Comparison of chemical and thermal protein denaturation by combination of computational and experimental approaches. II

Chemical and thermal denaturation methods have been widely used to investigate folding processes of proteins in vitro. However, a molecular understanding of the relationship between these two perturbation methods is lacking. Here, we combined computational and experimental approaches to investigate denaturing effects on three structurally different proteins. We derived a linear relationship between thermal denaturation at temperature T(b) and chemical denaturation at another temperature T(u) using the stability change of a protein (ΔG). For this, we related the dependence of ΔG on temperature, in the Gibbs-Helmholtz equation, to that of ΔG on urea concentration in the linear extrapolation method, assuming that there is a temperature pair from the urea (T(u)) and the aqueous (T(b)) ensembles that produces the same protein structures. We tested this relationship on apoazurin, cytochrome c, and apoflavodoxin using coarse-grained molecular simulations. We found a linear correlation between the temperature for a particular structural ensemble in the absence of urea, T(b), and the temperature of the same structural ensemble at a specific urea concentration, T(u). The in silico results agreed with in vitro far-UV circular dichroism data on apoazurin and cytochrome c. We conclude that chemical and thermal unfolding processes correlate in terms of thermodynamics and structural ensembles at most conditions; however, deviations were found at high concentrations of denaturant.     

Interaction of urea with amino acids: implications for urea-induced protein denaturation

The molecular mechanism of urea-induced protein denaturation is not yet fully understood. Mainly two opposing mechanisms are controversially discussed, according to which either hydrophobic, or polar interactions are the dominant driving force. To resolve this question, we have investigated the interactions between urea and all 20 amino acids by comprehensive molecular dynamics simulations of 22 tripeptides. Calculation of atomic contact frequencies between the amino acids and solvent molecules revealed a clear profile of solvation preferences by either water or urea. Almost all amino acids showed preference for contacts with urea molecules, whereas charged and polar amino acids were found to have slight preferences for contact with water molecules. Particularly strong preference for contacts to urea were seen for aromatic and apolar side-chains, as well as for the protein backbone of all amino acids. Further, protein-urea hydrogen bonds were found to be significantly weaker than protein-water or water-water hydrogen bonds. Our results suggest that hydrophobic interactions are the dominant driving force, while hydrogen bonds between urea and the protein backbone contribute markedly to the overall energetics by avoiding unfavorable unsatisfied hydrogen bond sites on the backbone. In summary, we suggest a combined mechanism that unifies the two current and seemingly opposing views.     

Atomic contacts via electrochemistry in water/cyclodextrin media: a step toward protected atomic contacts

Atomic contacts are nanoscience devices proposed for applications such as single-atom switches in nanoelectronic circuits or one-molecule sensing devices. The conductance of such contacts varies in a stepwise fashion with a tendency to quantize near integer multiples of the conductance quantum (G0) but can also deviate significantly from integer values upon molecular adsorption. However, for sensing applications it is first necessary to coat the contact permanently to avoid nonspecific adsorption. Here, we show that marked differences are observed between atomic contacts generated in water, and in water/beta-CD. In this latter medium, atomic contacts with unusual properties can be generated. They have below 1 G0 conductance, low conductance fluctuation with time, and appear to be protected or partially protected from salicylate external molecular probes. Such contacts are not obtained in water, in water/glucose, or when beta-CD is added after 1 G0 contacts have been generated in water. These results indicate specific adsorption of beta-cyclodextrin on the atomic contacts and are compatible with the formation of encapsulated atomic contacts. However, direct independent structural evidence is still needed to confirm or infirm this interpretation.     

Computational study of urea and its homologue glycinamide: conformations, rotational barriers, and relative interactions with sodium chloride

Conformational behaviors of urea and glycinamide have been investigated using the B3LYP functional with the 6-311+G* and 6-311+G** basis sets. Urea monomers have nonplanar minima at all the levels studied, even in the aqueous phase. In the case of glycinamide, the intramolecular hydrogen bond formed from the amide to the amine is important for stabilizing the global minimum. Bond rotations and nitrogen inversion barriers for glycinamide conformations have also been reported. The DFT calculated results suggest that urea conformers interact preferentially with the {111} surface of sodium chloride and such interactions can be responsible for the change in the habit of sodium chloride. Glycinamide conformers have a lower affinity toward the {111} surface of sodium chloride in water. The pyramidality of nitrogens in urea conformers does not influence the relative trends of interaction energies with sodium chloride surfaces. The mode of interactions predicted at the LDA/PWC/DND level for urea and glycinamide with sodium chloride for both slab and cluster models shows that the amide functionality (-CONH2) interacts with both Na(+) and Cl(-) ions on the {100} surface; however, the carbonyl oxygen of these additives predominantly interacts with the sodium ions on the {111} surface.     

Temperature dependence on the binding of butyl orange by bovine serum albumin: The effect of urea

The effect of urea on the extent of the binding of butyl orange by bovine serum albumin has been examined by an equilibrium dialysis method. The first binding constants and the thermodynamic parameters for the formation of the first dye anion–protein complex have been calculated. Addition of urea to the binding system causes a marked decrease in the absolute magnitude of the free energy change. The enthalpy change during binding becomes more exothermic, and the entropy change tends to decrease with increasing concentration of urea. These results can be interpreted in terms of the concept that urea reduces the structure of the aqueous environment and hence lowers the tendency of apolar groups of the dye and the albumin to participate in the formation of hydrophobic interactions.     

Urea Unfolding of Opsin in Phospholipid Bicelles†

Opsin is the unstable apo‐protein of the light‐activated G protein‐coupled receptor rhodopsin. We investigated the stability of bovine opsin, solubilized in 1,2‐dimyristoyl‐sn‐glycero‐3‐phosphocholine (DMPC)/detergent bicelles, against urea‐induced unfolding. A single irreversible protein unfolding transition was observed from changes in intrinsic tryptophan fluorescence and far‐UV circular dichroism. This unfolding transition correlated with loss of protein activity. Changes in tertiary structure, as indicated by fluorescence measurements, were concomitant with an approximate 50% reduction in α‐helical content of opsin, indicating that global unfolding had been induced by urea. The urea concentration at the midpoint of unfolding was dependent on the lipid/detergent environment, occurring at approximately 1.2 m urea in DMPC/1,2‐dihexanoyl‐sn‐glycero‐3‐phosphocholine bicelles, while being significantly stabilized to approximately 3.5 m urea in DMPC/3‐[(cholamidopropyl)dimethylammonio]‐1‐propanesulfonate bicelles. These findings demonstrate that interactions with the surrounding lipids and detergent are highly influential in the unfolding of membrane protein structure. The urea/bicelle system offers the possibility for a more detailed understanding of the structural changes that take place upon irreversible unfolding of opsin.     

New insights into urea action on proteins: a SANS study of the lysozyme case

We present a study on lysozyme dissolved in mixtures of water and urea, which is ubiquitously used as a protein denaturant. Despite the wide use of urea, the basic molecular mechanisms inducing protein unfolding are not still clarified. Small-angle neutron scattering (SANS) experiments have been performed using little amounts of denaturant in solutions in order to investigate the urea effect on lysozyme preceding the unfolding process. A global fit strategy, applied to analyze SANS experiments, provides an estimation of the average composition of the solvent in the close vicinity of the protein surface and the change of the protein-protein interactions due to the presence of urea. In particular, the thermodynamic equilibrium constant responsible for cosolvent balancing between the bulk and solvation layer has been determined. It turns out that urea is preferentially driven to the protein surface, confirming literature results at infinite dilute conditions. SANS data also reveal a possible variation of the protein net charge as a function of urea concentration, opening new perspectives and questions about the protein surface architecture at the first stages of unfolding processes.     

Insight into the Urea Binding and K166R Mutation Stabilizing Mechanism of TlpB: Molecular Dynamics and Principal Component Analysis Study

Chemoreceptor TlpB(Tlp=transducer-like protein), which has been demonstrated to respond to pH sensing function, is crucial for the survival of Helicobacter pylori(H. pylori) in host stomach. Urea was proposed to be essential for TlpB's pH sensing function via binding with the Per-ARNT-Sim(PAS) domain of TlpB. Additionally, K166R mutation of the TlpB protein has also been proven to have a similar effect on TlpB pH sensing as urea binding. Although X-ray crystallographic studies have been carried out for urea-bound TlpB, the molecular mechanism for the stabilization of TlpB induced by urea binding and K166R mutation remains to be elucidated. In this study, molecular dynamics simulations combined with principal component analysis(PCA) for the simulation results were used to gain an insight into the molecular mechanism of the stabilization of urea on TlpB protein. The formed H-bonds and salt-bridges surrounding Asp114, which were induced by both urea binding and K166R mutation of TlpB, were important to the stabilization of TlpB by urea. The similarity between the urea binding and K166R mutation as well as their differences in effect has been explicitly demonstrated with computer simulations at atomic-level. The findings may pave the way for the further researches of TlpB.     

A solution study on the local and global structure changes of cytochrome c: an unfolding process induced by urea

The local and global structural changes of cytochrome c induced by urea in aqueous solution have been studied using X-ray absorption spectroscopy (XAS) and small-angle X-ray scattering (SAXS). According to the XAS result, both the native (folded) protein and the unfolded protein exhibit the same preedge features taken at Fe K-edge, indicating that the Fe(III) in the heme group of the protein maintains a six-coordinated local structure in both the folded and unfolded states. Furthermore, the discernible differences in the X-ray absorption near-edge structure (XANES) of these two states are attributed to a possible spin transition of the Fe(III) from a low-spin state to a high-spin state during the unfolding process. The perseverance of six-coordination and the spin transition of the iron are reconciled by a proposed ligand exchange, with urea and water molecules replacing the methionine-80 and histidine-18 axial ligands, respectively. The SAXS result reveals a significant morphology change of cytochrome c from a globular shape of a radius of gyration R(g) = 12.8 A of the native protein to an elongated ellipsoid shape of R(g) = 29.7 A for the unfolded protein in the presence of concentrated urea. The extended X-ray absorption fine structure (EXAFS) data unveil the coordination geometries of Fe(III) in both the folded and unfolded state of cytochrome c. An initial spin transition of Fe(III) followed by an axial ligand exchange, accompanied by the change in the global envelope, is proposed for what happened in the protein unfolding process of cytochrome c.     

Isoelectric focusing in low-denaturing media: visualization in renal disease of variation of the isoelectric point of albumin not related to a remarkable conformational variation

The isoelectric properties of serum and urinary albumin from normal subjects and patients with nephrotic syndrome have been investigated in various conditions of denaturation, obtained by using urea (0-8 M) as a support in isoelectric focusing. In normal human serum, albumin is rather acidic (pI = 4.7) when focused in glycerol while the denatured form obtained by exposing the protein to 8 M urea has a much higher pI (6.1). Albumin from nephrotic patients is acidic in glycerol but at very low levels of urea (2M) it shifts from pI 4.7 to pI 6.1; the same effect has been induced by treating albumin with activated charcoal at low pH. In order to obtain more information on urea-induced changes, we have recorded the circular dichroic spectra of albumin when exposed to the concentration of urea used in gels, and we found that no conformational transition occurs for urea concentrations less than 5 M. Taken together, these observations reveal that variation of the pI of albumin in nephrotic syndrome occurs mainly due to a dissociating effect of urea on charged substances bound to this protein.     

The effects of urea and n-propanol on collagen denaturation: using DSC, circular dicroism and viscosity

The effect of urea and n-propanol on circular dichroism (CD) and viscosity of purified type1 collagen solution at various temperatures and differential scanning calorimetry (DSC) of rat-tail tendon (RTT) collagen fibre have been studied. CD reveals a spectrum with a positive peak at around 220 nm and a negative peak at 200 nm characteristics of collagen triple helix. The molar ellipticity decreases as the concentration of urea increases up to particular concentration (collagen solution treated with 265 μM of urea) and after that it increases (collagen solution treated with 500 μM of urea). There is a linear decrease in molar ellipticity as the concentration of n-propanol increases. Denaturation temperature of urea and n-propanol treated with purified collagen solution has been studied using viscosity method. Additives such as urea and n-propanol decrease the thermal stability of collagen triple helix in solution and in RTT collagen fibre. Thermal helix to coil transition of urea and n-propanol treated collagen depends on the degree of hydration and the concentration of these additives. Thermodynamic parameters such as the peak temperature, enthalpy of activation, and energy of activation for collagen-gelatin transition for native, urea and n-propanol treated RTT collagen fibre has been calculated using DSC. The change in the thermodynamic parameters has been observed for native, urea and n-propanol treated RTT collagen fibres. The experimental results show that the change in the water structure, dehydration and desolvation induced by different additives such as urea and n-propanol on RTT may vary with the type of denaturation.     

The Aminotriazole Antagonist Cmpd‐1 Stabilises a Distinct Inactive State of the Adenosine 2A Receptor

The widely expressed G‐protein coupled receptors (GPCRs) are versatile signal transducer proteins that are attractive drug targets but structurally challenging to study. GPCRs undergo a number of conformational rearrangements when transitioning from the inactive to the active state but have so far been believed to adopt a fairly conserved inactive conformation. Using ¹⁹F NMR spectroscopy and advanced molecular dynamics simulations we describe a novel inactive state of the adenosine 2A receptor which is stabilised by the aminotriazole antagonist Cmpd‐1. We demonstrate that the ligand stabilises a unique conformation of helix V and present data on the putative binding mode of the compound involving contacts to the transmembrane bundle as well as the extracellular loop 2.     

Dimerisation of urea in water solution: a quantum mechanical investigation

The effect of water solvation on the structure and stability of cyclic dimers of urea has been investigated with the aid of density functional theory at the B3LYP/6-311++G** level. Several hydration models have been discussed. Specific solvent effects have been simulated through single and multiple water-urea interactions involving all the hydration sites of urea. The bulk solvent effects have been estimated through polarised continuum models. Under all the hydration patterns cyclic dimers continue to be stable structures although the solvent weakens the urea-urea interaction. Single and multiple specific urea-water interactions are competitive with urea dimerisation. The anticooperative nature of the two intermolecular interactions is largely due to the changes on sigma- and pi-electron density of urea caused by hydrogen bonding with water. The stability of the dimer is however, lost within a few ps when the hydrated dimer is described by a quantum mechanical molecular dynamics approach (ADMP). The cyclic dimer evolves towards structures where urea molecules are linked not more directly but through water molecules which have a bridge function.     

Effect of urea on the behaviour of poly(2-hydroxyethyl methacrylate)-water mixtures

The effect of urea solutions on the equilibrium swelling of lightly crosslinked poly(2-hydroxyethyl methacrylate) (PHEMA) gels and on the viscometric behaviour of PHEMA, for various concentrations of urea and temperatures, has been studied. Urea raises the degree of swelling of gels and the intrinsic viscosity of PHEMA; the temperature coefficient of both quantities is negative. A thermodynamic analysis of the swelling data shows that a change in entropy is the driving force for the increase in swelling at low temperatures, while at higher temperatures (50–80°) a negative change in enthalpy prevails, both corresponding to the transport of PHEMA from the aqueous medium into urea solutions. The entropy and enthalpy of dilution parameters derived from viscometric measurements have negative values, and their absolute values decrease with increasing urea concentration. It has also been found that the PHEMA molecules in urea solutions under the θ-conditions are much more coiled than in an organic θ-solvent. The results are interpreted in terms of the existence of inter- and intramolecular hydrophobic bonds and by the destruction of hydrophobic clusters caused by urea.     

Close contacts between carbonyl oxygen atoms and aromatic centers in protein structures: pi...pi or lone-pair...pi interactions?

Lone-pair...pi and, more recently, pi...pi interactions have been studied in small molecule crystal structures, and they are the focus of attention in some biomolecules. In this study, we have systematically analyzed 500 high-resolution protein structures (resolution < or =1.8 A) and identified 286 examples in which carbonyl oxygen atoms approach the aromatic centers within a distance of 3.5 A. Contacts involving backbone carbonyl oxygens are frequently observed in helices and, to some extent, in strands. Geometrical characterization indicates that these contacts have geometry in between that of an ideal pi...pi and a lone-pair...pi interaction. Quantum mechanical calculations using 6-311++G** basis sets reveal that these contacts give rise to energetically favorable interactions and, along with MD simulations, indicate that such interactions could stabilize secondary structures.     

Theory Studies on the Intermolecular Interactions of Urea Nitrate with RDX

Six fully optimized geometries of urea nitrate cation and RDX complexes have been obtained with DFT-B3LYP and MP2 methods at the 6-311++G** level. The intermolecular interaction energies have been calculated with basis set superposition error (BSSE) and zero point energy (ZPE) correction. The nature of intermolecular interaction has been revealed by the analysis of AIM and NBO. The results indicate that the greatest binding energy of urea nitrate with RDX is –82.47kJ/mol. The O–H…O and N–H…O hydrogen bonds are important intermolecular interactions of urea nitrate cation with RDX, and the origin of hydrogen bonds is the oxygen atom offering its lone-pair electrons to the σ(O-H)* or σ(O-H)* antibonding orbital. The intermolecular interactions strengthen the N–NO2 bond, leading to the reduced sensitivity of urea nitrate and RDX mixture explosive.     

Raman spectroscopy of urea and urea-intercalated kaolinites at 77 K

The Raman spectra of urea and urea-intercalated kaolinites have been recorded at 77 K using a Renishaw Raman microprobe equipped with liquid nitrogen cooled microscope stage. The NH2 stretching modes of urea were observed as four bands at 3250, 3321, 3355 and 3425 cm(-1) at 77 K. These four bands are attributed to a change in conformation upon cooling to liquid nitrogen temperature. Upon intercalation of urea into both low and high defect kaolinites, only two bands were observed near 3390 and 3410 cm(-1). This is explained by hydrogen bonding between the amine groups of urea and oxygen atoms of the siloxane layer of kaolinite with only one urea conformation. When the intercalated low defect kaolinite was cooled to 77 K, the bands near 3700 cm(-1) attributed to the stretching modes of the inner surface hydroxyls disappeared and a new band was observed at 3615 cm(-1). This is explained by the breaking of hydrogen bonds involving OH groups of the gibbsite-like layer and formation of new bonds to the C=O group of the intercalated urea. Thus it is suggested that at low temperatures two kinds of hydrogen bonds are formed by urea molecules in urea-intercalated kaolinite.     

Complementary hydrogen bonding of a carboxylato-barbiturate with urea and acetamide: experimental and theoretical approach

A barbiturate derivative, 4-(2,4,6-trioxo-tetrahydro-pyrimidine-5-ylidenemethyl)-benzoic acid (L1) possessing functional complementarity to amides has been synthesized and characterized. Its binding separately with urea and acetamide was monitored using UV-vis, fluorescence and (1)H-NMR spectroscopic titrations. Experiments suggested stronger binding of L1 with urea as compared to acetamide. The solid adducts of L1 prepared separately with urea and acetamide were also characterized using IR, (1)H-NMR spectral and PXRD techniques. Theoretical studies on hydrogen bonded complexes of L1-urea and L1-acetamide in the gas phase, aqueous, and DMSO medium were carried out using density functional theory (DFT) at the B3LYP/6-31G** level. The theoretical calculations agreed to the experimental results.     

Effects of urea induced protein conformational changes on ion exchange chromatographic behavior

Urea is widely employed to facilitate protein separations in ion exchange chromatography at various scales. In this work, five model proteins were used to examine the chromatographic effects of protein conformational changes induced by urea in ion exchange chromatography. Linear gradient experiments were carried out at various urea concentrations and the protein secondary and tertiary structures were evaluated by far UV CD and fluorescence measurements, respectively. The results indicated that chromatographic retention times were well correlated with structural changes and that they were more sensitive to tertiary structural change. Steric Mass Action (SMA) isotherm parameters were also examined and the results indicated that urea induced protein conformational changes could affect both the characteristic charge and equilibrium constants in these systems. Dynamic light scattering analysis of changes in protein size due to urea-induced unfolding indicated that the size of the protein was not correlated with SMA parameter changes. These results indicate that while urea-induced structural changes can have a marked effect on protein chromatographic behavior in IEX, this behavior can be quite complicated and protein specific. These differences in protein behavior may provide insight into how these partially unfolded proteins are interacting with the resin material.