Microscopic mechanisms that govern the titration response and p K _a values of buried residues in staphylococcal nuclease mutants

Abstract

To probe the microscopic mechanisms that govern the titration behavior of buried ionizable groups, microsecond explicit solvent molecular dynamics simulations are carried out for several mutants of Staphylococcal nuclease using both fixed charge and polarizable force fields. While the ionization of Asp 66, Glu 66, and Lys 125 lead to enhanced structural fluctuations and partial unfolding of adjacent α-helical regions, the ionization of Lys 25 causes local unfolding of adjacent β sheets. Using the sampled conformational ensembles, good agreement with experimental pK values is obtained with Poisson-Boltzmann calculations using a protein dielectric constant of 2-4 for V66D/E; slightly larger dielectric constants are needed for Lys mutants especially L25K, suggesting that structural responses beyond microseconds are involved in ionization of Lys 25. Overall, the set of unbiased simulations provides insights into the spatial and temporal scales of protein and solvent motions that dictate the diverse titration behaviors of buried protein residues. Proteins 2017; 85:268-281. © 2016 Wiley Periodicals, Inc.

Prominent features of the amino acid mutation landscape in cancer

“…Charge-changing mutations, whether buried or surface-exposed, can alter protein charge, electrostatics, and conformation [16]. Electrostatics of surface residues have been shown to play a key role in protein-protein interactions [17], protein-membrane interactions [18, 19], and kinase substrate recognition [20].…”

Tracing the Pathways of Waters and Protons in Photosystem II and Cytochrome c Oxidase

“…A current work-around to the fixed backbone is to average the charge state distributions calculated in multiple snapshots from MD simulation or from multiple crystal structures, which provide a distribution of likely conformations. One problem is that an MD simulation will always seek to stabilize the charge states assigned to the simulation [73,74].…”

Conformational sampling and polarization of Asp26 in pKa calculations of thioredoxin

“…Calculations of the p K a of protein residues are highly dependent on the conformation of the protein and the description of the solvent . Starting from the X‐Ray structure, Thioredoxin was simulated in explicit solvent for 2 μ s with Asp26 in the protonated (state A) or deprotonated form (state B).…”

“…Calculations of the pK a of protein residues are highly dependent on the conformation of the protein and the description of the solvent. 10,39,42 Starting from the X-Ray structure, Thioredoxin was simulated in explicit solvent for 2 μs with Asp26 in the protonated (state A) or deprotonated form (state B). Slow conformational transitions related to changes in the position of backbone atoms were monitored by principal component analysis based on the backbone RMSD.…”

“…The importance of conformational changes in different protontation states and their effect on Δ p K a calculations has been recently addressed in staphylococoal nuclease mutants by Zheng and Cui with microsecond molecular dynamics simulation and polarizable and non‐polarizable force fields . The authors report that changes in the protonation state of buried titratable residues induce loss of secondary structure, rotations of side chains to be more solvent exposed and varying number of water molecules in hydrophobic pockets, which is only observed at relatively long time scales.…”