Article(id=1194684383262122405, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1194684377813717012, articleNumber=null, orderNo=null, doi=10.13343/j.cnki.wsxb.20250288, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1743955200000, receivedDateStr=2025-04-07, revisedDate=null, revisedDateStr=null, acceptedDate=1750176000000, acceptedDateStr=2025-06-18, onlineDate=1762764553132, onlineDateStr=2025-11-10, pubDate=1762185600000, pubDateStr=2025-11-04, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1762764553132, onlineIssueDateStr=2025-11-10, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1762764553132, creator=13701087609, updateTime=1762764553132, updator=13701087609, issue=Issue{id=1194684377813717012, tenantId=1146029695717560320, journalId=1192105938417971205, year='2025', volume='65', issue='11', pageStart='4721', pageEnd='5182', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1762764551833, creator=13701087609, updateTime=1762764551833, updator=13701087609, preIssue=null, nextIssue=null, ext=null, issueFiles=null}, startPage=4994, endPage=5007, ext={EN=ArticleExt(id=1194684383442477481, articleId=1194684383262122405, tenantId=1146029695717560320, journalId=1192105938417971205, language=EN, title=Improvement of the thermostability of the salt-tolerant xylanase XynRBM26 from GH10 family based on Pro effect, columnId=1192149543992045670, journalTitle=Acta Microbiologica Sinica, columnName=Research Article, runingTitle=null, highlight=null, articleAbstract=

Objective The mesophilic salt-tolerant xylanase XynRBM26, a member of the GH10 family, holds significant application value in industrial fields such as animal feed. This study improved the thermostability of this enzyme by protein modification via rational design, aiming to lay a foundation for the industrial application of XynRBM26 preparations. Methods The bioinformatics software FoldX was used to conduct positionscan of the 3D structure predicted by AlphaFold 2.0 for XynRBM26. The mutants with free energy changes less than -0.5 kcal/mol were selected to construct an initial electronic library. According to the Pro effect and screening principles for potential mutants, an electronic library composed of Pro mutations was subsequently established. Finally, site-directed mutagenesis was employed to construct mutant genes, and positive mutants were screened after heterologous expression, purification, and experimental verification. Results After screening of the initial potential mutants, a small and precise mutant library consisting of 21 Pro effect mutants was constructed. All the mutants were experimentally validated, and positive single-point mutants D222P, V182P, D344P, and A352P with significantly increased Tm values were screened out. Through subsequent stacking screening, a three-point stacked Pro effect mutant with superior properties was obtained. The combination of this mutant with the experimentally screened positive mutant G115D produced the most stable mutant M4 (G115D-D222P-D344P-A352P). Compared with wild-type XynRBM26, M4 showed increases of 6.5 °C and 5 °C in Tm and optimal temperature, respectively. Moreover, M4 presented the half-life (t1/2) at 55 °C 7.5-fold longer than the wild type, and its relative activity at the optimal temperature was 3.44 folds that of the wild type. Conclusion Screening thermostable mutants of the salt-tolerant xylanase XynRBM26 of the GH10 family based on the Pro effect and two different effect superimposing strategies is an effective approach.

, correspAuthors=Jinping WANG, authorNote=null, correspAuthorsNote=
*E-mail:
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目的 嗜中温GH10家族耐盐木聚糖酶XynRBM26在动物饲料等工业领域具有重要的应用价值。本研究基于理性设计方法对其进行蛋白质工程改造以提升其热稳定性,为后续XynRBM26酶制剂的工业化应用奠定基础。 方法 利用生物信息学软件FoldX对AlphaFold 2.0预测的XynRBM26的3D结构进行全序列扫描,将自由能变化小于-0.5 kcal/mol的突变体构建成一个初始电子文库;基于Pro效应及潜在突变体的筛选原则构建一个由Pro突变组成的电子文库;利用定点突变技术构建突变体基因,进一步对突变体进行异源表达和纯化,通过实验验证筛选出阳性突变体。 结果 初始潜在突变体经筛选后,构建了一个由21个Pro效应突变体组成的小而精的突变文库。对所有突变体进行实验验证,筛选出Tm值显著提高的阳性单点突变体D222P、V182P、D344P和A352P。后续通过叠加筛选获得了性质较优的3点叠加Pro突变体,并将其与实验筛选的阳性突变体G115D叠加,筛选出稳定性最优的叠加突变体M4 (G115D-D222P-D344P-A352P)。与XynRBM26野生型相比,其Tm值及最适温度分别提高了6.5 ℃和5 ℃,在55 ℃下的半衰期t1/2提高了7.5倍,最适温度下的相对活性是野生型的3.44倍。 结论 基于Pro效应及2种不同效应叠加方法筛选热稳定性GH10家族耐盐木聚糖酶XynRBM26突变体,是一种有效的策略。

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Food Chemistry, 2021, 342: 128270., articleTitle=Exploiting the activity-stability trade-off of glucose oxidase from Aspergillus niger using a simple approach to calculate thermostability of mutants, refAbstract=null), Reference(id=1194980454039270353, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, doi=null, pmid=null, pmcid=null, year=2024, volume=63, issue=29, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=[26], rfOrder=25, authorNames=ZHENG GS, YANG JX, ZHOU L, SINELSHCHIKOVA A, LEI Q, LIN JG, WUTTKE S, JEFFREY BRINKER C, ZHU W, journalName=Angewandte Chemie International Edition, refType=null, unstructuredReference=ZHENG GS, YANG JX, ZHOU L, SINELSHCHIKOVA A, LEI Q, LIN JG, WUTTKE S, JEFFREY BRINKER C, ZHU W. Multivariate silicification-assisted single enzyme structure augmentation for improved enzymatic activity-stability trade-off[J]. Angewandte Chemie International Edition, 2024, 63(29): e202406110., articleTitle=Multivariate silicification-assisted single enzyme structure augmentation for improved enzymatic activity-stability trade-off, refAbstract=null), Reference(id=1194980454102184915, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, doi=null, pmid=null, pmcid=null, year=2024, volume=283, issue=null, pageStart=137779, pageEnd=null, url=null, language=null, rfNumber=[27], rfOrder=26, authorNames=ZHANG YL, ZHANG T, MIAO M, journalName=International Journal of Biological Macromolecules, refType=null, unstructuredReference=ZHANG YL, ZHANG T, MIAO M. Semi-rational design in simultaneous improvement of thermostability and activity of β-1,3-glucanase from Alkalihalobacillus clausii KSMK16[J]. International Journal of Biological Macromolecules, 2024, 283: 137779., articleTitle=Semi-rational design in simultaneous improvement of thermostability and activity of β-1,3-glucanase from Alkalihalobacillus clausii KSMK16, refAbstract=null)], funds=[Fund(id=1194980452046975909, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, awardId=24B180015, language=EN, fundingSource=Key Scientific Research Project of Universities in Henan Province(24B180015), fundOrder=null, country=null), Fund(id=1194980452126667686, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, awardId=24B180015, language=CN, fundingSource=河南省高等学校重点科研项目(24B180015), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1194980443784196904, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, xref=null, ext=[AuthorCompanyExt(id=1194980443805168425, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, companyId=1194980443784196904, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1 School of Pharmacy, Xinyang Agriculture and Forestry University, Xinyang, Henan, China), AuthorCompanyExt(id=1194980443834528554, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, companyId=1194980443784196904, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1 信阳农林学院 药学院,河南 信阳)]), AuthorCompany(id=1194980444010689325, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, xref=null, ext=[AuthorCompanyExt(id=1194980444023272237, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, companyId=1194980444010689325, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2 Jiaozuo Technician College, Jiaozuo, Henan, China), AuthorCompanyExt(id=1194980444035855150, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, companyId=1194980444010689325, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2 焦作技师学院,河南 焦作)])], figs=[ArticleFig(id=1194980449144517506, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=EN, label=Figure 1, caption=3D structure of XynRBM26. A: Present the salad bowl-shaped structure of XynRBM26 in a cartoon form; B: Present the eight parallel β-sheets inside and the eight α-helices outside of XynRBM26 in a cartoon form., figureFileSmall=Fgu9yshWMF1Ro5e58T2LTw==, figureFileBig=Xme3ri0hd0ckIzRq3gSJQg==, tableContent=null), ArticleFig(id=1194980449236792196, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=CN, label=图1, caption=XynRBM26蛋白三维结构。A:以卡通形式展现XynRBM26的沙拉碗状结构;B:以卡通形式展现XynRBM26内部8个正向平行的β折叠和外部的8个α螺旋。, figureFileSmall=Fgu9yshWMF1Ro5e58T2LTw==, figureFileBig=Xme3ri0hd0ckIzRq3gSJQg==, tableContent=null), ArticleFig(id=1194980449312289671, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=EN, label=Figure 2, caption=SDS-PAGE diagram of a single point mutant. M: Protein marker; 1-21 are respectively the wild type of XynRBM26, mutant A32P, A117P, A99P, A128P, V140P, D222P, D221P, V190P, A189P, V182P, T323P, A141P, A254P, A295P, A298P, F300P, S360P, D344P, A352P, H335P, respectively., figureFileSmall=FJDa/HrokZ/dIb3FoJ9tvA==, figureFileBig=433nEFMloke1piKZgprJrQ==, tableContent=null), ArticleFig(id=1194980449362621320, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=CN, label=图2, caption=单点突变体的SDS-PAGE, figureFileSmall=FJDa/HrokZ/dIb3FoJ9tvA==, figureFileBig=433nEFMloke1piKZgprJrQ==, tableContent=null), ArticleFig(id=1194980449446507402, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=EN, label=Figure 3, caption=Tm values and optimal temperature of XynRBM26 wild type and combined mutant M4. A: The Tm values of XynRBM26 wild type and combined mutant M4; B: The optimal temperature of XynRBM26 wild type and combined mutant M4., figureFileSmall=R57bl+EGVEQGX0HBwJmd/w==, figureFileBig=meZj5dJDiCONX8JVEwveeg==, tableContent=null), ArticleFig(id=1194980449505227659, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=CN, label=图3, caption=XynRBM26野生型与叠加突变体M4Tm 值和最适温度。A:XynRBM26野生型与叠加突变体M4的Tm值;B:XynRBM26野生型与叠加突变体M4的最适温度。, figureFileSmall=R57bl+EGVEQGX0HBwJmd/w==, figureFileBig=meZj5dJDiCONX8JVEwveeg==, tableContent=null), ArticleFig(id=1194980449568142221, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=EN, label=Figure 4, caption=Half-life (t1/2)and activity of XynRBM26 wild type and superimposed mutant M4. A: The half-life (t1/2) of XynRBM26 wild type and superimposed mutant M4; B: The relative activity of XynRBM26 wild type and superimposed mutant M4., figureFileSmall=kaDJOwIc5ATQLuHsSr047A==, figureFileBig=OJNYKDqsh66OVwNpaanWQQ==, tableContent=null), ArticleFig(id=1194980449635251087, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=CN, label=图4, caption=XynRBM26野生型与叠加突变体M4的半衰期(t1/2)及活性。A:XynRBM26野生型与叠加突变体M4的半衰期(t1/2);B:XynRBM26野生型与叠加突变体M4的相对酶活。, figureFileSmall=kaDJOwIc5ATQLuHsSr047A==, figureFileBig=OJNYKDqsh66OVwNpaanWQQ==, tableContent=null), ArticleFig(id=1194980449710748561, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=EN, label=Figure 5, caption=Local structural characteristics of XynRBM26 wild type and superimposed mutant M4 mutation sites. A: The hydrogen bond formed by the G115 residue of the XynRBM26 wild type; B: The hydrogen bonds and salt bridges generated by superimposed mutant M4 D115 residue; C: The secondary structure position of the D222 residue in the XynRBM26 wild type; D: The secondary structure position of the P222 residue in the superimposed mutant M4; E: The secondary structure position of the D344 residue in the XynRBM26 wild type; F: The secondary structure position of the P344 residue in the superimposed mutant M4; G: The secondary structure position of the A352 residue in the XynRBM26 wild type; H: The secondary structure position of the P352 residue in the superimposed mutant M4., figureFileSmall=gnorTHzk8jOSpsYfRckidQ==, figureFileBig=9rFfA2lNVScaemtAG92low==, tableContent=null), ArticleFig(id=1194980449761080210, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=CN, label=图5, caption=XynRBM26野生型与叠加突变体M4各突变位点局部结构特征。A:XynRBM26野生型G115残基形成的氢键;B:叠加突变体M4 D115残基形成的氢键及盐桥;C:XynRBM26野生型D222残基所处的二级结构位置;D:叠加突变体M4 P222残基所处的二级结构位置;E:XynRBM26野生型D344残基所处的二级结构位置;F:叠加突变体M4 P344残基所处的二级结构位置;G:XynRBM26野生型A352残基所处的二级结构位置;H:叠加突变体M4 P352残基所处的二级结构位置。, figureFileSmall=gnorTHzk8jOSpsYfRckidQ==, figureFileBig=9rFfA2lNVScaemtAG92low==, tableContent=null), ArticleFig(id=1194980449823994772, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=EN, label=Figure 6, caption=Molecular dynamics simulation of XynRBM26 wild type and its superimposed mutant M4. A: The RMSD values of XynRBM26 wild type and superimposed mutant M4; B: The Rg values of XynRBM26 wild type and superimposed mutant M4; C: The RMSF values of XynRBM26 wild type and superimposed mutant M4., figureFileSmall=fDORn5XRBULawZgKp+5JPA==, figureFileBig=RliAmmy7ObQDIotMKQ2nYg==, tableContent=null), ArticleFig(id=1194980449941435286, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=CN, label=图6, caption=XynRBM26野生型及叠加突变体M4的分子动力学模拟。A:XynRBM26野生型及叠加突变体M4的RMSD值;B:XynRBM26野生型及叠加突变体M4的Rg值;C:XynRBM26野生型及叠加突变体M4的RMSF值。, figureFileSmall=fDORn5XRBULawZgKp+5JPA==, figureFileBig=RliAmmy7ObQDIotMKQ2nYg==, tableContent=null), ArticleFig(id=1194980450000155544, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=EN, label=Table 1, caption=

Pairs of the primers used in this study

, figureFileSmall=null, figureFileBig=null, tableContent=
PrimersMutationOligonucleotide sequences (5′→3′)
BF1FA32PCAAGACGCAGGTCCGCCGCTGAAAG
BF1RTTGCCAGATCTTTCAGCGGCGGACC
BF2FA117PAATTCGCGGTCACCCGCTGATTTGG
BF2RTCTTGCCAAATCAGCGGGTGACCGC
BF3FA99PTCAGTGGGGTCCGCCGGACGAAATG
BF3RGCAAACATTTCGTCCGGCGGACCCC
BF4FA128PCGAAATGGCTGCCGCCGTGGGTAAAC
BF4RAGTGCGTTTACCCACGGCGGCAGCC
BF5FV140PTCTGAAAAGCAAACCGCCGGCACATGC
BF5RTGCTTCAGCATGTGCCGGCGGTTTG
BF6FD222PCCGGGTCTGGGCGATCCGGCAAAAC
BF6RCTGCGCGATGTTTTGCCGGATCGCC
BF7FD221PCCGGGTCTGGGCCCGGATGCAAAAC
BF7RCGCGATGTTTTGCATCCGGGCCCAG
BF8FV190PCAAACGTATGGGCGCGCCGGAACAG
BF8RCAAATTCGATCTGTTCCGGCGCGCC
BF9FA189PACCAAACGTATGGGCCCGGTTGAAC
BF9RTCGATCTGTTCAACCGGGCCCATAC
BF10FV182PTAGCCTGATTCAGAACCCGTTCACC
BF10RCCATACGTTTGGTGAACGGGTTCTG
BE11FT323PACCCTGAGTTATCCGCCGTGTCGCG
BF11RCAGAAAATCGCGACACGGCGGATAACTC
BF12FA141PAAAAGCAAACCGGTCCCGCATGCTG
BF12RGAATTGCTTCAGCATGCGGGACCGG
BF13FA254PAAGTCACGTTTCTCCGGGCGATATG
BF13RAGACATCATATCGCCCGGAGAAACG
BF15FA295PACGTCAACGATAAACCGTTCCCGGC
BF15RCAAAATCCGCCGGGAACGGTTTATC
BF16FA298PATAAAGCGTTCCCGCCGGATTTTGC
BF16RACGTTTTGCAAAATCCGGCGGGAAC
BF17FF300PGCGTTCCCGGCGGATCCGGCAAAAC
BF17RTGCGTCACGTTTTGCCGGATCCGCC
BF18FS360PCCGACCCCGTACGATCCTCAACTGC
BF18RTAGCGCGCAGTTGAGGATCGTACG
BF19FG350PGCAAAACGTCCGGACCCGCTGGCAC
BF19RGGACGTTGTGCCAGCGGGTCCGGAC
BF20FD344PCTGCAAGTTTGGGCACCGGCAAAACG
BF20RCCGGACGTTTTGCCGGTGCCCAAAC
BF21FA352PGTCCGGACGGTCTGCCGCAACGTCC
BF21RACGGGGTCGGACGTTGCGGCAGACC
BF22FH335PGGGGTATGGCTGATCCGGTTAACTGG
BF22RTTGCAGCCAGTTAACCGGATCAGCC
), ArticleFig(id=1194980450096624538, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=CN, label=表1, caption=

本实验所用的PCR引物对

, figureFileSmall=null, figureFileBig=null, tableContent=
PrimersMutationOligonucleotide sequences (5′→3′)
BF1FA32PCAAGACGCAGGTCCGCCGCTGAAAG
BF1RTTGCCAGATCTTTCAGCGGCGGACC
BF2FA117PAATTCGCGGTCACCCGCTGATTTGG
BF2RTCTTGCCAAATCAGCGGGTGACCGC
BF3FA99PTCAGTGGGGTCCGCCGGACGAAATG
BF3RGCAAACATTTCGTCCGGCGGACCCC
BF4FA128PCGAAATGGCTGCCGCCGTGGGTAAAC
BF4RAGTGCGTTTACCCACGGCGGCAGCC
BF5FV140PTCTGAAAAGCAAACCGCCGGCACATGC
BF5RTGCTTCAGCATGTGCCGGCGGTTTG
BF6FD222PCCGGGTCTGGGCGATCCGGCAAAAC
BF6RCTGCGCGATGTTTTGCCGGATCGCC
BF7FD221PCCGGGTCTGGGCCCGGATGCAAAAC
BF7RCGCGATGTTTTGCATCCGGGCCCAG
BF8FV190PCAAACGTATGGGCGCGCCGGAACAG
BF8RCAAATTCGATCTGTTCCGGCGCGCC
BF9FA189PACCAAACGTATGGGCCCGGTTGAAC
BF9RTCGATCTGTTCAACCGGGCCCATAC
BF10FV182PTAGCCTGATTCAGAACCCGTTCACC
BF10RCCATACGTTTGGTGAACGGGTTCTG
BE11FT323PACCCTGAGTTATCCGCCGTGTCGCG
BF11RCAGAAAATCGCGACACGGCGGATAACTC
BF12FA141PAAAAGCAAACCGGTCCCGCATGCTG
BF12RGAATTGCTTCAGCATGCGGGACCGG
BF13FA254PAAGTCACGTTTCTCCGGGCGATATG
BF13RAGACATCATATCGCCCGGAGAAACG
BF15FA295PACGTCAACGATAAACCGTTCCCGGC
BF15RCAAAATCCGCCGGGAACGGTTTATC
BF16FA298PATAAAGCGTTCCCGCCGGATTTTGC
BF16RACGTTTTGCAAAATCCGGCGGGAAC
BF17FF300PGCGTTCCCGGCGGATCCGGCAAAAC
BF17RTGCGTCACGTTTTGCCGGATCCGCC
BF18FS360PCCGACCCCGTACGATCCTCAACTGC
BF18RTAGCGCGCAGTTGAGGATCGTACG
BF19FG350PGCAAAACGTCCGGACCCGCTGGCAC
BF19RGGACGTTGTGCCAGCGGGTCCGGAC
BF20FD344PCTGCAAGTTTGGGCACCGGCAAAACG
BF20RCCGGACGTTTTGCCGGTGCCCAAAC
BF21FA352PGTCCGGACGGTCTGCCGCAACGTCC
BF21RACGGGGTCGGACGTTGCGGCAGACC
BF22FH335PGGGGTATGGCTGATCCGGTTAACTGG
BF22RTTGCAGCCAGTTAACCGGATCAGCC
), ArticleFig(id=1194980450163733403, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=EN, label=Table 2, caption=

FoldX software predicts mutants with Pro effect

, figureFileSmall=null, figureFileBig=null, tableContent=
MutantΔΔG (kcal/mol)MutantΔΔG (kcal/mol)
A32P-1.077T323P-2.128
R61P-0.754A141P-1.065
A64P-0.724A254P-0.991
A78P-0.759A295P-0.538
Q85P-0.926A298P-1.273
A99P-0.968F300P-1.275
A117P-3.111M380P-1.187
D122P-2.238A364P-1.566
A128P-1.561S360P-1.531
V140P-1.547G350P-0.987
D222P-1.785D344P-1.782
D221P-0.510A352P-1.141
V190P-0.748A343P-1.611
A189P-1.168H335P-0.873
V182P-1.118
A143P-0.549
), ArticleFig(id=1194980450239230876, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=CN, label=表2, caption=

FoldX软件预测具有Pro效应的突变体

, figureFileSmall=null, figureFileBig=null, tableContent=
MutantΔΔG (kcal/mol)MutantΔΔG (kcal/mol)
A32P-1.077T323P-2.128
R61P-0.754A141P-1.065
A64P-0.724A254P-0.991
A78P-0.759A295P-0.538
Q85P-0.926A298P-1.273
A99P-0.968F300P-1.275
A117P-3.111M380P-1.187
D122P-2.238A364P-1.566
A128P-1.561S360P-1.531
V140P-1.547G350P-0.987
D222P-1.785D344P-1.782
D221P-0.510A352P-1.141
V190P-0.748A343P-1.611
A189P-1.168H335P-0.873
V182P-1.118
A143P-0.549
), ArticleFig(id=1194980450377642909, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=EN, label=Table 3, caption=

Construction of Pro effect mutation electronic library

, figureFileSmall=null, figureFileBig=null, tableContent=
MutantSecondary structure motifMutantSecondary structure motif
A32Pα-helix N capA254Pβ-turn
A99Pα-helix N capA298PLoop
A117PLoopA295PLoop
A128Pα-helix N capF300Pɑ-helix N cap
V140Pα-helix N capT323Pβ-turn
A141Pα-helix N capH335Pβ-turn
A189Pα-helix N capD344Pβ-turn
V182Pα-helix N capG350PLoop
V190Pα-helix N capA352PLoop
D221Pα-helix N capS360Pβ-turn
D222Pα-helix N cap
), ArticleFig(id=1194980450532832158, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=CN, label=表3, caption=

Pro效应突变电子文库的构建

, figureFileSmall=null, figureFileBig=null, tableContent=
MutantSecondary structure motifMutantSecondary structure motif
A32Pα-helix N capA254Pβ-turn
A99Pα-helix N capA298PLoop
A117PLoopA295PLoop
A128Pα-helix N capF300Pɑ-helix N cap
V140Pα-helix N capT323Pβ-turn
A141Pα-helix N capH335Pβ-turn
A189Pα-helix N capD344Pβ-turn
V182Pα-helix N capG350PLoop
V190Pα-helix N capA352PLoop
D221Pα-helix N capS360Pβ-turn
D222Pα-helix N cap
), ArticleFig(id=1194980450595746719, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=EN, label=Table 4, caption=

The melting temperature of XynRBM26 wild type and single point mutants

, figureFileSmall=null, figureFileBig=null, tableContent=
EnzymeTm/℃ΔTm/℃EnzymeTm/℃ΔTm/℃
Wild-type55.5
A32P56.3+0.8T323P52.5-3.0
A117P54.9-0.6A141P55.3-0.2
A99P55.2-0.3A254P53.3-2.2
A128P55.6+0.1A295P54.0-1.5
V140P53.8-1.7A298P52.4-3.1
D222P57.2+1.7F300P54.3-1.2
D221P49.5-6.0S360P48.5-7.0
V190P54.5-1.0D344P57.3+1.8
A189P55.5+0.0A352P58.3+2.8
V182P56.5+1.0H335P49.1-6.4
), ArticleFig(id=1194980450667049888, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=CN, label=表4, caption=

XynRBM26野生型和单点突变体的 Tm

, figureFileSmall=null, figureFileBig=null, tableContent=
EnzymeTm/℃ΔTm/℃EnzymeTm/℃ΔTm/℃
Wild-type55.5
A32P56.3+0.8T323P52.5-3.0
A117P54.9-0.6A141P55.3-0.2
A99P55.2-0.3A254P53.3-2.2
A128P55.6+0.1A295P54.0-1.5
V140P53.8-1.7A298P52.4-3.1
D222P57.2+1.7F300P54.3-1.2
D221P49.5-6.0S360P48.5-7.0
V190P54.5-1.0D344P57.3+1.8
A189P55.5+0.0A352P58.3+2.8
V182P56.5+1.0H335P49.1-6.4
), ArticleFig(id=1194980450742547361, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=EN, label=Table 5, caption=

The superimposed mutant Tm value was determined

, figureFileSmall=null, figureFileBig=null, tableContent=
EnzymeTm/℃ΔTm/℃
Wild type55.50.0
V182P-D222P57.1+1.6
V182P-D344P58.3+2.8
V182P-A352P58.6+3.1
D222P-D344P59.0+3.5
D222P-A352P60.3+4.8
D344P-A352P61.2+5.7
V182P-D222P-D344P60.6+5.1
V182P-D222P-A352P59.7+4.2
D222P-D344P-A352P61.7+6.2
V182P-D222P-D344P-A352P61.3+5.8
M4 (G115D-D222P-D344P-A352P)62.0+6.5
), ArticleFig(id=1194980451791123362, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=CN, label=表5, caption=

叠加突变体 Tm 值测定

, figureFileSmall=null, figureFileBig=null, tableContent=
EnzymeTm/℃ΔTm/℃
Wild type55.50.0
V182P-D222P57.1+1.6
V182P-D344P58.3+2.8
V182P-A352P58.6+3.1
D222P-D344P59.0+3.5
D222P-A352P60.3+4.8
D344P-A352P61.2+5.7
V182P-D222P-D344P60.6+5.1
V182P-D222P-A352P59.7+4.2
D222P-D344P-A352P61.7+6.2
V182P-D222P-D344P-A352P61.3+5.8
M4 (G115D-D222P-D344P-A352P)62.0+6.5
), ArticleFig(id=1194980451862426531, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=EN, label=Table 6, caption=

Dihedral angle statistics of positive mutants

, figureFileSmall=null, figureFileBig=null, tableContent=
Mutation siteΦΨ
182-55.829-32.765
222-55.015-37.362
344-68.529-15.345
352-64.594148.177
), ArticleFig(id=1194980451916952484, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1194684383262122405, language=CN, label=表6, caption=

阳性突变体二面角统计

, figureFileSmall=null, figureFileBig=null, tableContent=
Mutation siteΦΨ
182-55.829-32.765
222-55.015-37.362
344-68.529-15.345
352-64.594148.177
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基于Pro效应提高GH10家族耐盐木聚糖酶XynRBM26的热稳定性
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董盼盼 1 , 许海涛 2 , 王中雨 1 , 王琳 1 , 周星雨 1 , 刘林东 1 , 张婷婷 1 , 张娇娇 1 , 汪金萍 1, *
微生物学报 | 研究报告 2025,65(11): 4994-5007
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微生物学报 | 研究报告 2025, 65(11): 4994-5007
基于Pro效应提高GH10家族耐盐木聚糖酶XynRBM26的热稳定性
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董盼盼1, 许海涛2, 王中雨1, 王琳1, 周星雨1, 刘林东1, 张婷婷1, 张娇娇1, 汪金萍1, *
作者信息
  • 1 信阳农林学院 药学院,河南 信阳
  • 2 焦作技师学院,河南 焦作
Improvement of the thermostability of the salt-tolerant xylanase XynRBM26 from GH10 family based on Pro effect
Panpan DONG1, Haitao XU2, Zhongyu WANG1, Lin WANG1, Xingyu ZHOU1, Lindong LIU1, Tingting ZHANG1, Jiaojiao ZHANG1, Jinping WANG1, *
Affiliations
  • 1 School of Pharmacy, Xinyang Agriculture and Forestry University, Xinyang, Henan, China
  • 2 Jiaozuo Technician College, Jiaozuo, Henan, China
出版时间: 2025-11-04 doi: 10.13343/j.cnki.wsxb.20250288
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目的 嗜中温GH10家族耐盐木聚糖酶XynRBM26在动物饲料等工业领域具有重要的应用价值。本研究基于理性设计方法对其进行蛋白质工程改造以提升其热稳定性,为后续XynRBM26酶制剂的工业化应用奠定基础。 方法 利用生物信息学软件FoldX对AlphaFold 2.0预测的XynRBM26的3D结构进行全序列扫描,将自由能变化小于-0.5 kcal/mol的突变体构建成一个初始电子文库;基于Pro效应及潜在突变体的筛选原则构建一个由Pro突变组成的电子文库;利用定点突变技术构建突变体基因,进一步对突变体进行异源表达和纯化,通过实验验证筛选出阳性突变体。 结果 初始潜在突变体经筛选后,构建了一个由21个Pro效应突变体组成的小而精的突变文库。对所有突变体进行实验验证,筛选出Tm值显著提高的阳性单点突变体D222P、V182P、D344P和A352P。后续通过叠加筛选获得了性质较优的3点叠加Pro突变体,并将其与实验筛选的阳性突变体G115D叠加,筛选出稳定性最优的叠加突变体M4 (G115D-D222P-D344P-A352P)。与XynRBM26野生型相比,其Tm值及最适温度分别提高了6.5 ℃和5 ℃,在55 ℃下的半衰期t1/2提高了7.5倍,最适温度下的相对活性是野生型的3.44倍。 结论 基于Pro效应及2种不同效应叠加方法筛选热稳定性GH10家族耐盐木聚糖酶XynRBM26突变体,是一种有效的策略。

GH10家族  /  木聚糖酶XynRBM26  /  Pro效应  /  Tm值  /  半衰期t1/2

Objective The mesophilic salt-tolerant xylanase XynRBM26, a member of the GH10 family, holds significant application value in industrial fields such as animal feed. This study improved the thermostability of this enzyme by protein modification via rational design, aiming to lay a foundation for the industrial application of XynRBM26 preparations. Methods The bioinformatics software FoldX was used to conduct positionscan of the 3D structure predicted by AlphaFold 2.0 for XynRBM26. The mutants with free energy changes less than -0.5 kcal/mol were selected to construct an initial electronic library. According to the Pro effect and screening principles for potential mutants, an electronic library composed of Pro mutations was subsequently established. Finally, site-directed mutagenesis was employed to construct mutant genes, and positive mutants were screened after heterologous expression, purification, and experimental verification. Results After screening of the initial potential mutants, a small and precise mutant library consisting of 21 Pro effect mutants was constructed. All the mutants were experimentally validated, and positive single-point mutants D222P, V182P, D344P, and A352P with significantly increased Tm values were screened out. Through subsequent stacking screening, a three-point stacked Pro effect mutant with superior properties was obtained. The combination of this mutant with the experimentally screened positive mutant G115D produced the most stable mutant M4 (G115D-D222P-D344P-A352P). Compared with wild-type XynRBM26, M4 showed increases of 6.5 °C and 5 °C in Tm and optimal temperature, respectively. Moreover, M4 presented the half-life (t1/2) at 55 °C 7.5-fold longer than the wild type, and its relative activity at the optimal temperature was 3.44 folds that of the wild type. Conclusion Screening thermostable mutants of the salt-tolerant xylanase XynRBM26 of the GH10 family based on the Pro effect and two different effect superimposing strategies is an effective approach.

GH10 family  /  xylanase XynRBM26  /  Pro effect  /  Tm value  /  half-life t1/2
董盼盼, 许海涛, 王中雨, 王琳, 周星雨, 刘林东, 张婷婷, 张娇娇, 汪金萍. 基于Pro效应提高GH10家族耐盐木聚糖酶XynRBM26的热稳定性. 微生物学报, 2025 , 65 (11) : 4994 -5007 . DOI: 10.13343/j.cnki.wsxb.20250288
Panpan DONG, Haitao XU, Zhongyu WANG, Lin WANG, Xingyu ZHOU, Lindong LIU, Tingting ZHANG, Jiaojiao ZHANG, Jinping WANG. Improvement of the thermostability of the salt-tolerant xylanase XynRBM26 from GH10 family based on Pro effect[J]. Acta Microbiologica Sinica, 2025 , 65 (11) : 4994 -5007 . DOI: 10.13343/j.cnki.wsxb.20250288
木聚糖是植物半纤维素的重要组成部分,其主要由β-d-木糖、阿拉伯糖等通过β-1,4糖苷键连接而成。由于其结构具有异质性,因此实现其完全降解需要多种复合酶系共同参与。其中,内切木聚糖酶(endoxylanase, EC 3.2.1.8)是水解木聚糖的关键酶类,它作用于木聚糖的主链,水解吡喃木糖残基之间的β-1,4糖苷键,产生多种低聚木糖,包括木二糖、木三糖、木四糖及木寡糖[1]。与木聚糖酶相关的主要糖苷水解酶(glycoside hydrolase, GH)家族有5、7、8、9、10、11、12、16、26、30、43、44、51和62[2],其中多数木聚糖酶归属于GH10和GH11家族。GH10家族木聚糖酶具有对底物专一性高、活性强和稳定性好等优点,在造纸、纺织、食品加工、生物质能源生产及动物饲料加工等工业应用方面前景广阔。木聚糖酶的热稳定性是其实现工业化应用的前提,例如,动物饲料在加工成型过程中需要超过80 ℃的高温[3]。目前,文献中报道的GH10家族木聚糖酶主要以嗜中温为主,尽管有部分研究筛选出了嗜热GH10家族木聚糖酶,但因其活性和表达量较低等因素难以满足工业需求。因此,直接筛选嗜热木聚糖酶或对文献中报道的嗜中温木聚糖酶进行热稳定性改造是实现GH10家族木聚糖酶工业化应用目标的捷径。
目前,使用蛋白质工程提升酶热稳定性主要有3种策略:定向进化、半理性设计和理性设计[4]。定向进化策略是在不了解蛋白质结构的情况下,通过对目标基因进行反复随机突变来改进酶的特性,每轮进化通过替换一个残基来改进酶。半理性设计策略中最重要的一种方法是定点饱和突变,即选择酶结构中的一个残基,并用所有可能的19种天然氨基酸代替它进行位点饱和突变以提高热稳定性。在过去的20多年中,虽然定向进化和半理性设计策略已成功用于改造酶蛋白,且取得了不错的结果,但这2种方法不仅要建立庞大的突变文库,还需要高效的高通量筛选技术或价格昂贵的实验仪器设备,需要极大的人力物力资源作为支撑。近年来,随着蛋白质结晶技术和蛋白质结构预测软件日益成熟,蛋白质三维结构越来越多地被解析或预测出来。结合多种生物信息学软件,使用理性设计策略构建一个小而精的突变文库可大幅提高成功率,加快酶工程研究的进程[5]。目前,理性设计策略所涉及的方法主要有二硫键引入[6]、盐桥引入[7]、蛋白表面电荷分布优化[8]及Pro引入[9]等。大量文献研究表明,在蛋白质三维结构合适位置引入Pro所产生的Pro效应能够显著降低蛋白解折叠过程中的构象熵,增加蛋白质的稳定性。目前,完全基于Pro效应进行系统研究以提高GH10家族木聚糖酶热稳定性的文献屈指可数。
目前已有部分学者开展了对GH10家族木聚糖酶的热稳定性改造研究。Dotsenko等[10]基于吉布斯自由能的变化及结构分析改造了来自变灰青霉菌的GH10家族木聚糖酶XylE,筛选出的阳性突变体S104M的Tm值较野生型提高了3.1 ℃。You等[11]将来自密褐褶菌的GH10家族木聚糖酶GtXyn10中位于底物通道上产生空间位阻的氨基酸进行突变,筛选出热稳定性是野生型2倍的叠加突变体H51K/Q118A。Bai等[12]将来自威尼克外瓶霉的GH10家族木聚糖酶Hwxyl10A的灵活性区域进行改造,获得了在70 ℃下的t1/2值是野生型17倍的叠加突变体S21Y/N318W。然而,热稳定性较好的耐热木聚糖酶还需进一步开发,以满足饲料工业的需求。
来源于云南滇金丝猴肠道微生物的GH10家族木聚糖酶XynRBM26不仅对榉木木聚糖活性较好,而且耐盐性良好,经5 mol/L NaCl在37 ℃下放置1 h能保持86%的活性,还具有胰蛋白酶抗性,具有较大的工业化应用潜力[13]。然而,该酶在55 ℃下的半衰期(t1/2)仅为2 min,其热稳定性难以满足动物饲料加工成型过程的高温需求。本研究使用AlphaFold 2.0[14]在线软件预测了木聚糖酶XynRBM26的3D结构,并以此为基础对其进行基于Pro效应的热稳定性改造,筛选热稳定性突变体并揭示其耐热机制,以期为其他酶类的热稳定性改造提供参考。
大肠杆菌(Escherichia coli ) BL21(DE3)用于蛋白基因的克隆和表达,该菌株为本实验室保藏。蛋白重组表达质粒pET28a-XynRBM26由生工生物工程(上海)股份有限公司合成并构建。
蛋白纯化用镍柱填料、标准蛋白marker,北京全式金生物技术有限公司;Dpn I酶、DNA聚合酶和DNA marker,宝生物工程(大连)有限公司;硫酸卡那霉素和IPTG,生工生物工程(上海)股份有限公司;山毛榉木木聚糖和木糖,上海源叶生物科技有限公司;乙醇和甘油等其他试剂均为国药集团化学试剂有限公司所产分析纯;引物,铂尚生物技术(上海)有限公司,具体序列如表1所示。
蛋白纯化系统,泰渡生物科技(苏州)有限公司;落地式高速冷冻离心机,赛默飞世尔科技公司;全温大容量恒温摇床,上海旻泉仪器有限公司;蛋白电泳仪,上海一恒科学仪器有限公司;高压细胞破碎机,永联生物科技(上海)有限公司。
使用Expasy网站中的ProtParam程序对耐盐GH10家族木聚糖酶XynRBM26 (GenBank登录号ALO19936.1)的氨基酸序列进行等电点、分子量等基本性质的预测及分析。使用三维结构预测软件AlphaFold 2.0对XynRBM26及其突变体进行建模,利用Saves在线软件对该三维结构进行结构合理性评估。所有的三维结构图均使用PyMOL软件绘制。
基于XynRBM26的三维结构,使用FoldX软件对其进行全序列虚拟饱和突变,筛选出一个由自由能小于-0.5 kcal/mol的460个突变体组成的突变文库,其中涉及Pro突变的突变体共有30个。依据文献[15]中热稳定性突变体的筛选原则:Pro不得出现在α螺旋和β折叠中(α螺旋除N端帽子结构外),突变位点不得有较多盐桥和氢键,且突变后无其他作用力进行能量代偿,剔除不符合要求的突变体。
使用表1中的引物对,以野生型质粒pET28a-XynRBM26为模板,通过重叠延伸PCR引入突变。PCR反应体系:2×PrimeSTAR DNA Polymerase with GC Buffer 12.5 µL,模板0.5 µL,dNTPs (2.5 mmol/L) 2 µL,上、下游引物 (5 μmol/L)各1 µL,ddH2O 3 µL。PCR扩增条件:95 ℃ 3 min;95 ℃ 10 s,不同的引物对的退火温度不同,退火时间为15 s,72 ℃ 6 min,共20个循环;72 ℃10 min。使用Dpn I酶对PCR产物在37 ℃下酶切2 h。直接将酶切产物转入到Escherichia coli BL21(DE3)感受态细胞中。突变后的基因经生工生物工程(上海)股份有限公司测序验证。
吸取100 μL野生型及突变体的工程菌株菌液,接种于10 mL含卡那霉素(Kana)抗性的LB培养基中,在37 ℃、240 r/min条件下振荡培养6 h左右,至菌液OD600值达到0.6-0.9。随后将菌液转移至1 L LB液体培养基中,220 r/min摇菌4 h,待培养菌液OD600达到0.6-0.9时将摇床温度设置为16 ℃,待温度降至设定值后,加入300 μL 1 mol/L IPTG (终浓度0.3 mmol/L),于16 ℃、200 r/min培养13 h,在4 000 r/min下 离心10 min,去掉上清后,加入50 mL预冷 的裂解液buffer (50 mmol/L Tris-HCl pH 7.0,150 mmol/L NaCl)均匀重悬菌体。采用匀浆机在650 MPa下匀浆3 min,随后将蛋白倒入2个 50 mL离心管中,4 ℃、15 000 r/min离心20 min,将蛋白和细胞碎片分离,目的蛋白粗酶液在上清中,分别留取上清和沉淀各40 μL。参考重力Ni亲和层析柱使用说明书,利用亲和层析法进行目的蛋白的纯化,使用SDS-PAGE判断目的蛋白的纯度,并使用Bradford法测定野生型与突变体纯化后酶液的蛋白浓度。
将榉木木聚糖底物溶解于50 mmol/L缓冲液中,使木聚糖终浓度为0.5 mg/mL。酶的反应体系:将100 μL酶液加入到900 μL木聚糖底物中。在反应开始前,需将底物预热5-10 min,随后加入酶液在最适温度下反应10 min,稍后加入1.5 mL 3,5-二硝基水杨酸(dinitrosalicylic acid, DNS)试剂,随即在沸水中煮沸5 min,最后用自来水将样品冷却至室温,吸取200 μL溶液到96孔板中,设置3个平行,在540 nm特定波长下测定样品吸光值。对照为在同样的反应体系中用100 μL缓冲液替代酶液。酶活定义为:在最适温度、最适pH条件下,每分钟催化水解木聚糖生成1 μmol还原糖所需要的酶量为1 U。
本研究采用NanoDSF检测方法进行热稳定性的快速初筛,其基本原理是NanoDSF检测无需染料,通过色氨酸在350 nm和330 nm波长下荧光值的微量变化来揭示蛋白折叠状态转化过程,以2个波长下荧光值比值与温度的关系来确定解链温度(Tm)。在测定Tm前需对蛋白浓度进行摸索,确定实验蛋白样品浓度为1 mg/mL,检测温度范围为20-95 ℃,升温斜率为1 ℃/min。通过比较突变体的Tm值与野生型蛋白的Tm值,若突变体的Tm值增加则代表其热稳定性提高。
在30-65 ℃ (间隔5 ℃)的温度范围内以5 mg/mL榉木木聚糖作为底物,在金属浴中测定XynRBM26的最适温度,以吸光值最高温度下的酶活力为100%,对照组用相同体积的buffer替代加入的酶蛋白。在最适pH条件下将稀释好的酶在55 ℃下分别加热1、2、2.5、5、10、15、20、25、30 min,加热完后在冰上冷却20 min,分别测定不同处理时间下的活性,以加热后酶蛋白酶活力与未加热的酶蛋白活力的比值的百分数定义为残余酶活(residual activity),以此计算酶蛋白的失活速率kd,计算如公式(1)所示。最终计算酶蛋白的半衰期,如公式(2)所示。
Ln (Residual activity)=kd×t
t1/2=ln2/kd
式中:Residual activity为残余酶活;kd为酶蛋白的失活速率。
使用Gromacs 4.5.6[16]分别对AlphaFold 2.0预测的野生型及突变体三维结构进行分子动力学模拟。使用YASARA软件去除结构中的水分子和氢原子。使用CHARMM27作为力场来生成蛋白的坐标文件和拓扑数据。将目的蛋白加入到Space水盒子中(周期性边界条件),目的蛋白距离设置的水盒子边缘为1.0 nm。向水溶剂中加入Na+或者Cl-来中和体系中的离子,使体系维持电中性。系统的能量最小化采用最陡下降法,时间为100 ps。NVT平衡时间为100 ps,体系的温度在恒温恒压下提升至55 ℃。在 328 K、105 kPa压力下进行NPT体系平衡100 ps。对体系进行长达50 ns的分子动力学模拟(molecular dynamics),计算木聚糖酶XynRBM26骨架碳原子的均方根偏差(root mean square deviation)、回旋半径(radius of gyration)及体系平衡状态下原子的均方根波动(root mean square fluctuation)值。
木聚糖酶XynRBM26的基因序列(ALO19936.1)含1 152 bp,编码383个氨基酸,NCBI将其注释为木聚糖酶。XynRBM26蛋白预测分子量为42.35 kDa,等电点为8.95,280 nm的消光系数为64 065 [mol/(L·cm)],疏水性平均系数(GRAVY)为-0.297,不稳定指数(instability index)为31.34。使用AlphaFold 2.0对木聚糖酶XynRBM26进行同源建模,结果如图1所示。与几乎所有GH10家族的木聚糖酶一致,XynRBM26的整体三维结构呈现出Tim桶状结构,具有木聚糖酶第10家族经典的(β/α)8-barrel拓扑结构。其三维结构上端的直径明显大于下端,呈现出一种类似于沙拉碗的形状。XynRBM26主要由内部正向平行的8个β折叠和位于外部环绕β折叠的8个α螺旋组成。活性中心氨基酸Glu169和Glu288分别作为酶催化过程中的酸/碱和亲核试剂,位于蛋白结构的中心位置,2个氨基酸残基之间的距离为5.3 Å,这表明XynRBM26对底物的催化遵循保留机制。利用SAVES预测的拉式图评估XynRBM26三维结构模型质量,结果表明有91.8%的氨基酸残基位于核心区域,8.2%的氨基酸位于其他允许区。上述结果说明,木聚糖酶XynRBM26的三维模型结果较为可靠。
依据FoldX预测结果,从460个自由能小于-0.5 kcal/mol的突变体中筛选出30个具有Pro效应的突变体,其结果如表2所示。
基于1.4节中的筛选原则,剔除不符合筛选原则的突变体R61P、A64P、Q85P、A78P、D122P和A143P。由于在前期研究中突变体A343P、A364P和M380P已经构建,所以不在本研究的筛选范围内。最终创建了一个由21个Pro突变体组成的突变文库。突变体的组成及突变位点所在二级结构中的位置如表3所示。
表达并纯化所有的单点突变体,除G350P不能正常表达外,其余20个单点突变体均能正常表达。SDS-PAGE图显示,在40 kDa附近存在单一条带且较为清晰,与目的蛋白42 kDa的分子量相符(图2)。
XynRBM26野生型与单点突变体的Tm测定结果如表4所示,有14个突变体的热稳定性下降,1个保持不变,6个有所提高。其中,突变体D222P、V182P、D344P和A352P分别较野生型提高1.7、1.0、1.8和2.8 ℃,这4个突变体被选定用于下一步的叠加。
分别将V182P、D222P、D344P和A352P这4个阳性单点突变体进行2点、3点、4点叠加,叠加突变体的Tm值如表5所示。叠加突变体的Tm值提高幅度从1.6 ℃ (V182P-D222P)到6.2 ℃ (D222P-D344P-A352P)。V182P突变体在与其余3个突变体进行叠加时并未表现出明显的累积效应。表5中提高最多的是3点叠加突变体D222P-D344P-A352P,其Tm值明显高于其他叠加突变体,这表明由3个Pro单点突变组成的组合突变协同增加了XynRBM26的热稳定性。众所周知,不同效应的突变体之间的协同作用对热稳定性提高较单个效应更为显著,而筛选得到的突变体D222P-D344P-A352P只有一种Pro效应,所以将D222P-D344P-A352P与之前实验筛选的具有盐桥效应的阳性突变体G115D进行进一步叠加得到突变体G115D-D222P-D344P-A352P。为了实验方便将其命名为M4进行后续的实验。
同样采用NanoDSF测定出的Tm值来评估野生型及叠加突变体M4的热力学稳定性(图3A)。突变体M4的Tm值增加至62.0 ℃,比XynRBM26高6.5 ℃,这表明G115D的盐桥效应与D222P-D344P-A352P的Pro效应在提高酶热稳定性方面具有协同作用。
最适温度的升幅低于Tm值的升幅,M4的最适温度为55 ℃,较XynRBM26野生型提高了5 ℃,野生型在65 ℃下几乎完全丧失活性,而突变体M4在70 ℃下仍保留超过40%的活性(图3B)。
图4A所示,在55 ℃下,与XynRBM26野生型相比M4的动力学稳定性也得到了改善。XynRBM26野生型的半衰期t1/2为1.9 min,而M4的半衰期t1/2为14.3 min,是野生型的7.5倍。如图4B所示,在55 ℃、pH 6.5条件下测定M4的相对酶活,结果表明与XynRBM26野生型相比叠加突变体M4的活性是野生型的3.44倍。
为更好地解释组合突变体M4热稳定性提高的机制,对M4和XynRBM26野生型的三维结构进行对比分析并作图。如图5所示,115位点位于组成蛋白核心区域的β3上。突变前G115能与β3正向平行的β4的组成氨基酸S163和D165形成2个氢键(图5A);突变后D115不仅与上述2个氨基酸形成氢键,还能与β4的组成氨基酸H164形成一个距离为1.8 Å的盐桥(图5B)。D222位于α螺旋的N端帽子结构上,D222所在位置附近的氨基酸较为灵活,D221的B值排名第12,D220的B值排名第15位,D222的B值排名第33,由于Pro具有独特而稳定的吡咯环结构,不仅能刚化D222位置,还能限制其前面221所在位置的灵活性,使该区域的灵活性降低(图5C、5D)。D344不仅位于β转角的第二个位置,且其灵活性较高(B值排名第二)。一方面,β转角在第二个位置具有Pro偏好性;另一方面,突变后存在Pro效应,在这双重叠加效应下该突变的稳定性增强(图5E、5F)。A352位于一个灵活的Loop区域,突变为Pro后同样由于Pro效应增加了Loop区的局部刚性(图5G、5H)。
采用Gromacs软件进行分子动力学模拟,结合RMSD值、RMSF值和Rg值分析引入的盐桥和Pro效应对XynRBM26热稳定性的贡献。如图6A所示,随着分子动力学模拟的持续进行,XynRBM26野生型和突变体M4的RMSD值在开始阶段均有一个显著上升的过程。突变体M4在10 ns时达到平衡,而野生型在25 ns时才达到平衡。在野生型和突变体均处于平衡状态的25-50 ns时间段内,野生型的RMSD值一直高于叠加突变体M4。这表明与野生型相比M4的整体柔性显著下降,其结构更为稳定。如图6B所示,野生型和突变体M4的Rg值相差不大,说明突变对该酶的Rg值几乎无影响。
图6C所示,选取野生型和突变体M4均处于平衡状态的25-50 ns轨迹文件计算每一个氨基酸残基的RMSF值。结果发现,突变体M4在Loop 286-300、Loop 340-349、N端31-44及C端377-383等区域的柔性相较于野生型显著降低。这说明引入的4点突变可能通过提升该酶部分区域的刚性进而提高酶蛋白的整体稳定性。
Pro因其独特的侧链结构在组成蛋白的氨基酸中较为特殊。Pro的结构具有2个独有特征:(1) 与酰胺氮共价结合,这意味着该氮不能参与氢键的形成;(2) 脯氨酸的吡咯五元环结构使中心碳原子与主链氮之间的共价键更强,更不易旋转。基于上述原因,Pro在β折叠和α螺旋中不稳定。由于Pro独特的四氢吡咯环状结构能够对肽链及其周围的氨基酸残基起到加强限制作用,其构象的改变已成为一些蛋白质三维结构折叠与解折叠的限速步骤。由其引起的氨基酸替换所产生的结构限制可在一定程度上增强蛋白质三维结构中原先存在的各种作用,从而提高蛋白的热稳定性[17-19]。研究表明在β转角的第二个位置、α螺旋的N端帽子区域和柔性Loop区域引入Pro通常会增加酶的热稳定性[20]。因此,将Pro引入上述有利区域可能是提高热稳定性的有效策略。Pro突变筛选热稳定性突变体的难点在于正确寻找突变引入的位置。研究表明适合引入Pro的突变位点具有一个二面角范围(φ=-90°- -40°,ψ=120°-180°或ψ=-50-10°)[21]。统计本研究的4个阳性Pro突变位点的二面角如表6所示,所有阳性突变体的二面角均符合上述范围,进一步印证了文献的可靠性。
由热稳定性相关文献可知,单一突变效应引起的热稳定性提升是有限的。Huang等[22]通过对来源于米曲霉的脂肪酶ROL的底物结合腔的关键非保守性氨基酸使用Rosetta软件进行虚拟饱和突变,筛选出阳性突变体,进而与二硫键阳性突变体进行叠加,筛选出热稳定性叠加突变体M6,其中叠加的2点突变体E265V/S267W的Tm仅比野生型提高1.2 ℃,而叠加突变体M6的Tm较野生型提高8.5 ℃。由此可见,单个突变体引入的单个效应对提高酶热稳定性的幅度有限,而基于多个效应的多点叠加突变能大幅度提升酶的热稳定性。本研究在3点叠加的Pro效应基础上进一步引入了盐桥效应,得到的4点叠加突变体M4的热稳定性得到进一步提高。目前,关于通过改造提高GH10家族木聚糖酶热稳定性的研究相对较少。De Souza等[23]在GH10家族木聚糖酶XynA中引入突变体H209N,其Tm值较野生型仅提高0.4 ℃,而本研究构建的叠加突变体M4的Tm值较野生型提高6.5 ℃。本研究证实了基于FoldX计算和Pro效应的相结合方法是获得热稳定性酶的有效策略,为动物肠道微生物来源的耐盐酶热稳定性改造提供借鉴和参考。
酶常常表现出热稳定性和活性之间的平衡[24-27],这意味着增强一种属性通常是以牺牲另一种属性为代价的,这是研究人员在为工业应用设计酶时面临的一个挑战。然而,本研究筛选的叠加突变体M4的稳定性和活性均有一定程度的提高,这表明高热稳定性和高活性并不总是相互矛盾的。
董盼盼:开展试验及论文撰写;许海涛:数据分析;王中雨:负责部分试验;王琳:提供试验经费;周星雨:试验数据的验证;刘林东:文献查询;张婷婷:分子动力学模拟;张娇娇:试验仪器平台的提供;汪金萍:论文审阅及修订。
作者声明不存在任何可能会影响本文所报告工作的已知经济利益或个人关系。
  • 河南省高等学校重点科研项目(24B180015)
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doi: 10.13343/j.cnki.wsxb.20250288
  • 接收时间:2025-04-07
  • 首发时间:2025-11-10
  • 出版时间:2025-11-04
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  • 收稿日期:2025-04-07
  • 录用日期:2025-06-18
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Key Scientific Research Project of Universities in Henan Province(24B180015)
河南省高等学校重点科研项目(24B180015)
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    1 信阳农林学院 药学院,河南 信阳
    2 焦作技师学院,河南 焦作

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2种不同金属材料的力学参数

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种数
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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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