Proteins, Lipids, and Water in the Gas Phase

Abstract

Evidence from mass‐spectrometry experiments and molecular dynamics simulations suggests that it is possible to transfer proteins, or in general biomolecular aggregates, from solution to the gas‐phase without grave impact on the structure. If correct, this allows interpretation of such experiments as a probe of physiological behavior. Here, we survey recent experimental results from mass spectrometry and ion‐mobility spectroscopy and combine this with observations based on molecular dynamics simulation, in order to give a comprehensive overview of the state of the art in gas‐phase studies. We introduce a new concept in protein structure analysis by determining the fraction of the theoretical possible numbers of hydrogen bonds that are formed in solution and in the gas‐phase. In solution on average 43% of the hydrogen bonds is realized, while in vacuo this fraction increases to 56%. The hydrogen bonds stabilizing the secondary structure (α‐helices, β‐sheets) are maintained to a large degree, with additional hydrogen bonds occurring when side chains make new hydrogen bonds to rest of the protein rather than to solvent. This indicates that proteins that are transported to the gas phase in a native‐like manner in many cases will be kinetically trapped in near‐physiological structures. Simulation results for lipid‐ and detergent‐aggregates and lipid‐coated (membrane) proteins in the gas phase are discussed, which in general point to the conclusion that encapsulating proteins in “something” aids in the conservation of native‐like structure. Isolated solvated micelles of cetyl‐tetraammonium bromide quickly turn into reverse micelles whereas dodecyl phosphocholine micelles undergo much slower conversions, and do not quite reach a reverse micelle conformation within 100 ns. magnified image

Integrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiporters

“…We speculated that the most preferred lipid interactions observed by MD stabilize the protein in MS. We therefore carried out in vacuo MD simulations of detergent-free NapA with and without PE bound to mimic conditions inside the mass spectrometer2122. We therefore selected 23 PE molecules to represent the lipids in the first annular belt as observed in MD (Methods).…”

“…4d)21222324. CCS calculations of the equilibrated protein systems at the different temperatures allowed us to compare the predicted events with the unfolding steps observed by IM–MS.…”

Do Charge State Signatures Guarantee Protein Conformations?

“…Limited conformational changes were observed upon dehydration; these included the inward-folding of hydrophilic side chains, which tended to form new hydrogen bonds. In fact, more hydrogen bonds are typically observed in the gas-phase structures than for those same structures in solution [45]. These newly formed hydrogen bonds are likely to play a key role in the stabilization of secondary structure as the protein is transferred into vacuum conditions.…”

Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer

“…In addition, the fraction of hydrogen bonds (relative to the theoretical maximum) increases significantly upon passing from aqueous solution (on average 43%) to the gas phase (on average 56%) [41]. This suggests that proteins in the gas phase may be trapped in a low energy state, structurally close to the native state in water [42]. Our recent studies further indicate that the ionization state of a gas-phase protein is the result of the balance between repulsive electrostatic terms and stabilizing forces that include salt bridges, hydrogen bonds, π-charge and long-range electrostatic interactions [37], [38].…”