Solvation phenomena of a tetrapeptide in water/trifluoroethanol and water/ethanol mixtures: a diffusion NMR, intermolecular NOE, and molecular dynamics study

Alcohol-Induced Denaturation of Hen Egg White Lysozyme Studied by Infrared, Circular Dichroism, and Small-Angle Neutron Scattering

In aqueous binary solvents with fluorinated alcohols, 2,2,2-trifluoroethanol (TFE) and 1,1,1,3,3,3-hexafluoroisopropanol (HFIP), and aliphatic alcohols, ethanol (EtOH) and 2-propanol (2-PrOH), the denaturation of hen egg white lysozyme (HEWL) with increasing alcohol mole fraction xA has been investigated in a wide view from the molecular vibration to the secondary and ternary structures. Circular dichroism (CD) measurement showed that the secondary structure of α-helix content of HEWL increases on adding a small amount of the fluorinated alcohol to the aqueous solution, while the β-sheet content decreases. On the contrary, the secondary structure does not significantly change by the addition of the aliphatic alcohols. Correspondingly, the infrared (IR) spectroscopic measurements revealed that the amide I band red-shifts on the addition of the fluorinated alcohol. However, the band remains unchanged in the aliphatic alcohol systems with increasing alcohol content. To observe the ternary structure of HEWL, small-angle neutron scattering (SANS) experiments with H/D substitution technique have been applied to the HEWL solutions. The SANS experiments were successful in revealing the details of how the geometry of the HEWL changes as a function of xA. The SANS profiles indicated the spherical structure of HEWL in all of the alcohol systems in the xA range examined. The mean radius of HEWL in the two fluorinated alcohol systems increases from ∼16 to ∼18 Å during the change in the secondary structure against the increase in the fluorinated alcohol content. On contrast, the radius does not significantly change in both aliphatic alcohol systems below xA = 0.3 but expands to ∼19 Å as the alcohol content is close to the limitation of the HEWL solubility. According to the present results, together with our knowledge of the alcohol cluster formation and the interaction of the trifluoromethyl (CF3) groups with the hydrophobic moieties of biomolecules, the effects of alcohols on the denaturation of the protein have been discussed on a molecular scale.

Synthesis of robust underwater glues from common proteins via unfolding-aggregating strategy

Underwater adhesive proteins secreted by organisms greatly inspires the development of underwater glue. However, except for specific proteins such as mussel adhesive protein, barnacle cement proteins, curli protein and their related recombinant proteins, it is believed that abundant common proteins cannot be converted into underwater glue. Here, we demonstrate that unfolded common proteins exhibit high affinity to surfaces and strong internal cohesion via amyloid-like aggregation in water. Using bovine serum albumin (BSA) as a model protein, we obtain a stable unfolded protein by cleaving the disulfide bonds and maintaining the unfolded state by means of stabilizing agents such as trifluoroethanol (TFE) and urea. The diffusion of stabilizing agents into water exposes the hydrophobic residues of an unfolded protein and initiates aggregation of the unfolded protein into a solid block. A robust and stable underwater glue can thus be prepared from tens of common proteins. This strategy deciphers a general code in common proteins to construct robust underwater glue from abundant biomass.

Examination of Solvent Interactions with Trp-Cage in 1,1,1,3,3,3-Hexafluoro-2-propanol-water at 298 K through MD Simulations and Intermolecular Nuclear Overhauser Effects

MD simulations of the peptide Trp-cage dissolved in 28% hexafluoroisopropanol (HFIP)-water have been carried out at 298 K with the goal of exploring peptide hydrogen-solvent fluorine nuclear spin cross-relaxation. The work was motivated by the observation that most experimental fluoroalcohol-peptide cross-relaxation terms at 298 K are small, both positive and negative, and not always well predicted from simulations. The cross-relaxation terms for hydrogens of the caged tryptophan residue of Trp-cage are substantially negative, a result consistent with simulations. It was concluded that hexafluoroisopropanol interactions near this part of the peptide are particularly long-lived. While both HFIP and water are present in all regions of the simulation box, the composition of the solvent mixture is not homogeneous throughout the system. HFIP generally accumulates near the peptide surface, while water molecules are preferentially found in regions that are more than 1.5 nm from the surface of the peptide. However, some water remains in higher-than-expected amounts in the solvent layer surrounding 6Trp, 9Asp, Ser13, and Ser14 residues in the helical region of Trp-cage. As observed in simulations of this system at 278 K, HFIP molecules aggregate into clusters that continually form and re-form. Translational diffusion of both HFIP and water appears to be slowed near the surface of the peptide with reduction in diffusion near the 6Trp residue 2- to 3-fold larger than calculated for solvent interactions with other regions of Trp-cage.

Spectroscopic and Theoretical Studies on Conformational Stability of Benzyl Methyl Ether

Conformer-selected electronic and vibrational spectra of benzyl methyl ether and its terminal methyl group-substituted derivative in a supersonic jet have been measured using ultraviolet (UV)-UV hole burning and fluorescence-detected infrared spectroscopy to investigate the conformational stability of flexible molecules. Various quantum chemical calculations as well as experimental observations reveal the coexistence of three conformers with different CCOC dihedral angles and side-chain orientations relative to the benzene ring plane. Vibrational analysis in the excited state with time-dependent density functional theory and IR simulations containing anharmonic coupling sufficiently reproduce the experimental results, suggesting that these three conformers can be distinguished into one gauche-conformer and two trans-ones with respect to the CCOC dihedral angle. We also observe that the gauche conformer exhibits higher-frequency CH₂ modes. The natural bond orbital analysis indicates that this phenomenon is attributed to the electron delocalization from the non-bonding orbitals and the C-O orbitals associated with the neighboring oxygen atom, which leads to a conformer dependence of the methylene C-H bond strength.

Raising the benchmark potential of a simple alcohol-ketone intermolecular balance

2-Butanone offers two hydrogen bond docking variants to a solvating methanol which are cleanly separated by supersonic jet infrared absorption spectroscopy in the OH-stretching range, resolving earlier action spectroscopy indeterminacies for this elementary case of an intermolecular alcohol-ketone balance. The solvent preference for the shorter chain side is unambiguously derived from the spectra of homologous compounds. It is analysed in terms of competing steric and dispersion interactions and the resulting energy differences across a low interconversion barrier. Fortuitous cancellations are discussed and quantitative energy deficiencies of the employed DFT approaches are suggested. Some benchmarkable experimental observations: at low temperature, a single methanol molecule prefers the methyl-sided oxygen lone pair of 2-butanone over the ethyl-sided lone pair by 1-2 kJ mol^-1, the trans butane backbone is conserved in both low-lying isomers, the OH-stretching fundamentals differ by 47(2) cm^-1.

HFIP in Organic Synthesis

1,1,1,3,3,3-Hexafluoroisopropanol (HFIP) is a polar, strongly hydrogen bond-donating solvent that has found numerous uses in organic synthesis due to its ability to stabilize ionic species, transfer protons, and engage in a range of other intermolecular interactions. The use of this solvent has exponentially increased in the past decade and has become a solvent of choice in some areas, such as C-H functionalization chemistry. In this review, following a brief history of HFIP in organic synthesis and an overview of its physical properties, literature examples of organic reactions using HFIP as a solvent or an additive are presented, emphasizing the effect of solvent of each reaction.

Investigating the Bioactive Conformation of Angiotensin II Using Markov State Modeling Revisited with Web-Scale Clustering

Molecular dynamics simulation is a powerful technique for studying the structure and dynamics of biomolecules in atomic-level detail by sampling their various conformations in real time. Because of the long timescales that need to be sampled to study biomolecular processes and the big and complex nature of the corresponding data, relevant analyses of important biophysical phenomena are challenging. Clustering and Markov state models (MSMs) are efficient computational techniques that can be used to extract dominant conformational states and to connect those with kinetic information. In this work, we perform Molecular Dynamics simulations to investigate the free energy landscape of Angiotensin II (AngII) in order to unravel its bioactive conformations using different clustering techniques and Markov state modeling. AngII is an octapeptide hormone, which binds to the AT1 transmembrane receptor, and plays a vital role in the regulation of blood pressure, conservation of total blood volume, and salt homeostasis. To mimic the water-membrane interface as AngII approaches the AT1 receptor and to compare our findings with available experimental results, the simulations were performed in water as well as in water-ethanol mixtures. Our results show that in the water-ethanol environment, AngII adopts more compact U-shaped (folded) conformations than in water, which resembles its structure when bound to the AT1 receptor. For clustering of the conformations, we validate the efficiency of an inverted-quantized k-means algorithm, as a fast approximate clustering technique for web-scale data (millions of points into thousands or millions of clusters) compared to k-means, on data from trajectories of molecular dynamics simulations with reasonable trade-offs between time and accuracy. Finally, we extract MSMs using various clustering techniques for the generation of microstates and macrostates and for the selection of the macrostate representatives.

Ultrasmall MnSe Nanoparticles as T1-MRI Contrast Agents for In Vivo Tumor Imaging

Magnetic resonance imaging (MRI) has excellent potential in the clinical monitoring of tumors because it can provide high-resolution soft tissue imaging. However, commercial contrast agents (CAs) used in MRI still have some problems such as potential toxicity to the human body, low relaxivity, and a short MRI acquisition window. In this study, ultrasmall MnSe nanoparticles are synthesized by living Staphylococcus aureus cells. The as-prepared MnSe nanoparticles are monodispersed with a uniform particle size (3.50 ± 0.52 nm). Due to the ultrasmall particle size and good water solubility, the MnSe nanoparticles exhibit in vitro high longitudinal relaxivity properties (14.12 ± 1.85 mM-1·s-1). The CCK-8 colorimetric assay, histological analysis, and body weight results show that the MnSe nanoparticles do not have appreciable toxicity on cells and organisms. Besides, the MnSe nanoparticles as T1-MRI CAs offer a long MRI acquisition window to tumor imaging (∼7 h). This work provides a promising T1-MRI CA for clinical tumor imaging and a good reference for the application of functional MnSe nanoparticles in the biomedicine field.

Using Molecular Simulation to Guide Protein Engineering for Biocatalysis in Organic Solvents

Biocatalysis in organic solvents (OSs) is very appealing for the industry in producing bulk and/or fine chemicals, such as pharmaceuticals, biodiesel, and fragrances. The poor performance of enzymes in OSs (e.g., reduced activity, insufficient stability, and deactivation) negates OSs' excellent solvent properties. Molecular dynamics (MD) simulations provide a complementary method to study the relationship between enzymes dynamics and the stability in OSs. Here we describe computational procedure for MD simulation of enzymes in OSs with an example of Bacillus subtilis lipase A (BSLA) in dimethyl sulfoxide (DMSO) cosolvent with software GROMACS. We discuss main essential practical issues considered (such as choice of force field, parameterization, simulation setup, and trajectory analysis). The core part of this protocol (enzyme-OS system setup, analysis of structural-based and solvation-based observables) is transferable to other enzymes and any OS systems. Combining with experimental studies, the obtained molecular knowledge is most likely to guide researchers to access rational protein engineering approaches to tailor OS resistant enzymes and expand the scope of biocatalysis in OS media. Finally, we discuss potential solutions to overcome the remaining challenges of computational biocatalysis in OSs and briefly draw future directions for further improvement in this field.

Correlating solvation with conformational pathways of proteins in alcohol-water mixtures: a THz spectroscopic insight

Water, being an active participant in most of the biophysical processes, is important to trace how protein solvation changes as its conformation evolves in the presence of solutes or co-solvents. In this study, we investigate how the secondary structures of two diverse proteins - lysozyme and β-lactoglobulin - change in the aqueous mixtures of two alcohols - ethanol and 2,2,2-trifluoroethanol (TFE) using circular dichroism measurements. We observe that these alcohols change the secondary structures of these proteins and the changes are protein-specific. Subsequently, we measure the collective solvation dynamics of these two proteins both in the absence and in the presence of alcohols by measuring the frequency-dependent absorption coefficient (α(ν)) in the THz (0.1-1.2 THz) frequency domain. The alcohol-water mixtures exhibit a non-ideal behaviour with the highest absorption difference (Δα) obtained at X_alcohol = 0.2. The protein solvation in the presence of the alcohols shows an oscillating behaviour in which Δα_protein changes with X_alcohol. Such an oscillatory behaviour of protein solvation results from a delicate interplay between the protein-water, protein-alcohol and water-alcohol associations. We attempt to correlate the various structural conformations of the proteins with the associated solvation.

Examination of Interactions of Hexafluoro-2-propanol with Trp-Cage in Hexafluoro-2-propanol-Water by MD Simulations and Intermolecular Nuclear Overhauser Effects

All-atom molecular dynamic simulations of the peptide Trp-cage in 30% hexafluoro-2-propanol- water (V/V) at 278 K have been carried out with the goal of exploring peptide hydrogen-solvent fluorine nuclear spin cross relaxation. Force field parameters for HFIP reported by Fioroni et al. along with the fluorine parameters of the TFE5 model reported by this lab were used. Water was represented by the TIP5P-Ew model. Peptide modeling used the AMBER99SB-ILDN force field. Translational diffusion coefficients of solution components at 278 K were predicted to within 35% of experimental values using these parameter sets. The simulations indicate that the solvent mixture is not homogeneous, with HFIP molecules clustered into aggregates as large as 53 fluoroalcohol molecules. The solvent environment of surface atoms of Trp-cage fluctuates between being HFIP-rich and more water-rich about every 10 ns. In accord with previous studies by other groups, the average concentration of HFIP near the surface of the peptide is significantly enhanced over the concentration of HFIP in the bulk solvent. In the simulations, ∼7% of the initial contacts between HFIP molecules and Trp-cage develop into peptide-fluoroalcohol interactions that persist for times as long as 8 ns. Most of the available experimental nuclear spin cross-relaxation rates (Σ_HF) for hydrogens of the Trp-cage in 30% HFIP-water are reproduced from the MD trajectories to within uncertainties of the experimental data and the simulations. However, a few calculated Σ_HF values for hydrogens of the Trp-cage do not agree with experiment. These tend to be situations where long-lived peptide-HFIP interactions are predicted. The disagreements between observed and calculated Σ_HF in these instances signal defects in the modeling parameters and procedures that are presently unrecognized.

Solvation Structures of Tetraethylammonium Bromide and Tetrafluoroborate in Aqueous Binary Solvents with Ethanol, Trifluoroethanol, and Acetonitrile

The solvation structures of tetraethylammonium bromide and tetrafluoroborate (TEABr and TEABF₄) in aqueous binary solvents with ethanol (EtOH), 2,2,2-trifluoroethanol (TFE), and acetonitrile (AN) have been clarified by molecular dynamics (MD) simulations. In addition, ¹H and ¹³C NMR chemical shifts of the H and C atoms within TEA⁺ in the binary solvents have been measured as a function of the mole fraction of the organic solvent, x_OS. The variations of the chemical shifts with an increase in x_OS were interpreted according to the solvation structures of TEA⁺, Br^-, and BF₄^- obtained from the MD simulations. It has been found that TEABF₄ at 130 mmol dm^-3 cannot be dissolved into the EtOH and TFE solvents above x_OS ≈ 0.7 and 0.6, respectively, while TEABr can be done in both solvents. Interestingly, TEABr and TEABF₄ at the concentration can be dissolved in the AN solvents over the entire x_OS range. The solvation of TEA⁺, Br^-, and BF₄^- in each solvent has been discussed in terms of the electrostatic force, the weak hydrogen bond of C-H···F-C, and the dipole-dipole interaction.

Microscopic origin of breakdown of Stokes-Einstein relation in binary mixtures: Inherent structure analysis

Aqueous binary mixtures often exhibit dramatic departure from the predicted hydrodynamic behavior when transport properties are plotted against composition. We show by inherent structure (IS) analysis that this sharp composition dependent breakdown of the Stokes-Einstein relation can be attributed to the non-monotonic variation in the average inherent structure energy of these mixtures. Further IS analysis reveals the existence of a unique ground state, stabilized by both the formation of an optimum number of H-bonds and a favorable hydrophobic interaction at this composition. The surprisingly sharp turnaround behavior observed in the effective hydrodynamic radius also owes its origin to the same combination of these two factors. Interestingly, the temperature dependence of isothermal compressibility shows a minimum at the particular composition. Extensive studies on water-dimethyl sulfoxide and water-ethanol mixtures using two different force-fields of water reveal many features that are nearly universal. A justification of this quasi-universal behavior is provided in terms of a mode-coupling theory (MCT) of viscosity, which can serve as the starting point of a remarkable correlation observed with the nearest neighbor structure, as captured by the first peaks of the radial distribution function, and the slowdown in the intermediate scattering function at intermediate wavenumbers. Therefore, the formation of the local structure captured through IS analysis can be correlated with the MCT.

About TFE: Old and New Findings

The fluorinated alcohol 2,2,2-Trifluoroethanol (TFE) has been implemented for many decades now in conformational studies of proteins and peptides. In peptides, which are often disordered in aqueous solutions, TFE acts as secondary structure stabilizer and primarily induces an α -helical conformation. The exact mechanism through which TFE plays its stabilizing roles is still debated and direct and indirect routes, relying either on straight interaction between TFE and molecules or indirect pathways based on perturbation of solvation sphere, have been proposed. Another still unanswered question is the capacity of TFE to favor in peptides a bioactive or a native-like conformation rather than simply stimulate the raise of secondary structure elements that reflect only the inherent propensity of a specific amino-acid sequence. In protein studies, TFE destroys unique protein tertiary structure and often leads to the formation of non-native secondary structure elements, but, interestingly, gives some hints about early folding intermediates. In this review, we will summarize proposed mechanisms of TFE actions. We will also describe several examples, in which TFE has been successfully used to reveal structural properties of different molecular systems, including antimicrobial and aggregation-prone peptides, as well as globular folded and intrinsically disordered proteins.

Examination of Trifluoroethanol Interactions with Trp-Cage in Trifluoroethanol-Water at 298 K through Molecular Dynamics Simulations and Intermolecular Nuclear Overhauser Effects

Molecular dynamics simulations of the protein model Trp-cage in 42% trifluoroethanol (TFE)-water at 298 K have been carried out with the goal of exploring peptide hydrogen-solvent fluorine nuclear spin cross-relaxation. The TFE5 model of TFE developed in a previous work was used with the TIP5P-Ew model of water. System densities and component translational diffusion coefficients predicted by the simulations were within 20% of the experimental values. Consideration of the calculated relative amounts of TFE and water surrounding the hydrogens of Trp-cage indicated that the composition of the solvent mixture beyond ∼1.5 nm from the van der Waals surface of the peptide is close to the composition of the bulk solvent, but as observed by others, TFE accumulates preferentially near the peptide surface. In the simulations, both TFE and water molecules make contacts with the peptide surface; water molecules predominate in contacts with the peptide backbone atoms and TFE molecules generally preferentially interact with side chains. Translational diffusion of solvent molecules appears to be slowed near the surface of the peptide. Depending on the location in the structure, TFE molecules form complexes with the peptide that may persist for up to ∼7 ns. Many of the peptide spin-solvent fluorine cross-relaxation parameters (Σ_HF) for which experimental values are available are reasonably well-predicted from the simulations. However, the calculated Σ_HF values were too small for some hydrogens of the 6Trp indole ring and the amino acid hydrogens near this residue in the native structure, whereas Σ_HF values for hydrogens on the side chains of 1Asn, 4Ile, and 7Leu are too large. In 42% TFE-water, persistent conformations of Trp-cage are found, which differ from the conformation found in water by the orientation of the 3Tyr ring.

Structural Impact of Phosphorylation and Dielectric Constant Variation on Synaptotagmin's IDR

We used time-resolved Förster resonance energy transfer, circular dichroism, and molecular dynamics simulation to investigate the structural dependence of synaptotagmin 1's intrinsically disordered region (IDR) on phosphorylation and dielectric constant. We found that a peptide corresponding to the full-length IDR sequence, a ∼60-residue strong polyampholyte, can sample structurally collapsed states in aqueous solution, consistent with its κ-predicted behavior, where κ is a sequence-dependent parameter that is used to predict IDR compaction. In implicit solvent simulations of this same sequence, lowering the dielectric constant to more closely mimic the environment near a lipid bilayer surface promoted further sampling of collapsed structures. We then examined the structural tendencies of central region residues of the IDR in isolation. We found that the exocytosis-modulating phosphorylation of Thr¹¹² disrupts a local disorder-to-order transition induced by trifluoroethanol/water mixtures that decrease the solution dielectric constant and stabilize helical structure. Implicit solvent simulations on these same central region residues testing the impact of dielectric constant alone converge on a similar result, showing that helical structure is formed with higher probability at a reduced dielectric. In these helical conformers, lysine-aspartic acid salt bridges contribute to stabilization of transient secondary structure. In contrast, phosphorylation results in formation of salt bridges unsuitable for helix formation. Collectively, these results suggest a model in which phosphorylation and compaction of the IDR sequence regulate structural transitions that in turn modulate neuronal exocytosis.

Temperature-Induced Collapse of Elastin-like Peptides Studied by 2DIR Spectroscopy

Elastin-like peptides are hydrophobic biopolymers that exhibit a reversible coacervation transition when the temperature is raised above a critical point. Here, we use a combination of linear infrared spectroscopy, two-dimensional infrared spectroscopy, and molecular dynamics simulations to study the structural dynamics of two elastin-like peptides. Specifically, we investigate the effect of the solvent environment and temperature on the structural dynamics of a short (5-residue) elastin-like peptide and of a long (450-residue) elastin-like peptide. We identify two vibrational energy transfer processes that take place within the amide I' band of both peptides. We observe that the rate constant of one of the exchange processes is strongly dependent on the solvent environment and argue that the coacervation transition is accompanied by a desolvation of the peptide backbone where up to 75% of the water molecules are displaced. We also study the spectral diffusion dynamics of the valine(1) residue that is present in both peptides. We find that these dynamics are relatively slow and indicative of an amide group that is shielded from the solvent. We conclude that the coacervation transition of elastin-like peptides is probably not associated with a conformational change involving this residue.

Protein Environment: A Crucial Triggering Factor in Josephin Domain Aggregation: The Role of 2,2,2-Trifluoroethanol

The protein ataxin-3 contains a polyglutamine stretch that triggers amyloid aggregation when it is expanded beyond a critical threshold. This results in the onset of the spinocerebellar ataxia type 3. The protein consists of the globular N-terminal Josephin domain and a disordered C-terminal tail where the polyglutamine stretch is located. Expanded ataxin-3 aggregates via a two-stage mechanism: first, Josephin domain self-association, then polyQ fibrillation. This highlights the intrinsic amyloidogenic potential of Josephin domain. Therefore, much effort has been put into investigating its aggregation mechanism(s). A key issue regards the conformational requirements for triggering amyloid aggregation, as it is believed that, generally, misfolding should precede aggregation. Here, we have assayed the effect of 2,2,2-trifluoroethanol, a co-solvent capable of stabilizing secondary structures, especially α-helices. By combining biophysical methods and molecular dynamics, we demonstrated that both secondary and tertiary JD structures are virtually unchanged in the presence of up to 5% 2,2,2-trifluoroethanol. Despite the preservation of JD structure, 1% of 2,2,2-trifluoroethanol suffices to exacerbate the intrinsic aggregation propensity of this domain, by slightly decreasing its conformational stability. These results indicate that in the case of JD, conformational fluctuations might suffice to promote a transition towards an aggregated state without the need for extensive unfolding, and highlights the important role played by the environment on the aggregation of this globular domain.

Structure and dynamics of the extended-helix state of alpha-synuclein: Intrinsic lability of the linker region

The Parkinson's protein alpha-synuclein binds to synaptic vesicles in vivo and adopts a highly extended helical conformation when binding to lipid vesicles in vitro. High-resolution structural analysis of alpha-synuclein bound to small lipid or detergent micelles revealed two helices connected by a non-helical linker, but corresponding studies of the vesicle-bound extended-helix state are hampered by the size and heterogeneity of the protein-vesicle complex. Here we employ fluorinated alcohols (FAs) to induce a highly helical aggregation-resistant state of alpha-synuclein in solution that resembles the vesicle-bound extended-helix state but is amenable to characterization using high-resolution solution-state NMR. Analysis of chemical shift, NOE, coupling constant, PRE and relaxation measurements shows that the lipid-binding domain of alpha-synuclein in FA solutions indeed adopts a single continuous helix and that the ends of this helix do not come into detectable proximity to each other. The helix is well ordered in the center, but features an increase in fast internal motions suggestive of helix fraying approaching the termini. The central region of the helix exhibits slower time scale motions that likely result from flexing of the highly anisotropic structure. Importantly, weak or missing short- and intermediate-range NOEs in the region corresponding to the non-helical linker of micelle-bound alpha-synuclein indicate that the helical structure in this region of the protein is intrinsically unstable. This suggests that conversion of alpha-synuclein from the extended-helix to the broken-helix state represents a functionally relevant structural transition.

Real-time observation of the photoionization-induced water rearrangement dynamics in the 5-hydroxyindole-water cluster by time-resolved IR spectroscopy

Solvation plays an essential role in controlling the mechanism and dynamics of chemical reactions in solution. The present study reveals that changes in the local solute-solvent interaction have a great impact on the timescale of solvent rearrangement dynamics. Time-resolved IR spectroscopy has been applied to a hydration rearrangement reaction in the monohydrated 5-hydroxyindole-water cluster induced by photoionization of the solute molecule. The water molecule changes the stable hydration site from the indolic NH site to the substituent OH site, both of which provide a strongly attractive potential for hydration. The rearrangement time constant amounts to 8 ± 2 ns, and is further slowed down by a factor of more than five at lower excess energy. These rearrangement times are slower by about three orders of magnitude than those reported for related systems where the water molecule is repelled from a repulsive part of the interaction potential toward an attractive well. The excess energy dependence of the time constant is well reproduced by RRKM theory. Differences in the reaction mechanism are discussed on the basis of energy relaxation dynamics.

Conformational disorder and solvation properties of the key-residues of a protein in water-ethanol mixed solutions

A small number of key-residues in a protein sequence play vital roles in the function, stability, and folding of the protein. The nonuniform conformational disorder of a small protein Chymotrypsin Inhibitor 2 (CI2) and its secondary segments has been quantified in the ethanol governed temperature induced unfolding process by estimating its change in configurational entropy in several water-ethanol mixed solutions. Such calculations further assist us in identifying the key-residues, from where the unfolding of the protein was initiated. Our findings match well with the reported experimental results. We then make an attempt to explore the properties of the solvent water and ethanol around the key-residues of the protein in its folded and unfolded forms at ambient temperature to identify the individual role of ethanol and water in the protein unfolding. We find that the key-residues of the unfolded protein are in good contact with both water and ethanol as compared to those of the folded protein. In the presence of ethanol, water molecules are noticed to form a rigid structurally bound solvation layer around the key-residues of the protein, irrespective of its conformational state. The restricted translational motion and prominent caging effect of the water and ethanol molecules present around the key-residues of the unfolded protein are a signature of the existence of a rigid mixed water-ethanol layer as compared to that around the folded protein. Furthermore, comparable restricted structural relaxation of the key-residue-water and key-residue-ethanol hydrogen bonds in the unfolded protein as compared to that in the folded one implies that the formation of a strong long-lived hydrogen bonding environment nourishes the unfolding process. We believe that our findings will shed light to several co-solvent governed unfolding processes of a protein in general.

Can 2,2,2-trifluoroethanol be an efficient protein denaturant than methanol and ethanol under thermal stress?

We report the heterogeneous unfolding phenomenon of a small protein Chymotrypsin Inhibitor 2 in various concentrations of methanol, ethanol and TFE solutions by performing atomistic molecular dynamics simulation studies. Our study reveals that the unfolding phenomenon of CI2 under thermal stress majorly depends on the concentration and the nature of the alcohol.

Structural Characterization of the Intrinsically Disordered Protein p53 Using Raman Spectroscopy

The intrinsically disordered protein p53 has attracted a strong interest for its important role in genome safeguarding and potential therapeutic applications. However, its disordered character makes difficult a full characterization of p53 structural architecture. A deep knowledge of p53 structural motifs could significantly help the understanding of its functional properties, in connection with its complex binding network. We have applied Raman spectroscopy to investigate the structural composition and the conformational heterogeneity of both full-length p53 and its DNA binding domain (DBD), in different solvent environments. In particular, a careful analysis of the Amide I Raman band, which is highly sensitive to protein secondary structure elements such as α-helices, β-sheets and random coils, has revealed the presence of extended random coils in p53 and predominant β-sheet regions in its DBD. In addition, this analysis has allowed us to explore the ensemble of interchanging conformations in both p53 and its DBD, highlighting a higher conformational heterogeneity in p53 than in its DBD. Furthermore, by applying a principal components analysis, we have identified the principal spectral markers in both p53 and DBD samples. The combination of the two approaches could be insightful for the study of intrinsically disordered proteins, by offering increased versatility and wide application as a label-free, real-time and non-invasive detection method.

A Direct Link from the Gas to the Condensed Phase: A Rotational Spectroscopic Study of 2,2,2-Trifluoroethanol Trimers

Rotational spectra of the three most stable conformers (I, II, III) of the ternary 2,2,2-trifluoroethanol (TFE) cluster were measured using Fourier transform microwave spectrometers, and unambiguously assigned with the aid of ab initio calculations. The most stable conformer, I, contains one trans-TFE subunit which is unstable in its isolated gas phase form. The study offers new insights into how the trans conformation is stabilized in TFE clusters of increasing size, and eventually becomes a dominant conformation in the liquid phase. A detailed analysis shows that while O-H⋅⋅⋅O-H and O-H⋅⋅⋅F-C hydrogen bonds are the most significant attractive interactions which stabilize all three conformers, the main driving force for the stability of I over III, which has all gauche-TFE subunits, is the attractive interaction of C-F⋅⋅⋅F-C contact pairs. A new type of three-point F⋅⋅⋅F⋅⋅⋅F attractive contact interaction is also identified.

Binding of Amphipathic Cell Penetrating Peptide p28 to Wild Type and Mutated p53 as studied by Raman, Atomic Force and Surface Plasmon Resonance spectroscopies

BACKGROUND

Mutations within the DNA binding domain (DBD) of the tumor suppressor p53 are found in >50% of human cancers and may significantly modify p53 secondary structure impairing its function. p28, an amphipathic cell-penetrating peptide, binds to the DBD through hydrophobic interaction and induces a posttranslational increase in wildtype and mutant p53 restoring functionality. We use mutation analyses to explore which elements of secondary structure may be critical to p28 binding.

METHODS

Molecular modeling, Raman spectroscopy, Atomic Force Spectroscopy (AFS) and Surface Plasmon Resonance (SPR) were used to identify which secondary structure of site-directed and naturally occurring mutant DBDs are potentially altered by discrete changes in hydrophobicity and the molecular interaction with p28.

RESULTS

We show that specific point mutations that alter hydrophobicity within non-mutable and mutable regions of the p53 DBD alter specific secondary structures. The affinity of p28 was positively correlated with the β-sheet content of a mutant DBD, and reduced by an increase in unstructured or random coil that resulted from a loss in hydrophobicity and redistribution of surface charge.

CONCLUSIONS

These results help refine our knowledge of how mutations within p53-DBD alter secondary structure and provide insight on how potential structural alterations in p28 or similar molecules improve their ability to restore p53 function.

GENERAL SIGNIFICANCE

Raman spectroscopy, AFS, SPR and computational modeling are useful approaches to characterize how mutations within the p53DBD potentially affect secondary structure and identify those structural elements prone to influence the binding affinity of agents designed to increase the functionality of p53.

Hydrophobic fluorine mediated switching of the hydrogen bonding site as well as orientation of water molecules in the aqueous mixture of monofluoroethanol: IR, molecular dynamics and quantum chemical studies

Fluorination of ethanol changes orientation of water in its aqueous mixture.

Radical Formation Initiates Solvent-Dependent Unfolding and β-sheet Formation in a Model Helical Peptide

We examined the effects of Cα-centered radical formation on the stability of a model helical peptide, N-Ac-KK(AL)10KK-NH2. Three, 100 ns molecular dynamics simulations using the OPLS-AA force field were carried out on each α-helical peptide in six distinct binary TIP4P water/2,2,2-trifluoroethanol (TFE) mixtures. The α-helicity was at a maximum in 20% TFE, which was inversely proportional to the number of H-bonds between water molecules and the peptide backbone. The radial distribution of TFE around the peptide backbone was highest in 20% TFE, which enhanced helix stability. The Cα-centered radical initiated the formation of a turn within 5 ns, which was a smaller kink at high TFE concentrations, and a loop at lower TFE concentrations. The highest helicity of the peptide radical was measured in 100% TFE. The formation of hydrogen bonds between the peptide backbone and water destabilized the helix, whereas the clustering of TFE molecules around the radical center stabilized the helix. Following radical termination, the once helical structure converted to a β-sheet rich state in 100% water only, and this transition did not occur in the nonradical control peptide. This study gives evidence on how the formation of peptide radicals can initiate α-helical to β-sheet transitions under oxidative stress conditions.

Composition dependent multiple structural transformations of myoglobin in aqueous ethanol solution: a combined experimental and theoretical study

Experimental studies (circular dichroism and ultra-violet (UV) absorption spectra) and large scale atomistic molecular dynamics simulations (accompanied by order parameter analyses) are combined to establish a number of remarkable (and unforeseen) structural transformations of protein myoglobin in aqueous ethanol mixture at various ethanol concentrations. The following results are particularly striking. (1) Two well-defined structural regimes, one at xEtOH ∼ 0.05 and the other at xEtOH ∼ 0.25, characterized by formation of distinct partially folded conformations and separated by a unique partially unfolded intermediate state at xEtOH ∼ 0.15, are identified. (2) Existence of non-monotonic composition dependence of (i) radius of gyration, (ii) long range contact order, (iii) residue specific solvent accessible surface area of tryptophan, and (iv) circular dichroism spectra and UV-absorption peaks are observed. Interestingly at xEtOH ∼ 0.15, time averaged value of the contact order parameter of the protein reaches a minimum, implying that this conformational state can be identified as a molten globule state. Multiple structural transformations well known in water-ethanol binary mixture appear to have considerably stronger effects on conformation and dynamics of the protein. We compare the present results with studies in water-dimethyl sulfoxide mixture where also distinct structural transformations are observed along with variation of co-solvent composition.

Unusual H-Bond Topology and Bifurcated H-bonds in the 2-Fluoroethanol Trimer

By using a combination of rotational spectroscopy and ab initio calculations, an unusual H-bond topology was revealed for the 2-fluoroethanol trimer. The trimer exhibits a strong heterochiral preference and adopts an open OH⋅⋅⋅OH H-bond topology while utilizing two types of bifurcated H-bonds involving organic fluorine. This is in stark contrast to the cyclic OH⋅⋅⋅OH H-bond topology adopted by trimers of water and other simple alcohols. The strengths of different H-bonds in the trimer were analyzed by using the quantum theory of atoms in molecules. The study showcases a remarkable example of a chirality-induced switch in H-bond topology in a simple transient chiral fluoroalcohol. It provides important insight into the H-bond topologies of small fluoroalcohol aggregates, which are proposed to play a key role in protein folding and in enantioselective reactions and separations where fluoroalcohols serve as a (co)solvent.