PARAMETRIZATION, MD SIMULATION, CALCULATION OF POLYALANINE ALPHA-HELIX SPECTRA

参数化、分子动力学模拟、聚丙氨酸α螺旋谱的计算

• 批准号: 8364015
• 负责人: DENIZ SEZER
• 金额: $ 0.16万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-01 至 2012-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8364015
• 关键词: Affect; Alanine; Diffusion; Electron Spin Resonance Spectroscopy; Funding; Grant; Hydrophobic Interactions; Muramidase; National Center for Research Resources; Principal Investigator; Proteins; Research; Research Infrastructure; Resources; Side; Simulate; Site; Solutions; Solvents; Source; Spin Labels; Technology; Time; United States National Institutes of Health; alpha helix; cost; methyl methanethiosulfonate; molecular dynamics; polyalanine

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The nitroxide spin label 1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl-methanethiosulfonate (MTSSL), commonly used in site-directed spin labeling of proteins, was studied with molecular dynamics (MD) simulations. After developing force field parameters for the nitroxide moiety and the spin label linker, we simulated MTSSL attached to a polyalanine R-helix in explicit solvent to elucidate the factors affecting its conformational dynamics. Electron spin resonance spectra at 9 and 250 GHz were simulated in the time domain using the MD trajectories and including global rotational diffusion appropriate for the tumbling of T4 Lysozyme in solution. Analysis of the MD simulations reveals the presence of significant hydrophobic interactions of the spin label with the alanine side chains

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