泛素-蛋白酶体在真核生物的抗原呈递、细胞周期调控和转录因子激活等生理过程中发挥着极为重要的作用,其核心就是蛋白酶体对底物的选择性酶切作用,因此对选择性酶切位点的预测一直是计算生物学的一个重点研究内容.针对现有酶切位点预测...泛素-蛋白酶体在真核生物的抗原呈递、细胞周期调控和转录因子激活等生理过程中发挥着极为重要的作用,其核心就是蛋白酶体对底物的选择性酶切作用,因此对选择性酶切位点的预测一直是计算生物学的一个重点研究内容.针对现有酶切位点预测方法的非线性和物理意义不明确等问题,借鉴定量构效关系研究方法,采用基于氨基酸物理化学性质的描述子——VHSE(Principal component score vector of hydrophobic,steric,and electronic properties)对收集的2650个MHC-I配体的源蛋白序列进行了结构表征,在此基础上利用支持向量机建立了蛋白酶体酶切位点的预测模型,其最优线性模型的灵敏度(Sensitivity)、特异性(Specificity)、接受者操作特征曲线下面积(area under receiver operatingcharacteristics curve,AUC)和马休斯相关系数(Matthews coefficient of correlation,MCC)分别为90.18%,69.63%,0.8797和0.6131.模型分析结果表明:影响酶切位点选择性的氨基酸性质由大到小依次为:疏水性、电性和立体特征;P9,P8,P4,P1,P3',P4'和P5'位氨基酸对酶切位点的选择有重要影响,研究亦显示酶切位点上游P1位和下游P1'～P5'的"疏水势差"有利于蛋白酶体的切割作用.展开更多
Recently, genome wide association studies showed that there is a strong association between abacavir-induced serious, idio- syncratic, adverse drag reactions （ADRs） and human leukocyte antigen-B＊5701 （HLA-B＊5701...Recently, genome wide association studies showed that there is a strong association between abacavir-induced serious, idio- syncratic, adverse drag reactions （ADRs） and human leukocyte antigen-B＊5701 （HLA-B＊5701）. Studies also found that ab- acavir-induced ADRs were seldom observed in patients carrying the HLA-B＊5801 subtype. HLA-B＊5801 of the same sero- type （B17） as B＊5701 differs by only 4 amino acids from B＇5701. It is believed that because of these sequence differences, HLA-B＊5801 cannot bind the specific peptides which are required for HLA-B＊5701 to stimulate the T cell immune response. Thus, the difference in peptide binding profiles between HLA-B＊5701 and B＊5801 is an important clue for exploring the mechanisms of abacavir-induced ADRs. VHSE （principal component score vector of hydrophobic, steric, and electronic prop- erties）, a set of amino acid structural descriptors, was employed to establish QSAR models of peptide-binding affinities of HLA-B＊5701 and B＊5801. Optimal linear SVM （support vector machine） models with high predictive capabilities were ob- tained for both B＊5701 and B＇5801. The R2 （coefficient of determination）, Q2 （cross-validated R：）, and RpRE2 （R2 of test set） of two optimal models were 0,7530, 0.7037, 0.6153 （B＇5701） and 0.6074, 0.5966, 0.5762 （B＊5801）, respectively. For B＇5701 and B＇5801, the mutations in positions 45 （MET-THR） and 46 （ALA-GLU） have little influence on the selection specificity of the P2 position of the bound peptide. However, the mutation in position 97 （VAL-ARG） greatly influences the selection speci- ficity of the P7 position. HLA-B＊5701 prefers the bulky and positively charged amino acids at the P7 position. In contrast, HLA-B＊5801 prefers the non-polar hydrophobic amino acids at the P7 position while positively charged amino acids are un- favored.展开更多
文摘泛素-蛋白酶体在真核生物的抗原呈递、细胞周期调控和转录因子激活等生理过程中发挥着极为重要的作用,其核心就是蛋白酶体对底物的选择性酶切作用,因此对选择性酶切位点的预测一直是计算生物学的一个重点研究内容.针对现有酶切位点预测方法的非线性和物理意义不明确等问题,借鉴定量构效关系研究方法,采用基于氨基酸物理化学性质的描述子——VHSE(Principal component score vector of hydrophobic,steric,and electronic properties)对收集的2650个MHC-I配体的源蛋白序列进行了结构表征,在此基础上利用支持向量机建立了蛋白酶体酶切位点的预测模型,其最优线性模型的灵敏度(Sensitivity)、特异性(Specificity)、接受者操作特征曲线下面积(area under receiver operatingcharacteristics curve,AUC)和马休斯相关系数(Matthews coefficient of correlation,MCC)分别为90.18%,69.63%,0.8797和0.6131.模型分析结果表明:影响酶切位点选择性的氨基酸性质由大到小依次为:疏水性、电性和立体特征;P9,P8,P4,P1,P3',P4'和P5'位氨基酸对酶切位点的选择有重要影响,研究亦显示酶切位点上游P1位和下游P1'～P5'的"疏水势差"有利于蛋白酶体的切割作用.
基金supported by the National Natural Science Foundation of China (Grant No. 61073135)Chongqing Natural Science Foundation(Grant No. CSTC, 2009BA5068)
文摘Recently, genome wide association studies showed that there is a strong association between abacavir-induced serious, idio- syncratic, adverse drag reactions （ADRs） and human leukocyte antigen-B＊5701 （HLA-B＊5701）. Studies also found that ab- acavir-induced ADRs were seldom observed in patients carrying the HLA-B＊5801 subtype. HLA-B＊5801 of the same sero- type （B17） as B＊5701 differs by only 4 amino acids from B＇5701. It is believed that because of these sequence differences, HLA-B＊5801 cannot bind the specific peptides which are required for HLA-B＊5701 to stimulate the T cell immune response. Thus, the difference in peptide binding profiles between HLA-B＊5701 and B＊5801 is an important clue for exploring the mechanisms of abacavir-induced ADRs. VHSE （principal component score vector of hydrophobic, steric, and electronic prop- erties）, a set of amino acid structural descriptors, was employed to establish QSAR models of peptide-binding affinities of HLA-B＊5701 and B＊5801. Optimal linear SVM （support vector machine） models with high predictive capabilities were ob- tained for both B＊5701 and B＇5801. The R2 （coefficient of determination）, Q2 （cross-validated R：）, and RpRE2 （R2 of test set） of two optimal models were 0,7530, 0.7037, 0.6153 （B＇5701） and 0.6074, 0.5966, 0.5762 （B＊5801）, respectively. For B＇5701 and B＇5801, the mutations in positions 45 （MET-THR） and 46 （ALA-GLU） have little influence on the selection specificity of the P2 position of the bound peptide. However, the mutation in position 97 （VAL-ARG） greatly influences the selection speci- ficity of the P7 position. HLA-B＊5701 prefers the bulky and positively charged amino acids at the P7 position. In contrast, HLA-B＊5801 prefers the non-polar hydrophobic amino acids at the P7 position while positively charged amino acids are un- favored.
