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The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes, chemistries, and biological functions, and characterize their interactions with their hydration waters using molecular simulation and enhanced sampling techniques. We find that akin to extended hydrophobic surfaces, proteins situate their hydration waters at the edge of a dewetting transition, making them susceptible to unfavorable perturbations. We also find that the strength of the unfavorable potential needed to trigger dewetting is roughly the same, regardless of the protein being studied, and depends only the width of the hydration shell being perturbed. Our findings establish a framework for systematically classifying protein patches according to how favorably they interact with water.
An understanding of density fluctuations in bulk water has made significant contributions to our understanding of the hydration and interactions of idealized, purely repulsive hydrophobic solutes. To similarly inform the hydration of realistic hydrop
S-nitrosylation, the covalent addition of NO to the thiol side chain of cysteine, is an important post-transitional modification that can alter the function of various proteins. The structural dynamics and vibrational spectroscopy of S-nitrosylation
Native electrospray ionization/ion mobility-mass spectrometry (ESI/IM-MS) allows an accurate determination of low-resolution structural features of proteins. Yet, the presence of proton dynamics, observed already by us for DNA in the gas phase, and i
The recently proposed Hamiltonian Adaptive Resolution Scheme (H-AdResS) allows to perform molecular simulations in an open boundary framework. It allows to change on the fly the resolution of specific subset of molecules (usually the solvent), which
We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mecha