Abstract: Solvation of protein surface charges plays an important role for the protonation states of titratable surface groups and is routinely incorporated in low dielectric protein models using surface accessible areas. For many-body protein simulations, however, such dielectric boundary methods are rarely tractable and a greater level of simplification is desirable. In this work, we scrutinize how charges on a high dielectric surface are affected by the nonpolar interior core of the protein. A simple dielectric model, which models the interior as a low dielectric sphere, combined with Monte Carlo simulations, shows that for small, hydrophilic proteins the effect of the low dielectric interior is largely negligible and that the protein (and solution) can be approximated with a uniform high dielectric constant equal to that of the solvent. This is verified by estimates of titration curves and acidity constants for four different proteins (BPTI, calbindin D(9k), ribonuclease A, and turkey ovomucoid third domain) that all correlate well with experimental data. Furthermore, the high dielectric approximation follows as a natural consequence of the multipole expansion of the potential due to embedded protein charges in the presence of the low dielectric core region.
Abstract: For a series of biologically relevant anions, we present free energy changes upon replacing potassium with sodium in a contact ion pair. Calculations performed using a combination of molecular dynamics simulations and ab initio methods demonstrate the ordering of anions in a Hofmeister series. Small anionic groups such as carboxylates preferentially pair with sodium, while intermediate cases such as chloride or monovalent phosphate exhibit almost no specificity, and large anions (e.g., methylsulfonate) prefer potassium over sodium. These results can rationalize different behavior of Na+ versus K+ at the surface of hydrated proteins, DNA, and reversed micelles.
Abstract: Proteins in the living cell can interact with a wide variety of solutes, ranging from ions, peptides, other proteins, DNA to membranes. Charged groups play a major role and solution conditions such as pH and ionic strength can modulate the interactions significantly. Describing these systems in a statistical mechanical framework involves thousands of pair-interactions and therefore a certain amount of coarse graining is often required. We here present a conceptually simple mesoscopic protein model where the detailed charge distribution and surface topology is well preserved. Monte Carlo simulations based on this model can be used to accurately reproduce second virial coeffients, pH titration curves and binding constants of proteins.
Abstract: Both natural and synthetic polyelectrolytes form strong complexes with a variety of proteins. One peculiar phenomenon is that association can take place even when the protein and the polyelectrolyte carry the same charge. This has been interpreted as if the ion-dipole interaction can overcome the repulsive ion-ion interaction. On the basis of Monte Carlo simulations and perturbation theory, we propose a different explanation for the association, namely, charge regulation. We have investigated three different protein-polymer complexes and found that the induced ionization of amino acid residues due to the polyelectrolyte leads to a surprisingly strong attractive interaction between the protein and the polymer. The extra attraction from this charge-induced charge interaction can be several kT and is for the three cases studied here, lysozyme, alpha-lactalbumin, and beta-lactoglobulin, of the same magnitude or stronger than the ion-dipole interaction. The magnitude of the induced charge is governed by a response function, the protein charge capacitance Z2-Z2. This fluctuation term can easily be calculated in a simulation or measured in a titration experiment.
Abstract: When a protein molecule approaches a charged surface, its protonation state can undergo dramatic changes due to the imposed electric potential. This has a large impact on adsorption strengths that may be enhanced by several kT. Using mesoscopic simulation techniques as well as analytical theories, we have investigated this regulation mechanism and demonstrate how it is influenced by salt concentration and solution pH. Using hisactophilin as a test case, we show how the binding to a lipid membrane is governed by small changes in pH and that this is intimately coupled to the charge regulation mechanism.
Abstract: It is known that the overall charge of a protein can change as the molecule approaches a charged object like another protein or a cell membrane. We have formalized this mechanism using a statistical mechanical framework and show how this rather overlooked interaction increases the attraction between protein molecules. From the theory, we can identify a unique property, the protein charge capacitance, that contains all information needed to describe the charge regulation mechanism. The capacitance can be obtained from experiment or theory and is a function of pH, salt concentration, and the number of titrating residues. For a range of different protein molecules, we calculate the capacitance and demonstrate how it can be used to quantify the charge regulation interaction. With minimal effort, the derived formulas can be used to improve existing models by including a charge regulation term. Good agreement is found between theory, simulations, and experimental data.
Abstract: Concentrations of ammonia in air and ammonium in surface water were measured from a platform in the Southern North Sea close to the Dutch coast. Fluxes were derived from the measurements applying Monin-Obukhov similarity theory and exchange velocities calculated. The fluxes and air concentrations of ammonia were compared to results obtained from the Lagrangian transport-chemistry model ACDEP with and without a parameterisation of outgoing fluxes of ammonia from the sea. The results indicate that the flux may in fact be upward during periods with low atmospheric ammonia concentrations and that the calculated overall ammonia dry deposition may be overestimated by a factor two or more in the coastal region. A more detailed study is needed in order to quantify how this may influence overall deposition to given marine waters. In some cases the deposition may solely be redistributed whereas the total deposition is only marginally influenced.
Abstract: Protein self-association may be detrimental in biological systems, but can be utilized in a controlled fashion for protein crystallization. It is hence of considerable interest to understand how factors like solution conditions prevent or promote aggregation. Here we present a computational model describing interactions between protein molecules in solution. The calculations are based on a molecular description capturing the detailed structure of the protein molecule using x-ray or nuclear magnetic resonance structural data. Both electrostatic and van der Waals interactions are included and the salt particles are explicitly treated allowing investigations of systems containing mono-, di-, and trivalent ions. For three different proteinsâlysozyme, -chymotrypsinogen, and calbindin D9kâwe have investigated under which conditions (salt concentration, ion valency, pH, and/or solvent) the proteins are expected to aggregate via evaluation of the second virial coefficient. Good agreement is found with experimental data where available. Calbindin is investigated in more detail, and it is demonstrated how changes in solvent and/or counterion valency lead to attractive ion-ion correlation effects. For high valency counterions we have found abnormal trends in the second virial coefficient. With trivalent counterions, attraction of two negatively charged protein molecules can be favored because the repulsive term is decreased for entropic reasons due to the low number of particles present.
Abstract: Electrostatic interactions in bio-molecular systems are important
not only in the living cell but also in more technical applications.
Using molecular simulation as well as approximate theories the
properties of a number of aqueous protein solutions have been
studied. This include interactions with other proteins, protons,
charged membranes as well as flexible polyelectrolytes. The focus
is on electrostatic interactions and special attention is put on
charge regulation. I.e. how the protonation state of a biomolecule
is influenced by nearby charged species. We show that this gives an
important contribution to the free energy and that the mechanism
can be accounted for by a simple statistical mechanical model. In
particular we introduce the concept of âprotein capacitanceâ that
is the key intrinsic property for quantifying the charge regulation.
