Formation Of Contact Pairs Research Articles

Hofmeister Effects of Group II Cations as Seen in the Unfolding of Ribonuclease A.

This work studies the effects of alkaline-earth cation addition on the unfolding free energy of a model protein, pancreatic Ribonuclease A (RNase A) by differential scanning calorimetry analysis. RNase A was chosen because: a) it does not specifically bind Mg2+ , Ca2+ and Sr2+ cations and b) maintains its structural integrity throughout a large pH range. We have measured and compared the effects of NaCl, MgCl2 , CaCl2 and SrCl2 addition on the melting point of RNase A. Our results show that even though the addition of group II cations to aqueous solvent reduces the solubility of nonpolar residues (and enhances the hydrophobic effect), their interactions with the amide moieties are strong enough to "salt-them-in" the solvent, thereby causing an overall protein stability reduction. We demonstrate that the amide-cation interactions are a major contributor to the observed "Hofmeister Effects" of group II cations in protein folding. Our analysis suggests that protein folding "Hofmeister Effects" of group II cations, are mostly the aggregate sum of how cation addition simultaneously salts-out hydrophobic moieties by increasing the cavitation free energy, while promoting the salting-in of amide moieties through contact pair formation.

Thermodynamics of association of water soluble fullerene derivatives [ $$\hbox {C}_{60}\hbox {(OH)}_{\mathrm{n}}$$ C 60 (OH) n , n = 0, 2, 4, 8 and 12] in aqueous media

The thermodynamics of association of fullerene [ $$\hbox {C}_{60}$$ ] and water-soluble fullerene derivatives, i.e., fullerols [ $$\hbox {C}_{60}\hbox {(OH)}_{\mathrm{n}}$$ , where, n = 2, 4, 8, 12] in aqueous solutions have been studied using molecular dynamics simulations. The potentials of mean force (PMFs) bring out the tendency of aggregation of these nanostructures in water. The extent of hydroxylation seems to have a minor effect on the depth of the contact minima (the first minimum in the PMFs). The positions of the subsequent minima and maxima in the PMFs change with the size of the solute molecules. Higher stability of the contact state of highly hydroxylated fullerols is due to the van der Waals interactions whereas intermolecular solute-solvent hydrogen bonding nearly flattens the PMFs beyond the $$2{\mathrm{nd}}$$ minima for higher fullerols. The solvent contributions to the PMFs for all the solute particles studied here are positive. Entropic and enthalpic contributions to the association of solute molecules are calculated in the isothermal-isobaric (NPT) ensemble. We find that the contact pair formation is governed by entropy with the enthalpic contributions being highly unfavorable, whereas the solvent assisted and solvent separated configurations show entropy-enthalpy compensation. Synopsis: Aqueous solutions of fullerene have found applications in molecular sensing devices, biochemistry and environmental science. Therefore, it is necessary to have a microscopic understanding of the solvation structure of such macromolecules. Association and dynamics of fullerene and fullerols [ $$\hbox {C}_{60}\hbox {(OH)}_{\mathrm{n}}$$ ] in water are addressed by molecular dynamics simulations.

Coordination ability of N,N’-disubstituted 9,10-phenanthrenediimines

The ability of N,N’-disubstituted 9,10-phenanthrenediimines in neutral, monoand direduced states to act as bidentate ligands in main-group-metal and transition-metal complexes has been demonstrated for the first time. The formation of metal complexes with the radical anion form of phenanthrenediimines stabilized through the formation of contact pairs (for Li) or chelate complexes (for Rh) has been detected.

Effects of the protein denaturant guanidinium chloride on aqueous hydrophobic contact-pair interactions

Guanidinium chloride (GdmCl) is one of the most common protein denaturants. Although GdmCl is well known in the field of protein folding, the mechanism by which it denatures proteins is not well understood. In fact, there are few studies looking at its effects on hydrophobic interactions. In this work the effect of GdmCl on hydrophobic interactions has been studied by observing how the denaturant influences model systems of phenyl and alkyl hydrophobic contact pairs. Contact pair formation is monitored through the use of fluorescence spectroscopy, i.e., measuring the intrinsic phenol fluorescence being quenched by carboxylate ions. Hydrophobic interactions are isolated from other interactions through a previously developed methodology. The results show that GdmCl does not significantly affect hydrophobic interactions between small moieties such as methyl groups and phenol; while on the other hand, the interaction of larger hydrophobes such as hexyl and heptyl groups with phenol is significantly destabilized.

Infrared spectroscopic studies on hydrogen-bonded water networks in gas phase clusters

Size-selective infrared (IR) spectroscopy of gas phase water-containing clusters is performed to probe microscopic natures of hydrogen-bonded water networks. Size-selective observation is extended to the size range of a few tens to hundreds of molecules to bridge the gap between simple but unique networks in small-sized water clusters and those in bulk water. IR spectra of two types of large water-containing clusters, phenol-(H2O) n (n < ∼50) and H+(H2O) n (n ⩽ 221), are measured in the OH stretching vibrational region. Clear size dependence of the observed spectra is interpreted in terms of coordination numbers of water molecules, ring sizes of hydrogen bond networks and interior crystallisation of the clusters. Structural features of hydrogen bond networks seen in bulk water are confirmed in these large-sized clusters. For more detailed analyses of spectra of H+(H2O) n , the inert gas ‘tagging’ technique is employed. Tuning of internal energy and isomer distribution of H+(H2O) n is achieved by a choice of inert gas species. An effective approach to spectral isomer separation is proposed on the basis of unexpected inert gas dependence of isomer distribution. Inert gas tagging is also applied to probe hydrogen bond network motifs of large-sized H+(H2O) n in the size range of n = 20−50. A particular success of the tagging is demonstrated on the n = 22 cluster, which has been known as an anti-magic number cluster. An important application of gas phase water clusters is simplification of a complicated phenomenon in liquid water and such model clusters allow us to extract the physical essence of the phenomenon. Radiation chemistry of water (ionisation and following processes) is studied by IR spectroscopy of water cluster radical cations, (H2O) n +. The H3O+–OH ion-radical contact pair formation upon ionisation of water is confirmed in n ⩽ 4. Separation of the ion-radical pair by hydration processes is observed in n ⩾ 5. This result shows the intrinsic instability of the H3O+–OH ion-radical contact pair in water networks, and implies higher mobility of the OH radical due to its release from the charged site.

Cations Bind Only Weakly to Amides in Aqueous Solutions

We investigated salt interactions with butyramide as a simple mimic of cation interactions with protein backbones. The experiments were performed in aqueous metal chloride solutions using two spectroscopic techniques. In the first, which provided information about contact pair formation, the response of the amide I band to the nature and concentration of salt was monitored in bulk aqueous solutions via attenuated total reflection Fourier transform infrared spectroscopy. It was found that molar concentrations of well-hydrated metal cations (Ca(2+), Mg(2+), Li(+)) led to the rise of a peak assigned to metal cation-bound amides (1645 cm(-1)) and a decrease in the peak associated with purely water-bound amides (1620 cm(-1)). In a complementary set of experiments, the effect of cation identity and concentration was investigated at the air/butyramide/water interface via vibrational sum frequency spectroscopy. In these studies, metal ion-amide binding led to the ordering of the adjacent water layer. Such experiments were sensitive to the interfacial partitioning of cations in either a contact pair with the amide or as a solvent separated pair. In both experiments, the ordering of the interactions of the cations was: Ca(2+) > Mg(2+) > Li(+) > Na(+) ≈ K(+). This is a direct cationic Hofmeister series. Even for Ca(2+), however, the apparent equilibrium dissociation constant of the cation with the amide carbonyl oxygen was no tighter than ∼8.5 M. For Na(+) and K(+), no evidence was found for any binding. As such, the interactions of metal cations with amides are far weaker than the analogous binding of weakly hydrated anions.

The effect of urea on aqueous hydrophobic contact-pair interactions

Urea is perhaps the most common denaturant used for studying proteins. However the mechanism of denaturation is still not well understood. Recent theoretical work suggests that van der Waals interactions between urea and non-polar amino acid residues are a major contributor to the protein denaturation process. However, there are few experimental data measuring the effect of urea on hydrophobic interactions. In this work we have determined how the addition of urea to the aqueous solvent affects the contact-pair formed between alkyl and phenyl groups in model compounds: the data indicate that for solutes having a radius smaller than 2.87 Å cavity formation energetics dominate, therefore the addition of urea promotes the formation of hydrophobic contact pairs; while for larger solutes, van der Waals interactions have the largest magnitude, causing urea to disrupt the formation of contact pairs. The influence of urea on hydrophobic interactions is shown to be continuous in the 1-8 M concentration range and is well-correlated with the predictions of scaled particle theory. This demonstrates that the effect of urea on hydrophobic contact pairs can be explained by the changes observed in the solvent packing density, without having to invoke changes in the hydrogen bonding network of water.

Atomistic Simulations of Dilute Polyelectrolyte Solutions

The properties of short chains of poly-(styrene)-co-(styrene sulfonate) are studied using atomistic molecular dynamics simulations with explicit solvent. We study single 8-mers and 16-mers with two species of counterions, Na(+) and Mg(2+), and for various degrees of sulfonation, f. We find that single trajectories do not efficiently sample configurational space, even for fairly long 100-ns simulations, because of rotational barriers caused by nonbonded interactions. Hamiltonian replica exchange molecular dynamics (HREMD) simulations or averages over multiple trajectories are required in order to obtain equilibrium properties. A polystyrene sulfonate chain adopts collapsed conformations at low f, in which the sulfonate groups are located outside the globule and benzene rings form the inner region, and adopts extended conformations as f is increased. Interestingly, the pair correlation functions between side groups of polystyrene chains are not sensitive to f and species of counterion, i.e., the balance of electrostatic repulsion between charged groups and hydrophobic attraction between benzene rings is achieved by conformational change in a way preserving pair correlations between side groups in a polymer chain. For Na(+) counterions, no localization is observed in the simulations. For Mg(2+) counterions, there is a large free energy barrier to contact pair formation between the sulfonate groups and the Mg(2+) counterions. As a consequence we do not observe the formation or breaking of contact pairs during the course of a simulation. The simulations provide insight into the important interactions and correlations in polyelectrolyte solutions.

Study on The Characters of Different Types of Amino-acid Networks and Their Relations With Protein Folding*

The theoretical and experimental studies have showed that the topology of the native structure of protein plays an important role in determining its folding process. The complex network approach was used to analyze the topological characters of the native structure of protein and then explore the relationship between these characters and the experimental folding rates. Several types of network were constructed, including all-amino-acids network, hydrophobic amino acid network, hydrophilic amino acid, hydrophobic-hydrophilic amino acid network and their corresponding long-range interaction network. The statistic characters of the assortativity coefficient and the clustering coefficient were studied. The results indicate that all types of network except for the hydrophobic-hydrophilic one are of the positive assortativity coefficient. Furthermore, there is an obvious linear positive correlation between the assortativity coefficient and the folding rate for the all amino acids network and the hydrophobic amino acid network, which implies that the cooperative interactions of the hydrophobic amino acids are important for proteins rapidly folding into their native states. Moreover, it is found that there is a clear linear negative correlation between the clustering coefficient of the hydrophobic amino acid networks and the experimental folding rates of the corresponding proteins, which indicates that the formation of the triangle construction among the amino acids reduces the folding rates. It is also found that in the long-range interaction networks, the formation of contact pairs linking two distant residues in sequence would slow down the process of protein folding.

Enthalpy−Entropy Contributions to the Potential of Mean Force of Nanoscopic Hydrophobic Solutes

Entropic and enthalpic contributions to the hydrophobic interaction between nanoscopic hydrophobic solutes, modeled as graphene plates in water, have been calculated using molecular dynamics simulations in the isothermal-isobaric (NPT) ensemble with free energy perturbation methodology. We find the stabilizing contribution to the free energy of association (contact pair formation) to be the favorable entropic part, the enthalpic contribution being highly unfavorable. The desolvation barrier is dominated by the unfavorable enthalpic contribution, despite a fairly large favorable entropic compensation. The enthalpic contributions, incorporating the Lennard-Jones solute-solvent terms, largely determine the stability of the solvent separated configuration. We decompose the enthalpy into a direct solute-solute term, the solute-solvent interactions, and the remainder that contains pressure-volume work as well as contributions due to solvent reorganization. The enthalpic contribution due to changes in water-water interactions arising from solvent reorganization around the solute molecules is shown to have major contribution in the solvent induced enthalpy change.

Contact pair dynamics during folding of two small proteins: chicken villin head piece and the Alzheimer protein beta-amyloid.

The folding of an extended protein to its unique native state requires establishment of specific, predetermined, often distant, contacts between amino acid residue pairs. The dynamics of contact pair formation between various hydrophobic residues during folding of two different small proteins, the chicken villin head piece (HP-36) and the Alzheimer protein beta-amyloid (betaA-40), are investigated by Brownian dynamics (BD) simulations. These two proteins represent two very different classes-HP-36 being globular while betaA-40 is nonglobular, stringlike. Hydropathy scale and nonlocal helix propensity of amino acids are used to model the complex interaction potential among the various amino acid residues. The minimalistic model we use here employs a connected backbone chain of atoms of equal size while an amino acid is attached to each backbone atom as an additional atom of differing sizes and interaction parameters, determined by the characteristics of each amino acid. Even for such simple models, we find that the low-energy structures obtained by BD simulations of both the model proteins mimic the native state of the real protein rather well, with a best root-mean-square deviation of 4.5 A for HP-36. For betaA-40 (where a single well-defined structure is not available), the simulated structures resemble the reported ensemble rather well, with the well-known beta-bend correctly reproduced. We introduce and calculate a contact pair distance time correlation function, C(P) (ij)(t), to quantify the dynamical evolution of the pair contact formation between the amino acid residue pairs i and j. The contact pair time correlation function exhibits multistage dynamics, including a two stage fast collapse, followed by a slow (microsecond long) late stage dynamics for several specific pairs. The slow late stage dynamics is in accordance with the findings of Sali et al. Analysis of the individual trajectories shows that the slow decay is due to the attempt of the protein to form energetically more favorable pair contacts to replace the less favorable ones. This late stage contact formation is a highly cooperative process, involving participation of several pairs and thus entropically unfavorable and expected to face a large free energy barrier. This is because any new pair contact formation among hydrophobic pairs will require breaking of several contacts, before the favorable ones can be formed. This aspect of protein folding dynamics is similar to relaxation in glassy liquids, where also alpha relaxation requires highly cooperative process of hopping. The present analysis suggests that waiting time for the necessary pair contact formation may obey the Poissonian distribution. We also study the dynamics of Forster energy transfer during folding between two tagged amino acid pairs. This dynamics can be studied by fluorescence resonance energy transfer (FRET). It is found that suitably placed donor-acceptor pairs can capture the slow dynamics during folding. The dynamics probed by FRET is predicted to be nonexponential.

Study of Pair Contact Formation among Hydrophobic Residues in a Model HP-36 Protein: Relationship between Contact Order Parameter and Rate of Folding and Collapse

Recent analysis of the structures of a large number of proteins in their native state has demonstrated a close relation between relative contact order parameter (COP) (which gives the average contact distance among hydrophobic residues) and the rate of protein folding (Grantcharova et al. Curr. Opin. Struct. Biol. 2001, 11, 70). We have explored the existence of such a relationship by carrying out Brownian dynamics simulations of a model protein. The model consists of 36 amino acid residues and mimics a thermostable single domain headpiece of chicken villin (HP-36) protein. Long range interactions across the protein are obtained by using a simplified hydropathy scale. The heteropolymer exhibits qualitative features of folding and correlates with the COP. We have defined and calculated the distance dependent pair correlation function among the hydrophobic residues. Nativelike states are characterized by distinct pair contacts which are mostly absent in other collapsed non-native states. Contact pair formation shows a strong dependence on contour distance separation between the pairs. Study of the dynamics of specific contact pair formation during folding shows different characteristics depending on whether the final state is (near) native or far from the native configuration. Approach to the final collapsed state is almost always faster when the final state is nativelike. Fluctuations in pair contacts are found to be smaller in nativelike conformations compared to those of higher energy configurations. This is in agreement with a recent theoretical prediction.

Understanding the Hygroscopic Properties of Supersaturated Droplets of Metal and Ammonium Sulfate Solutions Using Raman Spectroscopy

The hygroscopic properties of sulfate-containing particles are important to understanding the behavior of atmospheric aerosols. At high concentrations, chemical interactions between sulfate ions with the countercations are significant and lead to the formation of contact pairs. In this paper, Raman spectroscopy was used to study the structural changes of single aqueous droplets of equal molar Na2SO4/MgSO4 mixture, Na2SO4, (NH4)2SO4, MgSO4, ZnSO4, and CdSO4 in relation to their hygroscopic properties in an electrodynamic balance. The molar water-to-solute ratio (WSR) and the Raman spectra of droplets equilibrated at different ambient relative humidities were measured. When RH is reduced, the WSR of the Na2SO4/MgSO4 droplet decreases from 25.3 to 4.2 without crystallization but with two distinct transition points. The first one appears at WSR = 18.9, where the WSR is more sensitive to RH and the shoulder at 995 cm-1 of the ν1-SO42- band of the Raman spectrum shows an abrupt change in the ratio of the intens...

Rate constants of singlet exciton fission in a tetracene crystal determined from the rydmr spectral linewidth

The lifetime τ of a correlated pair of triplet excitons has been determined from the linewidth of the RYDMR spectrum. The value τ = 7 × 10 −9 s obtained has been used to calculate the rate constants of the singlet exciton fission into a pair of triplet excitons in a tetracene single crystal. The fission was shown to go via three steps: the first one is contact pair formation, the second step is its transformation into a diffusive pair, and the third one is the dissociation of the diffusive pair into free triplet excitons. Both the values of the rate constants of every step and the entropy growth in the transition from contact pair to diffusive pair have been evaluated.