论文库首页  论文库
 
论文编号:
论文题目: Elucidation of Single Hydrogen Bonds in GTPases via Experimental and Theoretical Infrared Spectroscopy
英文论文题目: Elucidation of Single Hydrogen Bonds in GTPases via Experimental and Theoretical Infrared Spectroscopy
第一作者: Mann, D; Howeler, U; Kotting, C; Gerwert, K
英文第一作者: Mann, D; Howeler, U; Kotting, C; Gerwert, K
联系作者: Gerwert, K (reprint author), CAS MPG Partner Inst Computat Biol PICB Shanghai, Shanghai, Peoples R China.
英文联系作者: Gerwert, K (reprint author), CAS MPG Partner Inst Computat Biol PICB Shanghai, Shanghai, Peoples R China.
外单位作者单位:
英文外单位作者单位:
发表年度: 2017
卷: 112
期: 1
页码: 66-77
摘要: Time-resolved Fourier transform infrared (FTIR) spectroscopy is a powerful tool to elucidate label-free the reaction mechanisms of proteins. After assignment of the absorption bands to individual groups of the protein, the order of events during the reaction mechanism can be monitored and rate constants can be obtained. Additionally, structural information is encoded into infrared spectra and can be decoded by combining the experimental data with biomolecular simulations. We have determined recently the infrared vibrations of GTP and guanosine diphosphate (GDP) bound to Gail, a ubiquitous GTPase. These vibrations are highly sensitive for the environment of the phosphate groups and thereby for the binding mode the GTPase adopts to enable fast hydrolysis of GTP. In this study we calculated these infrared vibrations from biomolecular simulations to transfer the spectral information into a computational model that provides structural information far beyond crystal structure resolution. Conformational ensembles were generated using 15 snapshots of several 100 ns molecular-mechanics/molecular-dynamics (MM-MD) simulations, followed by quantum-mechanics/molecular-mechanics (QM/MM) minimization and normal mode analysis. In comparison with other approaches, no time-consuming QM/MM-MD simulation was necessary. We carefully bench marked the simulation systems by deletion of single hydrogen bonds between the GTPase and GTP through several G alpha(i1) point mutants. The missing hydrogen bonds lead to blue-shifts of the corresponding absorption bands. These band shifts for alpha-GTP (G alpha(i1)-T48A), gamma-GTP (G alpha(i1)-R178S), and for both beta-GTP/gamma-GTP (G alpha(i1)-K46A, G alpha(i1)-D200E) were found in agreement in the experimental and the theoretical spectra. We applied our approach to open questions regarding G alpha(i1): we show that the GDP state of Gail carries a Mg2+, which is not found in x-ray structures. Further, the catalytic role of K46, a central residue of the P-loop, and the protonation state of the GTP are elucidated.
英文摘要: Time-resolved Fourier transform infrared (FTIR) spectroscopy is a powerful tool to elucidate label-free the reaction mechanisms of proteins. After assignment of the absorption bands to individual groups of the protein, the order of events during the reaction mechanism can be monitored and rate constants can be obtained. Additionally, structural information is encoded into infrared spectra and can be decoded by combining the experimental data with biomolecular simulations. We have determined recently the infrared vibrations of GTP and guanosine diphosphate (GDP) bound to Gail, a ubiquitous GTPase. These vibrations are highly sensitive for the environment of the phosphate groups and thereby for the binding mode the GTPase adopts to enable fast hydrolysis of GTP. In this study we calculated these infrared vibrations from biomolecular simulations to transfer the spectral information into a computational model that provides structural information far beyond crystal structure resolution. Conformational ensembles were generated using 15 snapshots of several 100 ns molecular-mechanics/molecular-dynamics (MM-MD) simulations, followed by quantum-mechanics/molecular-mechanics (QM/MM) minimization and normal mode analysis. In comparison with other approaches, no time-consuming QM/MM-MD simulation was necessary. We carefully bench marked the simulation systems by deletion of single hydrogen bonds between the GTPase and GTP through several G alpha(i1) point mutants. The missing hydrogen bonds lead to blue-shifts of the corresponding absorption bands. These band shifts for alpha-GTP (G alpha(i1)-T48A), gamma-GTP (G alpha(i1)-R178S), and for both beta-GTP/gamma-GTP (G alpha(i1)-K46A, G alpha(i1)-D200E) were found in agreement in the experimental and the theoretical spectra. We applied our approach to open questions regarding G alpha(i1): we show that the GDP state of Gail carries a Mg2+, which is not found in x-ray structures. Further, the catalytic role of K46, a central residue of the P-loop, and the protonation state of the GTP are elucidated.
刊物名称: BIOPHYSICAL JOURNAL
英文刊物名称: BIOPHYSICAL JOURNAL
论文全文:
英文论文全文:
全文链接:
其它备注:
英文其它备注:
学科: Biophysics
英文学科: Biophysics
影响因子: 3.656
第一作者所在部门:
英文第一作者所在部门:
论文出处:
英文论文出处:
论文类别: Article
英文论文类别: Article
参与作者:
英文参与作者:
 
2014 中国科学院上海生命科学研究院 版权所有