多肽不但具有较好的水溶性，而且具有典型的蛋白质二级结构特征和少量的疏水结构域。辅因子能够诱导随机多肽发生构象转变，而且各种辅因子诱导随机多肽发生构象转变的特点各不相同。ATP的诱导效应主要表现为β片层和无规则卷曲含量的减少，β转角和α螺旋含量的增加。NADP+的诱导效应表现为β片层的增加和无规则卷曲含量的减少，α螺旋和β转角的含量变化不大。NAD~+的诱导效应表现β片层的增加和α螺旋、β转角的减少，无规则卷曲含量变化不大。NADH的诱导效应表现为β片层略有增加和α螺旋略有减少，β转角和无规则卷曲含量变化不大。Mg~(2+)的诱导效应表现为β片层少量增加和β转角的略有减少，α螺旋和无规则卷曲含量变化不大。ATP、NAD~+和NADH能够诱导随机多肽产生更多的疏水结构域。
研究意义：本论文的研究结果不但证实了起源较早的氧化还原蛋白可以仅由14种早起源氨基酸组成，而且发现由简约化的氨基酸子集组成的随机多肽具有蛋白质二级结构特征且具有可折叠性，辅因子能够诱导早起源氨基酸组成的随机多肽发生构象转变并产生更多的疏水结构域。上述实验结果不但能够为辅因子诱导蛋白质起源假说提供了实验验证，而且为蛋白质工程的相关研究提供了新的思路。
“How did life begin?” is one of three central topics in the natural science field whichrequired to be answered. Since protein is not only an important biomacromolecule, but alsothe performer of vitual movement. So, origin of proteins is one of the central topics in thestudy of origin of life. Although there is no fossile of primitive protein left, we can infer thecharacteristic of ancient protein with the help of “molecular fossile” accompanied by rapiddevelopment of all kinds of “omics”. Through analyzing the distribution patterns ofsmall-molecule ligands in protein space, we proposed that the primitive protein architectureswere generated by the induction/selection of small molecules. In this thesis, this hypothesiswas preliminarily valiadated by the study of characteristic and structure of ancient proteinconstructed by primitive amino acids, and the study of cofactors induced effects on theconformation transfer of random peptides consisting of primitive amino acids set.
Objectives: To elucidate whether an ancient redox protein can be construsted by aprimitive amino acids set? Secondary structure characteristic of random polypeptidesconsisting of4kinds of primitive amino acids, secondary structure characteristic of randompolypeptides consisting of15kinds of amino acids which encode by VNM, and whethercofactors can induce transfer of the conformation of random polypeptides?
Methods: Through substituting “Late amino acids” by “Early amino acids” of aflavodoxin by rational design, mutant flavodoxin recombinant vector was constructed and itscharacteristic properties were evaluated.(Val~x/Glu~y/Lys~z/Ser~Z) random co-polypeptides wassynthesized by N-carboxyanhydride open-ring reaction, the secondary structure characteristicof random co-polypeptides and the effect of organic cofactor on the conformation transitionof random co-polypeptides were determined by Circular Dichroism spectrum analysis. ADNA library encoding random polypeptides consisting of15kinds of primitive amino acidswas constructed by strategy of library in small cassette, consequentlyly a random peptideslibrary was obtained by in vitro translation. The secondary structure characteristic andhydrophobic domain of random polypeptides were determined by Circular Dichroismspectrum analysis bis-ANS binding assay. The effects of cofactors on the conformationtransition of random co-polypeptides were invested by Circular Dichroism spectrum analysis bis-ANS binding assay also.
Results: Mutant flavodoxin has similar structural characteristics to wild-type protein,although the semiquinone and hydroquinone flavodoxin mutants possess lower stability incomparison with corresponding form of wild-type flavodoxin, the redox potential of doubleelectron reduction（E_(ox/hq)）arrived at-360mV, indicating that flavodoxin mutant consititutedsolely by early amino acids can exert effectively electron transfer activity. The secondarystructure of (Val~x/Glu~y/Lys~z/Ser~Z) random co-polypeptides include α helix and random coil,there is no β sheet was induced by ATP, NAD and NADH. The β turn were induced by lowconcentration organic cofactors, the conformation transition of β turn, α helix and randomcoil were induced by higher concentration organic cofactors. Random polypeptides consistingof15kinds of primitive amino acids which encoded by VNM is not only soluable but alsohas a secondary structure characteristic of protein. Cofactors can induce conformationtransition of random polypeptides and the effect is different between different cofactors. Theinducing effect of ATP shows as decrease of β sheet and random coil, and the increasedcontents of α helix and β turn. The inducing effect of NADP+shows as increase of β sheetand decreased content of random coil, the contents of α helix and β turn changed slightly. Theinducing effect of NAD~+shows as increase of β sheet and decreased content of α helix and βturn, the contents of random coil changed slightly. The inducing effect of NADH shows asa slightly increased β sheet and a slightly decreased α helix, the contents of β turn andrandom coil changed very slightly. The inducing effect of Mg~(2+)shows as a slightly increasedβ sheet and a slightly decreased β turn, the contents of α helix and random coil changed veryslightly. ATP, NAD~+and NADH can induced the formation of hydrophobic domain ofrandom polypeptides.
Significance: An ancient redox protein constructed by14kinds of primitive amino acidswas validated in this paper. Furthermore, it was finded that random polypeptides consisting ofreduced amino acids set has secondary structural characteristic of protein,15kinds ofprebiotic amino acids set is a foldable set, cofactors can induce the conformation transition ofrandom polypeptides, ATP, NAD~+and NADH can induce the formation of hydrophobicdomain of random polypeptides. These results not only provide an experimental verificationfor “small molecular induced the origin of protein” hypothesis, but also can provide a novel solution for protein engineering.
研究目的：明确起源较早的氧化还原蛋白能否仅由早起源氨基酸构成；明确由四种早起源氨基酸组成的随机聚肽的二级结构特征；明确由VNM编码的早起源氨基酸子集组成随机多肽的二级结构特征；明确辅因子能否诱导早起源氨基酸组成的随机多肽产生构象转变。
研究方法：采用理性设计方法将起源较早的黄素氧化还原蛋白2FZ5中的晚起源氨基酸用早起源氨基酸进行替换，据此构建了突变型黄素氧化还原蛋白原核表达载体，并对其进行了原核表达、纯化及相关氧化还原性质测定。通过N-内羧酸酐开环聚合反应合成了（Val~x/Glu~y/Lys~z/Ser~Z）n随机共聚肽，采用圆二色性光谱研究了随机共聚肽的二级结构特点及三种有机辅因子对随机共聚肽构象转变的影响。采用两轮组装的小盒式DNA编码文库经体外翻译生成由VNM编码的15种氨基酸组成的随机多肽，采用圆二色性光谱和bis-ANS荧光结合实验研究了随机多肽的二级结构和疏水结构域的特征，研究了五种辅因子对随机多肽构象转变和疏水结构域的影响。
研究结论：实验结果表明突变型黄素氧化还原蛋白具有与野生型相似的结构特征，半醌型和氢醌型黄素氧化还原蛋白突变体较野生型的稳定性低，双电子氧化还原电位（E_(ox/hq)）达到-360mV，表明仅由早起源氨基酸和有机辅因子构成的突变型黄素氧化还原蛋白具有氧化还原蛋白活性。（Val~x/Glu~y/Lys~z/Ser~Z）n随机共聚肽的二级结构包括无规则卷曲和α螺旋，添加ATP、NAD或NADH均未诱导产生β片层结构；低浓度的有机辅因子诱导β转角的产生，高浓度的有机辅因子倾向于使β转角转变为无规则卷曲或α螺旋。由VNM编码的15种早起源氨基酸子集组成的随机多肽不但具有较好的水溶性，而且具有典型的蛋白质二级结构特征和少量的疏水结构域。辅因子能够诱导随机多肽发生构象转变，而且各种辅因子诱导随机多肽发生构象转变的特点各不相同。ATP的诱导效应主要表现为β片层和无规则卷曲含量的减少，β转角和α螺旋含量的增加。NADP+的诱导效应表现为β片层的增加和无规则卷曲含量的减少，α螺旋和β转角的含量变化不大。NAD~+的诱导效应表现β片层的增加和α螺旋、β转角的减少，无规则卷曲含量变化不大。NADH的诱导效应表现为β片层略有增加和α螺旋略有减少，β转角和无规则卷曲含量变化不大。Mg~(2+)的诱导效应表现为β片层少量增加和β转角的略有减少，α螺旋和无规则卷曲含量变化不大。ATP、NAD~+和NADH能够诱导随机多肽产生更多的疏水结构域。
研究意义：本论文的研究结果不但证实了起源较早的氧化还原蛋白可以仅由14种早起源氨基酸组成，而且发现由简约化的氨基酸子集组成的随机多肽具有蛋白质二级结构特征且具有可折叠性，辅因子能够诱导早起源氨基酸组成的随机多肽发生构象转变并产生更多的疏水结构域。上述实验结果不但能够为辅因子诱导蛋白质起源假说提供了实验验证，而且为蛋白质工程的相关研究提供了新的思路。
“How did life begin?” is one of three central topics in the natural science field whichrequired to be answered. Since protein is not only an important biomacromolecule, but alsothe performer of vitual movement. So, origin of proteins is one of the central topics in thestudy of origin of life. Although there is no fossile of primitive protein left, we can infer thecharacteristic of ancient protein with the help of “molecular fossile” accompanied by rapiddevelopment of all kinds of “omics”. Through analyzing the distribution patterns ofsmall-molecule ligands in protein space, we proposed that the primitive protein architectureswere generated by the induction/selection of small molecules. In this thesis, this hypothesiswas preliminarily valiadated by the study of characteristic and structure of ancient proteinconstructed by primitive amino acids, and the study of cofactors induced effects on theconformation transfer of random peptides consisting of primitive amino acids set.
Objectives: To elucidate whether an ancient redox protein can be construsted by aprimitive amino acids set? Secondary structure characteristic of random polypeptidesconsisting of4kinds of primitive amino acids, secondary structure characteristic of randompolypeptides consisting of15kinds of amino acids which encode by VNM, and whethercofactors can induce transfer of the conformation of random polypeptides?
Methods: Through substituting “Late amino acids” by “Early amino acids” of aflavodoxin by rational design, mutant flavodoxin recombinant vector was constructed and itscharacteristic properties were evaluated.(Val~x/Glu~y/Lys~z/Ser~Z) random co-polypeptides wassynthesized by N-carboxyanhydride open-ring reaction, the secondary structure characteristicof random co-polypeptides and the effect of organic cofactor on the conformation transitionof random co-polypeptides were determined by Circular Dichroism spectrum analysis. ADNA library encoding random polypeptides consisting of15kinds of primitive amino acidswas constructed by strategy of library in small cassette, consequentlyly a random peptideslibrary was obtained by in vitro translation. The secondary structure characteristic andhydrophobic domain of random polypeptides were determined by Circular Dichroismspectrum analysis bis-ANS binding assay. The effects of cofactors on the conformationtransition of random co-polypeptides were invested by Circular Dichroism spectrum analysis bis-ANS binding assay also.
Results: Mutant flavodoxin has similar structural characteristics to wild-type protein,although the semiquinone and hydroquinone flavodoxin mutants possess lower stability incomparison with corresponding form of wild-type flavodoxin, the redox potential of doubleelectron reduction（E_(ox/hq)）arrived at-360mV, indicating that flavodoxin mutant consititutedsolely by early amino acids can exert effectively electron transfer activity. The secondarystructure of (Val~x/Glu~y/Lys~z/Ser~Z) random co-polypeptides include α helix and random coil,there is no β sheet was induced by ATP, NAD and NADH. The β turn were induced by lowconcentration organic cofactors, the conformation transition of β turn, α helix and randomcoil were induced by higher concentration organic cofactors. Random polypeptides consistingof15kinds of primitive amino acids which encoded by VNM is not only soluable but alsohas a secondary structure characteristic of protein. Cofactors can induce conformationtransition of random polypeptides and the effect is different between different cofactors. Theinducing effect of ATP shows as decrease of β sheet and random coil, and the increasedcontents of α helix and β turn. The inducing effect of NADP+shows as increase of β sheetand decreased content of random coil, the contents of α helix and β turn changed slightly. Theinducing effect of NAD~+shows as increase of β sheet and decreased content of α helix and βturn, the contents of random coil changed slightly. The inducing effect of NADH shows asa slightly increased β sheet and a slightly decreased α helix, the contents of β turn andrandom coil changed very slightly. The inducing effect of Mg~(2+)shows as a slightly increasedβ sheet and a slightly decreased β turn, the contents of α helix and random coil changed veryslightly. ATP, NAD~+and NADH can induced the formation of hydrophobic domain ofrandom polypeptides.
Significance: An ancient redox protein constructed by14kinds of primitive amino acidswas validated in this paper. Furthermore, it was finded that random polypeptides consisting ofreduced amino acids set has secondary structural characteristic of protein,15kinds ofprebiotic amino acids set is a foldable set, cofactors can induce the conformation transition ofrandom polypeptides, ATP, NAD~+and NADH can induce the formation of hydrophobicdomain of random polypeptides. These results not only provide an experimental verificationfor “small molecular induced the origin of protein” hypothesis, but also can provide a novel solution for protein engineering.
引文
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