肿瘤相关Smads家族蛋白的计算机模拟修饰
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摘要
本文旨在比较分析Smad蛋白家族的结构与功能特性,进而对不稳定蛋白进行模拟修饰,为深入开展Smad蛋白功能研究奠定基础;应用生物信息学对比分析Smad蛋白质家族成员的理化特性、结构特点及功能差异,基于各自特征对不稳定蛋白质进行修饰预测并评估其稳定性;结果表明氨基酸序列的相似性在Smad亚家族内极高;亚家族间则较低。家族各成员分子量、等电点、消光系数等理化性质差异显著,各成员均为疏水性蛋白(GRAVY <0)且体外稳定性较差(Instability index>40)。测定Smad蛋白质的p I值和消光系数能够有效对Smad进行快速分类。比较分析亚家族间蛋白质结合位点和三维结构均具有与蛋白质的功能相对应的标志性特征,体现了各成员的功能多样性。最后就研究热点蛋白Smad4,6,7的不稳定结构进行模拟突变,预测蛋白质在体外环境15～50℃区间相对稳定;对Smad蛋白家族进行了系统的对比分析,并对不稳定蛋白进行了理想的模拟修饰,为进一步开展Smad在肿瘤发生途径与作用机制中的研究提供依据。
To lay a foundation for further research on the function of Smad protein,this paper analyzes the protein structure,functional characteristics of Smad protein family,modify and predict the unstable protein.The physicochemical properties,structural features and functional difference of Smad protein family are compariatively analyzed by Applied Bioinformatics.Based on its different characteristics,the modification of unstable protein is predicted and its stability is evaluated.The result shows that the similarity of the amino acid sequence is very high in Smad subfamily but very low in other subfamilies.Significant differences are found in the molecular weight,isoelectric point,extinction coefficient and other physical and chemical properties of each member of the family.All of the proteins are hydrophobic(GRAVY < 0) but with poor stability in vitro(Instability index > 40).The measured pI value and extinction coefficient of protein are efficient in classifying Smad in a quick way.The binding sites and 3 D structures are consistent with the functional difference of proteins,reflecting the diversity of protein functions.The simulated mutation of unstable protein 4,6,7 are carried out to predict the stability of protein in an external enviroment of 15～50 ℃.The comparative analysis and ideal modification of Smad protein family can provide a basis for the further study of Smad in pathogenesis and mechanism of tumorigenesis.
To lay a foundation for further research on the function of Smad protein,this paper analyzes the protein structure,functional characteristics of Smad protein family,modify and predict the unstable protein.The physicochemical properties,structural features and functional difference of Smad protein family are compariatively analyzed by Applied Bioinformatics.Based on its different characteristics,the modification of unstable protein is predicted and its stability is evaluated.The result shows that the similarity of the amino acid sequence is very high in Smad subfamily but very low in other subfamilies.Significant differences are found in the molecular weight,isoelectric point,extinction coefficient and other physical and chemical properties of each member of the family.All of the proteins are hydrophobic(GRAVY < 0) but with poor stability in vitro(Instability index > 40).The measured pI value and extinction coefficient of protein are efficient in classifying Smad in a quick way.The binding sites and 3 D structures are consistent with the functional difference of proteins,reflecting the diversity of protein functions.The simulated mutation of unstable protein 4,6,7 are carried out to predict the stability of protein in an external enviroment of 15～50 ℃.The comparative analysis and ideal modification of Smad protein family can provide a basis for the further study of Smad in pathogenesis and mechanism of tumorigenesis.
引文
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[22]常凯,童立冬,江忠勇,等.醛脱氢酶(ALDH)蛋白家族的信息学比较分析与修饰预测[J].基因组学与应用生物学,2016,35(1):28-33.
[2]JR F P,CREIGHTON C J,MATZUK M M.Insights Into SMAD4 Loss in Pancreatic Cancer From Inducible Restoration of TGF-βSignaling.[J].Molecular Endocrinology,2015,29(10):1440.
[3]XU J,LI J,WANG H,et al.A novel SMAD family protein,SMAD9 is involved in follicular initiation and changes egg yield of geese via synonymous mutations in exon1 and intron2[J].Molecular Biology Reports,2015,42(1):289.
[4]ZHANG T,WEN F,WU Y,et al.Cross-talk between TGF-beta/SMAD and integrin signaling pathways in regulating hypertrophy of mesenchymal stem cell chondrogenesis under deferral dynamic compression[J].Biomaterials,2015,38:72-85.
[5]WANG X B,WANG W,ZHU X C,et al.The potential of asiaticoside for TGF-β1/Smad signaling inhibition in prevention and progression of hypoxia-induced pulmonary hypertension.[J].Life Sciences,2015,137(4):56-64.
[6]DA C,LIU Y,ZHAN Y,et al.Nobiletin inhibits epithelial-mesenchymal transition of human non-small cell lung cancer cells by antagonizing the TGF-β1/Smad3 signaling pathway[J].Oncology Reports,2016,35(5):2767.
[7]MACIAS M J,MARTINMALPARTIDA P,MASSAGUéJ.Structural determinants of SMAD function in TGF-βsignaling[J].Trends in Biochemical Sciences,2015,40(6):296.
[8]苟凡铖,侯怡铃,宋波,等.r DNA-ITS序列分析法和传统分类法对真菌进行分类鉴定[J].西华师范大学学报(自然科学版),2017(4):382-386.
[9]EBEL M E,KANSAS G S.Functions of smad transcription factors in TGF-β1-induced selectin ligand expression on murine CD4Th cells[J].Journal of Immunology,2016,197(7):2627-2634.
[10]BILLING M,R RBY E,DAHL M,et al.Signaling via Smad2 and Smad3 is dispensable for adult murine hematopoietic stem cell function in vivo[J].Experimental Hematology,2017,55:34-44.
[11]DEPKE M,MICHALIK S,RABE A,et al.A peptide resource for the analysis of Staphylococcus aureus in host-pathogen interaction studies.[J].Proteomics,2015,15(21):3648-3661.
[12]MISHRA A,IQBAL S,HOQUE M T.Discriminate protein decoys from native by using a scoring function based on ubiquitous Phi and Psi angles computed for all atom[J].Journal of Theoretical Biology,2016,398:112-121.
[13]QIN B Y,CHACKO B M,LAM S S,et al.Structural basis of Smad1 activation by receptor kinase phosphorylation.[J].Molecular Cell,2001,8(6):1303.
[14]QIN B,LAM S S,LIN K.Crystal structure of a transcriptionally active Smad4 fragment.[J].Structure,1999,7(12):1493.
[15]WU J W,HU M,CHAI J,et al.Crystal Structure of a Phosphorylated Smad2:Recognition of Phosphoserine by the MH2 Domain and Insights on Smad Function in TGF-βSignaling[J].Molecular Cell,2001,8(6):1277.
[16]CAPRIOTTI E,FARISELLI P,Casadio R.I-Mutant2.0:predicting stability changes upon mutation from the protein sequence or structure.[J].Nucleic Acids Research,2005,33(Web Server issue):306-10.
[17]DENNLER S,HUET S,GAUTHIER J M.A short amino-acid sequence in MH1 domain is responsible for functional differences between Smad2 and Smad3[J].Oncogene,1999,18(8):1643.
[18]HAEGER S M,THOMPSON J J,KALRA S,et al.Smad4 loss promotes lung cancer formation but increases sensitivity to DNAtopoisomerase inhibitors[J].Oncogene,2016,35(5):577-586.
[19]KANG C M,KYOUNG H H,JIAE P,et al.Maximum standard uptake value as a clinical biomarker for detecting loss of SMAD4expression and early systemic tumor recurrence in resected left-sided pancreatic cancer[J].Medicine,2016,95(17):e3452.
[20]NAKAO A,AFRAKHTE M,MORN A,et al.Identification of SMAD7,a TGFβ-inducible antagonist of TGF-βsignalling[J].Nature,2015,389(6651):631-635.
[21]LIU X,LEE J,COOLEY M,et al.Smad7 but not Smad6 cooperates with Oncogenic ras to cause malignant conversion in a mouse model for squamous cell carcinoma[J].Cancer Research,2003,63(22):7760.
[22]常凯,童立冬,江忠勇,等.醛脱氢酶(ALDH)蛋白家族的信息学比较分析与修饰预测[J].基因组学与应用生物学,2016,35(1):28-33.