Free enthalpies of replacing water molecules in protein binding pockets

Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. The free enthalpy difference between a water molecule and a CH3 group at the same location in the pocket in comparison to their presence in bulk solution calculated from EDS molecular dynamics simulations corresponds to the binding free enthalpy of CH3 at this location. From the free enthalpy difference and the enthalpy difference, the entropic contribution of the displacement can be obtained too. The overlay of the resulting occupancy volumes of the water molecules with crystal structures of analogous ligands shows qualitative correlation between experimentally measured inhibition constants and the calculated free enthalpy differences. Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug desig

Phage display identification of nanomolar ligands for human NEDD4-WW3: Energetic and dynamic implications for the development of broad-spectrum antivirals

This research has been financed by grants BIO2016-78746-C2-1-R and PID2020-112895RB-100 from the Spanish Ministry of Education and Science (I.L.) including AEI/FEDER EU funds. R.N.H. was funded in part by National Institutes of Health grants AI138052 and AI138630. M. I.B. and J.M.C. were recipients of a research contract from the Spanish Ministry of Education and Science. F.C. was funded by a predoctoral fellowship from the Andalusian Government P10-CVI-5915. J.M.C. ac-knowledges a reincorporation research contract from the University of Granada. We thank Dr. Sachdev Sidhu for his invaluable assistance setting up the phage display techniques in our laboratory. We also thank the support of the C.I.C. of the University of Granada.The recognition of PPxY viral Late domains by the third WW domain of the human HECT-E3 ubiquitin ligase NEDD4 (NEDD4-WW3) is essential for the budding of many viruses. Blocking these interactions is a promising strategy to develop broad-spectrum antivirals. As all WW domains, NEDD4-WW3 is a challenging therapeutic target due to the low binding affinity of its natural interactions, its high conformational plasticity, and its complex thermodynamic behavior. In this work, we set out to investigate whether high affinity can be achieved for monovalent ligands binding to the isolated NEDD4-WW3 domain. We show that a competitive phage-display set-up allows for the identification of high-affinity peptides showing inhibitory activity of viral budding. A detailed biophysical study combining calorimetry, nuclear magnetic resonance, and molecular dynamic simulations reveals that the improvement in binding affinity does not arise from the establishment of new interactions with the domain, but is associated to conformational restrictions imposed by a novel C-terminal -LFP motif in the ligand, unprecedented in the PPxY interactome. These results, which highlight the complexity of WW domain interactions, provide valuable insight into the key elements for high binding affinity, of interest to guide virtual screening campaigns for the identification of novel therapeutics targeting NEDD4-WW3 interactions.Spanish Government BIO2016-78746-C2-1-R PID2020-112895RB-100 AEI/FEDER EU funds AI138052 AI138630United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA P10-CVI-5915German Research Foundation (DFG)University of Granad

Symmetric Allosteric Mechanism of Hexameric Escherichia coli Arginine Repressor Exploits Competition between L-Arginine Ligands and Resident Arginine Residues

An elegantly simple and probably ancient molecular mechanism of allostery is described for the Escherichia coli arginine repressor ArgR, the master feedback regulator of transcription in L-arginine metabolism. Molecular dynamics simulations with ArgRC, the hexameric domain that binds L-arginine with negative cooperativity, reveal that conserved arginine and aspartate residues in each ligand-binding pocket promote rotational oscillation of apoArgRC trimers by engagement and release of hydrogen-bonded salt bridges. Binding of exogenous L-arginine displaces resident arginine residues and arrests oscillation, shifting the equilibrium quaternary ensemble and promoting motions that maintain the configurational entropy of the system. A single L-arg ligand is necessary and sufficient to arrest oscillation, and enables formation of a cooperative hydrogen-bond network at the subunit interface. The results are used to construct a free-energy reaction coordinate that accounts for the negative cooperativity and distinctive thermodynamic signature of L-arginine binding detected by calorimetry. The symmetry of the hexamer is maintained as each ligand binds, despite the conceptual asymmetry of partially-liganded states. The results thus offer the first opportunity to describe in structural and thermodynamic terms the symmetric relaxed state predicted by the concerted allostery model of Monod, Wyman, and Changeux, revealing that this state is achieved by exploiting the dynamics of the assembly and the distributed nature of its cohesive free energy. The ArgR example reveals that symmetry can be maintained even when binding sites fill sequentially due to negative cooperativity, which was not anticipated by the Monod, Wyman, and Changeux model. The molecular mechanism identified here neither specifies nor requires a pathway for transmission of the allosteric signal through the protein, and it suggests the possibility that binding of free amino acids was an early innovation in the evolution of allostery

Systematic Correlation of Structural, Thermodynamic and Residual Solvation Properties of Hydrophobic Substituents in Hydrophobic Pockets Using Thermolysin as a Case Study

Water molecules participate besides protein and ligand as an additional binding partner in every in vivo protein–ligand binding process. The displacement of water molecules from apolar surfaces of solutes is considered the driving force of the hydrophobic effect. It is generally assumed that the mobility of the water molecules increases through the displacement, and, as a consequence, entropy increases. This explanation, which is based on experiments with simple model systems, is, however, insufficient to describe the hydrophobic effect as part of the highly complex protein–ligand complex formation process. For instance, the displacement of water molecules from apolar surfaces that already exhibit an increased mobility before their displacement can result in an enthalpic advantage. Furthermore, it has to be considered that by the formation of the protein–ligand complex a new solvent-exposed surface is created, around which water molecules have to rearrange. The present thesis focuses on the impact of the latter effect on the thermodynamic and kinetic binding properties of a given ligand. A congeneric ligand series comprised of nine ligands binding to the model protein thermolysin (TLN) was analyzed to determine the impact of the rearrangement of water molecules around the surface of a newly formed protein–ligand complex on the thermodynamic binding properties of a ligand. The protein–ligand complexes were characterized structurally by X-ray crystallography and thermodynamically by isothermal titration calorimetry (ITC). The only structural difference between the ligands was their strictly apolar P2’ substituent, which changed in size from a methyl to a phenylethyl group. The P2’ group interacts with the flat, apolar, and well-solvated S2’ pocket of TLN. Depending on the bound ligand, the solvent-exposed surface of the protein–ligand complex changes. The ITC measurements revealed strong thermodynamic differences between the different ligands. The structural analysis showed ligand-coating water networks pronounced to varying degrees. A pronounced water network clearly correlated with a favorable enthalpic and less favorable entropic term, and overall resulted in an affinity gain. Based on these results, new P2’ substituents were rationally designed with the aim to achieve stronger stabilization of the adjacent water networks and thereby further increase ligand affinity. First, the quality of the putative water networks was validated using molecular dynamics (MD) simulations. Subsequently, the proposed ligands were synthesized, crystallized in complex with TLN, and analyzed thermodynamically. Additionally, a kinetic characterization using surface plasmon resonance (SPR) was performed. The crystallographically determined water networks adjacent to the P2’ substituents were in line with their predictions conducted by MD simulations. The ligands showed increasingly pronounced water networks as well as a slight enthalpy-drive affinity increase compared to the ligands from the initial study. The ligand with the highest affinity showed an almost perfect water network as well as a significantly reduced dissociation constant. To analyze the influence of the ligand-coating water networks on the kinetic binding properties of a ligand, seventeen congeneric TLN ligands exhibiting different P2’ groups were kinetically (by SPR) and crystallographically characterized. The different degree of the water network stabilization showed only a minor influence on the binding kinetic properties. By contrast, the strength of the interaction between the ligand and Asn112 proved crucial for the magnitude of the dissociation rate constant. A strong interaction resulted in a considerably prolonged residence time of the ligand by hindering TLN to undergo a conformational transition that is necessary for ligand release. In the last study, the reason for the exceptionally high affinity gain for addressing the deep, apolar S1’ pocket of TLN with apolar ligand portions was investigated. Therefore, a congeneric TLN ligand series substituted with differently large apolar P1’ substituents (ranging from a single hydrogen atom to an iso-butyl group) was analyzed. The exchange of the hydrogen atom at the P1’ position with a single methyl group already results in a 100-fold affinity increase of the ligand. To elucidate the molecular mechanism behind this considerable affinity gain, the solvation state of the S1’ pocket was carefully analyzed. The results strongly indicate that the S1’ pocket is completely free of the presence of any water molecules. Thus, the huge affinity gain was attributed to the absence of an energetically costly desolvation step. The data presented in this thesis show that to describe the thermodynamic signature of the hydrophobic effect it is necessary to explicitly consider the change of the thermodynamic properties of every involved water molecule. Solely considering the buried apolar surface area and assigning an entropic term to it is not sufficient. The increasing stabilization of the water network adjacent to the protein-bound ligand represents a promising approach — quite independent of specific properties of the target protein — to optimize the thermodynamic profile of a given ligand. This approach also allows fine-tuning of the kinetic binding parameters

The Role of Water in Protein-Ligand Binding: A Comprehensive Study by Crystallography and Isothermal Titration Calorimetry

The aim of this work is to investigate the impact of desolvation effects on protein-ligand interactions. In all complex structures with thrombin and pyridine, it is evident that preserving the original solvation state of Asp189 is a crucial and a common feature upon binding of the pyridine inhibitors. However, the associated entropic losses are immense. In two ligand complexes even disordered ligand portions are found in the S1 pocket, which evade full desolvation of Asp189 compared with the apo form of thrombin. The price for the desolvation of a charged amino acid is simply too large to ensure in this case a complete displacement of all waters. The determined complex structures reveal that the charged methylpyridinium derivatives do not optimally address the negatively charged Asp189 at the bottom of the S1 pocket. A short distance to the deprotonated Asp189 cannot be achieved either due to steric reasons or the bulky methyl group provides a good protection to interact in a proper way with the negatively charged Asp189. The optimal interaction geometry to Asp189 cannot be realized in this series. Therefore, the energy released from the suboptimal interaction between methylpyridinium and Asp189 is not high enough to compensate for the large desolvation price required for the charged ligands. Additionally, water effects have been studied in hydrophobic interactions in thrombin and thermolysin. The thermodynamic characterization shows a hydrophobic effect in thrombin which is clearly entropically driven. In the study, the S3/4 pocket has been gradually desolvated using increasing hydrophobic modifications in P3. In both series, the binding affinity improved by about 40-fold. The binding affinity has been optimized hydrophobically from nanomolar to low picomolar affinity. The benzamidine derivatives are even characterized by a binding mode showing two ligands to be bound simultaneously. Surprisingly, the additionally bound ligand traces remarkable well the recognition area that accommodates fibrinopeptide A (cleavage product of fibrinogen). In contrast, the examined S2' pocket of thermolysin is less well shaped, but ideally solvated because of its exposure to the protein surface. The ligands differ only by a terminal carboxylate and/or methyl group. A surprising nonadditivity of functional group contributions for the carboxylate and/or methyl groups is detected. Adding first the methyl and then the carboxylate group results in a small Gibbs free energy increase and minor enthalpy/entropy partitioning for the first modification, whereas the second involves strong affinity increase combined with huge enthalpy/entropy changes. Adding however first the carboxylate and then the methyl group yields reverse effects: now the acidic group attachment causes minor effects whereas the added methyl group provokes huge changes. The added COO- groups perturb the local water network in both carboxylated complexes and the attached methyl groups provide favorable interaction sites for water molecules. In all complexes, apart one example, a contiguously connected water network between protein and ligand functional groups is observed. In the complex with the carboxylated ligand, still lacking the terminal methyl group, the water network is unfavorably ruptured. This results in the surprising thermodynamic signature showing only minor affinity increase upon COO- group attachment. Since the further added methyl group provides a favorable interaction site for water, the network can be re-established and strong affinity increase with huge enthalpy/entropy signature is then detected. Addressing the S2' pocket of thermolysin with hydrophobic molecule portions generates also an entropically dominated signal similarly to the thrombin series. The present series of closely related thermolysin complexes shows that both thermodynamic properties are involved and many detailed structural phenomena determine the final signature. If a contiguously connected water network ruptures, an enthalpic loss and entropic gain is experienced. Particularly, in case of accommodation of ligand portions in pockets opening to the bulk solvent and exposing parts of the placed ligand to the water phase, new binding sites for water molecules can be generated, e.g. as in our study at the capping position above the carboxylate group or the site on top of the benzyl ring. Also such phenomena contribute on the molecular level to the finally determined hydrophobic effect. In summary, there are no arguments why the hydrophobic effect should be predominantly entropic or enthalpic. Small structural changes on the molecular level determine whether hydrophobic binding to hydrophobic pockets results in a more enthalpy or entropy-driven signature

Understanding the Molecular Mechanism underlying the Great Thermal Stability of Thermophilic Enzymes using Aminoglycoside Nucleotidyltransferase 4\u27 as a Model

The aminoglycoside nucleotidyltransferase 4\u27 (ANT) is a homodimeric enzyme that detoxifies antibiotics by nucleotidylating at the C4\u27-OH site. Two thermostable variants T130K and D80Y generated by direct evolution in laboratory differ by only a single residue replacement compared to the wild type mesophilic enzyme. Both variants display enhanced melting temperatures and execute catalysis at temperatures the wild type would be inactive. However, T130K variant still keeps molecular properties of mesophilic enzyme. T130àK130 does not trigger significant change in enzyme’s local flexibility or thermodynamics of ligand binding while D80Y variant has distinct properties in ligand recognition and dynamics. We hypothesize that T130K and D80Y variants adopt different strategies to achieve thermal stability. In this respect, T130K is a heat stable mesophilic enzyme with simply higher melting temperature due to more stabilizing intramolecular interactions and may not be a true “thermophilic” enzyme. Thermophilic variant D80Y, on the other hand, displays higher atomic fluctuations than mesophilic enzyme thus increasing the entropic change associated with enzyme denaturation. Here we attempt to draw a line separating heat resistant enzymes like T130K from true thermophilic enzyme like D80Y. Numerous studies compared the differences in various structural features of thermophilic/thermostable-mesophilic enzymes in order to reach unifying and general mechanisms of greater thermostability/thermophilicity for such enzymes. To date, not a single molecular feature emerged as the parameter defining “thermophilic” properties. We believe that this is because these comparisons included all heat stable enzymes, some of which may simply be heat stable versions of mesophilic enzymes, such as those with added stabilizing interactions (disulfide bonds or salt bridges) based on structural analyses. In this work, we demonstrated that thermodynamic properties of protein-ligand interactions may yield molecular properties of true thermophilic enzymes by using two heat stable variants of ANT to demonstrate that one of them, T130K is simply a heat stable enzyme with proper ties of the wild type while the other, D80Y, shows properties that are significantly different and alters the dynamics of the enzyme

Water in Protein Cavities: Free Energy, Entropy, Enthalpy, and its Influences on Protein Structure and Flexibility

Complexes of the antibiotics novobiocin and clorobiocin with DNA gyrase are illustrative of the importance of bound water to binding thermodynamics. Mutants resistantto novobiocin as well as those with a decreased affinity for novobiocin over clorobiocinboth involve a less favorable entropy of binding, which more than compensates for amore favorable enthalpy, and additional water molecules at the proteinligandinterface.Free energy, enthalpy, and entropy for these water molecules were calculated by thermodynamicintegration computer simulations. The calculations show that addition of thewater molecules is entropically unfavorable, with values that are comparable to the measuredentropy differences. The free energies and entropies correlate with the change inthe number of hydrogen bonds due to the addition of water molecules.To examine the wide variety of cavities available to water molecules inside proteins,a model of the protein cavities is developed with the local environment treated at atomicdetail and the nonlocal environment treated approximately. The cavities are then changedto vary in size and in the number of hydrogen bonds available to a water molecule insidethe cavity. The free energy, entropy, and enthalpy change for the transfer of a watermolecule to the cavity from the bulk liquid is calculated from thermodynamic integration.The results of the model are close to those of similar cavities calculated using the fullprotein and solvent environment. As the number of hydrogen bonds resulting from theaddition of the water molecule increases, the free energy decreases, as the enthalpic gainof making a hydrogen bond outweighs the entropic cost. Changing the volume of thecavity has a smaller effect on the thermodynamics. Once the hydrogen bond contributionis taken into account, the volume dependence on free energy, entropy, and enthalpy issmall and roughly the same for a hydrophobic cavity as a hydrophilic cavity.The influences of bound water on protein structure and influences are also evaluatedby performing molecular dynamics simulation for proteins with and without boundwater. Four proteins are simulated, the wildtypebovine pancreatic trypsin inhibitor(BPTI), the wildtypehen egg white lysozyme (HEWL), and two variants of the wildtypeStaphylococcal nuclease (SNase), PHS and PHS/V66E. The simulation reveals that allthese four proteins suffer structural changes upon the removing of bound water molecules,as indicating by their increased RMSD values with respect to the crystal structures. Threeout of the four proteins, BPTI, HEWL, and the PHS mutant of SNase have increased flexibility,while no apparent flexibility change is seen in the PHS/V66E variant of SNase

Water in Protein Cavities: Free Energy, Entropy, Enthalpy, and its Influences on Protein Structure and Flexibility

Complexes of the antibiotics novobiocin and clorobiocin with DNA gyrase are illustrative of the importance of bound water to binding thermodynamics. Mutants resistantto novobiocin as well as those with a decreased affinity for novobiocin over clorobiocinboth involve a less favorable entropy of binding, which more than compensates for amore favorable enthalpy, and additional water molecules at the proteinligandinterface.Free energy, enthalpy, and entropy for these water molecules were calculated by thermodynamicintegration computer simulations. The calculations show that addition of thewater molecules is entropically unfavorable, with values that are comparable to the measuredentropy differences. The free energies and entropies correlate with the change inthe number of hydrogen bonds due to the addition of water molecules.To examine the wide variety of cavities available to water molecules inside proteins,a model of the protein cavities is developed with the local environment treated at atomicdetail and the nonlocal environment treated approximately. The cavities are then changedto vary in size and in the number of hydrogen bonds available to a water molecule insidethe cavity. The free energy, entropy, and enthalpy change for the transfer of a watermolecule to the cavity from the bulk liquid is calculated from thermodynamic integration.The results of the model are close to those of similar cavities calculated using the fullprotein and solvent environment. As the number of hydrogen bonds resulting from theaddition of the water molecule increases, the free energy decreases, as the enthalpic gainof making a hydrogen bond outweighs the entropic cost. Changing the volume of thecavity has a smaller effect on the thermodynamics. Once the hydrogen bond contributionis taken into account, the volume dependence on free energy, entropy, and enthalpy issmall and roughly the same for a hydrophobic cavity as a hydrophilic cavity.The influences of bound water on protein structure and influences are also evaluatedby performing molecular dynamics simulation for proteins with and without boundwater. Four proteins are simulated, the wildtypebovine pancreatic trypsin inhibitor(BPTI), the wildtypehen egg white lysozyme (HEWL), and two variants of the wildtypeStaphylococcal nuclease (SNase), PHS and PHS/V66E. The simulation reveals that allthese four proteins suffer structural changes upon the removing of bound water molecules,as indicating by their increased RMSD values with respect to the crystal structures. Threeout of the four proteins, BPTI, HEWL, and the PHS mutant of SNase have increased flexibility,while no apparent flexibility change is seen in the PHS/V66E variant of SNase