Article(id=1210518238786621868, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1210518228766421884, articleNumber=null, orderNo=null, doi=10.16438/j.0513-4870.2022-0631, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1653408000000, receivedDateStr=2022-05-25, revisedDate=1654531200000, revisedDateStr=2022-06-07, acceptedDate=null, acceptedDateStr=null, onlineDate=1766539638468, onlineDateStr=2025-12-24, pubDate=1670774400000, pubDateStr=2022-12-12, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1766539638468, onlineIssueDateStr=2025-12-24, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1766539638468, creator=13701087609, updateTime=1766539638468, updator=13701087609, issue=Issue{id=1210518228766421884, tenantId=1146029695717560320, journalId=1189982191388893191, year='2022', volume='57', issue='12', pageStart='0', pageEnd='3698', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1766539636078, creator=13701087609, updateTime=1766539730802, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1210518626109624560, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1210518228766421884, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1210518626109624561, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1210518228766421884, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=3669, endPage=3674, ext={EN=ArticleExt(id=1210518239285744089, articleId=1210518238786621868, tenantId=1146029695717560320, journalId=1189982191388893191, language=EN, title=Semi-rational design improves the catalytic activity of phenylalanine ammonia lyase from Anabaena variabilis, columnId=1190335348761793317, journalTitle=Acta Pharmaceutica Sinica, columnName=Original Articles, runingTitle=null, highlight=null, articleAbstract=

Phenylalanine ammonia lyase (PAL) can catalyze L-phenylalanine to produce trans-cinnamic acid, which is widely used in the fields of pharmacy, food and agriculture. In particular, phenylalanine ammonia lyase from Anabaena variabilis (AvPAL) is the only protein drug for the treatment of phenylketonuria. However, the poor activity and low stability limit the application in industry of AvPAL. In this study, the key amino acids of substrate-binding cavity in AvPAL were identified by screening the single site saturation mutagenesis library. Subsequently, the impact of replacing M222 with the additional 19 amino acids on activity was also evaluated by site-directed mutagenesis. It was found that the kcat values of mutants M222L and M222V were 90% and 60% higher than that of AvPAL, and the kcat/Km was 1.4 and 1.5 times as that of AvPAL. Molecular docking results revealed that the higher activity of M222L and M222V may be due to the increase of hydrophobicity favorable for the substrate-binding cavity. This study is important for elucidating the structure-function relationship of AvPAL.

, correspAuthors=Zhao-yong YANG, Zhi-fei ZHANG, authorNote=null, correspAuthorsNote=null, copyrightStatement=Copyright ©2022 Acta Pharmaceutica Sinica. All rights reserved., copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, authorCompany=null, fund=null, authors=null, authorsList=Xi-yu WEI, Cui-yue FENG, Rui-jie LV, Shuai FAN, Zhao-yong YANG, Zhi-fei ZHANG), CN=ArticleExt(id=1210518243949810283, articleId=1210518238786621868, tenantId=1146029695717560320, journalId=1189982191388893191, language=CN, title=半理性设计提高Anabaena variabilis来源的苯丙氨酸解氨酶的催化活性, columnId=1190335348896011050, journalTitle=药学学报, columnName=研究论文, runingTitle=null, highlight=null, articleAbstract=

苯丙氨酸解氨酶(phenylalanine ammonia lyase, PAL) 可催化L-苯丙氨酸生成反式肉桂酸, 广泛应用在制药、食品和农业等领域中, 尤其来源于多变鱼腥藻(Anabaena variabilis) 的PAL (AvPAL) 是现有唯一治疗苯丙酮尿症的蛋白类药物。但较低的活性和较差的稳定性限制了PAL在工业中广泛的应用。本研究针对组成AvPAL底物结合腔的氨基酸, 通过点饱和突变文库筛选获得了活性提高的突变体, 并通过定点突变探讨了M222位点对活性的影响。研究发现突变体M222L和M222V的kcat值相比于AvPAL提高90%和60%, 同时kcat/Km较AvPAL提高至1.4和1.5倍。结合分子对接结果显示, 突变体M222L和M222V通过增加底物结合腔的疏水性提高AvPAL的催化活性。本研究对于阐明AvPAL关键底物结合位点结构与活性的关系具有重要的意义。

, correspAuthors=杨兆勇, 张志斐, authorNote=null, correspAuthorsNote=
*杨兆勇, E-mail: ;
张志斐, E-mail:
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A: AvPAL contains four chains in crystal asymmetric unit, and are colored in green, red, blue, and yellow for the subunits, respectively; B: Residues in substrate and its binding cavity of AvPAL are shown in sticks , figureFileSmall=jxkhERjPZkld/eQ+RXQTFw==, figureFileBig=hkB5Qtyb71Mmdm4+cZm94Q==, tableContent=null), ArticleFig(id=1210518251910599596, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518238786621868, language=EN, label=null, caption=null, figureFileSmall=QtiXbjEyC8TH5TosJGCkDw==, figureFileBig=AdHh7aB4woQln7rprHcyRQ==, tableContent=null), ArticleFig(id=1210518251998679984, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518238786621868, language=CN, label=Figure 2, caption= The recombinant AvPAL expressed in different strains of <i>E. coli.</i> Data are shown as the mean ± SD (<i>n</i> = 3). M: Marker; 1: Rosetta-gami2 (DE3); 2: ArcticExpress (DE3) pRARE2; 3: Origami2 (DE3); 4: BL21-CodonPlus (DE3)-RIPL; 5: Rosetta (DE3); 6: OverExpress C43 (DE3); 7: <i>E. coli</i> BL21 (DE3) , figureFileSmall=QtiXbjEyC8TH5TosJGCkDw==, figureFileBig=AdHh7aB4woQln7rprHcyRQ==, tableContent=null), ArticleFig(id=1210518252069983162, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518238786621868, language=EN, label=null, caption=null, figureFileSmall=GP68g1G7rFOvngxj8GjKVQ==, figureFileBig=x31DZYll9TZsLYbyRyT2NQ==, tableContent=null), ArticleFig(id=1210518252145480640, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518238786621868, language=CN, label=Figure 3, caption= The activity of mutants of M222. Data are shown as the mean ± SD (<i>n</i> = 3) , figureFileSmall=GP68g1G7rFOvngxj8GjKVQ==, figureFileBig=x31DZYll9TZsLYbyRyT2NQ==, tableContent=null), ArticleFig(id=1210518252262921160, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518238786621868, language=EN, label=null, caption=null, figureFileSmall=WDFjjUeAeSisUFR7+QgHgQ==, figureFileBig=7MRUTDI+lrVATYmmwFIiSg==, tableContent=null), ArticleFig(id=1210518252367778769, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518238786621868, language=CN, label=Figure 4, caption= Effects of pH (A) and temperature (B) on AvPAL and its mutants. 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Primer namePrimer sequence (5'-3')
AvPAL-FGAAGGAGATATACATATGAAAACCCT GAGCCAGGCGC
AvPAL-RGTGGTGGTGGTGCTCGAGATGCAGG CACGGCAGAATA
L104-FTGCAGACCAATNNKGTGTGGTTTCT
L104-RAGAAACCACACMNNATTGGTCTGCA
L108-FTGGTGTGGTTTNNKAAAACCGGCGC
L108-RGCGCCGGTTTTMNNAAACCACACCA
L219-FCGAAAGAAGGCNNKGCGATGATGAA
L219-RTTCATCATCGCMNNGCCTTCTTTCG
M222-FGCCTGGCGATGNNKAACGGCACCAG
M222-RCTGGTGCCGTTMNNCATCGCCAGGC
N223-FTGGCGATGATGNNKGGCACCAGCGT
N223-RACGCTGGTGCCMNNCATCATCGCCA
N451-FCGGAACAGTTTNNKCAGAACATTAA
N451-RTTAATGTTCTGMNNAAACTGTTCCG
F363-FATGGCGGCAACNNKCTGGGCCAGTA
F363-RTACTGGCCCAGMNNGTTGCCGCCAT
), ArticleFig(id=1210518252866900976, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518238786621868, language=CN, label=Table 1, caption=

Primers used in this study. M = A or C; N = A, C, G, or T; K = G or T

, figureFileSmall=null, figureFileBig=null, tableContent=
Primer namePrimer sequence (5'-3')
AvPAL-FGAAGGAGATATACATATGAAAACCCT GAGCCAGGCGC
AvPAL-RGTGGTGGTGGTGCTCGAGATGCAGG CACGGCAGAATA
L104-FTGCAGACCAATNNKGTGTGGTTTCT
L104-RAGAAACCACACMNNATTGGTCTGCA
L108-FTGGTGTGGTTTNNKAAAACCGGCGC
L108-RGCGCCGGTTTTMNNAAACCACACCA
L219-FCGAAAGAAGGCNNKGCGATGATGAA
L219-RTTCATCATCGCMNNGCCTTCTTTCG
M222-FGCCTGGCGATGNNKAACGGCACCAG
M222-RCTGGTGCCGTTMNNCATCGCCAGGC
N223-FTGGCGATGATGNNKGGCACCAGCGT
N223-RACGCTGGTGCCMNNCATCATCGCCA
N451-FCGGAACAGTTTNNKCAGAACATTAA
N451-RTTAATGTTCTGMNNAAACTGTTCCG
F363-FATGGCGGCAACNNKCTGGGCCAGTA
F363-RTACTGGCCCAGMNNGTTGCCGCCAT
), ArticleFig(id=1210518252988535797, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518238786621868, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
Enzymekcat/s-1Km/mmol·L-1kcat/Km/s-1·(mmol·L-1)-1
AvPAL1.390.662.1
M222L2.590.892.9
M222V2.210.683.2
M222I1.991.421.4
M222N2.691.631.7
), ArticleFig(id=1210518253265359869, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210518238786621868, language=CN, label=Table 2, caption=

Kinetic parameters of AvPAL and its mutants

, figureFileSmall=null, figureFileBig=null, tableContent=
Enzymekcat/s-1Km/mmol·L-1kcat/Km/s-1·(mmol·L-1)-1
AvPAL1.390.662.1
M222L2.590.892.9
M222V2.210.683.2
M222I1.991.421.4
M222N2.691.631.7
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半理性设计提高Anabaena variabilis来源的苯丙氨酸解氨酶的催化活性
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魏西羽 1 , 冯翠月 1 , 吕瑞杰 1 , 樊帅 2 , 杨兆勇 2, * , 张志斐 1, *
药学学报 | 研究论文 2022,57(12): 3669-3674
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药学学报 | 研究论文 2022, 57(12): 3669-3674
半理性设计提高Anabaena variabilis来源的苯丙氨酸解氨酶的催化活性
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魏西羽1, 冯翠月1, 吕瑞杰1, 樊帅2, 杨兆勇2, * , 张志斐1, *
作者信息
  • 1.华北理工大学药学院, 河北 唐山 063200
  • 2.中国医学科学院、北京协和医学院医药生物技术研究所, 北京 100050

通讯作者:

*杨兆勇, E-mail: ;
张志斐, E-mail:
Semi-rational design improves the catalytic activity of phenylalanine ammonia lyase from Anabaena variabilis
Xi-yu WEI1, Cui-yue FENG1, Rui-jie LV1, Shuai FAN2, Zhao-yong YANG2, * , Zhi-fei ZHANG1, *
Affiliations
  • 1. School of Pharmacy, North China University of Science and Technology, Tangshan 063200, China
  • 2. Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
出版时间: 2022-12-12 doi: 10.16438/j.0513-4870.2022-0631
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苯丙氨酸解氨酶(phenylalanine ammonia lyase, PAL) 可催化L-苯丙氨酸生成反式肉桂酸, 广泛应用在制药、食品和农业等领域中, 尤其来源于多变鱼腥藻(Anabaena variabilis) 的PAL (AvPAL) 是现有唯一治疗苯丙酮尿症的蛋白类药物。但较低的活性和较差的稳定性限制了PAL在工业中广泛的应用。本研究针对组成AvPAL底物结合腔的氨基酸, 通过点饱和突变文库筛选获得了活性提高的突变体, 并通过定点突变探讨了M222位点对活性的影响。研究发现突变体M222L和M222V的kcat值相比于AvPAL提高90%和60%, 同时kcat/Km较AvPAL提高至1.4和1.5倍。结合分子对接结果显示, 突变体M222L和M222V通过增加底物结合腔的疏水性提高AvPAL的催化活性。本研究对于阐明AvPAL关键底物结合位点结构与活性的关系具有重要的意义。

苯丙氨酸解氨酶  /  饱和突变  /  催化效率  /  分子对接

Phenylalanine ammonia lyase (PAL) can catalyze L-phenylalanine to produce trans-cinnamic acid, which is widely used in the fields of pharmacy, food and agriculture. In particular, phenylalanine ammonia lyase from Anabaena variabilis (AvPAL) is the only protein drug for the treatment of phenylketonuria. However, the poor activity and low stability limit the application in industry of AvPAL. In this study, the key amino acids of substrate-binding cavity in AvPAL were identified by screening the single site saturation mutagenesis library. Subsequently, the impact of replacing M222 with the additional 19 amino acids on activity was also evaluated by site-directed mutagenesis. It was found that the kcat values of mutants M222L and M222V were 90% and 60% higher than that of AvPAL, and the kcat/Km was 1.4 and 1.5 times as that of AvPAL. Molecular docking results revealed that the higher activity of M222L and M222V may be due to the increase of hydrophobicity favorable for the substrate-binding cavity. This study is important for elucidating the structure-function relationship of AvPAL.

phenylalanine ammonia lyase  /  saturation mutation  /  catalytic efficiency  /  molecular docking
魏西羽, 冯翠月, 吕瑞杰, 樊帅, 杨兆勇, 张志斐. 半理性设计提高Anabaena variabilis来源的苯丙氨酸解氨酶的催化活性. 药学学报, 2022 , 57 (12) : 3669 -3674 . DOI: 10.16438/j.0513-4870.2022-0631
Xi-yu WEI, Cui-yue FENG, Rui-jie LV, Shuai FAN, Zhao-yong YANG, Zhi-fei ZHANG. Semi-rational design improves the catalytic activity of phenylalanine ammonia lyase from Anabaena variabilis[J]. Acta Pharmaceutica Sinica, 2022 , 57 (12) : 3669 -3674 . DOI: 10.16438/j.0513-4870.2022-0631
苯丙酮尿症(phenylketonuria, PKU) 是由于苯丙氨酸羟化酶缺乏而影响苯丙氨酸代谢的一种遗传疾病[1]。高苯丙氨酸血症会出现严重的神经和认知并发症, 最终导致癫痫发作和智力低下[2, 3]。现阶段, 饮食疗法可将血液中的苯丙氨酸浓度降至非神经毒性范围内, 但是, 很多PKU患者并不能始终严格遵守这些饮食要求[4], 因此, 开发替代饮食疗法的治疗药物已成为现阶段研究的焦点。1961年, Koukol等[5]首次在植物中发现苯丙氨酸解氨酶(EC 4.3.1.5, phenylalanine ammonia-lyase, PAL) 以来, 越来越多的PAL基因已经从植物、真菌和原核生物中分离和鉴定出来, 如丹参(Salvia miltiorrhiza)[6]、粘红酵母(Rhodotorula glutinis)[7]、拟南芥(Arabidopsis thaliana)[8]、绿竹(Bambusa oldhamii)[9]、粗糙链孢霉(Neurospora crassa)[10]等, 而来源于Anabaena variabilis的PAL (AvPAL) 经定点突变和聚乙二醇修饰, 已被证明是治疗效果最好、人体内稳定性最高的PAL[11, 12], 并于2018年被美国Food and Drug Administration (FDA) 批准作为PKU的酶替代疗法[13]。同时, PAL是苯丙烷类代谢途径的关键酶, 可催化L-苯丙氨酸非氧化脱氨生成反式肉桂酸[14], 再进一步代谢转化为一系列苯丙素类化合物, 如黄酮类、木质素、香豆素、植物抗毒素等[15], 苯丙素因具有抗氧化、抗癌、抗动脉粥样硬化、抗炎和抗病毒等特性, 在医药和营养领域广泛应用而备受关注[16]。同时, AvPAL催化反应为可逆反应, 也可以催化廉价的氨水和芳基丙烯酸绿色合成高价值的非天然氨基酸[17], 从而具有在精细化工中广泛应用的潜力, 然而, AvPAL酶活显著低于真核生物来源的PAL[18], 在一定程度上限制了该酶的应用。
大部分PAL均由4个相同的亚基形成四聚体发挥生物活性, 单个亚基均有辅因子4-甲基二烯-咪唑-5酮(MIO), 其由高度保守的Ala-Ser-Gly三联体自环化脱水形成。虽然PAL的三维结构[19]、酶学性质[20-22]有了广泛的研究, 但其较低的催化效率和稳定性限制了PAL在制药和工业上的广泛应用[23]。目前通过易错PCR[24]、定点突变[25]或PEG修饰[26]提高了PAL的活性和稳定性, 但对于制药和精细化工所要求酶的性能还远远不够。因此, 对于PAL, 仍需要通过蛋白质工程手段来提高酶的性质以满足制药和精细化工工艺的要求。
本研究针对组成AvPAL底物结合腔的关键氨基酸构建点饱和突变文库, 筛选获得活性提高的突变体, 并优化了AvPAL大肠杆菌表达菌株, 再结合定点突变探讨M222位点对活性的影响, 最终获得具有更好催化性能的突变体。
菌株与试剂  菌株TOP10用于表达质粒的构建和克隆, 菌株E. coli K12、E. coli BL21 (DE3)、Rosetta-gami2 (DE3)、ArcticExpress (DE3) pRARE2、OverExpress C43 (DE3)、Rosetta (DE3)、Origami2 (DE3)、BL21-CodonPlus (DE3)-RIPL用于表达质粒的表达, 克隆和表达菌株购自美国Agilent Technologies或Novagen公司; 表达质粒pET-21a (+) 购自Novagen公司; 质粒提取试剂盒、PCR纯化试剂盒、内切酶购自康润生物公司; 氨苄青霉素、异丙基-β-D-硫代半乳糖苷(IPTG) 购自上海生物工程有限公司; Co2+-NTA填料购自日本TaKaRa公司; 30 K超滤浓缩管购自美国Millipore公司; 其余试剂均为国产分析纯。
构建点饱和突变文库和定点突变  来源于Anabaena variabilis的AvPAL (NCBI: WP_011320679.1) 经密码子优化基因全合成(华大基因), 经酶切连接得到表达质粒pET-21AvPAL, 以此为模板, 设计兼并引物, 针对不同位点, 采用ClonExpress® Ultra One Step Cloning Kit (诺唯赞) 突变试剂盒进行实验。PCR扩增反应体系为: 模板DNA 1 µL, buffer 25 µL, dNTP (2 mmol·L-1) 4 µL, ddH2O 17 µL, KOD 1 µL, 上下游引物各1 µL。PCR条件为: 94 ℃预变性2 min; 94 ℃变性15 s, 58 ℃退火15 s, 68 ℃延伸30 s, 30个循环; 最后68 ℃延伸7 min。将构建的突变体质粒转入E. coli K12, 从而得到单位点饱和突变文库。定点突变过程与上述流程一致, 点饱和突变引物和定点突变引物见表 1
突变文库筛选  利用AvPAL催化活性偶联菌体生长的高通量筛选已被报道[24], 具体过程如下: 在缺乏氮源的基础培养基上添加苯丙氨酸, E. coli K12菌株无法生长, 而AvPAL可催化苯丙氨酸生成反式肉桂酸和NH4+, E. coli K12可利用NH4+作为氮源生长, 因此AvPAL及其突变体催化活性高低可与菌株生长A600值偶联, 通过96孔板筛选可以获得活性提高的突变体。
AvPAL及其突变体的表达与纯化  经测序验证正确的质粒转化到OverExpress C43 (DE3) 中, 并于LB固体培养基上37 ℃过夜培养, 挑选菌落接种到2 mL含氨苄霉素(100 μg·mL-1) 的LB培养基中, 37 ℃下200 r·min-1过夜活化, 把活化后的菌液按照1∶100比例接种到含有氨苄霉素(100 μg·mL-1) 的LB液体培养基中, 37 ℃下培养至吸光度值为0.4~0.6时, 加入终浓度为0.2 mmol·L-1的异丙基-β-D-硫代半乳糖苷(IPTG) 诱导蛋白表达, 16 ℃下继续振荡培养16 h; 4 ℃、6 000 r·min-1离心5 min收集菌体, 并在裂解缓冲液(50 mmol·L-1 NaH2PO4, 300 mmol·L-1 NaCl, 10 mmol·L-1咪唑, pH 8.0) 中用高压均质器进行破碎, 在4 ℃、6 000 r·min-1离心30 min后将上清液通过0.45 μm的过滤膜, 装入平衡好的Co2+-NTA亲和柱中, 用冲洗缓冲液(50 mmol·L-1磷酸缓冲液, 300 mmol·L-1 NaCl, 20 mmol·L-1咪唑, pH 7.4) 冲洗, 再用洗脱液(50 mmol·L-1 NaH2PO4, 300 mmol·L-1 NaCl, 250 mmol·L-1咪唑, pH 8.0) 洗脱目的蛋白。使用超滤浓缩管将含有AvPAL的组分汇集并浓缩至1 mL。所有突变体的纯度通过12.5%的SDS-PAGE电泳分析, 并用考马斯亮蓝R250染色。以牛血清白蛋白为标准, 采用Bradford法测定蛋白质浓度。
AvPAL及其突变体酶活性测定  酶催化反应体系为450 µL, 将5 µg蛋白加入到含10 mmol·L-1苯丙氨酸的50 mmol·L-1 Tris-HCl (pH 7.5) 中, 40 ℃反应5 min, 加入50 µL TCA终止反应, 12 000 r·min-1离心5 min, 于紫外分光光度计下290 nm处测量吸光度值, 并通过标准曲线确定生成肉桂酸的量, 计算PAL酶活。每分钟催化生成1 μmol反式肉桂酸所需的PAL量定义为1 U。
AvPAL及其突变体酶动力学测定  为评估酶的动力学参数Kmkcat, 以溶于50 mmol·L-1 Tris-HCl (pH 7.5) 的10~20 000 µmol·L-1苯丙氨酸作为底物, 分别与适当稀释的酶液反应, 测定酶活性, 利用GraphPad Prism 8.0中Michaelis-Menten非线性拟合作图法计算KmVmax值, 并通过测定的蛋白浓度计算出对应的kcat
AvPAL及其突变体最适反应温度与最适pH  配制pH值分别为5.0、5.5、6.0、6.5的50 mmol·L-1醋酸钠缓冲液, 7.0、7.5、8.0、8.5的50 mmol·L-1 Tris-HCl缓冲液, 9.0、9.5、10.0和10.5的50 mmol·L-1碳酸钠缓冲液, 在40 ℃, 不同pH条件下反应5 min, 以最高活性为100%, 计算相对酶活性以确定酶的最适反应pH。将适量酶液与底物在不同温度(30、35、40、45、50、55、60、65、70、75、80、85、90、95和100 ℃) 反应5 min, 以最高活性为100%, 测定相对酶活, 以确定酶反应的最适温度。
AvPAL分子对接  分子对接由AutoDock Vina[27]完成, 以AvPAL (PDB: 2NYN) 为目标蛋白, 将小分子L-苯丙氨酸对接至底物结合腔, 选取合适构象进行分析。三维结构图片由PyMOL (www.pymol.org) 绘制。
AvPAL三维结构中不对称单位包含两个二聚体, 经两个对称操作后形成完整的四聚体结构(图 1A), 分子对接结果显示, 组成L-苯丙氨酸的底物结合腔的氨基酸有: L104、L108、L219、M222、N223、F363和N451 (图 1B), 一般认为组成底物结合腔的氨基酸会明显影响蛋白活性, 因此选择上述7个位点进行点饱和突变研究。
建立不同位点的饱和突变文库利用96孔板进行筛选, 菌体A600值越大预示突变体的酶活越高[24]。通过酶标仪测定96孔板每孔在600 nm下的吸光度值, 获得突变库中活力提高的突变体, 7个突变体库中得到的阳性突变体经华大基因有限公司测序后, 确定其具体信息如下: 突变体M222-23, 将222位M突变为N, 命名为突变体M222N; 突变体M222-67和M222-122, 将222位M突变为L, 命名为突变体M222L; 突变体N451-16, 将451位N突变为A, 命名为突变体N451A。
将上述所有测序验证的突变体, 经过重新上摇瓶发酵破碎纯化得到对应蛋白后, 经体外酶活测定, 最终确定突变体M222L和M222N的活性均分别提高了60%和23%, 而突变体N451A的活性在体外测活实验中无提高, 因此后续实验不对其进行研究, 鉴于M222位点在96孔板筛选可能会有遗漏, 针对M222位点分别做定点突变, 探究M222位点各个突变体对活性的影响。
因常规大肠杆菌表达菌株BL21 (DE3) 表达AvPAL大部分为包涵体(数据未显示), 不利于后续实验, 因此考察了E. coli BL21 (DE3)、Rosetta-gami2 (DE3)、ArcticExpress (DE3) pRARE2、OverExpress C43 (DE3)、Rosetta (DE3)、Origami2 (DE3)、BL21-CodonPlus (DE3)-RIPL不同菌株表达AvPAL的情况, 在20 ℃和0.2 mmol·L-1 IPTG浓度的条件下, 低温诱导12 h, 离心收集菌体, 破碎纯化后, 同体积取样进行SDS-PAGE电泳, 结果显示(图 2), OverExpress C43 (DE3) 的可溶性表达量最高, 达2 mg·L-1, 因此, 本实验后续选择OverExpress C43 (DE3) 作为表达菌株。
针对M222位点对活性的影响, 通过定点突变探究M222位点对活性的影响, 初步获得此位点突变为其余19种氨基酸的活性数据, 如图 3所示, M222位点突变为任意氨基酸的活性均能保持在65%以上, 其中突变体M222L、M222I、M222N和M222V的活性相较于AvPAL分别提高了60%、4%、23%、16%。
突变体M222L、M222V、M222I和M222N的酶动力学实验结果(表 2) 显示, 突变体M222L、M222V、M222I和M222N的kcat值相比于AvPAL提高90%、60%、40%和90%, 但突变体的Km值均不同程度的提高, 表示突变体对底物的亲和力有所下降, 最终突变体M222L和M222V的kcat/Km是AvPAL的1.4、1.5倍。
对突变体M222L和M222V的酶学性质进行了研究, 如图 4A所示, AvPAL和突变体M222L的最适pH值为7.5, 而突变体M222V的最适pH值为8.5; AvPAL和突变体M222L的最适反应温度为55 ℃ (图 4B), 突变体M222V的最适反应温度提高5 ℃, 达到60 ℃, 并且在50~75 ℃内维持较高的活性, 在75 ℃时, 突变体M222V能维持89%的残余活性, 而AvPAL为71%。
AvPAL的晶体结构已被解析[18], 晶体结构显示, AvPAL有4个亚基(亚基A~D), 4个亚基结合稳定组成一个寡聚体(图 1A), 活性中心由辅因子MIO和Y314组成, 其中MIO来自亚基A, 而Y314来自亚基D (图 5), 由此, 四聚体AvPAL具有4个活性中心。尽管AvPAL的晶体已被报道多年, 但AvPAL与底物L-苯丙氨酸的复合结构未见报道, 因此采用分子对接的方式将底物L-苯丙氨酸对接到AvPAL活性腔。分子对接结果显示, L-苯丙氨酸苯基在由T102、L108、G218和M222组成的结合腔内, 并且第102位的苏氨酸突变为疏水性的脯氨酸, 提高了AvPAL的活性[28], 而本研究中, 将第222位的蛋氨酸突变为疏水性氨基酸(缬氨酸和亮氨酸), 增加了与苯丙氨酸苯基的疏水相互作用, 从而提高了突变体的活性。
来源于Anabaena variabilis的AvPAL是2018年被美国FDA批准的唯一用于治疗PKU的酶类药物, AvPAL和目前已大量报道的植物[29]及酵母[30]等真核生物来源的苯丙氨酸脱氨酶在活性中心的结构上高度保守, 催化部位都是由Ala-Ser-Gly经环化脱水形成的MIO基团和一个含有Tyr的高度柔性的loop区组成。在三维结构上, 真核生物来源的PAL与AvPAL的C端多一段多螺旋区域, 此区域不稳定且对蛋白酶敏感[31], 因此AvPAL的稳定性和抗降解能力要比真核生物来源的PAL更好, 但AvPAL的催化速度要比真核来源的PAL低。
本研究利用PAL分解苯丙氨酸生成NH4+, 可作为大肠杆菌生长氮源的筛选方法, 偶联点饱和突变文库, 筛选获得了可提高AvPAL活性的位点, 并结合定点突变探究了AvPAL结合底物苯丙氨酸的关键位点M222对反应活性的影响, 结果显示, 突变体M222L和M222V的kcat值分别为AvPAL的1.9和1.6倍, 通过分子对接分析, M222处于底物L-Phe的苯基结合部位, 由极性氨基酸突变为疏水氨基酸, 有利于苯丙氨酸锚定于结合腔, 从而提高了催化效率。
作者贡献: 魏西羽撰写了论文; 魏西羽、冯翠月、吕瑞杰完成了实验; 魏西羽、樊帅分析了实验数据; 杨兆勇、张志斐负责设计本项实验; 全部作者均阅读并参与修改了本文。
利益冲突: 本文的作者声明无任何利益冲突。
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2022年第57卷第12期
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doi: 10.16438/j.0513-4870.2022-0631
  • 接收时间:2022-05-25
  • 首发时间:2025-12-24
  • 出版时间:2022-12-12
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  • 收稿日期:2022-05-25
  • 修回日期:2022-06-07
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国家自然科学基金面上项目(81872782)
中国医学科学院医学与健康科技创新工程(2021-I2M-1-055)
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    1.华北理工大学药学院, 河北 唐山 063200
    2.中国医学科学院、北京协和医学院医药生物技术研究所, 北京 100050

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*杨兆勇, E-mail: ;
张志斐, E-mail:
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2种不同金属材料的力学参数

Family
属数
Number of
genus
种数
Number of
species
占总种数比例
Percentage of
total species (%)

Genus
种数
Number of
species
占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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