Statistical proofs of the interdependence between nearest neighbor effects on polypeptide backbone conformations

Backbone dihedral angles ϕ and ψ are the main structural descriptors of proteins and peptides. The distribution of these angles has been investigated over decades as they are essential for the validation and refinement of experimental measurements, as well as for structure prediction and design methods. The dependence of these distributions, not only on the nature of each amino acid but also on that of the closest neighbors, has been the subject of numerous studies. Although neighbor-dependent distributions are nowadays generally accepted as a good model, there is still some controversy about the combined effects of left and right neighbors. We have investigated this question using rigorous methods based on recently-developed statistical techniques. Our results unambiguously demonstrate that the influence of left and right neighbors cannot be considered independently. Consequently, three-residue fragments should be considered as the minimal building blocks to investigate polypeptide sequence-structure relationships.

Exploring Nearest Neighbor Interactions and Their Influence on the Gibbs Energy Landscape of Unfolded Proteins and Peptides

The Flory isolated pair hypothesis (IPH) is one of the corner stones of the random coil model, which is generally invoked to describe the conformational dynamics of unfolded and intrinsically disordered proteins (IDPs). It stipulates, that individual residues sample the entire sterically allowed space of the Ramachandran plot without exhibiting any correlations with the conformational dynamics of its neighbors. However, multiple lines of computational, bioinformatic and experimental evidence suggest that nearest neighbors have a significant influence on the conformational sampling of amino acid residues. This implies that the conformational entropy of unfolded polypeptides and proteins is much less than one would expect based on the Ramachandran plots of individual residues. A further implication is that the Gibbs energies of residues in unfolded proteins or polypeptides are not additive. This review provides an overview of what is currently known and what has yet to be explored regarding nearest neighbor interactions in unfolded proteins.

Randomizing of Oligopeptide Conformations by Nearest Neighbor Interactions between Amino Acid Residues

Flory’s random coil model assumes that conformational fluctuations of amino acid residues in unfolded poly(oligo)peptides and proteins are uncorrelated (isolated pair hypothesis, IPH). This implies that conformational energies, entropies and solvation free energies are all additive. Nearly 25 years ago, analyses of coil libraries cast some doubt on this notion, in that they revealed that aromatic, but also β-branched side chains, could change the ³J(H^NH^Cα) coupling of their neighbors. Since then, multiple bioinformatical, computational and experimental studies have revealed that conformational propensities of amino acids in unfolded peptides and proteins depend on their nearest neighbors. We used recently reported and newly obtained Ramachandran plots of tetra- and pentapeptides with non-terminal homo- and heterosequences of amino acid residues to quantitatively determine nearest neighbor coupling between them with a Ising type model. Results reveal that, depending on the choice of amino acid residue pairs, nearest neighbor interactions either stabilize or destabilize pairs of polyproline II and β-strand conformations. This leads to a redistribution of population between these conformations and a reduction in conformational entropy. Interactions between residues in polyproline II and turn(helix)-forming conformations seem to be cooperative in most cases, but the respective interaction parameters are subject to large statistical errors.

Amino acid conformations control the morphological and chiral features of the self-assembled peptide nanostructures: Young investigators perspective

HYPOTHESIS

A variety of nanostructures with different chiral features can be self-assembled from short peptides with highly similar sequences. We hypothesize that these supramolecular nanostructures are ruled by the constituent amino acid residues which adopt their conformations under the influence of intra-/inter-molecular interactions during peptide self-assembly.

APPROACH

Through reviewing recent advances in the self-assembly of short peptides and focusing on the relationship between amino acid conformations, peptide secondary structures and intra-/inter-molecular interactions within the supramolecular architectures, we aim to rationalize the complex interactive processes involved in the self-assembly of short, designed peptides.

RESULTS

Given the highly complexing interactive processes, the adoption of amino acid conformations and their control over peptide self-assembly consist of 4 main steps: (1) Each amino acid residue adopts its unique conformation in a specific sequence; (2) The sequence exhibits its own main chain geometry and determines the propensity of the intermolecular alignment within the building block; (3) The structural propensity of the building block and the packing mode between them determine the self-assembled structural features such as twisting, growth and chirality; (4) In addition to intra-/inter-molecular interactions, inter-sheet and inter-building block interactions could also affect the residue conformations and nanostructures, causing structural readjustment.

Hydration effects on Leu's polyproline II population in AcLXPNH2

Hydration is important in many fundamental processes. To investigate hydration effects on peptide conformations, we examined neighboring-residue and side-chain blocking effects in AcLXPNH2. A correlation between two effects suggests that hydration stabilizes PII more than β-structures. Our results are important for understanding the hydration effects on peptide conformations and hydration-forces in general.

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.

Sequence-Dependent Interfacial Adsorption and Permeation of Dipeptides across Phospholipid Membranes

We investigate permeation of three blocked dipeptides with different side chain polarity across a phospholipid membrane and their behavior at the water-membrane interface by way of molecular dynamics simulations. Hydrophilic serine-serine dipeptide is found to desorb from the interface to aqueous phase, whereas hydrophobic phenylalanine-leucine and amphiphilic serine-leucine tend to accumulate at the interface with a free energy minimum of -3 kcal/mol. All three dipeptides exhibit free energy barriers to permeation across the membrane located at the center of the bilayer. The height of the barrier is strongly sequence dependent and increases with the dipeptide polarity. It is equal to 3.5, 6.4, and 10.0 kcal/mol for phenylalanine-leucine, serine-leucine, and serine-serine, respectively. The corresponding permeability coefficients are equal to 4.6 × 10^-3, 4.5 × 10^-5, and 8.7 × 10^-8 cm/s. The apparent insensitivity of membrane permeability to hydrophobicity of dipeptides, found in some experiments, is attributed to neglecting corrections for unstirred water layers near membrane surface, which are significant for hydrophobic species. Different hydrophobicity of the dipeptides also influences their conformations and orientations, both at the interface and inside the membrane. In particular, penetration of hydrophilic serine-serine dipeptide causes the formation of water-filled defects in the bilayer. These results are relevant to the delivery of peptide-based therapeutic agents.

Conformational analysis of short polar side-chain amino-acids through umbrella sampling and DFT calculations

Molecular and quantum mechanics calculations were carried out in a series of tripeptides (GXG, where X = D, N and C) as models of the unfolded states of proteins. The selected central amino acids, especially aspartic acid (D) and asparagine (N) are known to present significant average conformations in partially allowed areas of the Ramachandran plot, which have been suggested to be important in unfolded protein regions. In this report, we present the calculation of the propensity values through an umbrella sampling procedure in combination with the calculation of the NMR J-coupling constants obtained by a DFT model. The experimental NMR observations can be reasonably explained in terms of a conformational distribution where PP_II and β basins sum up propensities above 0.9. The conformational analysis of the side chain dihedral angle (χ₁), along with the computation of ³J(H^αH^β), revealed a preference for the g _- and g ₊ rotamers. These may be connected with the presence of intermolecular H-bonding and carbonyl-carbonyl interactions sampled in the PP_II and β basins. Taking into account all those results, it can be established that these residues show a similar behavior to other amino acids in short peptides regarding backbone φ,ψ dihedral angle distribution, in agreement with some experimental analysis of capped dipeptides.

Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series

Various host-guest peptide series are used by experimentalists as reference conformational states. One such use is as a baseline for random-coil NMR chemical shifts. Comparison to this random-coil baseline, through secondary chemical shifts, is used to infer protein secondary structure. The use of these random-coil data sets rests on the perception that the reference chemical shifts arise from states where there is little or no conformational bias. However, there is growing evidence that the conformational composition of natively and nonnatively unfolded proteins fail to approach anything that can be construed as random coil. Here, we use molecular dynamics simulations of an alanine-based host-guest peptide series (AAXAA) as a model of unfolded and denatured states to examine the intrinsic propensities of the amino acids. We produced ensembles that are in good agreement with the experimental NMR chemical shifts and confirm that the sampling of the 20 natural amino acids in this peptide series is be far from random. Preferences toward certain regions of conformational space were both present and dependent upon the environment when compared under conditions typically used to denature proteins, i.e., thermal and chemical denaturation. Moreover, the simulations allowed us to examine the conformational makeup of the underlying ensembles giving rise to the ensemble-averaged chemical shifts. We present these data as an intrinsic backbone propensity library that forms part of our Structural Library of Intrinsic Residue Propensities to inform model building, to aid in interpretation of experiment, and for structure prediction of natively and nonnatively unfolded states.

Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field

Understanding the intrinsic conformational preferences of amino acids and the extent to which they are modulated by neighboring residues is a key issue for developing predictive models of protein folding and stability. Here we present the results of 441 independent explicit-solvent MD simulations of all possible two-residue peptides that contain the 20 standard amino acids with histidine modeled in both its neutral and protonated states. (3)J(HNHα) coupling constants and δ(Hα) chemical shifts calculated from the MD simulations correlate quite well with recently published experimental measurements for a corresponding set of two-residue peptides. Neighboring residue effects (NREs) on the average (3)J(HNHα) and δ(Hα) values of adjacent residues are also reasonably well reproduced, with the large NREs exerted experimentally by aromatic residues, in particular, being accurately captured. NREs on the secondary structure preferences of adjacent amino acids have been computed and compared with corresponding effects observed in a coil library and the average β-turn preferences of all amino acid types have been determined. Finally, the intrinsic conformational preferences of histidine, and its NREs on the conformational preferences of adjacent residues, are both shown to be strongly affected by the protonation state of the imidazole ring.

The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design

The conformational propensities of amino acids are an amalgamation of sequence effects, environmental effects and underlying intrinsic behavior. Many have attempted to investigate neighboring residue effects to aid in our understanding of protein folding and improve structure prediction efforts, especially with respect to difficult to characterize states, such as disordered or unfolded states. Host-guest peptide series are a useful tool in examining the propensities of the amino acids free from the surrounding protein structure. Here, we compare the distributions of the backbone dihedral angles (φ/ψ) of the 20 proteogenic amino acids in two different sequence contexts using the AAXAA and GGXGG host-guest pentapeptide series. We further examine their intrinsic behaviors across three environmental contexts: water at 298 K, water at 498 K, and 8 M urea at 298 K. The GGXGG systems provide the intrinsic amino acid propensities devoid of any conformational context. The alanine residues in the AAXAA series enforce backbone chirality, thereby providing a model of the intrinsic behavior of amino acids in a protein chain. Our results show modest differences in φ/ψ distributions due to the steric constraints of the Ala side chains, the magnitudes of which are dependent on the denaturing conditions. One of the strongest factors modulating φ/ψ distributions was the protonation of titratable side chains, and the largest differences observed were in the amino acid propensities for the rarely sampled αL region.

Populations of the Minor α-Conformation in AcGXGNH2 and the α-Helical Nucleation Propensities

Intrinsic backbone conformational preferences of different amino acids are important for understanding the local structure of unfolded protein chains. Recent evidence suggests α-structure is relatively minor among three major backbone conformations for unfolded proteins. The α-helices are the dominant structures in many proteins. For these proteins, how could the α-structures occur from the least in unfolded to the most in folded states? Populations of the minor α-conformation in model peptides provide vital information. Reliable determination of populations of the α-conformers in these peptides that exist in multiple equilibriums of different conformations remains a challenge. Combined analyses on data from AcGXPNH₂ and AcGXGNH₂ peptides allow us to derive the populations of PII, β and α in AcGXGNH₂. Our results show that on average residue X in AcGXGNH₂ adopt PII, β, and α 44.7%, 44.5% and 10.8% of time, respectively. The contents of α-conformations for different amino acids define an α-helix nucleation propensity scale. With derived PII, β and α-contents, we can construct a free energy-conformation diagram on each AcGXGNH₂ in aqueous solution for the three major backbone conformations. Our results would have broad implications on early-stage events of protein folding.

Interplay between Intrinsic Conformational Propensities and Intermolecular Interactions in the Self-Assembly of Short Surfactant-like Peptides Composed of Leucine/Isoleucine

To study how the conformational propensities of individual amino acid residues, primary structures (i.e., adjacent residues and molecular lengths), and intermolecular interactions of peptides affect their self-assembly properties, we report the use of replica exchange molecular dynamics (REMD) to investigate the monomers, dimers, and trimers of a series of short surfactant-like peptides (I3K, L3K, L4K, and L5K). For four-residue peptides X3K (I3K and L3K), the results show that their different aggregation behaviors arise from the different intrinsic conformational propensities of isoleucine and leucine. For LmK peptides (L3K, L4K, and L5K), the molecular length is found to dictate their aggregation via primarily modulating intermolecular interactions. Increasing the number of hydrophobic amino acid residues of LmK peptides enhances their intermolecular H-bonding and promotes the formation of β-strands in dimer and trimer aggregates, overwhelming the intrinsic preference of Leu for helical structures. Thus, the interplay between the conformational propensities of individual amino acid residues for secondary structures and molecular interactions determines the self-assembly properties of the peptides, and the competition between intramolecular and intermolecular H-bonding interactions determines the probability of β-sheet alignment of peptide molecules. These results are validated by comparing simulated and experimental CD spectra of the peptides. This study will aid the design of short peptide amphiphiles and improve the mechanistic understanding of their self-assembly behavior.

Dynamical Network of HIV-1 Protease Mutants Reveals the Mechanism of Drug Resistance and Unhindered Activity

HIV-1 protease variants resist drugs by active and non-active-site mutations. The active-site mutations, which are the primary or first set of mutations, hamper the stability of the enzyme and resist the drugs minimally. As a result, secondary mutations that not only increase protein stability for unhindered catalytic activity but also resist drugs very effectively arise. While the mechanism of drug resistance of the active-site mutations is through modulating the active-site pocket volume, the mechanism of drug resistance of the non-active-site mutations is unclear. Moreover, how these allosteric mutations, which are 8-21 Å distant, communicate to the active site for drug efflux is completely unexplored. Results from molecular dynamics simulations suggest that the primary mechanism of drug resistance of the secondary mutations involves opening of the flexible protease flaps. Results from both residue- and community-based network analyses reveal that this precise action of protease is accomplished by the presence of robust communication paths between the mutational sites and the functionally relevant regions: active site and flaps. While the communication is more direct in the wild type, it traverses across multiple intermediate residues in mutants, leading to weak signaling and unregulated motions of flaps. The global integrity of the protease network is, however, maintained through the neighboring residues, which exhibit high degrees of conservation, consistent with clinical data and mutagenesis studies.

Randomizing the unfolded state of peptides (and proteins) by nearest neighbor interactions between unlike residues

To explore the influence of nearest neighbors on conformational biases in unfolded peptides, we combined vibrational and 2D NMR spectroscopy to obtain the conformational distributions of selected "GxyG" host-guest peptides in aqueous solution: GDyG, GSyG, GxLG, GxVG, where x/y=A, K, L, V. Large changes of conformational propensities were observed due to nearest-neighbor interactions, at variance with the isolated pair hypothesis. We found that protonated aspartic acid and serine lose their above-the-average preference for turn-like structures in favor of polyproline II (pPII) populations in the presence of neighbors with bulky side chains. Such residues also decrease the above-the-average pPII preference of alanine. These observations suggest that the underlying mechanism involves a disruption of the hydration shell. Thermodynamic analysis of (3) J(H(N) ,H(α) ) (T) data for each x,y residue reveals that modest changes in the conformational ensemble masks larger changes of enthalpy and entropy governing the pPII↔β equilibrium indicating a significant residue dependent temperature dependence of the peptides' conformational ensembles. These results suggest that nearest-neighbor interactions between unlike residues act as conformational randomizers close to the enthalpy-entropy compensation temperature, eliminating intrinsic biases in favor of largely balanced pPII/β dominated ensembles at physiological temperatures.

Local order in the unfolded state: conformational biases and nearest neighbor interactions

The discovery of Intrinsically Disordered Proteins, which contain significant levels of disorder yet perform complex biologically functions, as well as unwanted aggregation, has motivated numerous experimental and theoretical studies aimed at describing residue-level conformational ensembles. Multiple lines of evidence gathered over the last 15 years strongly suggest that amino acids residues display unique and restricted conformational preferences in the unfolded state of peptides and proteins, contrary to one of the basic assumptions of the canonical random coil model. To fully understand residue level order/disorder, however, one has to gain a quantitative, experimentally based picture of conformational distributions and to determine the physical basis underlying residue-level conformational biases. Here, we review the experimental, computational and bioinformatic evidence for conformational preferences of amino acid residues in (mostly short) peptides that can be utilized as suitable model systems for unfolded states of peptides and proteins. In this context particular attention is paid to the alleged high polyproline II preference of alanine. We discuss how these conformational propensities may be modulated by peptide solvent interactions and so called nearest-neighbor interactions. The relevance of conformational propensities for the protein folding problem and the understanding of IDPs is briefly discussed.

Biophysical properties of intrinsically disordered p130Cas substrate domain--implication in mechanosensing

Mechanical stretch-induced tyrosine phosphorylation in the proline-rich 306-residue substrate domain (CasSD) of p130Cas (or BCAR1) has eluded an experimentally validated structural understanding. Cellular p130Cas tyrosine phosphorylation is shown to function in areas without internal actomyosin contractility, sensing force at the leading edge of cell migration. Circular dichroism shows CasSD is intrinsically disordered with dominant polyproline type II conformations. Strongly conserved in placental mammals, the proline-rich sequence exhibits a pseudo-repeat unit with variation hotspots 2–9 residues before substrate tyrosine residues. Atomic-force microscopy pulling experiments show CasSD requires minimal extension force and exhibits infrequent, random regions of weak stability. Proteolysis, light scattering and ultracentrifugation results show that a monomeric intrinsically disordered form persists for CasSD in solution with an expanded hydrodynamic radius. All-atom 3D conformer sampling with the TraDES package yields ensembles in agreement with experiment when coil-biased sampling is used, matching the experimental radius of gyration. Increasing β-sampling propensities increases the number of prolate conformers. Combining the results, we conclude that CasSD has no stable compact structure and is unlikely to efficiently autoinhibit phosphorylation. Taking into consideration the structural propensity of CasSD and the fact that it is known to bind to LIM domains, we propose a model of how CasSD and LIM domain family of transcription factor proteins may function together to regulate phosphorylation of CasSD and effect machanosensing.

Mechanical stretching of cells causes the substrate domain of p130Cas (CasSD) to be phosphorylated on 15 tyrosine residues embedded along its length. CasSD is rich in proline and surprisingly well conserved in placental mammals. Stretching of CasSD by atomic force microscopy has identified that it requires far less force than normal folded proteins. Classical biophysical analyses have determined that CasSD is a typical intrinsically disordered protein, a difficult-to-study group of molecules covering about 30% of human proteins. The average size of CasSD is larger and elongated than folded globular proteins but smaller than chemically denatured proteins. We have simulated a large number of all-atom protein structures using a fast all-atom sampling method. The result is in good agreement with the experimental observation. As it is already known that stretching somehow exposes the tyrosine residues to phosphorylation, a mechanism is proposed where straightening of the p130Cas substrate domain backbone conformation through mechanical stretching can lead to dissociation of p130Cas-binding LIM domain proteins and exposure of CasSD tyrosine residues for phosphorylation. This study has led to a new model of a protein-based mechanism of force sensing at the leading edge of cells that allows the cells to feel their way as they move.

pH-Independence of trialanine and the effects of termini blocking in short peptides: a combined vibrational, NMR, UVCD, and molecular dynamics study

Several lines of evidence now well establish that unfolded peptides in general, and alanine in specific, have an intrinsic preference for the polyproline II (pPII) conformation. Investigation of local order in the unfolded state is, however, complicated by experimental limitations and the inherent dynamics of the system, which has in some cases yielded inconsistent results from different types of experiments. One method of studying these systems is the use of short model peptides, and specifically short alanine peptides, known for predominantly sampling pPII structure in aqueous solution. Recently, He et al. ( J. Am. Chem. Soc. 2012 , 134 , 1571 - 1576 ) proposed that unblocked tripeptides may not be suitable models for studying conformational propensities in unfolded peptides due to the presence of end effect, that is, electrostatic interactions between investigated amino acid residues and terminal charges. To determine whether changing the protonation states of the N- and C-termini influence the conformational manifold of the central amino acid residue in tripeptides, we have examined the pH-dependence of unblocked trialanine and the conformational preferences of alanine in the alanine dipeptide. To this end, we measured and globally analyzed amide I' band profiles and NMR J-coupling constants. We described conformational distributions as the superposition of two-dimensional Gaussian distributions assignable to specific subspaces of the Ramachandran plot. Results show that the conformational ensemble of trialanine as a whole, and the pPII content (χpPII = 0.84) in particular, remains practically unaffected by changing the protonation state. We found that compared to trialanine, the alanine dipeptide has slightly lower pPII content (χpPII = 0.74) and an ensemble more reminiscent of the unblocked Gly-Ala-Gly model peptide. In addition, a two-state thermodynamic analysis of the conformational sensitive Δε(T) and (3)J(H(N)H(α))(T) data obtained from electronic circular dichroism and H NMR spectra indicate that the free energy landscape of trialanine is similar in all protonation states. MD simulations for the investigated peptides corroborate this notion and show further that the hydration shell around unblocked trialanine is unaffected by the protonation/deprotonation of the C-terminal group. In contrast, the alanine dipeptide shows a reduced water density around the central residue as well as a less ordered hydration shell, which decreases the pPII propensity and reduces the lifetime of sampled conformations.

Disorder and order in unfolded and disordered peptides and proteins: a view derived from tripeptide conformational analysis. I. Tripeptides with long and predominantly hydrophobic side chains

We performed a conformational analysis of the central residues of three tripeptides glycyl-L-isoleucyl-glycine (GIG), glycyl-L-tyrosyl-glycine (GYG) and glycyl-L-arginyl-glycine (GRG) in aqueous solution, based on a global analysis of amide I' band profiles and NMR J-coupling constants. The results are compared with recently reported distributions of GVG, GFG and GEG. For GIG and GYG, we found that even though the polyproline II (pPII) fraction is below 0.5, it is still the most populated conformation, whereas GVG and GFG show both a larger β-strand fraction. For GRG, we observed a clear dominance of pPII over β-strand, reminiscent of observations for GEG and GKG. This finding indicates that terminal charges on otherwise hydrophobic residue side chains stabilize pPII over β-strand conformations. For all peptides investigated we found that a variety of compact and turn-like conformations constitute nearly 20 percent of their conformational distributions. Attempts to analyze our data with a simple two-state pPII-->/<--β model therefore do not yield any satisfactory reproduction of experimental results. A comparison of the obtained GxG ensembles with conformational distributions of GxG segments in truncated coil libraries (helices and sheets omitted) revealed a much larger fraction of type II β(i+2) and type III β like conformations for the latter. Thus, a comparison of conformational distributions of unfolded peptide segments in solution and in coil libraries reveal interesting information on how the interplay between intrinsic propensities of amino acid residues and non-local interactions in polypeptide chains determine the conformations of loop segments in proteins.

Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites

Intrinsically disordered (ID) proteins function in the absence of a unique stable structure and appear to challenge the classic structure-function paradigm. The extent to which ID proteins take advantage of subtle conformational biases to perform functions, and whether signals for such mechanism can be identified in proteome-wide studies is not well understood. Of particular interest is the polyproline II (PII) conformation, suggested to be highly populated in unfolded proteins. We experimentally determine a complete calorimetric propensity scale for the PII conformation. Projection of the scale into representative eukaryotic proteomes reveals significant PII bias in regions coding for ID proteins. Importantly, enrichment of PII in ID proteins, or protein segments, is also captured by other PII scales, indicating that this enrichment is robustly encoded and universally detectable regardless of the method of PII propensity determination. Gene ontology (GO) terms obtained using our PII scale and other scales demonstrate a consensus for molecular functions performed by high PII proteins across the proteome. Perhaps the most striking result of the GO analysis is conserved enrichment (P < 10(-8) ) of phosphorylation sites in high PII regions found by all PII scales. Subsequent conformational analysis reveals a phosphorylation-dependent modulation of PII, suggestive of a conserved "tunability" within these regions. In summary, the application of an experimentally determined polyproline II (PII) propensity scale to proteome-wide sequence analysis and gene ontology reveals an enrichment of PII bias near disordered phosphorylation sites that is conserved throughout eukaryotes.

Temperature and urea have opposing impacts on polyproline II conformational bias

The native states of globular proteins have been accessed in atomic detail by X-ray crystallography and nuclear magnetic resonance spectroscopy, yet characterization of denatured proteins beyond global metrics has proven to be elusive. Denatured proteins have been observed to exhibit global geometric properties of a random coil polymer. However, this does not preclude the existence of nonrandom, local conformational bias that may be significant for protein folding and function. Indeed, circular dichroism (CD) spectroscopy and other methods have suggested that the denatured state contains considerable local bias to the polyproline II (PII) conformation. Here, we develop predictive models to determine the extent that temperature and the chemical denaturant urea modulate PII propensity. In agreement with our predictive model, PII propensity is observed experimentally to decrease with an increase in temperature. Conversely, urea appears to promote the PII conformation as determined by CD and isothermal titration calorimetry. Importantly, the calorimetric data are in quantitative agreement with a model that predicts the stability of the PII helix relative to other denatured state conformations based upon solvent accessible surface area and experimentally measured Gibbs transfer free energies. The ability of urea to promote the PII conformation can be attributed to the favorable interaction of urea with the peptide backbone. Thus, perturbing denatured states by temperature or cosolutes has subtle, yet opposing, impacts on local PII conformational biases. These results have implications for protein folding as well as for the function of signaling proteins that bind proline-rich targets in globular or intrinsically disordered proteins.