Dewetting transitions in protein cavities

Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies

The independent trajectory thermodynamic integration (IT-TI) approach (Lawrenz et. al J. Chem. Theory. Comput. 2009, 5:1106-1116(1)) for free energy calculations with distributed computing is employed to study two distinct cases of protein-ligand binding: first, the influenza surface protein N1 neuraminidase bound to the inhibitor oseltamivir, and second, the M. tuberculosis enzyme RmlC complexed with the molecule CID 77074. For both systems, finite molecular dynamics (MD) sampling and varied molecular flexibility give rise to IT-TI free energy distributions that are remarkably centered on the target experimental values, with a spread directly related to protein, ligand, and solvent dynamics. Using over 2 μs of total MD simulation, alternative protocols for the practical, general implementation of IT-TI are investigated, including the optimal use of distributed computing, the total number of alchemical intermediates, and the procedure to perturb electrostatics and van der Waals interactions. A protocol that maximizes predictive power and computational efficiency is proposed. IT-TI outperforms traditional TI predictions and allows a straightforward evaluation of the reliability of free energy estimates. Our study has broad implications for the use of distributed computing in free energy calculations of macromolecular systems.

Advances in all atom sampling methods for modeling protein-ligand binding affinities

Conformational dynamics plays a fundamental role in the regulation of molecular recognition processes. Conformational heterogeneity and entropy variations upon binding, although not always evident from the analysis of structural data, can substantially affect affinity and specificity. Computer modeling is able to provide some of the most direct insights into these aspects of molecular recognition. We review recent physics-based computational studies that employ advanced conformational sampling algorithms and effective potentials to model the three main classes of degrees of freedom relevant to the binding process: ligand positioning relative to the receptor, ligand and receptor internal reorganization, and hydration. Collectively these studies show that all of these elements are important for proper modeling of protein-ligand interactions.

Ligand binding to protein-binding pockets with wet and dry regions

Biological processes often depend on protein-ligand binding events, yet accurate calculation of the associated energetics remains as a significant challenge of central importance to structure-based drug design. Recently, we have proposed that the displacement of unfavorable waters by the ligand, replacing them with groups complementary to the protein surface, is the principal driving force for protein-ligand binding, and we have introduced the WaterMap method to account this effect. However, in spite of the adage "nature abhors vacuum," one can occasionally observe situations in which a portion of the receptor active site is so unfavorable for water molecules that a void is formed there. In this paper, we demonstrate that the presence of dry regions in the receptor has a nontrivial effect on ligand binding affinity, and suggest that such regions may represent a general motif for molecular recognition between the dry region in the receptor and the hydrophobic groups in the ligands. With the introduction of a term attributable to the occupation of the dry regions by ligand atoms, combined with the WaterMap calculation, we obtain excellent agreement with experiment for the prediction of relative binding affinities for a number of congeneric ligand series binding to the major urinary protein receptor. In addition, WaterMap when combined with the cavity contribution is more predictive than at least one specific implementation [Abel R, Young T, Farid R, Berne BJ, Friesner RA (2008) J Am Chem Soc 130:2817-2831] of the popular MM-GBSA approach to binding affinity calculation.

How Can Hydrophobic Association Be Enthalpy Driven?

Hydrophobic association is often recognized as being driven by favorable entropic contributions. Here, using explicit solvent molecular dynamics simulations we investigate binding in a model hydrophobic receptor-ligand system which appears, instead, to be driven by enthalpy and opposed by entropy. We use the temperature dependence of the potential of mean force to analyze the thermodynamic contributions along the association coordinate. Relating such contributions to the ongoing changes in system hydration allows us to demonstrate that the overall binding thermodynamics is determined by the expulsion of disorganized water from the receptor cavity. Our model study sheds light on the solvent-induced driving forces for receptor-ligand association of general, transferable relevance for biological systems with poorly hydrated binding sites.

Mechanisms underlying dioxygen reduction in laccases. Structural and modelling studies focusing on proton transfer

BACKGROUND

Laccases are enzymes that couple the oxidation of substrates with the reduction of dioxygen to water. They are the simplest members of the multi-copper oxidases and contain at least two types of copper centres; a mononuclear T1 and a trinuclear that includes two T3 and one T2 copper ions. Substrate oxidation takes place at the mononuclear centre whereas reduction of oxygen to water occurs at the trinuclear centre.

RESULTS

In this study, the CotA laccase from Bacillus subtilis was used as a model to understand the mechanisms taking place at the molecular level, with a focus in the trinuclear centre. The structures of the holo-protein and of the oxidised form of the apo-protein, which has previously been reconstituted in vitro with Cu(I), have been determined. The former has a dioxygen moiety between the T3 coppers, while the latter has a monoatomic oxygen, here interpreted as a hydroxyl ion. The UV/visible spectra of these two forms have been analysed in the crystals and compared with the data obtained in solution. Theoretical calculations on these and other structures of CotA were used to identify groups that may be responsible for channelling the protons that are needed for reduction of dioxygen to water.

CONCLUSIONS

These results present evidence that Glu 498 is the only proton-active group in the vicinity of the trinuclear centre. This strongly suggests that this residue may be responsible for channelling the protons needed for the reduction. These results are compared with other data available for these enzymes, highlighting similarities and differences within laccases and multicopper oxidases.