Hydronium Ions Accompanying Buried Acidic Residues Lead to High Apparent Dielectric Constants in the Interior of Proteins

Selective Inhibitor Design against Thymidylate Synthase of Mycobacterium tuberculosis Using Alchemical Simulations

Thymidylate synthase is an essential enzyme that catalyzes the conversion of deoxyuridine monophosphate (dUMP) to deoxythymidine monophosphate (dTMP). Thymidylate synthase from Mycobacterium tuberculosis(MtbThyX) recognizes the deprotonated substrate dUMP(d) (ionized at N3, charge = -3) involving the cationic side chain of Arg199, whereas the human analogue (hThyA) selects the natural substrate dUMP (charge = -2) by involving the polar side chain of Asn226 in the binding pocket. Distinctly different protonation states of the substrate and the catalytic pocket architecture make MtbThyX an attractive drug target for combating Mycobacterium tuberculosis. Fluorodeoxyuridylate (FdUMP) is a known inhibitor of thymidylate synthase, which is severely limited by poor selectivity (it is more potent against hThyA relative to MtbThyX). Using FdUMP as a template, we designed three drug-like ligands, L1, L2, and L3, by (1) removing the proton from the Watson-Crick edge and (2) substituting the ketone/hydroxyl group with fluorine and/or a carboxylic moiety. The absence of a proton on the N3 atom of the ligand is intended to ensure selectivity by favoring MtbThyX binding (skipping the N3 ionization requirement) but penalizing hThyA binding (disrupting the interaction with Asn226). Ionization of the carboxyl group in the ligands was expected to increase the affinity in the cationic binding pocket of MtbThyX. Alchemical simulations confirmed that the designed ligands are strongly favored and disfavored relative to the substrate (dUMP) by MtbThyX and hThyA, respectively. In contrast to hThyA, the catalytic pocket of MtbThyX proved to be relatively dry and stabilized the relatively compact conformation of the ligand (which had a noticeable effect on sugar puckering). Favorable protein-ligand electrostatic interactions in the dry MtbThyX pocket strongly favored ligand binding. In contrast, the interaction between the Watson-Crick edge of the ligands and hThyA was compromised, resulting in water exposure. Ligand L2 is particularly advantageous for its highest affinity for MtbThyX and weak affinity for hThyA. The L2:MtbThyX complex is stabilized by a new salt-bridge interaction (COO- of L2···Arg107 of protein) and a bridging water molecule (between COO- of L2 and E92 of protein) in the binding pocket. Moreover, our estimated pK a of +4.5 units of N3 (dUMP) in the MtbThyX catalytic pocket indicated the strong acidic nature of the uracil, corroborating previous experimental and computational claims. These findings provide insights into the protein-ligand binding affinity in atomic detail and a rational approach for inhibitor design against MtbThyX.

Uracil/H+ Symport by FurE Refines Aspects of the Rocking-bundle Mechanism of APC-type Transporters

Transporters mediate the uptake of solutes, metabolites and drugs across the cell membrane. The eukaryotic FurE nucleobase/H+ symporter of Aspergillus nidulans has been used as a model protein to address structure-function relationships in the APC transporter superfamily, members of which are characterized by the LeuT-fold and seem to operate by the so-called 'rocking-bundle' mechanism. In this study, we reveal the binding mode, translocation and release pathway of uracil/H+ by FurE using path collective variable, funnel metadynamics and rational mutational analysis. Our study reveals a stepwise, induced-fit, mechanism of ordered sequential transport of proton and uracil, which in turn suggests that FurE, functions as a multi-step gated pore, rather than employing 'rocking' of compact domains, as often proposed for APC transporters. Finally, our work supports that specific residues of the cytoplasmic N-tail are involved in substrate translocation, in line with their essentiality for FurE function.

Accurate pKa Calculations in Proteins with Reactive Molecular Dynamics Provide Physical Insight Into the Electrostatic Origins of Their Values

Classical molecular dynamics simulations are a versatile tool in the study of biomolecular systems, but they usually rely on a fixed bonding topology, precluding the explicit simulation of chemical reactivity. Certain modifications can permit the modeling of reactions. One such method, multiscale reactive molecular dynamics, makes use of a linear combination approach to describe condensed-phase free energy surfaces of reactive processes of biological interest. Before these simulations can be performed, models of the reactive moieties must first be parametrized using electronic structure data. A recent study demonstrated that gas-phase electronic structure data can be used to derive parameters for glutamate and lysine which reproduce experimental pKa values in both bulk water and the staphylococcal nuclease protein with remarkable accuracy and transferability between the water and protein environments. In this work, we first present a new model for aspartate derived in similar fashion and demonstrate that it too produces accurate pKa values in both bulk and protein contexts. We also describe a modification to the prior methodology, involving refitting some of the classical force field parameters to density functional theory calculations, which improves the transferability of the existing glutamate model. Finally and most importantly, this reactive molecular dynamics approach, based on rigorous statistical mechanics, allows one to specifically analyze the fundamental physical causes for the marked pKa shift of both aspartate and glutamate between bulk water and protein and also to demonstrate that local steric and electrostatic effects largely explain the observed differences.

Formation of the Metal-Binding Core of the ZRT/IRT-like Protein (ZIP) Family Zinc Transporter

Zinc homeostasis in mammals is constantly and precisely maintained by sophisticated regulatory proteins. Among them, the Zrt/Irt-like protein (ZIP) regulates the influx of zinc into the cytoplasm. In this work, we have employed all-atom molecular dynamics simulations to investigate the Zn²⁺ transport mechanism in prokaryotic ZIP obtained from Bordetella bronchiseptica (BbZIP) in a membrane bilayer. Additionally, the structural and dynamical transformations of BbZIP during this process have been analyzed. This study allowed us to develop a hypothesis for the zinc influx mechanism and formation of the metal-binding site. We have created a model for the outward-facing form of BbZIP (experimentally only the inward-facing form has been characterized) that has allowed us, for the first time, to observe the Zn²⁺ ion entering the channel and binding to the negatively charged M2 site. It is thought that the M2 site is less favored than the M1 site, which then leads to metal ion egress; however, we have not observed the M1 site being occupied in our simulations. Furthermore, removing both Zn²⁺ ions from this complex resulted in the collapse of the metal-binding site, illustrating the "structural role" of metal ions in maintaining the binding site and holding the proteins together. Finally, due to the long Cd²⁺-residue bond distances observed in the X-ray structures, we have proposed the existence of an H₃O⁺ ion at the M2 site that plays an important role in protein stability in the absence of the metal ion.

Electrostatic Environment of Proteorhodopsin Affects the pKa of Its Buried Primary Proton Acceptor

The protonation state of embedded charged residues in transmembrane proteins (TMPs) can control the onset of protein function. It is understood that interactions between an embedded charged residue and other charged or polar residues in the moiety would influence its pKa, but how the surrounding environment in which the TMP resides affects the pKa of these residues is unclear. Proteorhodopsin (PR), a light-responsive proton pump from marine bacteria, was used as a model to examine externally accessible factors that tune the pKa of its embedded charged residue, specifically its primary proton acceptor D97. The pKa of D97 was compared between PR reconstituted in liposomes with different net headgroup charges and equilibrated in buffer with different ion concentrations. For PR reconstituted in net positively charged compared to net negatively charged liposomes in low-salt buffer solutions, a drop of the apparent pKa from 7.6 to 5.6 was observed, whereas intrinsic pKa modeled with surface pH calculated from Gouy-Chapman predictions found an opposite trend for the pKa change, suggesting that surface pH does not account for the main changes observed in the apparent pKa. This difference in the pKa of D97 observed from PR reconstituted in oppositely charged liposome environments disappeared when the NaCl concentration was increased to 150 mM. We suggest that protein-intrinsic structural properties must play a role in adjusting the local microenvironment around D97 to affect its pKa, as corroborated with observations of changes in protein side-chain and hydration dynamics around the E-F loop of PR. Understanding the effect of externally controllable factors in tuning the pKa of TMP-embedded charged residues is important for bioengineering and biomedical applications relying on TMP systems, in which the onset of functions can be controlled by the protonation state of embedded residues.