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Full-Text Articles in Physical Sciences and Mathematics
Testing The Robustness Of Solution Force Fields For Md Simulations On Gaseous Protein Ions., Justin H Lee, Katja Pollert, Lars Konermann
Testing The Robustness Of Solution Force Fields For Md Simulations On Gaseous Protein Ions., Justin H Lee, Katja Pollert, Lars Konermann
Chemistry Publications
It is believed that electrosprayed proteins and protein complexes can retain solution-like conformations in the gas phase. However, the lack of high-resolution structure determination methods for gaseous protein ions implies that their properties remain poorly understood. Many practitioners tackle this difficulty by complementing mass spectrometry-based experiments with molecular dynamics (MD) simulations. It is a potential problem that the standard MD force fields used for this purpose (such as OPLS-AA/L and CHARMM) were optimized for solution conditions. The question whether these force fields produce meaningful gas-phase data has received surprisingly little attention. Standard force fields are overpolarized to account for an …
Protein Ions Generated By Native Electrospray Ionization: Comparison Of Gas Phase, Solution, And Crystal Structures., Maryam Bakhtiari, Lars Konermann
Protein Ions Generated By Native Electrospray Ionization: Comparison Of Gas Phase, Solution, And Crystal Structures., Maryam Bakhtiari, Lars Konermann
Chemistry Publications
Experiments and molecular dynamics (MD) simulations in the literature indicate that gaseous proteins generated by electrospray ionization (ESI) can retain native-like structures. However, the exact properties of these ions remain to be explored. Focusing on ubiquitin and lysozyme, we examined several pertinent questions. (1) We applied solvent MD runs to test whether the X-ray structures of both proteins are affected by crystal packing. Main and side-chain orientations were retained in solution, providing a justification for the hitherto unscrutinized approach of relying on crystal data for "solution" versus gas-phase comparisons. (2) Most earlier gas-phase protein MD investigations employed short (ns) simulation …