Influence of the solvent on the conformational-dependent properties of random-coil polypeptides. I. The mean-square of the end-to-end distance and of the dipole moment

Conformational energies for the N-acetyl-N'-methylamides of the 20 natural amino acids were calculated, including the solvent effects, as functions of the angles phi and psi for rotation of the main chain and for six positions chi 1 of the C alpha-C beta bond in the side chain (fixed values for chi 2, chi 3, ...). The computed energies were used to evaluate the mean-square end-to-end distance and mean-square dipole moment of homopolypeptides of the 20 natural amino acids. Ten proteins and three enzymes of current interest were also studied. Slight differences in both properties are found on taking the effects of solvent into consideration. Comparison with other computational and experimental results is made.     

Reassessment of the random coil conformation: vibrational CD study of proline oligopeptides and related polypeptides.

The "random coil" conformational problem is examined by comparison of vibrational CD (VCD) spectra of various polypeptide model systems with that of proline oligomers [(Pro)n] and poly(L-proline). VCD, ir and uv CD spectra of blocked L-proline oligopeptides [(Pro)n, n = 2-12] in different solvents are reported and compared to the spectra of poly(L-proline) II, poly(L-glutamic acid), and unblocked proline oligomers. Based on the chain-length dependence of the VCD and electronic CD (ECD) spectra of proline oligomers, it is established that VCD spectra are dominated by short-range interactions. The VCD of random coil model polypeptides is shown to be identical in shape but smaller in magnitude than poly(L-proline) II and of similar magnitude to that of (Pro)n (n = 3, 4). Based on the spectral evidence, it is concluded that the "random coil" conformation has a large fraction of helical regions, conformationally similar to the left-handed, 3(1) polyproline II helix, as was previously suggested by Krimm and co-workers. This conclusion is further supported by studies of effects of salt (CaCl2, LiBr, LiClO4), temperature (5-75 degrees C), and pH on the VCD spectra of L-proline oligomers, poly(L-proline) II, and poly(L-glutamic acid). These show that, after each of these perturbations, a significant local ordering remains in the oligomers and polymers studied, and that charged polypeptides such as poly(L-glutamic acid) are more flexible than are polyproline or even L-proline oligomers.     

Adsorption of polypeptides on the solid surface. II. Effect of secondary chain structure and helix–coil transition

The theory of adsorption of semistiff chains on a planar surface developed by the authors previously has been used to consider the helix–coil transition in single-stranded macromolecule interacting with an adsorbent plane. The cases of nonselective interaction when the adsorption energy is independent of the unit conformation (a) and selective interaction with only helical (b) or coiled (c) sequences active in adsorption were investigated. In case (b) the existence of secondary structure favors chain bonding to the surface. This leads to the increase in the stability of the helical state and complete polypeptide chain spiralization. The profile of the conformational helix–coil transition acquires an asymmetrical shape inherent to the second-order phase transition. In case (c) the bonding of a partially helical chain to the surface is similar to the adsorption of Gaussian coils and is accompanied by the destruction of secondary structure, this destruction being appreciable even if the helical state in space was favorable.     

Influence of carbamoylation on some analytical properties of basic polypeptides

The effect of carbamoylation on the assay or identification of histones and polylysine was investigated. Incubation with sodium cyanate decreased the positive charge on these polypeptides as judged by changes in the binding of methyl orange or the electrophoretic mobility. Histones in chromatin appeared less accessible to carbamoylation than isolated histones. Carbamoylation of proteins under conditions in which there was little or no effect on the Lowry procedure could affect their assay by methods utilizing metachromasia with Coomassie Blue G. The Bradford assay has low sensitivity for Hl histone and polylysine but this can be increased by preincubation with sodium cyanate. More extensive carbamoylation of polylysine caused decreased sensitivity which was the only response seen with core nucleosomal histones and bovine serum albumin when preincubated with sodium cyanate. It was concluded that the sensitivity for Hl histone and polylysine in assays dependent on metachromasia with Coomassie Blue G may be changed by factors which decrease the positive charge on these polypeptides.     

Experimental theromodynamics of the helix-random coil transition. I. Influence of polymer concentration and solvent composition in the PBG-DCA-EDC system

The course of the reversible helix formation of poly(γ-benzyl L -glutamate) (PBG) dissolved in a mixture of dichloroacetic acid (DCA) and 1,2-dichloroethane (EDC) was followed by measuring the heat capacity and the optical rotation of the system through the transition region. The results of these measurements indicate that the transition enthalpy ΔH the transition temperature T_c, and the Zimm-Bragg parameter σ depend considerably on the PBG concentration as well as on the composition of the solvent. For the standard state of infinite dilution, however, a linear extrapolation of the measured ΔH if values results in a standard value ΔH° = 950 cal./mole, independent of the solvent composition. The results of the calorimetric measurements are discussed in relationship to changes in optical rotation. Some peculiarities in the measured thermodynamic and optical properties in solutions with relatively high content of dichloroacetic acid are reported.     

Influence of solvent composition on the mechanical properties of arterial elastin

We have investigated the effects of changes in solution composition on the mechanical properties of rings of arterial elastin. The time course of force equilibration at constant strain following a change in the composition of the bathing solution was measured. Both the force developed during slow extension and force relaxation following rapid straining were also measured in each of the test solutions. The results are difficult to summarize because all of the primitive quantities measured--sample dimension, slope of the force-extension curve, force overshoot and time of relaxation--as well as the derived quantities such as elastic modulus changed in different and apparently uncorrelated ways. Changes in pH and ionic composition of the bathing solution had small effects consistent with the low fixed charge density of elastin. Solutions of glucose, sucrose, and ethylene glycol had larger effects consistent with changes in hydrophobic interactions. The viscosity of the solution that penetrated the intrafibrillar space of the elastin appeared to be a major determinant of the dynamic response.     

Understanding the alpha-helix to coil transition in polypeptides using network rigidity: predicting heat and cold denaturation in mixed solvent conditions

Thermodynamic stability in polypeptides is described using a novel Distance Constraint Model (DCM). Here, microscopic interactions are represented as constraints. A topological arrangement of constraints define a mechanical framework. Each constraint in the framework is associated with an enthalpic and entropic contribution. All accessible topological arrangements of distance constraints form an ensemble of mechanical frameworks, each representing a microstate of the polypeptide. A partition function is calculated exactly using a transfer matrix approach, where in many respects the DCM is similar to the Lifson-Roig model. The crucial difference is that the effect of network rigidity is explicitly calculated for each mechanical framework in the ensemble. Network rigidity is a mechanical interaction that provides a mechanism for long-range molecular cooperativity and enables a proper treatment of the nonadditivity of a microscopic free energy decomposition. Accounting for (1) helix <--> coil conformation changes along the backbone similar to the Lifson-Roig model, (2) i to i + 4 hydrogen-bond formation <--> breaking similar to the Zimm-Bragg model, and (3) structured <--> unstructured solvent interaction (hydration effects), a six-parameter DCM describes normal and inverted helix-coil transitions in polypeptides. Under suitable mixed solvent conditions heat and cold denaturation is predicted. Model parameters are fitted to experimental data showing different degrees of cold denaturation in monomeric polypeptides in aqueous hexafluoroisopropanol (HFIP) solution at various HFIP concentrations. By assuming a linear HFIP concentration dependence (up to 6% by mole fraction) on model parameters, all essential experimentally observed features are captured.     

Dielectric properties of hemoglobin and myoglobin. I. Influence of solvent and particle size on the dielectric dispersion

Dielectric dispersion measurements with aqueous solutions of hemoglobin and myoglobin have been performed in the frequency range from 100 kcps to 15 Mcps. The influence of preparation, particle size, and solvent conditions was studied. The results are analyzed in terms of an orientational polarization mechanism.     

Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. II. Amide absorption bands of polypeptides and fibrous proteins in alpha-, beta-, and random coil conformations.

Infrared spectra of poly(D,L-alanine), poly(L-glutamic acid), poly(L-lysine), silk fibroin, and tropomyosin have been registered for various conformations of the polypeptide chain. Assuming additivity of the main- and side-chain absorption, spectral parameters of amide I and II absorption bands corresponding to alpha-, beta-, and random coil conformations have been derived. The amide I band parameters for H2O and D2O have been compared.     

Influence of decreased solvent permittivity on the structure and magnesium(II)-binding properties of the catalytic domain 5 of a group II intron ribozyme

Although it is well known that the so-called “equivalent solution” or “effective” solvent permittivity (dielectric constant) in proteins and nucleic acids is lower than in bulk water, this fact is commonly neglected in (bioinorganic) studies of such compounds. Using domain 5 of the group II intron ribozyme Sc.ai5γ, we describe here the influence of 1,4-dioxane-d₈ on the structure and magnesium(II)-binding properties of this catalytic domain. Applying one- and two-dimensional NMR, we observe distinct structural changes in the functionally important bulge region following a decrease in solvent permittivity. Concomitantly, an increase by a factor of 1.5 in the affinity of Mg²⁺ towards the individual-binding sites in the catalytic core domain is observed upon addition of 1,4-dioxane-d₈. This has led to the detection of a new metal ion coordination site near the GU wobble pair in the catalytic triad. Our results show that solvent permittivity is an important factor in the formation of intrinsic RNA structures and affects their metal ion-binding properties. Hence, solvent permittivity should be taken into account in future studies.     

Vibrational circular dichroism of polypeptides. II. Solution amide II and deuteration results

Vibrational CD (VCD) of amide I and II vibrations of several α-helical polypeptides have been measured in solution. For the amide II as well as the amide I [previously published: Lal, B.B. & Nafie, L.A. (1982) Biopolymers 21 , 2161] we find the VCD to be characteristic of the polypeptide secondary structure. Amide II bands of right-handed α helices were all found to have negative VCD and to have their maximum rotational strength for the parallel (low-energy) component. However, left-handed α helices formed from L -amino acids gave positive amide II bands at higher frequencies than found for the right-handed helices, indicating that the VCD was sensitive to the stereochemical difference. The amide-I VCD spectra of some deuterated right-handed α-helical polypeptides have a new negative feature to low frequency that does not reflect theoretical predictions but also appears to be stereochemically sensitive. Amide-II and amide-A VCD of a few deuterated polypeptides imply retention of the secondary-structure-dependent characteristics seen in the hydrogenated VCD.     

Mean square fluctuations of hydrogen atoms and water-biopolymer interactions in hydrated saccharides.

We have used the elastic neutron scattering technique to investigate the dynamics of the two main saccharidic components of starch: amylose and amylopectin. The measurements were carried out in the temperature range of 20 to 320 K and at different hydration levels from the dry state up to 0.47 g saccharide/g D(2)O. In the dry samples, the atomic dynamics is harmonic up to approximately 300 K. In the hydrated samples a "glass-like" transition leading to an anharmonic dynamics is observed. The onset of the anharmonicity occurs at temperatures that increase from approximately 180 K to 260 K upon decreasing hydration from 0.5 to 0.1 g saccharide/g D(2)O. This behavior is qualitatively similar to that observed in hydrated globular proteins, but quantitative differences are present. Assuming a simple asymmetric double-well potential model, the temperature and hydration dependence of the transition have been described in terms of few physical parameters.     

Spontaneous degradation of polypeptides at aspartyl and asparaginyl residues: effects of the solvent dielectric.

We have investigated the spontaneous degradation of aspartate and asparagine residues via succinimide intermediates in model peptides in organic co-solvents. We find that the rate of deamidation at asparagine residues is markedly reduced in solvents of low dielectric strength. Theoretical considerations suggest that this decrease in rate is due to the destabilization of the deprotonated peptide bond nitrogen anion that is the postulated attacking species in succinimide formation. This result suggests that asparagine residues in regions with low dielectric constants, such as the interior of a protein or in a membrane bilayer, are protected from this type of degradation reaction. On the other hand, we found little or no effect on the rate of succinimide-mediated isomerization of aspartate residues when subjected to the same changes in dielectric constant. In this case, the destabilization of the attacking peptide bond nitrogen anion may be balanced by increased protonation of the aspartyl side chain carboxyl group, a reaction that results in a superior leaving group. Consequently, any protein structure or conformation that would increase the protonation of an aspartate side chain carboxyl group can be expected to render that residue more labile. These results may help explain why particular aspartate residues have been found to degrade in proteins at rates comparable to those of asparagine residues, even though aspartyl-containing peptides degrade more slowly than corresponding asparaginyl-containing peptides in aqueous solutions.     

Studies on the polypeptides of poxvirus. II. Comparison of virus-induced polypeptides in cells infected with vaccinia, cowpox and Shope fibroma viruses.

Virus-induced polypeptides in cells infected with vaccinia, cowpox and Shope fibroma viruses were examined by SDS-polyacrylamide gel electrophoresis followed by autoradiography. At least 42 vaccinia virus-induced polypeptides were identified among the polypeptides of cells pulse-labeled with [35S]-methionine and/or of fractionated cells labeled with [14C]-leucine for 24 hr. They consisted of 15 polypeptides (early polypeptides) which were synthesized even in the presence of cytosine-1-beta-D-arabinofuranosyl-HCl, and 27 polypeptides (late polypeptides) which were synthesized only in the absence of cytosine-1-beta-D-arabinofuranosyl-HCl. By the same procedure at least 40 cowpox virus-induced polypeptides (14 early polypeptides and 26 late polypeptides) and at least 31 Shope fibroma virus-induced polypeptides (13 early polypeptides and 18 late polypeptides) were identified. Comparative studies of virus-induced polypeptides on the basis of migration in SDS-polyacrylamide gel electrophoresis revealed that 11 polypeptides were early polypeptides common to both vaccinia and cowpox viruses; 21 were late polypeptides common to both vaccinia and cowpox viruses; 4 were early polypeptides common to both vaccinia and Shope fibroma viruses; 7 were late polypeptides common to both vaccinia and Shope fibroma viruses; 5 were early polypeptides common to both cowpox and Shope fibroma viruses; 9 were late polypeptides common to both cowpox and Shope fibroma viruses; 4 were early polypeptides common to all three viruses; and 7 were late polypeptides common to all three viruses.