Unfolded State Of Peptides Research Articles

Quantum Mechanics Study on Hydrophilic and Hydrophobic Interactions in the Trivaline-Water System.

With the aim to elucidate hydrophobic effects in the unfolded state of peptides, DFT-M062X computations on the Val3H+· nH2O ( n up to 22) clusters have been accomplished. As far as the main chain is concerned, four conformers with β-strand and/or polyproline type II conformations, PPII (indicated as β-β, β-PPII, PPII-β, and PPII-PPII), have been found by changing the ϕ and ψ angles. For bare peptide, the side chain (isopropyl) of each residue can independently take on three different orientations with negligible effects on energetics. The great isopropyl spatial separations in β-β and β-PPII conformers allow for the construction of synergic and extensive water-water and water-peptide H-bonding in the minimal hydration Val3H+·22H2O models without significant steric encumbrance. Conversely, due to the proximity of the isopropyl of the central residue with the other two, some restrictions in the water shell construction around the peptide become evident for the PPII-PPII conformer and the number of energetically accessible structures decreases. This is indicative of correlated motion involving isopropyls and backbone mediated by water molecules, the origin of the nearest neighbor effects. Comparing the thermodynamic data of Ala3H+·22H2O and Val3H+·22H2O, what emerges is that both hydration enthalpy and entropy drive the β-strand stability of the latter.

Anti-cooperative Nearest Neighbor Coupling Determines the Statistical Coil State of Peptides and Proteins at High Temperatures

The interest in the unfolded state of peptides and proteins stems partially from the observation that conformational distributions of amino acid residues are more restricted and residue specific than expected for an ideal random coil. Moreover, multiple lines of evidence suggest that contrary to the isolated pair hypothesis the conformational propensity of a distinct residue depends on the properties of its neighbors. We analyzed the recently reported conformational propensities of the two guest residues of GxyG peptides in terms of a statistical thermodynamics model that allows for cooperative as well as anti-cooperative interactions between adjacent residues adopting either a polyproline II (pPII) or a β-strand conformation. Our analysis revealed that the nearest neighbor interactions between most of the central residues in the investigated GxyG peptides is anti-cooperative. Interaction Gibbs energies become significant at high temperature (350 K) at which most proteins undergo thermal unfolding. At room temperature, these interaction energies are less pronounced. We utilized the obtained interaction parameters in an Ising-type approach to calculate the temperature dependence of the UV circular dichroism (CD) of the so-called MAX3 peptide that is predominantly built by KV-repeats. The agreement between simulation and experimental data is very good. Finally, we analyzed the temperature dependence of the CD spectra and selected 3J(HNHα ) parameters of the Aβ(1-9) fragment. The results corroborated the occurrence of anti-cooperative nearest neighbor interactions. A comparison of CD spectra of unfolded and intrinsically disordered proteins with predictions of our model suggests that anti-cooperative interactions govern their experimentally obtained temperature dependence. Generally, our results suggest that unfolded peptides and proteins behave like antiferromagnetic systems in the presence of a magnetic field of intermediate strength.

Ionized Trilysine: A Model System for Understanding the Nonrandom Structure of Poly-l-lysine and Lysine-Containing Motifs in Proteins

It is now well-established that different amino acid residues can exhibit different conformational distributions in the unfolded state of peptides and proteins. These conformational propensities can be modulated by nearest neighbors. In the current study, we combined vibrational and NMR spectroscopy to determine the conformational distributions of the central and C-terminal residues in trilysine peptides in aqueous solution. The study was motivated by earlier observations suggesting that interactions between ionized nearest neighbor residues can substantially change conformational propensities. We found that the central lysine residue predominantly adopts conformations that are located at the upper border of the upper left quadrant of the Ramachandran plot and the left border of the polyproline II region. We term this type of conformation deformed polyproline II (pPII(d)). The structures of less populated subensembles of trilysine resemble are comparable with structures at the i + 1 position of type I and type II β-turns. For the C-terminal residue, however, we obtained a mixture of polyproline II, β-strand, and right-handed helical conformations, which is typical for lysine residues in alanine- and glycine-based peptides. Our data thus indicate that the terminal lysines modify and restrict the conformational distribution of the central lysine residue. DFT calculations for ionized trilysine and lysyllysyllysylglycine in vacuo indicate that the pPII(d) is stabilized by a rather strong hydrogen bond between the NH3(+) group of the central lysine and the carbonyl group of the C-terminal peptide. This intramolecular hydrogen bonding induces optical activity in the C-terminal CO stretching vibration, which leads to an unusual and relatively intense positive Cotton band. Additionally, we analyzed the amide I' band profile of ionized triornithine in water. Ornithine is structurally similar to lysine in that its side chain is terminated with an amino group; however, the side chain of ornithine is shorter than lysine's side chain by one methylene group. We found that the conformational distribution of the central ornithine in this peptide must be very similar to that of the central lysine residue in trilysine. This suggests that the ionized ammonium group, which lysine and ornithine side chains have in common, is the main determinant of their conformational propensities at the central position in the respective tripeptides. The results of a DFT-based geometry optimization confirm this notion. In principle, our results suggest that lysine-rich segments in unfolded/disordered proteins and peptides can switch between different types of local order, i.e., an extended pPII(d)-like conformation and transient turns. However, for longer polylysine segments nonlocal interactions between side chains might impede the formation of turns, thus enabling the formation of pPII(d)-helix segments.

Amino Acids with Hydrogen‐Bonding Side Chains have an Intrinsic Tendency to Sample Various Turn Conformations in Aqueous Solution

Local structure in unfolded proteins, especially turn segments, has been suggested to initiate the hierarchical protein-folding process. To determine the intrinsic propensity to form such turn structures, amide I' band profiles of the Raman, IR, and vibrational circular dichroism (VCD) spectra, and several structure-sensitive NMR J-coupling constants, have been measured for a series of GxG (x=D, N, T, C) peptides, in which the central x residues are abundant in various turn motifs in folded proteins. In addition, we revisited earlier measured GSG experimental data. To check whether this relatively high propensity for these residues to sample turns reflects an intrinsic propensity, the experimental data were analyzed in terms of conformational distributions that can be described as a superposition of two-dimensional Gaussian distributions associated with different so-called mesostates. The analysis reveals that the investigated residues sample dihedral angles similar to those found in the corner residues of various turns, namely, type I/I', II/II', and IV β-turns. Aspartic acid (D) was found to predominantly sample regions attributed to turns, including distributions at the upper border of the upper-right quadrant of the Ramachandran plot, which bear some resemblance to asx-turns observed in proteins. This conformation enables hydrogen bonding between the side-chain carboxylate and the C-terminal amide group. Altogether, the study shows that the high propensity for T, S, C, N, and D to be located in turn motifs reflects, to a substantial degree, an intrinsic property and supports the role of these residues as initiation sites for hierarchical folding processes that can lead to compact structures in the unfolded state of peptides and proteins.

Distribution of Conformations Sampled by the Central Amino Acid Residue in Tripeptides Inferred From Amide I Band Profiles and NMR Scalar Coupling Constants

The conformational preference of individual amino acid residues in the unfolded state of peptides and proteins is the subject of a continuous debate. Research has mostly been focused on alanine, owing to its abundance in proteins and its relevance for the understanding of helix <----> coil transitions. In the current study, we have analyzed the amide I band profiles of the IR, isotropic and anisotropic Raman, and VCD profiles of trialanine in terms of a conformational model which, for the first time, explicitly considers the entire ensemble of possible conformations rather than representative structures. The distribution function utilized for a satisfactory simulation of the amide I band profiles was found to also reproduce a set of five J coupling constants reported by Graf et al. (Graf, J.; et al. J. Am. Chem. Soc. 2007, 129, 1179). The results of our analysis reveal a PPII fraction of approximately 0.84 for the central alanine residue, which strongly corroborates the notion that alanine has a very high PPII propensity, exceeding the values obtained from restricted coil libraries. We performed a similar analysis for trivaline and found that the dominant fraction of its central residue is a beta-strand. The fraction of the respective distribution is 0.68. The remaining fraction contains contributions from helical and PPII conformations. The results of our analysis enable us to decide on the suitability of force fields used for MD simulations of short alanine-containing peptides. The paper establishes vibrational spectroscopy as a suitable method to explore the energy landscape of amino acid residues.

Preferred peptide backbone conformations in the unfolded state revealed by the structure analysis of alanine-based (AXA) tripeptides in aqueous solution.

We have combined Fourier transform IR, polarized Raman spectroscopy, and vibrational CD measurements of the amide I' band profile of alanyl-X-alanine tripeptides in (2)H(2)O to obtain the dihedral angles of their central amino acid residue. X represents glycine, valine, methionine, histidine, serine, proline, lysine, leucine, tryptophan, tyrosine, and phenylalanine. The experimental data were analyzed by means of a recently developed algorithm, which exploits the excitonic coupling between the amide modes of the two peptide groups. The results were checked by measuring the respective electronic CD spectra. The investigated peptides can be sorted into three classes. Valine, phenylalanine, tryptophan, histidine, and serine predominantly adopt an extended beta-strand conformation. Cationic lysine and proline prefer a polyproline II-like structure. Alanine, methionine, glycine, and leucine populate these two conformations with comparable probability. Our results are in variance with the prediction of the random-coil model, but supportive of Flory's isolated-pair hypothesis. We combined the obtained structural propensities of the investigated residues and similar information about other residues in the literature (i.e., glutamate, aspartate, isoleucine, and glutamine) to predict possible conformations of the monomeric amyloid beta peptide A beta(1-42) in aqueous solution, which reproduces results from most recent spectroscopic studies. Thus, it is demonstrated that the unfolded state of peptides can be understood in terms of the intrinsic structural propensities of their amino acid residues.

Methinks it is like a folding curve

Most often, the unfolded state of peptides and proteins has been modeled as a statistical random coil. Here, we suggest an alternative model based on the presence of a significant, temperature-dependent conformational bias in the unfolded population. Conformational bias is suggested by our calculations [Proc. Natl. Acad. Sci. USA 96 (1999) 14258–14263], and it is found in recent studies of both proteins and peptides. The imposition of even a modest bias would transform our assessment of the folding problem.

Unfolded state of peptides

Publisher Summary This chapter illustrates the current knowledge on the unfolded state of peptides. Currently, the characterization of the populated microscopic states of a peptide is possible only by simulation methods. The focus is on molecular dynamics simulations of spontaneous (i.e., lacking biasing potentials or directed-sampling algorithms) and reversible folding of peptides in solution (i.e., with explicit solvent molecules), since the results from this type of studies are the least dependent on the methodology. A full characterization of the unfolded state becomes as essential as the determination of the folded conformation in two scenarios. The first is in the study of the physical, chemical, and biological properties of peptides. The folded conformation of a peptide is, in general, only marginally more stable than the lowest-free-energy unfolded conformation. As a result, any macroscopic observable of a peptide is weighted with both the folded and the unfolded states. Interpreting such observables in terms of the folded conformation only is therefore not correct. The second scenario is related to the study of peptide and protein folding. The description of equilibrium requires knowledge about each of the states involved. Therefore, it is fundamental to describe not only the folded state but also the unfolded state accurately in order to draw conclusions on the nature and mechanisms of peptide and protein folding.