Local Mutations Can Serve as a Game Changer for Global Protein Solvent Interaction

Abstract

Although it is well-known that limited local mutations of enzymes, such as matrix metalloproteinases (MMPs), may change enzyme activity by orders of magnitude as well as its stability, the completely rational design of proteins is still challenging. These local changes alter the electrostatic potential and thus local electrostatic fields, which impacts the dynamics of water molecules close the protein surface. Here we show by a combined computational design, experimental, and molecular dynamics (MD) study that local mutations have not only a local but also a global effect on the solvent: In the specific case of the matrix metalloprotease MMP14, we found that the nature of local mutations, coupled with surface morphology, have the ability to influence large patches of the water hydrogen-bonding network at the protein surface, which is correlated with stability. The solvent contribution can be experimentally probed via terahertz (THz) spectroscopy, thus opening the door to the exciting perspective of rational protein design in which a systematic tuning of hydration water properties allows manipulation of protein stability and enzymatic activity.

Spectroscopic Fingerprints of Cavity Formation and Solute Insertion as a Measure of Hydration Entropic Loss and Enthalpic Gain

“…water‐mediated catalysis [10–12] and electro‐catalysis [13–15] . Going from small solutes all the way up to large biomolecules, a subtle balance between hydrophilic and hydrophobic interactions is what dictates hydration free energies [16–24] . Evaluating such balance requires a local mapping of hydrophilic and hydrophobic contributions, which remains a challenge for both theory and experiments [18, 19, 25–29] .…”

“…[13][14][15] Going from small solutes all the way up to large biomolecules, a subtle balance between hydrophilic and hydrophobic interactions is what dictates hydration free energies. [16][17][18][19][20][21][22][23][24] Evaluating such balance requires a local mapping of hydrophilic and hydrophobic contributions, which remains a challenge for both theory and experiments. [18,19,[25][26][27][28][29] From the experimental side, these contributions are notoriously difficult to probe and cannot be dissected by standard calorimetry approaches.…”

“…[16][17][18][19][20][21][22][23][24] Evaluating such balance requires a local mapping of hydrophilic and hydrophobic contributions, which remains a challenge for both theory and experiments. [18,19,[25][26][27][28][29] From the experimental side, these contributions are notoriously difficult to probe and cannot be dissected by standard calorimetry approaches. Nevertheless, several attempts have been undertaken since the ability to characterize hydration thermodynamic properties would guarantee major economic advantages for e.g.…”

On the trail of molecular hydrophilicity and hydrophobicity at aqueous interfaces

“…In other words, the spatial distribution of the hydrophobic/hydrophilic sites has a large influence on global hydrophobicity, as it is well documented in previous theoretical works. 33,43,[50][51][52][53] . As a result of dangling-OH suppression for the uniform mixing adopted in our simulation, the tiny free OH peak in the BIL-SFG spectrum of the mixed PEG-OTS/water system is hardly distinguishable from the PEG/water interface, both with approximately zero free OH signal.…”

Hydration Dynamics in Biological Membranes: Emerging Applications of Terahertz Spectroscopy

“…However, gaining quantitative insights on membrane hydration dynamics in complex cellular systems is strongly contingent on the availability of comprehensive literature on changes in THz patterns with differences in microenvironment (including pH and presence of salt, metal ions, and small molecules) commonly experienced by biological membranes. Incidentally, such a strategy has been successfully employed for THz-based studies of proteins, with systematic characterization of hydration of individual amino acids, amino acid mixtures and dipeptides, and peptide tetramers complementing investigations on more complex biologically relevant proteins, ,− including GPCRs and the SecY translocon …”