Peptide-urea interactions as observed in diketopiperazine-urea cocrystal

Structural Elucidation of a Polypeptoid Chain in a Crystalline Lattice Reveals Key Morphology-Directing Role of the N-Terminus

The ability to engineer synthetic polymers with the same structural precision as biomacromolecules is crucial to enable the de novo design of robust nanomaterials with biomimetic function. Peptoids, poly(N-substituted) glycines, are a highly controllable bio-inspired polymer family that can assemble into a variety of functional, crystalline nanostructures over a wide range of sequences. Extensive investigation on the molecular packing in these lattices has been reported; however, many key atomic-level details of the molecular structure remain underexplored. Here, we use cryo-TEM 3D reconstruction to directly visualize the conformation of an individual polymer chain within a peptoid nanofiber lattice in real space at 3.6 Å resolution. The backbone in the N-decylglycine hydrophobic core is shown to clearly adopt an extended, all-cis-sigma strand conformation, as previously suggested in many peptoid lattice models. We also show that packing interactions (covalent and noncovalent) at the solvent-exposed N-termini have a dominant impact on the local chain ordering and hence the ability of the chains to pack into well-ordered lattices. Peptoids in pure water form fibers with limited growth in the a direction (<14 molecules in width), whereas in the presence of formamide, they grow to over microns in length in the a direction. This dependence points to the significant role of the chain terminus in determining the long-range order in the packing of peptoid lattices and provides an opportunity to modulate lattice stability and nanoscale morphology by the addition of exogenous small molecules. These findings help resolve a major challenge in the de novo structure-based design of sequence-defined biomimetic nanostructures based on crystalline domains and should accelerate the design of functional nanostructures.

Effects of guanidine hydrochloride on the conformation and enzyme activity of streptomycin adenylyltransferase monitored by circular dichroism and fluorescence spectroscopy

Equilibrium denaturation of streptomycin adenylyltransferase (SMATase) has been studied by CD spectroscopy, fluorescence emission spectroscopy, and binding of the hydrophobic dye 1-anilino-8-naphthalene sulfonic acid (ANS). Far-UV CD spectra show retention of 90% native-like secondary structure at 0.5 M guanidine hydrochloride (GdnHCl). The mean residue ellipticities at 222 nm and enzyme activity plotted against GdnHCl concentration showed loss of about 50 and 75% of secondary structure and 35 and 60% of activity at 0.75 and 1.5 M GdnHCl, respectively. At 6 M GdnHCl, there was loss of secondary structure and activity leading to the formation of GdnHCl-induced unfolded state as evidenced by CD and fluorescence spectroscopy as well as by measuring enzymatic activity. The denaturant-mediated decrease in fluorescence intensity and 5 nm red shift of lambda(max) point to gradual unfolding of SMATase when GdnHCl is added up from 0.5 M to a maximum of 6 M. Decreasing of ANS binding and red shift (approximately 5 nm) were observed in this state compared to the native folded state, indicating the partial destruction of surface hydrophobic patches of the protein molecule on denaturation. Disruption of disulfide bonds in the protein resulted in sharp decrease in surface hydrophobicity of the protein, indicating that the surface hydrophobic patches are held by disulfide bonds even in the GdnHCl denatured state. Acrylamide and potassium iodide quenching of the intrinsic tryptophan fluorescence of SMATase showed that the native protein is in folded conformation with majority of the tryptophan residues exposed to the solvent, and about 20% of them are in negatively charged environment.

Kinetic measurements of protein conformation in a microchip

This paper presents a microchip-based system for collecting kinetic time-based information on protein refolding and unfolding. Dynamic protein conformational change pathways were studied in microchannel flow using a microfluidic device. We present a protein-conserving approach for quantifying refolding by dynamically varying the concentration of the chemical denaturants, guanidine hydrochloride and urea. Short diffusion distances in the microchannel result in rapid equilibrium between protein and titrating solutions. Dilutions on the chip were tightly regulated using pressure controls rather than syringe-based flow, as verified with extensive on-chip tracer dye controls. To validate this protein assay method, folding transition experiments were performed using two well-characterized proteins, human serum albumin (HSA) and bovine carbonic anhydrase (BCA). Transition events were monitored through fluorescence intensity shifts of the protein dye 8-anilino-1-naphthalenesulfonic acid (ANS) during dilutions of protein from urea or guanidine hydrochloride solutions. The enzymatic activity of refolded BCA was measured by UV absorption through the conversion of p-nitrophenyl acetate (p-NPA). The microchip protein refolding transitions using ANS were well-correlated with conventional plate-based experiments. The microfluidic platform enables refolding studies to identify rapidly the optimal folding strategy for a protein using small quantities of material.

Probing the binding states of GDP to Cdc42 using urea interaction

The inactive state of the small G protein Cdc42, the Cdc42.GDP.Mg(2+) ternary complex, was investigated using fluorescence, Mn(2+) substituted electron paramagnetic resonance, and (31)P nuclear magnetic resonance spectroscopy at various urea concentrations. The urea interaction with the protein was used to probe the binding state of GDP.Mg(2+) to Cdc42. Two binding states of the Cdc42.GDP.Mg(2+) ternary complex with different binding stability were observed. The two binding states were characterized by two sets of (31)P resonance of GDP phosphate groups, namely P(alpha) and P(beta), P('alpha), and P('beta). The high populated binding state I (P(alpha) and P(beta)) was more stable and less sensitive to the urea interaction. Yet the population of binding state II (P('alpha) and P('beta)) was lower, and the binding of GDP.Mg(2+) to Cdc42 in this state was more sensitive to the urea interaction. The release of GDP.Mg(2+) from the ternary complex in binding state II was faster than in state I.

Comparing tolerance of Ichthyophthirius multifiliis and Tetrahymena thermophila for new cryopreservation methods

Ichthyophthirius multifiliis is an obligate protozoan parasite of freshwater fishes that has a complex developmental cycle. It has not been successfully cryopreserved, so management studies are restricted to parasites obtained during outbreaks or perpetuated by passage in live fishes. To overcome this serious limitation, free-swimming I. multifiliis parasites were tested in a cryopreservation protocol routinely used for a related ciliate, Tetrahymena. In this protocol, I. multifiliis theronts retained infectivity for 3 days, although the protocol itself was ultimately lethal. Exposure of I. multifiliis and Tetrahymena thermophila to a battery of media and cryopreservative reagents showed that I. multifiliis was less hardy than T. thermophila and likely had significant biological and cytoskeletal differences. No combination of reagents, media, freezing rates, or dilution media permitted cryopreservation of I. multifiliis parasites that could then undergo development or infect fish. However, a vitrification protocol was formulated using Ficoll, 1,2-propanediol, and N,N-dimethylacetamide from which intact cryopreserved theronts with some motility were recovered. Understanding the effects of these reagents may lead to both a cryopreservation method for I. multifiliis and to improved understanding of the biology of ciliates.

Structural characterization of protein-denaturant interactions: crystal structures of hen egg-white lysozyme in complex with DMSO and guanidinium chloride

A variety of physico-chemical methods employ chemical denaturants to unfold proteins, and study different biophysical processes involved therein. Chemical denaturants are believed to induce unfolding by stabilizing the unfolded state of proteins over the folded state, either macroscopically or through specific interactions. In order to characterize the nature of specific interactions between proteins and denaturants, we have solved crystal structures of hen egg-white lysozyme complexed with denaturants, and report here dimethyl sulfoxide and guanidinium chloride complexes. The dimethyl sulfoxide molecules and guanidinium ions were seen to bind the protein at specific sites and were involved in characteristic interactions. They share a major binding site between them, the C site in the sugar binding cleft of the enzyme. Although the overall conformations of the complexes were very similar to the native structure, spectacular conformational changes were seen to occur locally. Temperature factors were also seen to drop dramatically in the local regions close to the denaturant binding sites. An interesting observation of the present study was the generation of a sodium ion binding site in hen egg-white lysozyme in the presence of denaturants, which was hitherto unknown in any of the other lysozyme structures solved so far. Loss of some of the crucial side chain-main chain interactions may form the initial events in lysozyme unfolding.

Structural details of urea binding to barnase: a molecular dynamics analysis

BACKGROUND

The molecular mechanism of urea-induced protein unfolding has not been established. It is generally thought that denaturation results from the stabilizing interactions of urea with portions of the protein that are buried in the native state and become exposed upon unfolding of the protein.

RESULTS

We have performed molecular dynamics simulations of barnase (a 110 amino acid RNase from Bacillus amyloliquefaciens) with explicit water and urea molecules at 300 K and 360 K. The native conformation was unaffected in the 300 K simulations at neutral and low pH. Two of the three runs at 360 K and low pH showed some denaturation, with partial unfolding of the hydrophobic core 2. The first solvation shell has a much higher density of urea molecules (water/urea ratio ranging from 2.07 to 2.73) than the bulk (water/urea ratio of 4.56). About one half of the first-shell urea molecules are involved in hydrogen bonds with polar or charged groups on the barnase surface, and between 15% and 18% of the first-shell urea molecules participate in multiple hydrogen bonds with barnase. The more stably bound urea molecules tend to be in crevices or pockets on the barnase surface.

CONCLUSIONS

The simulation results indicate that an aqueous urea solution solvates the surface of a polypeptide chain more favorably than pure water. Urea molecules interact more favorably with nonpolar groups of the protein than water does, and the presence of urea improves the interactions of water molecules with the hydrophilic groups of the protein. The results suggest that urea denaturation involves effects on both nonpolar and polar groups of proteins.

Anion binding to the ubiquitin molecule

Effects of different salts (NaCl, MgCl2, CaCl2, GdmCl, NaBr, NaClO4, NaH2PO4, Na2SO4) on the stability of the ubiquitin molecule at pH 2.0 have been studied by differential scanning calorimetry, circular dichroism, and Tyr fluorescence spectroscopies. It is shown that all of the salts studied significantly increase the thermostability of the ubiquitin molecule, and that this stabilization can be interpreted in terms of anion binding. Estimated thermodynamic parameters of binding for Cl- show that this binding is relatively weak (Kd = 0.15 M) and is characterized by a negative enthalpy of -15 kJ/mol per site. Particularly surprising was the observed stabilizing effect of GdmCl through the entire concentration range studied (0.01-2 M), however, to a lesser extent than stabilization by NaCl. This stabilizing effect of GdmCl appears to arise from the binding of Cl- ions. Analysis of the observed changes in the stability of the ubiquitin molecule in the presence of GdmCl can be adequately described by combining the thermodynamic model of denaturant binding with Cl- binding effects.

The effect of denaturants on protein structure

Virtually all studies of the protein-folding reaction add either heat, acid, or a chemical denaturant to an aqueous protein solution in order to perturb the protein structure. When chemical denaturants are used, very high concentrations are usually necessary to observe any change in protein structure. In a solution with such high denaturant concentrations, both the structure of the protein and the structure of the solvent around the protein can be altered. X-ray crystallography is the obvious experimental technique to probe both types of changes. In this paper, we report the crystal structures of dihydrofolate reductase with urea and of ribonuclease A with guanidinium chloride. These two classic denaturants have similar effects on the native structure of the protein. The most important change that occurs is a reduction in the overall thermal factor. These structures offer a molecular explanation for the reduction in mobility. Although the reduction is observed only with the native enzyme in the crystal, a similar decrease in mobility has also been observed in the unfolded state in solution (Makhatadze G, Privalov PL. 1992. Protein interactions with urea and guanidinium chloride: A calorimetric study.

Calorimetrically-derived parameters for protein interactions with urea and guanidine-HCl are not consistent with denaturant m values

A recent study used calorimetric data and a stoichiometric binding model to derive binding constants, enthalpies, and stoichiometries describing the interaction between proteins and the chemical denaturants, urea and guanidine-HCl (Makhatadze and Privalov, J. Mol. Biol., 226 (1992) 491). In the present study, these parameters have been used to calculate the excess free energy, delta Gex, associated with interactions between chemical denaturants and the three proteins examined in the calorimetric study: ribonuclease A, cytochrome c, and lysozyme. This free energy and its dependence on denaturant concentration, the denaturant m value, have then been compared to experimental results from chemical denaturation experiments. The magnitudes of m values calculated from the calorimetric studies are significantly greater, 20 to 100%, than the observed values in urea. Calculated m values for guanidine-HCl range from about 10% greater than observed values for cytochrome c to over 100% greater for lysozyme. Discrepancies between calculated and observed m values are probably attributable to incomplete binding isotherms in the calorimetric studies. An additional issue raised in this study concerns the correlation of m values with changes in accessible surface areas upon unfolding. For proteins that undergo a two-state unfolding reaction, experimental m values can vary by more than a factor of two for a given protein, depending on the solution conditions. This observation suggests that factors beyond changes in accessible surface areas play a major role in determining m values.

Interactions of alpha-chymotrypsinogen A with alkylureas

Solvation of alpha-chymotrypsinogen A (alpha-ctg A) in aqueous urea, methylurea, N,N'-dimethylurea and ethylurea was studied by density measurements. From the densities at constant molality and at constant chemical potential the preferential solvation parameters were determined. In urea and methylurea preferential solvation was observed, whereas in N,N'-dimethylurea and ethylurea at higher concentration water is preferentially bound. From preferential solvation data Gibbs free energy of transfer of alpha-ctg A from water to urea and alkylurea solutions were calculated. Since the enthalpies of transfer were determined previously, the entropies of transfer could also be obtained so that a complete thermodynamic description is available. An attempt is made to interpret the values of the thermodynamic quantities in terms of various interactions involved in solvation as well as to calculate the exchange constant by using the model of weak interactions. In solvation of alkylureas the hydrophobic nature of the alkyl groups is clearly reflected.

Thermodynamics of denaturation of alpha-chymotrypsinogen A in aqueous urea and alkylurea solutions

The effects of pH, urea, and alkylureas on the thermal stability of alpha-chymotrypsinogen A (alpha-ctg A) have been investigated by differential scanning calorimetry (DSC) and UV spectroscopy. Heat capacity changes and enthalpies of transition of alpha-ctg A in the presence of urea and alkylureas were measured at the transition temperature. Using these data, the corresponding Gibbs free energies, enthalpies, and entropies of denaturation at 25 degrees C were calculated. Comparison of these values shows that at 25 degrees C denaturation with urea is characterized by a significantly smaller enthalpy and entropy of denaturation. At all denaturant concentrations the enthalpy term slightly dominates the entropy term in the Gibbs free energy function. The most obvious effect of alkylureas was lowering of the temperature of transition, which was increasing with alkylurea concentration and the size of alkyl chain. Destabilization of the folded protein in the presence of alkylureas appears to be primarily the result of the weakening of hydrophobic interactions due to diminished solvent ordering around the protein-molecules. At pH lower than 2.0, alpha-ctg A still exists in a very stable form, probably the acid-denatured from (A-form).

Salt-stabilized globular protein structure in 7 M aqueous urea solution

A 7 M aqueous urea solution of the 63-residue N-terminal domain of the 434-repressor at pH 7.5 and 18 degrees C contains a mixture of about 10% native, folded protein and 90% unfolded protein. Interconversion between the two conformations is slow on the NMR chemical shift time scale, so that observation of separate resonances can be used to monitor the equilibrium between folded and unfolded protein when changing the solution conditions. In this paper we describe the influence of various salts or non-ionic compounds on this conformational equilibrium. Solution conditions are described which contain a homogenous preparation of the folded protein in the presence of 6 to 7 M urea, providing a basis for an NMR structure determination in concentrated urea and for studies of the solvation of the folded protein in mixed water/urea/salt environments.

The solubilities of five cyclic dipeptides in water and in aqueous urea at 298.15 K: a quantitative model for the denaturation of proteins in aqueous urea solutions

The solubilities of cyclo(L-alanylglycine), cyclo(L-alanyl-L-alanine), cyclo(glycyl-L-leucine), cyclo(L-valyl-L-valine) and cyclo(glycyl-L-phenylalanine) were determined in water and in aqueous urea solutions up to concentrations of 9 molar urea at 298.15 K. The solubilities of all cyclic dipeptides increase with increasing urea concentration. A simple equilibrium model, taking into account the activity of urea and that of water, fits the solubility data yielding apparent equilibrium constants describing the interactions occurring between urea and the peptide groups plus the alkyl groups that are next to these peptide groups. The apparent equilibrium constants were converted to Gibbs energy parameters for each amino acid residue which were then used to make a quantitative estimate of the contribution of urea to the denaturation of proteins.

Protein internal flexibility and global stability: effect of urea on hydrogen exchange rates of bovine pancreatic trypsin inhibitor

The hydrogen isotope exchange kinetics of buried NH protons in bovine pancreatic trypsin inhibitor (BPTI) was measured in 8 M urea at 30 degrees C and pH 3.5. The data were analyzed by the two-process model in which slower exchanging protons utilize an unfolding mechanism and more rapidly exchanging protons exchange from the folded state. Urea accelerates the set of protons exchanging by the unfolding mechanism, all of which have approximately the same exchange rate constants in urea. For protons in this set, the ratio of exchange rate constants in the presence and absence of urea is used to estimate delta delta G(0-->8M urea) = 6.6 kcal/mol. For the set of protons exchanging from the folded state, 8 M urea either has no effect or slows exchange. Slowing of exchange by urea implies binding of urea to sites at or near the exchanging proton. Some buried protons exchanging from the folded state have diminished rates in 8 M urea, meaning that urea is accessible to these buried sites. Several unassigned side-chain NH's of arginine or lysine are highly protected from exchange by urea, suggesting that they are the location of urea binding sites on the surface of the molecule.

Urea-diketopiperazine interactions: a model for urea induced denaturation of proteins

The solubility of diketopiperazine (DKP) in aqueous urea (U) solutions with molalities ranging from 0 to 16 mol kg-1 (corresponding to urea activities ranging from 0 to 10 mol kg-1) has been measured as a function of the urea activity at 298.15 K. In accordance with a previous study the solubility of diketopiperazine increases with increasing urea activity but drops sharply at a urea activity of 5.7 +/- 0.2 mol kg-1. This drop in solubility can be attributed to the formation of a DKP.U2 cocrystal. The solubility data were fitted to a simple model based on the stoichiometry of the DKP.U2 to yield an intrinsic equilibrium constant kappa describing the interactions occurring between a urea molecule and a peptide group of diketopiperazine in aqueous solution, its value being kappa = 0.0447 +/- 0.0007 kg mol-1. When the activity of water is taken into account, kappa has a lower value of 0.0398 +/- 0.0007 kg mol-1.