The binding of Endonuclease colicin 9 (E9) by Immunity protein 9 (Im9) was found to involve some hotspots from helix III of Im9 on protein-protein interface that contribute the dominant binding energy to the complex.I...The binding of Endonuclease colicin 9 (E9) by Immunity protein 9 (Im9) was found to involve some hotspots from helix III of Im9 on protein-protein interface that contribute the dominant binding energy to the complex.In the current work,MD simulations of the WT and three hotspot mutants (D51A,Y54A and Y55A of Im9) of the E9-Im9 complexes were carried out to investigate specific interaction mechanisms of these three hotspot residues.The changes of binding energy between the WT and mutants of the complex were computed by the MM/PBSA method using a polarized force field and were in excellent agreement with experiment values,verifying that these three residues were indeed hotspots of the binding complex.Energy decomposition analysis revealed that binding by D51 to E9 was dominated by electrostatic interaction due to the presence of the carboxyl group of Asp51 which hydrogen bonds to K89.For binding by hotspots Y54 and Y55,van der Waals interaction from the aromatic side chain of tyrosine provided the dominant interaction.For comparison,calculation by using the standard (nonpolarizable) AMBER99SB force field produced binding energy changes from these mutations in opposite direction to the experimental observation.Dynamic hydrogen bond analysis showed that conformations sampled from MD simulation in the standard AMBER force field were distorted from the native state and they disrupted the inter-protein hydrogen bond network of the protein-protein complex.The current work further demonstrated that electrostatic polarization plays a critical role in modulating protein-protein binding.展开更多
beta-Galactosidase, a kind of endoenzyme in E. coli cells. can be released by the pore-forming action of colicin El. and E. coli can be detected rapidly by enzymatic method.
目的:表达并纯化大肠杆菌素Ia通道结构域(Colicin Ia channel domain)与变异链球菌感受刺激多肽(CSP)的融合蛋白。方法:将编码大肠杆菌素Ia通道结构域的基因与编码变异链球菌感受刺激多肽CSP的基因导入带有麦芽糖结合蛋白(MBP)基因的pMA...目的:表达并纯化大肠杆菌素Ia通道结构域(Colicin Ia channel domain)与变异链球菌感受刺激多肽(CSP)的融合蛋白。方法:将编码大肠杆菌素Ia通道结构域的基因与编码变异链球菌感受刺激多肽CSP的基因导入带有麦芽糖结合蛋白(MBP)基因的pMAL-c2x质粒中,构建pMAL-c2x-Colicin Ia channeldomain-CSP融合表达载体,将重组质粒转化大肠埃希菌BL21后,IPTG诱导融合蛋白表达,裂解后得到目的蛋白。结果:通过双酶切、电泳分析、测序,证明成功构建了pMAL-c2x-Colicin Ia channel domain-CSP融合表达载体,目的蛋白产物经SDS-PAGE分析,与预期一致。结论:成功构建了pMAL-c2x-Colicin Ia channeldomain-CSP,表达并纯化目的蛋白,为进一步研究Colicin Ia channel domain-CSP的功能奠定了基础。展开更多
基金the National Natural Science Foundation of China(21003048,10974054,and 20933002)Shanghai PuJiang Program (09PJ1404000) for financial support XXY is also supported by "Scientific Research Foundation for Agricultural Machinery Bureau of Jiangsu Province (gxz10008)"CGJ is also supported by "the Fundamental Research Funds for the Central Universities"
文摘The binding of Endonuclease colicin 9 (E9) by Immunity protein 9 (Im9) was found to involve some hotspots from helix III of Im9 on protein-protein interface that contribute the dominant binding energy to the complex.In the current work,MD simulations of the WT and three hotspot mutants (D51A,Y54A and Y55A of Im9) of the E9-Im9 complexes were carried out to investigate specific interaction mechanisms of these three hotspot residues.The changes of binding energy between the WT and mutants of the complex were computed by the MM/PBSA method using a polarized force field and were in excellent agreement with experiment values,verifying that these three residues were indeed hotspots of the binding complex.Energy decomposition analysis revealed that binding by D51 to E9 was dominated by electrostatic interaction due to the presence of the carboxyl group of Asp51 which hydrogen bonds to K89.For binding by hotspots Y54 and Y55,van der Waals interaction from the aromatic side chain of tyrosine provided the dominant interaction.For comparison,calculation by using the standard (nonpolarizable) AMBER99SB force field produced binding energy changes from these mutations in opposite direction to the experimental observation.Dynamic hydrogen bond analysis showed that conformations sampled from MD simulation in the standard AMBER force field were distorted from the native state and they disrupted the inter-protein hydrogen bond network of the protein-protein complex.The current work further demonstrated that electrostatic polarization plays a critical role in modulating protein-protein binding.
文摘beta-Galactosidase, a kind of endoenzyme in E. coli cells. can be released by the pore-forming action of colicin El. and E. coli can be detected rapidly by enzymatic method.
文摘目的:表达并纯化大肠杆菌素Ia通道结构域(Colicin Ia channel domain)与变异链球菌感受刺激多肽(CSP)的融合蛋白。方法:将编码大肠杆菌素Ia通道结构域的基因与编码变异链球菌感受刺激多肽CSP的基因导入带有麦芽糖结合蛋白(MBP)基因的pMAL-c2x质粒中,构建pMAL-c2x-Colicin Ia channeldomain-CSP融合表达载体,将重组质粒转化大肠埃希菌BL21后,IPTG诱导融合蛋白表达,裂解后得到目的蛋白。结果:通过双酶切、电泳分析、测序,证明成功构建了pMAL-c2x-Colicin Ia channel domain-CSP融合表达载体,目的蛋白产物经SDS-PAGE分析,与预期一致。结论:成功构建了pMAL-c2x-Colicin Ia channeldomain-CSP,表达并纯化目的蛋白,为进一步研究Colicin Ia channel domain-CSP的功能奠定了基础。
