目的分析1个遗传性蛋白C(protein C,PC)缺陷症家系的表型和基因变异。方法检测先证者及其家系成员(共3代7人)的血浆蛋白C活性(protein C activity,PC:A)、蛋白C抗原(protein C antigen,PC:Ag)含量及其他凝血指标。用PCR对先证者PROC基因...目的分析1个遗传性蛋白C(protein C,PC)缺陷症家系的表型和基因变异。方法检测先证者及其家系成员(共3代7人)的血浆蛋白C活性(protein C activity,PC:A)、蛋白C抗原(protein C antigen,PC:Ag)含量及其他凝血指标。用PCR对先证者PROC基因的9个外显子及其侧翼序列进行扩增,将产物纯化后进行直接测序。对候选变异通过反向测序进行验证,并对家系其他成员的相同位点进行检测。用生物信息学软件分析变异的致病性和保守性。用Swiss-PdbViewer软件分析蛋白质三维模型以及变异氨基酸之间的相互作用。结果先证者及其祖母、父亲和哥哥的PC:A和PC:Ag分别降至55%、52%、48%、51%和53%、55%、50%、56%。测序分析显示,上述成员PROC基因的第9外显子均存在c.1318C>T(p.Arg398Cys)杂合错义变异。MutationTaster评分为0.991、PROVEAN为评分-3.72、FATHMM为评分-2.49,均提示为有害变异;保守性分析显示Arg398在同源物种间呈弱保守性;蛋白质模型分析显示变异前Arg398与Glu341和Lys395各形成1个氢键,变异为Cys398后与Glu341之间的氢键消失,与Lys395之间则增加了1个氢键,使蛋白质的结构发生了改变。结论先证者PROC第9外显子c.1318C>T(p.Arg398Cys)杂合错义变异可能是导致该家系PC:A和PC:Ag减少的原因。展开更多
Metalloproteins have inspired chemists for many years to synthesize artificial catalysts that mimic native enzymes.As a complementary approach to studying native enzymes or making synthetic models,biosynthetic approac...Metalloproteins have inspired chemists for many years to synthesize artificial catalysts that mimic native enzymes.As a complementary approach to studying native enzymes or making synthetic models,biosynthetic approach using small and stable proteins to model native enzymes has offered advantages of incorporating non-covalent secondary sphere interactions under physiological conditions.However,most biosynthetic models are restricted to natural amino acids.To overcome this limitation,incorporating unnatural amino acids into the biosynthetic models has shown promises.In this review,we summarize first synthetic,semisynthetic and biological methods of incorporates unnatural amino acids(UAAs)into proteins,followed by progress made in incorporating UAAs into both native metalloproteins and their biosynthetic models to fine-tune functional properties beyond native enzymes or their variants containing natural amino acids,such as reduction potentials of azurin,O_2 reduction rates and percentages of product formation of HCO models in Mb,the rate of radical transport in ribonucleotide reductase(RNR)and the proton and electron transfer pathways in photosystemⅡ(PSⅡ).We also discuss how this endeavour has allowed systematic investigations of precise roles of conserved residues in metalloproteins,such as Metl21 in azurin,Tyr244 that is cross-linked to one of the three His ligands to CuB in HCO,Tyr122,356,730 and 731 in RNR and TyrZ in PSⅡ.These examples have demonstrated that incorporating UAAs has provided a new dimension in our efforts to mimic native enzymes and in providing deeper insights into structural features responsible high enzymatic activity and reaction mechanisms,making it possible to design highly efficient artificial catalysts with similar or even higher activity than native enzymes.展开更多
目的:通过检测复合杂合突变导致遗传性凝血因子Ⅴ(FⅤ)缺陷家系的表型和基因突变分析,探讨其分子发病机制。方法:检测先证者及其家系成员(共3代10人)血浆凝血酶原时间(PT)、活化部分凝血活酶时间(APTT)、纤维蛋白原(FIB)、FⅤ促凝活性(...目的:通过检测复合杂合突变导致遗传性凝血因子Ⅴ(FⅤ)缺陷家系的表型和基因突变分析,探讨其分子发病机制。方法:检测先证者及其家系成员(共3代10人)血浆凝血酶原时间(PT)、活化部分凝血活酶时间(APTT)、纤维蛋白原(FIB)、FⅤ促凝活性(FⅤ∶C)、FⅤ抗原(FⅤ∶Ag)及其他相关凝血指标以明确诊断。采用DNA直接测序分析F5基因的所有外显子、侧翼、5'和3'非翻译区及家系成员相应的突变位点区域,发现突变位点用反向测序证实。使用ClustalX-2.1-win软件分析突变氨基酸的保守性,PROVEAN和MutationTaster在线生物信息学软件预测突变对蛋白质功能的影响,Swiss-PdbViewer软件在突变位点上进行蛋白质模型和氨基酸相互作用分析。结果:先证者PT和APTT较正常对照健康体检者显著延长,分别为34.2 vs 13.2 s和119.3 vs 36.0 s;FⅤ∶C和FⅤ∶Ag极度降低,分别为3%和6%。先证者的第二子、第三子、女儿和孙子的PT和APTT略有延长,FⅤ∶C和FⅤ∶Ag均有不同程度的降低,其他家庭成员的相关凝血参数均在正常范围内。先证者6号外显子上存在c.911G>A杂合错义突变,导致p.Gly276Glu;16号外显子上存在c.5343C>G杂合错义突变,导致p.Ser1781Arg。其第二子、第三子和孙子均携带p.Gly276Glu的杂合子,其女儿携带p.Ser1781Arg的杂合子,其他家庭成员均为野生型。保守分析结果表明,Gly276和Ser1781在同源物种中高度保守。2种生物信息学软件的预测结果相同,PROVEAN(得分-6.214和-12.79)表明,该复合杂合突变是一种有害突变;MutationTaster(得分0.976和0.999)提示,这些突变可能引起相应疾病。p.Gly276Glu蛋白质模型分析显示,Glu侧链延长,分子量变大,这将增加它与周围氨基酸之间的空间位阻,影响FⅤ蛋白的正常局部折叠,最终导致蛋白质活性和含量降低。由于尚无16号外显子FⅤ的X射线3D结构文件,本研究无法对p.Ser1781Arg突变蛋白进行空间结构展开更多
Lysozyme, myoglobin and BSA were used as models of globular proteins covering a wide range of pl. The purpose is to extend the studies to anionic lipid bilayers. Electrostatics is studied in cationic protein adsorptio...Lysozyme, myoglobin and BSA were used as models of globular proteins covering a wide range of pl. The purpose is to extend the studies to anionic lipid bilayers. Electrostatics is studied in cationic protein adsorption to zwitterionic PC and anionic mixed PC/PG SUVs. Protein adsorption is investigated in SUVs along with changes of fluorescence emission spectra. Partition coefficients and cooperativity parameters are calculated. At pl binding obtains maximum while at lower or higher pHs binding decreases. In Gouy-Chapman formalism activity coefficient goes with square charge, which deviations indicate asymmetric location of anionic phospholipid in the inner leaflet, in mixed SUVs for lysozyme- and myoglobin-PC/PG systems, in agreement with experiments and molecular dynamics simulations. Vesicles bind myoglobin anti-cooperatively while lysozyme-BSA cooperativitivey. A model is proposed for both, which composes two protein sub-layers with different structures and properties. Hill coefficient reflects subunit cooperativity of bi and tridomain proteins.展开更多
蛋白质模型质量评估是指对计算手段预测出的蛋白质结构进行评分,以选择尽可能接近天然结构的蛋白质模型,这对在蛋白质结构预测中挑选最优的蛋白质模型和在生物医学研究中恰当使用它们起到至关重要的作用.随着3D蛋白质数据的不断增长,基...蛋白质模型质量评估是指对计算手段预测出的蛋白质结构进行评分,以选择尽可能接近天然结构的蛋白质模型,这对在蛋白质结构预测中挑选最优的蛋白质模型和在生物医学研究中恰当使用它们起到至关重要的作用.随着3D蛋白质数据的不断增长,基于深度学习的蛋白质模型质量评估方法得到了快速发展,但该领域只探索了深度学习方向较浅层的应用.本文为了探索更精确的质量评估方法,提出了一个基于多尺度卷积(MCNN)和双向门控循环神经网络(BiGRU)的深度模型,预测蛋白质模型的GDT_TS(Global Distance Test_Total Score)分数,并将这一方法命名为BMBQA(Quality Assessment Base on MCNN-BiGRU).其中,多尺度卷积神经网络用来提取蛋白质模型中浅层的细节信息以及深层的抽象信息,双向门控循环神经网络用来提取每个残基的长程相互作用信息,通过数据增强来提高深度模型在目标蛋白质中挑选最优蛋白质模型的性能.本文利用CASP13中的数据集与现有的先进方法进行比较,实验结果表明本文方法在4个经典的评价指标中均具有很强的竞争力.展开更多
文摘目的分析1个遗传性蛋白C(protein C,PC)缺陷症家系的表型和基因变异。方法检测先证者及其家系成员(共3代7人)的血浆蛋白C活性(protein C activity,PC:A)、蛋白C抗原(protein C antigen,PC:Ag)含量及其他凝血指标。用PCR对先证者PROC基因的9个外显子及其侧翼序列进行扩增,将产物纯化后进行直接测序。对候选变异通过反向测序进行验证,并对家系其他成员的相同位点进行检测。用生物信息学软件分析变异的致病性和保守性。用Swiss-PdbViewer软件分析蛋白质三维模型以及变异氨基酸之间的相互作用。结果先证者及其祖母、父亲和哥哥的PC:A和PC:Ag分别降至55%、52%、48%、51%和53%、55%、50%、56%。测序分析显示,上述成员PROC基因的第9外显子均存在c.1318C>T(p.Arg398Cys)杂合错义变异。MutationTaster评分为0.991、PROVEAN为评分-3.72、FATHMM为评分-2.49,均提示为有害变异;保守性分析显示Arg398在同源物种间呈弱保守性;蛋白质模型分析显示变异前Arg398与Glu341和Lys395各形成1个氢键,变异为Cys398后与Glu341之间的氢键消失,与Lys395之间则增加了1个氢键,使蛋白质的结构发生了改变。结论先证者PROC第9外显子c.1318C>T(p.Arg398Cys)杂合错义变异可能是导致该家系PC:A和PC:Ag减少的原因。
基金supported by the US National Science Foundation(CHE-1413328)the Major State Basic Research Program of China(2015CB856203)+1 种基金the National Natural Science Foundation of China (21325211,31500641)theTianjinMunicipalGrant(13ZCZDSY04800, 14ZCZDSY00059,14JCYBJC43400)
文摘Metalloproteins have inspired chemists for many years to synthesize artificial catalysts that mimic native enzymes.As a complementary approach to studying native enzymes or making synthetic models,biosynthetic approach using small and stable proteins to model native enzymes has offered advantages of incorporating non-covalent secondary sphere interactions under physiological conditions.However,most biosynthetic models are restricted to natural amino acids.To overcome this limitation,incorporating unnatural amino acids into the biosynthetic models has shown promises.In this review,we summarize first synthetic,semisynthetic and biological methods of incorporates unnatural amino acids(UAAs)into proteins,followed by progress made in incorporating UAAs into both native metalloproteins and their biosynthetic models to fine-tune functional properties beyond native enzymes or their variants containing natural amino acids,such as reduction potentials of azurin,O_2 reduction rates and percentages of product formation of HCO models in Mb,the rate of radical transport in ribonucleotide reductase(RNR)and the proton and electron transfer pathways in photosystemⅡ(PSⅡ).We also discuss how this endeavour has allowed systematic investigations of precise roles of conserved residues in metalloproteins,such as Metl21 in azurin,Tyr244 that is cross-linked to one of the three His ligands to CuB in HCO,Tyr122,356,730 and 731 in RNR and TyrZ in PSⅡ.These examples have demonstrated that incorporating UAAs has provided a new dimension in our efforts to mimic native enzymes and in providing deeper insights into structural features responsible high enzymatic activity and reaction mechanisms,making it possible to design highly efficient artificial catalysts with similar or even higher activity than native enzymes.
文摘目的:通过检测复合杂合突变导致遗传性凝血因子Ⅴ(FⅤ)缺陷家系的表型和基因突变分析,探讨其分子发病机制。方法:检测先证者及其家系成员(共3代10人)血浆凝血酶原时间(PT)、活化部分凝血活酶时间(APTT)、纤维蛋白原(FIB)、FⅤ促凝活性(FⅤ∶C)、FⅤ抗原(FⅤ∶Ag)及其他相关凝血指标以明确诊断。采用DNA直接测序分析F5基因的所有外显子、侧翼、5'和3'非翻译区及家系成员相应的突变位点区域,发现突变位点用反向测序证实。使用ClustalX-2.1-win软件分析突变氨基酸的保守性,PROVEAN和MutationTaster在线生物信息学软件预测突变对蛋白质功能的影响,Swiss-PdbViewer软件在突变位点上进行蛋白质模型和氨基酸相互作用分析。结果:先证者PT和APTT较正常对照健康体检者显著延长,分别为34.2 vs 13.2 s和119.3 vs 36.0 s;FⅤ∶C和FⅤ∶Ag极度降低,分别为3%和6%。先证者的第二子、第三子、女儿和孙子的PT和APTT略有延长,FⅤ∶C和FⅤ∶Ag均有不同程度的降低,其他家庭成员的相关凝血参数均在正常范围内。先证者6号外显子上存在c.911G>A杂合错义突变,导致p.Gly276Glu;16号外显子上存在c.5343C>G杂合错义突变,导致p.Ser1781Arg。其第二子、第三子和孙子均携带p.Gly276Glu的杂合子,其女儿携带p.Ser1781Arg的杂合子,其他家庭成员均为野生型。保守分析结果表明,Gly276和Ser1781在同源物种中高度保守。2种生物信息学软件的预测结果相同,PROVEAN(得分-6.214和-12.79)表明,该复合杂合突变是一种有害突变;MutationTaster(得分0.976和0.999)提示,这些突变可能引起相应疾病。p.Gly276Glu蛋白质模型分析显示,Glu侧链延长,分子量变大,这将增加它与周围氨基酸之间的空间位阻,影响FⅤ蛋白的正常局部折叠,最终导致蛋白质活性和含量降低。由于尚无16号外显子FⅤ的X射线3D结构文件,本研究无法对p.Ser1781Arg突变蛋白进行空间结构
文摘Lysozyme, myoglobin and BSA were used as models of globular proteins covering a wide range of pl. The purpose is to extend the studies to anionic lipid bilayers. Electrostatics is studied in cationic protein adsorption to zwitterionic PC and anionic mixed PC/PG SUVs. Protein adsorption is investigated in SUVs along with changes of fluorescence emission spectra. Partition coefficients and cooperativity parameters are calculated. At pl binding obtains maximum while at lower or higher pHs binding decreases. In Gouy-Chapman formalism activity coefficient goes with square charge, which deviations indicate asymmetric location of anionic phospholipid in the inner leaflet, in mixed SUVs for lysozyme- and myoglobin-PC/PG systems, in agreement with experiments and molecular dynamics simulations. Vesicles bind myoglobin anti-cooperatively while lysozyme-BSA cooperativitivey. A model is proposed for both, which composes two protein sub-layers with different structures and properties. Hill coefficient reflects subunit cooperativity of bi and tridomain proteins.
文摘蛋白质模型质量评估是指对计算手段预测出的蛋白质结构进行评分,以选择尽可能接近天然结构的蛋白质模型,这对在蛋白质结构预测中挑选最优的蛋白质模型和在生物医学研究中恰当使用它们起到至关重要的作用.随着3D蛋白质数据的不断增长,基于深度学习的蛋白质模型质量评估方法得到了快速发展,但该领域只探索了深度学习方向较浅层的应用.本文为了探索更精确的质量评估方法,提出了一个基于多尺度卷积(MCNN)和双向门控循环神经网络(BiGRU)的深度模型,预测蛋白质模型的GDT_TS(Global Distance Test_Total Score)分数,并将这一方法命名为BMBQA(Quality Assessment Base on MCNN-BiGRU).其中,多尺度卷积神经网络用来提取蛋白质模型中浅层的细节信息以及深层的抽象信息,双向门控循环神经网络用来提取每个残基的长程相互作用信息,通过数据增强来提高深度模型在目标蛋白质中挑选最优蛋白质模型的性能.本文利用CASP13中的数据集与现有的先进方法进行比较,实验结果表明本文方法在4个经典的评价指标中均具有很强的竞争力.
