Binding Enthalpy Research Articles

Hydrophobic-Interaction-Induced Stiffening of α-Synuclein Fibril Networks.

In water, networks of semiflexible fibrils of the protein α-synuclein stiffen significantly with increasing temperature. We make plausible that this reversible stiffening is a result of hydrophobic contacts between the fibrils that become more prominent with increasing temperature. The good agreement of our experimentally observed temperature dependence of the storage modulus of the network with a scaling theory linking network elasticity with reversible cross-linking enables us to quantify the endothermic binding enthalpy and estimate the effective size of hydrophobic patches on the fibril surface. Our findings may not only shed light on the role of amyloid deposits in disease conditions, but can also inspire new approaches for the design of thermoresponsive materials.

Selective Removal of B800 Bacteriochlorophyll a from Light-Harvesting Complex 2 of the Purple Photosynthetic Bacterium Phaeospirillum molischianum.

The selective removal of B800 bacteriochlorophyll (BChl) a from light-harvesting complex 2 (LH2) in purple photosynthetic bacteria is a clue about elucidation of the mechanism for the transfer of energy from these pigments to B850 BChl a and their roles in the LH2 protein structure. We demonstrated that the kinetics of the removal of B800 BChl a from two representative LH2 proteins derived from Phaeospirillum molischianum and Rhodoblastus acidophilus differed significantly, in contrast to the calculated binding enthalpy. These results may be interpreted as changes in the local structure near B800 BChl a with respect to the geometries of the original crystal structures upon removal of B800 BChl a. Despite the difficulty of removing B800 BChl a from molischianum-LH2, we prepared the molischianum-LH2 protein lacking B800 BChl a by combination of two detergents, n-dodecyl β-d-maltoside and n-octyl β-d-glucoside, under acidic conditions. Spectral and atomic force microscopy analyses indicated that the absence of B800 BChl a had little effect on the local structure in the vicinity of B850 BChl a and the circular arrangement in this protein. These results suggest that the hydrophobic domain near B850 BChl a is rigid and plays a major role in the structural formation of molischianum-LH2.

Energetics underlying hemin extraction from human hemoglobin by Staphylococcus aureus

Staphylococcus aureus is a leading cause of life-threatening infections in the United States. It actively acquires the essential nutrient iron from human hemoglobin (Hb) using the iron-regulated surface-determinant (Isd) system. This process is initiated when the closely related bacterial IsdB and IsdH receptors bind to Hb and extract its hemin through a conserved tri-domain unit that contains two NEAr iron Transporter (NEAT) domains that are connected by a helical linker domain. Previously, we demonstrated that the tri-domain unit within IsdH (IsdHN2N3) triggers hemin release by distorting Hb's F-helix. Here, we report that IsdHN2N3 promotes hemin release from both the α- and β-subunits. Using a receptor mutant that only binds to the α-subunit of Hb and a stopped-flow transfer assay, we determined the energetics and micro-rate constants of hemin extraction from tetrameric Hb. We found that at 37 °C, the receptor accelerates hemin release from Hb up to 13,400-fold, with an activation enthalpy of 19.5 ± 1.1 kcal/mol. We propose that hemin removal requires the rate-limiting hydrolytic cleavage of the axial HisF8 Nϵ-Fe3+ bond, which, based on molecular dynamics simulations, may be facilitated by receptor-induced bond hydration. Isothermal titration calorimetry experiments revealed that two distinct IsdHN2N3·Hb protein·protein interfaces promote hemin release. A high-affinity receptor·Hb(A-helix) interface contributed ∼95% of the total binding standard free energy, enabling much weaker receptor interactions with Hb's F-helix that distort its hemin pocket and cause unfavorable changes in the binding enthalpy. We present a model indicating that receptor-introduced structural distortions and increased solvation underlie the IsdH-mediated hemin extraction mechanism.

The binding of boronated peptides to low affinity mammalian saccharides

AbstractA 54‐member library of boronated octapeptides, with all but the boronated residue being proteinogenic, was tested for affinity to a set of saccharides commonly found on the terminus of mammalian glycans. After experimentation with a high‐throughput dye‐displacement assay, attention was focused on isothermal titration calorimetry as a tool to provide reliable affinity data, including enthalpy and entropy of binding. A small number of boronated peptides showed higher affinity and significant selectivity for N‐acetylneuraminic acid over methyl‐α‐d‐galactopyranoside, methyl‐α/β‐l‐fucopyranoside and N‐acetyl‐d‐glucosamine. Thermodynamic data showed that for most of the boronated peptides studied, saccharide binding was associated with a significant increase in entropy, presumably resulting from the displacement of semiordered water molecules from around the sugar and/or peptide.

Dynamics, Conformational Entropy, and Frustration in Protein-Protein Interactions Involving an Intrinsically Disordered Protein Domain.

Intrinsically disordered proteins (IDPs) are abundant in the eukaryotic proteome. However, little is known about the role of subnanosecond dynamics and the conformational entropy that it represents in protein-protein interactions involving IDPs. Using nuclear magnetic resonance side chain and backbone relaxation, stopped-flow kinetics, isothermal titration calorimetry, and computational studies, we have characterized the interaction between the globular TAZ1 domain of the CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2). We show that the TAZ1/TAD-STAT2 complex retains considerable subnanosecond motions, with TAD-STAT2 undergoing only a partial disorder-to-order transition. We report here the first experimental determination of the conformational entropy change for both binding partners in an IDP binding interaction and find that the total change even exceeds in magnitude the binding enthalpy and is comparable to the contribution from the hydrophobic effect, demonstrating its importance in the binding energetics. Furthermore, we show that the conformational entropy change for TAZ1 is also instrumental in maintaining a biologically meaningful binding affinity. Strikingly, a spatial clustering of very high amplitude motions and a cluster of more rigid sites in the complex exist, which through computational studies we found to overlap with regions that experience energetic frustration and are less frustrated, respectively. Thus, the residual dynamics in the bound state could be necessary for faster dissociation, which is important for proteins that interact with multiple binding partners.

Multivalent Binding of a Ligand-Coated Particle: Role of Shape, Size, and Ligand Heterogeneity

We utilize a multiscale modeling framework to study the effect of shape, size, and ligand composition on the efficacy of binding of a ligand-coated particle to a substrate functionalized with the target receptors. First, we show how molecular dynamics along with steered molecular dynamics calculations can be used to accurately parameterize the molecular-binding free energy and the effective spring constant for a receptor-ligand pair. We demonstrate this for two ligands that bind to the α5β1-domain of integrin. Next, we show how these effective potentials can be used to build computational models at the meso- and continuum-scales. These models incorporate the molecular nature of the receptor-ligand interactions and yet provide an inexpensive route to study the multivalent interaction of receptors and ligands through the construction of Bell potentials customized to the molecular identities. We quantify the binding efficacy of the ligand-coated-particle in terms of its multivalency, binding free-energy landscape, and the losses in the configurational entropies. We show that 1) the binding avidity for particle sizes less than 350 nm is set by the competition between the enthalpic and entropic contributions, whereas that for sizes above 350 nm is dominated by the enthalpy of binding; 2) anisotropic particles display higher levels of multivalent binding compared to those of spherical particles; and 3) variations in ligand composition can alter binding avidity without altering the average multivalency. The methods and results presented here have wide applications in the rational design of functionalized carriers and also in understanding cell adhesion.

Evidence for Ion-Templation During Macrocyclooligomerization of Depsipeptides.

The ion-mediated Mitsunobu macrocyclooligomerization (M-MCO) reaction of hydroxy acid depsipeptides provides small collections of cyclic depsipeptides with good mass recovery. The approach can produce good yields of a single macrocycle or provide rapid access to multiple oligomeric macrocycles in good overall yield. While Lewis acidic alkali metal salts are known to play a role in the outcome of MCO reactions, it is unclear whether their effect is due to an organizational (e.g., templating) mechanism. Isothermal titration calorimetry (ITC) was used to study macrocycle-metal ion binding interactions, and this report correlates these thermodynamic measurements to the (kinetically determined) size distributions of depsipeptides formed during a Mitsunobu-based macrocyclooligomerization (MCO). Key trends have been identified in quantitative metal ion-cyclic depsipeptide binding affinity ( Ka), enthalpy of binding (Δ H), and stoichiometry of complexation across discrete series of macrocycles, and they provide the first analytical platform to rationally select a metal-ion template for a targeted size regime of cyclic oligomeric depsipeptides.

Protein Separation Coacervation with Carboxymethyl Cellulose of Different Substitution Degree: Noninteracting Behavior of Bowman-Birk Chymotrypsin Inhibitor.

We first observed that protein/polysaccharide interaction exhibited noninteracting behavior which makes Bowman-Birk chymotrypsin inhibitor (BBI) always free of complexation, being separated from another protein with similar isoelectric points, Kunitz trypsin inhibitor (KTI). Turbidity titrations showed that the electrostatic attractions were much stronger between KTI/BBI (KBi) and carboxymethyl cellulose of higher substitution degree. Unchanged chymotrypsin inhibitory activity (CIA) indicated that BBI had negligible contribution to protein recovery and trypsin inhibitory activity (TIA). Tricine-SDS-PAGE revealed that, at r = 20:1-2:1, unbound BBI was left in the supernatant when bound KTI transferred into precipitates, even if there was excess negative charge. Thus, purified KTI or BBI was achieved easily at the given conditions. The noninteracting behavior of BBI was further confirmed by ITC, where the binding enthalpy of BBI to CMC was negligible compared with the high binding affinity ( Kb) of KTI. This work will be beneficial to protein purification based on protein-polysaccharide coacervation.

Structural Investigation of the Dopamine-2 Receptor Agonist Bromocriptine Binding to Dimeric D2HighR and D2LowR States.

The active (D2HighR) and inactive (D2LowR) states of dimeric dopamine D2 receptor (D2R) models were investigated to clarify the binding mechanisms of the dopamine agonist bromocriptine, using Molecular Dynamics (MD) simulation. The aim of this comprehensive study was to investigate the critical effects of bromocriptine binding on each distinct receptor conformation. The different binding modes of the bromocriptine ligand in the active and inactive states have a significant effect on the conformational changes of the receptor. Based on the MM/GBSA approach, the calculated binding enthalpies of bromocriptine demonstrated selectivity toward the D2HighR active state. There is good agreement between the calculated and experimentally measured D2HighR selectivity. In the ligand-binding site, the key amino acids identified for D2HighR were Asp114(3.32) and Glu95(2.65), and for D2LowR, it was Ser193(5.42). Moreover, analysis of replicate MD trajectories demonstrated that the bromocriptine structure was more rigid at the D2HighR state and more flexible at the D2LowR state. However, the side chains of the ligand-receptor complex of D2HighR showed larger variations relative to the corresponding regions of D2LowR. The present study is part of an ongoing research program to study D2R conformational changes during ligand activation and to evaluate the conformational state selectivity for ligand binding.

Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding.

The structure-thermodynamics correlation analysis was performed for a series of fluorine- and chlorine-substituted benzenesulfonamide inhibitors binding to several human carbonic anhydrase (CA) isoforms. The total of 24 crystal structures of 16 inhibitors bound to isoforms CA I, CA II, CA XII, and CA XIII provided the structural information of selective recognition between a compound and CA isoform. The binding thermodynamics of all structures was determined by the analysis of binding-linked protonation events, yielding the intrinsic parameters, i.e., the enthalpy, entropy, and Gibbs energy of binding. Inhibitor binding was compared within structurally similar pairs that differ by para- or meta-substituents enabling to obtain the contributing energies of ligand fragments. The pairs were divided into two groups. First, similar binders—the pairs that keep the same orientation of the benzene ring exhibited classical hydrophobic effect, a less exothermic enthalpy and a more favorable entropy upon addition of the hydrophobic fragments. Second, dissimilar binders—the pairs of binders that demonstrated altered positions of the benzene rings exhibited the non-classical hydrophobic effect, a more favorable enthalpy and variable entropy contribution. A deeper understanding of the energies contributing to the protein-ligand recognition should lead toward the eventual goal of rational drug design where chemical structures of ligands could be designed based on the target protein structure.

Piperine Encapsulation within Cucurbit[n]uril (n=6,7): A Combined Experimental and Density Functional Study

AbstractThe formation of host‐guest between piperine and cucurbit[n]uril (n=6,7) molecules were studied using experimental and density functional theory (DFT) calculations. The host‐guest complexation was monitored using UV‐Visible and isothermal calorimetric (ITC) methods. The obtained Jobs plot indicate the formation of 1:1 complex. ITC analysis shows a moderate binding of the guest to the host molecules. The enthalpy of binding and the free energy of formation were negative indicating the facile formation of inclusion complex at room temperature. DFT studies confirm the formation of stable inclusion complexes. In stable inclusion complex of piperine with cucurbit[6]uril, the aromatic moiety was found to be inside the cucurbituril cavity, while in the cucurbit[7]uril inclusion complex, the piperidine moiety was inside the cavity, which was further confirmed by time dependent‐DFT study. The global reactivity descriptors analysis, indicate the formation of piperine inclusion complex with cucurbit[7]uril, could prevent the isomerization reaction of piperine. Atoms‐in‐molecules analysis shows the presence of extra inter and intramolecular bond critical points in the piperine inclusion complex with cucurbit[7]uril, which accounts for its extra stability. The computed intermolecular bond parameters confirm the existence of a non‐covalent with partial electrostatic interactions between the guest and host molecules. Energy decomposition analysis, suggest the Pauli repulsion to be higher for the cucurbit[6]uril inclusion complex, while the dispersion plays a major role in stabilizing the cucurbit[7]uril inclusion complex, which was further corroborated by noncovalent index analysis.

The binding of boronated peptides to low affinity mammalian saccharides.

A 54-member library of boronated octapeptides, with all but the boronated residue being proteinogenic, was tested for affinity to a set of saccharides commonly found on the terminus of mammalian glycans. After experimentation with a high-throughput dye-displacement assay, attention was focused on isothermal titration calorimetry as a tool to provide reliable affinity data, including enthalpy and entropy of binding. A small number of boronated peptides showed higher affinity and significant selectivity for N-acetylneuraminic acid over methyl-α-d-galactopyranoside, methyl-α/β-l-fucopyranoside and N-acetyl-d-glucosamine. Thermodynamic data showed that for most of the boronated peptides studied, saccharide binding was associated with a significant increase in entropy, presumably resulting from the displacement of semiordered water molecules from around the sugar and/or peptide.

Boron Nanowheels with Axles Containing Noble Gas Atoms: Viable Noble Gas Bound M©B10- Clusters (M=Nb, Ta).

The viability of noble gas axled boron nanowheels Ngn M©B10- (Ng=Ar-Rn; M=Nb, Ta; n=1, 2) is explored by ab initio computations. In the resulting Ng2 -M complexes, the Ng-M-Ng nanorod passes through the center of the B10- ring, providing them with an inverse sandwich-like structure. While in the singly Ng bound analogue, the Ng binding enthalpy Hb at 298 K ranges from 2.5 to 10.6 kcal mol-1 , in doubly Ng bound cases it becomes very low for the Ng2 M©B10- →Ng+NgM©B10- dissociation channel, except for the case of Rn, for which the corresponding Hb values are 3.4 (Nb) and 4.0 kcal mol-1 (Ta). For a given Ng, Ta has slightly higher Ng-binding ability than Nb. The corresponding free-energy changes indicate that these systems, particularly the Xe and Rn complexes, are good candidates for experimental realization in a low-temperature matrix. The Ng-M bonds were found to be covalent in nature, as reflected in their large Wiberg bond indices, formation of a 2c-2e σ orbital between Ng and M centers in natural bond orbital and adaptive natural density partitioning (AdNDP) analyses, and the short Ng-M distances. Energy decomposition analysis and a study on the natural orbitals for chemical valence show that the Ng-M contact is supported mainly by the orbital and electrostatic interactions, with almost equal contributions. Although both the Ng→M σ donation and Ng←M π backdonation play roles in the origin of orbital interaction, the former is significantly dominant over the latter. Further, AdNDP analysis indicates that the doubly aromatic character (both σ and π) in MB10- clusters is not perturbed by the interaction with Ng atoms.

Analysis of Evolutionarily Independent Protein-RNA Complexes Yields a Criterion to Evaluate the Relevance of Prebiotic Scenarios

A central difficulty facing study of the origin of life on Earth is evaluating the relevance of different proposed prebiotic scenarios. Perhaps the most established feature of the origin of life was the progression through an RNA World, a prebiotic stage dominated by functional RNA. We use the appearance of proteins in the RNA World to understand the prebiotic milieu and develop a criterion to evaluate proposed synthetic scenarios. Current consensus suggests that the earliest amino acids of the genetic code were anionic or small hydrophobic or polar amino acids. However, the ability to interact with the RNA World would have been a crucial feature of early proteins. To determine which amino acids would be important for the RNA World, we analyze non-biological protein-aptamer complexes in which the RNA or DNA is the result of invitro evolution. This approach avoids confounding effects of biological context and evolutionary history. We use bioinformatic analysis and molecular dynamics simulations to characterize these complexes. We find that positively charged and aromatic amino acids are over-represented whereas small hydrophobic amino acids are under-represented. Binding enthalpy is found to be primarily electrostatic, with positively charged amino acids contributing cooperatively to binding enthalpy. Arginine dominates all modes of interaction at the interface. These results suggest that proposed prebiotic syntheses must be compatible with cationic amino acids, particularly arginine or a biophysically similar amino acid, in order to be relevant to the invention of protein by the RNA World.

Is Water at the Graphite Interface Vapor-like or Ice-like?

Graphitic surfaces are the main component of soot, a major constituent of atmospheric aerosols. Experiments indicate that soots of different origins display a wide range of abilities to heterogeneously nucleate ice. The ability of pure graphite to nucleate ice in experiments, however, seems to be almost negligible. Nevertheless, molecular simulations with the monatomic water model mW with water-carbon interactions parameterized to reproduce the experimental contact angle of water on graphite predict that pure graphite nucleates ice. According to classical nucleation theory, the ability of a surface to nucleate ice is controlled by the binding free energy between ice immersed in liquid water and the surface. To establish whether the discrepancy in freezing efficiencies of graphite in mW simulations and experiments arises from the coarse resolution of the model or can be fixed by reparameterization, it is important to elucidate the contributions of the water-graphite, water-ice, and ice-water interfaces to the free energy, enthalpy, and entropy of binding for both water and the model. Here we use thermodynamic analysis and free energy calculations to determine these interfacial properties. We demonstrate that liquid water at the graphite interface is not ice-like or vapor-like: it has similar free energy, entropy, and enthalpy as water in the bulk. The thermodynamics of the water-graphite interface is well reproduced by the mW model. We find that the entropy of binding between graphite and ice is positive and dominated, in both experiments and simulations, by the favorable entropy of reducing the ice-water interface. Our analysis indicates that the discrepancy in freezing efficiencies of graphite in experiments and the simulations with mW arises from the inability of the model to simultaneously reproduce the contact angle of liquid water on graphite and the free energy of the ice-graphite interface. This transferability issue is intrinsic to the resolution of the model, and arises from its lack of rotational degrees of freedom.

A structurally-characterized peroxomanganese(iv) porphyrin from reversible O2 binding within a metal-organic framework.

The role of peroxometal species as reactive intermediates in myriad biological processes has motivated the synthesis and study of analogous molecular model complexes. Peroxomanganese(iv) porphyrin complexes are of particular interest, owing to their potential ability to form from reversible O2 binding, yet have been exceedingly difficult to isolate and characterize in molecular form. Alternatively, immobilization of metalloporphyrin sites within a metal-organic framework (MOF) can enable the study of interactions between low-coordinate metal centers and gaseous substrates, without interference from bimolecular reactions and axial ligation by solvent molecules. Here, we employ this approach to isolate the first rigorously four-coordinate manganese(ii) porphyrin complex and examine its reactivity with O2 using infrared spectroscopy, single-crystal X-ray diffraction, EPR spectroscopy, and O2 adsorption analysis. X-ray diffraction experiments reveal for the first time a peroxomanganese(iv) porphyrin species, which exhibits a side-on, η2 binding mode. Infrared and EPR spectroscopic data confirm the formulation of a peroxomanganese(iv) electronic structure, and show that O2 binding is reversible at ambient temperature, in contrast to what has been observed in molecular form. Finally, O2 gas adsorption measurements are employed to quantify the enthalpy of O2 binding as hads = -49.6(8) kJ mol-1. This enthalpy is considerably higher than in the corresponding Fe- and Co-based MOFs, and is found to increase with increasing reductive capacity of the MII/III redox couple.

Evaluations of the accuracies of DMol3 density functionals for calculations of experimental binding enthalpies of N2, CO, H2, C2H2 at catalytic metal sites

The density functionals that can be used with numerical basis sets in the density functional methodology of the programme DMol3 are evaluated by comparison with experimental data. The objective is to identify and validate the most accurate and computationally efficient density functional to be used in DMol3 simulations that use large molecular models (many hundreds of atoms) of the reaction steps involved in the chemical mechanisms of metalloenzymes and synthetic metallocatalysts. The experimental systems focus on enthalpy data for reactions analogous to those involved in the chemical mechanism of nitrogenase, including coordination of N2, CO, H2 and C2H4 and hydrogen bonding. Some geometric and vibrational frequency data are included in the 19 test systems. The conclusion is that the gradient-corrected functionals PBE, PW91 and BP provide acceptably accurate results, with the best functional being PBE, which yields reaction energies within or very close the experimental error range. These functionals are also the most computationally efficient.

Ligand-Directed Reactivity in Dioxygen and Water Binding to cis-[Pd(NHC)2(η2-O2)

Reaction of [Pd(IPr)2] (IPr = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) and O2 leads to the surprising discovery that at low temperature the initial reaction product is a highly labile peroxide complex cis-[Pd(IPr)2(η2-O2)]. At temperatures ≳ -40 °C, cis-[Pd(IPr)2(η2-O2)] adds a second O2 to form trans-[Pd(IPr)2(η1-O2)2]. Squid magnetometry and EPR studies yield data that are consistent with a singlet diradical ground state with a thermally accessible triplet state for this unique bis-superoxide complex. In addition to reaction with O2, cis-[Pd(IPr)2(η2-O2)] reacts at low temperature with H2O in methanol/ether solution to form trans-[Pd(IPr)2(OH)(OOH)]. The crystal structure of trans-[Pd(IPr)2(OOH)(OH)] is reported. Neither reaction with O2 nor reaction with H2O occurs under comparable conditions for cis-[Pd(IMes)2(η2-O2)] (IMes = 1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene). The increased reactivity of cis-[Pd(IPr)2(η2-O2)] is attributed to the enthalpy of binding of O2 to [Pd(IPr)2] (-14.5 ± 1.0 kcal/mol) that is approximately one-half that of [Pd(IMes)2] (-27.9 ± 1.5 kcal/mol). Computational studies identify the cause as interligand repulsion forcing a wider C-Pd-C angle and tilting of the NHC plane in cis-[Pd(IPr)2(η2-O2)]. Arene-arene interactions are more favorable and serve to further stabilize cis-[Pd(IMes)2(η2-O2)]. Inclusion of dispersion effects in DFT calculations leads to improved agreement between experimental and computational enthalpies of O2 binding. A complete reaction diagram is constructed for formation of trans-[Pd(IPr)2(η1-O2)2] and leads to the conclusion that kinetic factors inhibit formation of trans-[Pd(IMes)2(η1-O2)2] at the low temperatures at which it is thermodynamically favored. Failure to detect the predicted T-shaped intermediate trans-[Pd(NHC)2(η1-O2)] for either NHC = IMes or IPr is attributed to dynamic effects. A partial potential energy diagram for initial binding of O2 is constructed. A range of low-energy pathways at different angles of approach are present and blur the distinction between pure "side-on" or "end-on" trajectories for oxygen binding.

Molecular interactions between warfarin and human (HSA) or bovine (BSA) serum albumin evaluated by isothermal titration calorimetry (ITC), fluorescence spectrometry (FS) and frontal analysis capillary electrophoresis (FA/CE)

Interaction thermodynamics between warfarin, a very popular anticoagulant, and Sudlow I binding site of human (HSA) or bovine (BSA) serum albumin have been examined in strictly controlled experimental conditions (HEPES buffer 50 mM, pH 7.4 and 25 °C) by means of isothermal titration calorimetry (ITC), fluorescence spectrometry (FS) and frontal analysis capillary electrophoresis (FA/CE). Each technique is based on measurements of a different property of the biochemical system, and then the results allow a critical discussion about the suitability of each approach to estimate the drug-protein binding parameters. The strongest interaction step is properly evaluated by the three assayed approaches being the derived binding constants strongly consistent: from 4 × 104 to 7 × 104 for HSA and from 0.8 × 105 to 1.2 × 105 for BSA. Binding enthalpy variations also show consistent results: −5.4 and −5.6 Kcal/mol for HSA and −4.3 and −3.7 Kcal/mol for BSA, as measured by ITC and FS, respectively. Further high order interaction events for both albumins are detected only by FA/CE.

Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition.

Understanding the fine balance between changes of entropy and enthalpy and the competition between a guest and water molecules in molecular binding is crucial in fundamental studies and practical applications. Experiments provide measurements. However, illustrating the binding/unbinding processes gives a complete picture of molecular recognition not directly available from experiments, and computational methods bridge the gaps. Here, we investigated guest association/dissociation with β-cyclodextrin (β-CD) by using microsecond-time-scale molecular dynamics (MD) simulations, postanalysis and numerical calculations. We computed association and dissociation rate constants, enthalpy, and solvent and solute entropy of binding. All the computed values of kon, koff, ΔH, ΔS, and ΔG using GAFF-CD and q4MD-CD force fields for β-CD could be compared with experimental data directly and agreed reasonably with experiment findings. In addition, our study further interprets experiments. Both force fields resulted in similar computed ΔG from independently computed kinetics rates, ΔG = -RT ln(kon·C0/koff), and thermodynamics properties, ΔG = ΔH - TΔS. The water entropy calculations show that the entropy gain of desolvating water molecules are a major driving force, and both force fields have the same strength of nonpolar attractions between solutes and β-CD as well. Water molecules play a crucial role in guest binding to β-CD. However, collective water/β-CD motions could contribute to different computed kon and ΔH values by different force fields, mainly because the parameters of β-CD provide different motions of β-CD, hydrogen-bond networks of water molecules in the cavity of free β-CD, and strength of desolvation penalty. As a result, q4MD-CD suggests that guest binding is mostly driven by enthalpy, while GAFF-CD shows that gaining entropy is the major driving force of binding. The study deepens our understanding of ligand-receptor recognition and suggests strategies for force field parametrization for accurately modeling molecular systems.