Polyproline II Research Articles

Structural landscape of the proline-rich domain of Sos1 nucleotide exchange factor

Despite its key role in mediating a plethora of cellular signaling cascades pertinent to health and disease, little is known about the structural landscape of the proline-rich (PR) domain of Sos1 guanine nucleotide exchange factor. Herein, using a battery of biophysical tools, we provide evidence that the PR domain of Sos1 is structurally disordered and adopts an extended random coil-like conformation in solution. Of particular interest is the observation that while chemical denaturation of PR domain results in the formation of a significant amount of polyproline II (PPII) helices, it has little or negligible effect on its overall size as measured by its hydrodynamic radius. Our data also show that the PR domain displays a highly dynamic conformational basin in agreement with the knowledge that the intrinsically unstructured proteins rapidly interconvert between an ensemble of conformations. Collectively, our study provides new insights into the conformational equilibrium of a key signaling molecule with important consequences on its physiological function.

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.

Synthesis of peptides and glycopeptides with polyproline II helical topology as potential antifreeze molecules

A library of peptides and glycopeptides containing (4R)-hydroxy-l-proline (Hyp) residues were designed with a view to providing stable polyproline II (PPII) helical molecules with antifreeze activity. A library of dodecapeptides containing contiguous Hyp residues or an Ala-Hyp-Ala tripeptide repeat sequence were synthesized with and without α-O-linked N-acetylgalactosamine and α-O-linked galactose-β-(1→3)-N-acetylgalactosamine appended to the peptide backbone. All (glyco)peptides possessed PPII helical secondary structure with some showing significant thermal stability. The majority of the (glyco)peptides did not exhibit thermal hysteresis (TH) activity and were not capable of modifying the morphology of ice crystals. However, an unglycosylated Ala-Hyp-Ala repeat peptide did show significant TH and ice crystal re-shaping activity suggesting that it was capable of binding to the surface of ice. All (glyco)peptides synthesized displayed some ice recrystallization inhibition (IRI) activity with unglycosylated peptides containing the Ala-Hyp-Ala motif exhibiting the most potent inhibitory activity. Interestingly, although glycosylation is critical to the activity of native antifreeze glycoproteins (AFGPs) that possess an Ala-Thr-Ala tripeptide repeat, this same structural modification is detrimental to the antifreeze activity of the Ala-Hyp-Ala repeat peptides studied here.

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.

Polyproline fold—In imparting kinetic stability to an alkaline serine endopeptidase

Polyproline II (PPII) fold, an unusual structural element was detected in the serine protease from Nocardiopsis sp. NCIM 5124 (NprotI) based on far UV circular dichroism spectrum, structural transitions of the enzyme in presence of GdnHCl and a distinct isodichroic point in chemical and thermal denaturation. The functional activity and conformational transitions of the enzyme were studied under various denaturing conditions. Enzymatic activity of NprotI was stable in the vicinity of GdnHCl upto 6.0M concentration, organic solvents viz. methanol, ethanol, propanol (all 90% v/v), acetonitrile (75% v/v) and proteases such as trypsin, chymotrypsin and proteinase K (NprotI:protease 10:1). NprotI seems to be a kinetically stable protease with a high energy barrier between folded and unfolded states. Also, an enhancement in the activity of the enzyme was observed in 1M GdnHCl upto 8h, in organic solvents (75% v/v) for 72h and in presence of proteolytic enzymes. The polyproline fold remained unaltered or became more prominent under the above mentioned conditions. However, it diminished gradually during thermal denaturation above 60°C. Thermal transition studies by differential scanning calorimetry (DSC) showed scan rate dependence as well as irreversibility of denaturation, the properties characteristic of kinetically stable proteins. This is the first report of PPII helix being the global conformation of a non structural protein, an alkaline serine protease, from a microbial source, imparting kinetic stability to the protein.

Polyproline and Triple Helix Motifs in Host-Pathogen Recognition

Secondary structure elements often mediate protein-protein interactions. Despite their low abundance in folded proteins, polyproline II (PPII) and its variant, the triple helix, are frequently involved in protein-protein interactions, likely due to their peculiar propensity to be solvent-exposed. We here review the role of PPII and triple helix in mediating host-pathogen interactions, with a particular emphasis to the structural aspects of these processes. After a brief description of the basic structural features of these elements, examples of host-pathogen interactions involving these motifs are illustrated. Literature data suggest that the role played by PPII motif in these processes is twofold. Indeed, PPII regions may directly mediate interactions between proteins of the host and the pathogen. Alternatively, PPII may act as structural spacers needed for the correct positioning of the elements needed for adhesion and infectivity. Recent investigations have highlighted that collagen triple helix is also a common target for bacterial adhesins. Although structural data on complexes between adhesins and collagen models are rather limited, experimental and theoretical studies have unveiled some interesting clues of the recognition process. Interestingly, very recent data show that not only is the triple helix used by pathogens as a target in the host-pathogen interaction but it may also act as a bait in these processes since bacterial proteins containing triple helix regions have been shown to interact with host proteins. As both PPII and triple helix expose several main chain non-satisfied hydrogen bond acceptors and donors, both elements are highly solvated. The preservation of the solvation state of both PPII and triple helix upon protein-protein interaction is an emerging aspect that will be here thoroughly discussed.

Water interaction differences determine the relative energetic stability of the polyproline II conformation of the alanine dipeptide in aqueous environments

Although subsequent studies have provided extensive support for the 1968 Tiffany and Krimm proposal (Biopolymers 6, 1379) that the polyproline II (PPII) conformation is a significant component of the structure of unordered polypeptide chains, two issues are still not fully resolved: the PPII persistence length in a chain and the source of its relative stability with respect to the β-conformation. We examine the latter question by studying the B97-D/6-31++G(**) energy, in the absence and presence of a reaction field, of the alanine dipeptide hydrated by various amounts of explicit waters and resolving this into its three components: the energies of the individual solvated peptides and water structures plus the interaction energy involving them. We find that the relative stability of the PPII conformation is determined mainly by the difference in the interaction energies of the water structures in the near-peptide layers.

Infrared Probing of 4-Azidoproline Conformations Modulated by Azido Configurations

4-Azidoproline (Azp) can tune the stability of the polyproline II (P(II)) conformation in collagen. The azido group in the 4R and 4S configurations stabilizes and destabilizes the P(II) conformation, respectively. To obtain insights into the dependence of the conformational stability on the azido configuration, we carried out Fourier transform (FT) IR experiments with four 4-azidoproline derivatives, Ac-(4R/S)-Azp-(NH/O)Me. We found that the amide I and azido IR spectra are different depending on the azido configuration and C-terminal structure. The origin of such spectral differences between 4R and 4S configurations and between C-terminal methylamide and ester ends was elucidated by quantum chemistry calculations in combination with (1)H NMR and time- and frequency-resolved IR pump-probe spectroscopy. We found that the azido configurations and C-terminal structures affect intramolecular interactions, which are responsible for the ensuing conformational and thereby IR spectral differences. Consequently, 4-azidoproline conformations modulated by azido configurations can be probed by IR spectroscopy. These findings suggest that 4-azidoproline can be both a structure-control and -probing element, which enables the infrared tracking of proline roles in protein structure, function, and dynamics.

Investigation of self-assembling proline- and glycine-rich recombinant proteins and peptides inspired by proteins from a symbiotic fungus using atomic force microscopy and circular dichroism spectroscopy

Fiber-forming proteins and peptides are being scrutinized as a promising source of building blocks for new nanomaterials. Arabinogalactan-like (AGL) proteins expressed at the symbiotic interface between plant roots and arbuscular mycorrhizal fungi have novel sequences, hypothesized to form polyproline II (PPII) helix structures. The functional nature of these proteins is unknown but they may form structures for the establishment and maintenance of fungal hyphae. Here we show that recombinant AGL1 (rAGL1) and recombinant AGL3 (rAGL3) are extended proteins based upon secondary structural characteristics determined by electronic circular dichroism (CD) spectroscopy and can self-assemble into fibers and microtubes as observed by atomic force microscopy (AFM) and scanning electron microscopy (SEM). CD spectroscopy results of synthetic peptides based on repeat regions in AGL1, AGL2 and AGL3 suggest that the synthetic peptides contain significant amounts of extended PPII helices and that these structures are influenced by ionic strength and, at least in one case, by concentration. Point mutations of a single residue of the repeat region of AGL3 resulted in altered secondary structures. Self-assembly of these repeats was observed by means of AFM and optical microscopy. Peptide (APADGK)6 forms structures with similar morphology to rAGL1 suggesting that these repeats are crucial for the morphology of rAGL1 fibers. These novel self-assembling sequences may find applications as precursors for bioinspired nanomaterials.

Effects of solvents on the intrinsic propensity of peptide backbone conformations

We investigated the effects of solvents on the intrinsic propensity of peptide backbone conformations based on molecular dynamics simulations. The results show that compared with pure water, aqueous urea decreases the helix propensity. In comparison, methanol decreases the polyproline II (PPII) propensity. Such a solvent dependence of the intrinsic propensity of the backbone conformation is correlated with the solvent dependence of the hydration of the backbone groups and the formation probability of the local intrapeptide hydrogen bonds. Aqueous urea which has low ability to stabilize the local intrapeptide hydrogen bonds disfavors the helical conformation. Whereas, methanol which has low ability to hydrate the backbone groups disfavors the polyproline II conformation. In addition, the solvent effects can be further modulated by the side chains of the peptides. The solvent effects of the intrinsic propensity of peptide backbone conformations observed in this work suggest that changing the intrinsic propensity of the protein backbone conformations can partly contribute to the solvent-induced protein structure and dynamics variations. These results will be useful in understanding the solvent dependence of the conformational distributions of the unfolded proteins or peptides (or intrinsically disordered proteins) in which the global tertiary interactions are less important than that in the well-folded proteins.

Phosphorylation alters backbone conformational preferences of serine and threonine peptides

Despite the notion that a control of protein function by phosphorylation works mainly by inducing its conformational changes, the phosphorylation effects on even small peptide conformation have not been fully understood yet. To study its possible effects on serine and threonine peptide conformations, we recently carried out pH- and temperature-dependent circular dichroism (CD) as well as (1)H NMR studies of the phosphorylated serine and threonine peptides and compared them with their unphosphorylated analogs. In the present article, by performing the self-consistent singular value decomposition analysis of the temperature-dependent CD spectra and by analyzing the (3)J(H(N),H(α)) coupling constants extracted from the NMR spectra, the populations of the polyproline II (PPII) and β-strand conformers of the phosphorylated Ser and Thr peptides are determined. As temperature is increased, the β-strand populations of both phosphorylated serine and threonine peptides increase. However, the dependences of PPII/β-strand population ratio on pH are different for these two cases. The phosphorylation of the serine peptide enhances the PPII propensity, whereas that of the threonine peptide has the opposite effect. This suggests that the serine and threonine phosphorylations can alter the backbone conformational propensity via direct but selective intramolecular hydrogen-bonding interactions with the peptide N--H groups. This clearly indicates that the phosphoryl group actively participates in modulating the peptide backbone conformations.

Perturbation analyses of intermolecular interactions

Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the α state and PPII (polyproline II) + β states) for larger cutoff length, the separation between the PPII state and the β state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the IPA. To test the feasibility of the DIPA for larger molecules, we apply the DIPA to the ten-residue chignolin folding in explicit water. The top three principal components identify the four states (native state, two misfolded states, and unfolded state) and their corresponding eigenfunctions identify important chignolin-water interactions to each state. Thus, the DIPA provides the practical method to identify conformational states and their corresponding important intermolecular interactions with distance information.

Conformational Changes of Trialanine Induced by Direct Interactions between Alanine Residues and Alcohols in Binary Mixtures of Water with Glycerol and Ethanol

Despite the increasing relevance of characterizing local conformational distributions in the unfolded state, an unambiguous description of the role that solvation and the addition of certain cosolvents play in altering this ensemble has yet to emerge. Alcohol cosolvents, and specifically glycerol, are known to act as protein stabilizers. The underlying mechanism of this effect is, however, still debated. Short alanine-based peptides provide a suitable model system for exploring the influence of cosolvents on backbone conformations, as ample experimental evidence now indicates that alanine does not exhibit a true statistical coil behavior but rather shows strong preference for sampling the polyproline II (PPII) region of the Ramachadran map when solvated in water. To explore the effect glycerol and ethanol cosolvents have on the conformational distribution of trialanine, we combined UV-CD and H NMR spectroscopies. The temperature dependence of the conformationally sensitive maximum dichroism (Δε) and (3)J(H(α)H(N)) coupling constants of two amide protons (N- and C-terminal) was subjected to a global thermodynamic analysis based on simple two-state PPII↔β models. Interestingly, our results show that even small admixtures of alcohol (5% v/v) considerably change the spectral parameters, Δε(PPII) and Δε(β), as well as the enthalpic and entropic differences between the two states. For the central residue of trialanine in 5% glycerol, we obtained a gain in enthalpy favoring PPII of ΔΔH(n) = -4.80 kJ/mol and a compensating increase in entropy favoring the β-strand of ΔΔS(n) = -13.53[J/mol K]. This causes increases in -ΔG and slight increases in PPII content. Further addition of alcohol, however, reverses the trend in that it causes a destabilization of the hydration shell and a shift toward β-strand conformations. The combined manifold of ΔH and ΔS values obtained for the investigated binary mixtures and the pure aqueous solvent exhibits an excellent linear correlation, which reflects enthalpy-entropy compensation and a common transition temperature. The latter can be considered an indication of a weak binding between cosolvent and peptide. A comparison of infrared and Raman spectra of trialanine in water and in water-alcohol mixtures indeed reveals a close proximity between aliphatic side chains of alanine residues and alcohol molecules even for 5% (v/v) alcohol-water mixtures. Hence, our results provide the first experimental evidence for direct interactions between, e.g., glycerol and peptides in aqueous solutions, in line with the result of recent calculations by Vagenende et al. (Biochemistry 2009, 48, 11084-11096) but at variance with preferential exclusion theories.

Polyproline II structure is critical for the enzyme protective function of soybean Em (LEA1) conserved domains

Group 1 late embryogenesis-abundant (LEA1) proteins protect enzyme activity from dehydration and are structurally conserved with three different 20 amino acid motifs in the N-terminal, middle and C-terminal domains. Three soybean Em (LEA1) domain peptides (Em-N, Em-2M and Em-C) covering these respective motifs were constructed and had differential protective ability on lactate dehydrogenase against freeze-thaw: Em-C>Em-2M>Em-N. CD spectroscopy revealed that Em-2M and Em-C contained both polyproline II (PII) helical structure and α-helix, while Em-N had a high potential to form α-helix but did not contain PII structure. The PII helical structure between the third and fifth glycine in the middle motif was shown, through site mutation, to be critical for the enzyme protective function of soybean Em (LEA1) conserved domain under freezing stress.

Assignment of PolyProline II Conformation and Analysis of Sequence – Structure Relationship

BackgroundSecondary structures are elements of great importance in structural biology, biochemistry and bioinformatics. They are broadly composed of two repetitive structures namely α-helices and β-sheets, apart from turns, and the rest is associated to coil. These repetitive secondary structures have specific and conserved biophysical and geometric properties. PolyProline II (PPII) helix is yet another interesting repetitive structure which is less frequent and not usually associated with stabilizing interactions. Recent studies have shown that PPII frequency is higher than expected, and they could have an important role in protein – protein interactions.Methodology/Principal FindingsA major factor that limits the study of PPII is that its assignment cannot be carried out with the most commonly used secondary structure assignment methods (SSAMs). The purpose of this work is to propose a PPII assignment methodology that can be defined in the frame of DSSP secondary structure assignment. Considering the ambiguity in PPII assignments by different methods, a consensus assignment strategy was utilized. To define the most consensual rule of PPII assignment, three SSAMs that can assign PPII, were compared and analyzed. The assignment rule was defined to have a maximum coverage of all assignments made by these SSAMs. Not many constraints were added to the assignment and only PPII helices of at least 2 residues length are defined.Conclusions/SignificanceThe simple rules designed in this study for characterizing PPII conformation, lead to the assignment of 5% of all amino as PPII. Sequence – structure relationships associated with PPII, defined by the different SSAMs, underline few striking differences. A specific study of amino acid preferences in their N and C-cap regions was carried out as their solvent accessibility and contact patterns. Thus the assignment of PPII can be coupled with DSSP and thus opens a simple way for further analysis in this field.

Study of Membrane-Induced Conformations of Substance P: Detection of Extended Polyproline II Helix Conformation

We study the conformation of substance P (SP), a ligand of neurokinin 1 receptor, and its analogue [Trp8]SP in membrane-mimetic media to provide further insights into membrane-ligand interactions and the factors determining and modulating the peptide structure. CD data revealed that the neuropeptide attains α-helical fold in negatively charged SDS micelles and DMPG liposomes but not in zwitterionic DMPC. The fluorescence experiments reported that the Trp side chain of [Trp8]SP inserts into the hydrophobic core of the SDS micelles and DMPG liposomes but faces the DMPC hydrophilic region, indicating that electrostatic interactions between membrane and SP are essential for the α-helical fold. Formation of extended polyproline II (PPII) helical structure in aqueous solutions and in submicellar concentrations of SDS and DMPC liposomes was confirmed by comparing CD spectra at increasing temperatures. Moreover, in all conditions where PPII conformation was detected, the Trp was totally exposed to the bulk. The PPII structure may be vital for recognition processes of SP by neurokinin receptors.

Direct Calorimetric Determination of a Complete Polyproline II (pII) Propensity Scale Reveals PII Enhancement in Intrinsically Disordered Proteins

Circular dichroism spectropolarimetry experiments and other studies have suggested that the denatured states of polypeptides may comprise a smaller conformational space than previously thought, and that the polyproline II (PII) helix is one of the conformations that is highly populated in the denatured state. Src-homology 3 (SH3) is a modular domain that recognizes and binds peptide in the PII conformation, such as SosY, with high specificity. Our experimental strategy is to use isothermal titration calorimetry (ITC) to monitor the binding of SH3 to engineered SosY peptides, enabling the direct detection of ligand population that is in the PII conformation. Importantly, our model system allows direct access to free energy information concerning the context dependent PII propensity of amino acids at specific sites in the SosY peptide. Binding isotherms have been measured and quantitative estimates made for the PII propensity all twenty amino acids, developing a complete PII scale. Correlations of the calorimetrically determined scale to the GenomeNet database of amino acid physico-chemical property and secondary structure propensity scales revealed no significant correlations. An algorithm is developed to calculate the average PII propensities of different sequences, revealing that intrinsically disordered proteins have an enhancement of PII compared to sequences that fold. Upon random shuffling, the high PII regions within intrinsically disordered segments are lost, demonstrating local enrichment of high PII bias within these sequences.

Solvent Dependence of Trialanine Conformers

Determining the conformational propensities of amino acid residues in short peptides is increasingly recognized as pivotal for obtaining a reliable picture of the unfolded states of peptides and proteins. In this context, ample experimental evidence indicates that alanine does not exhibit a statistical coil behavior, but rather shows a strong preference for sampling the polyproline II (PPII) region of the Ramachadran plot. Solvation in water has been proposed as the main reason for PPII stabilization. The mechanisms involved in the respective peptide-solvent interactions are still debated. Results from DFT-calculations on dialanine suggest that water stabilizes PPII conformers by forming hydrogen bond bridges between adjacent carbonyl and amide groups. Other models have invoked electrostatic interactions. To explore the solvent dependence of PPII stabilization, we used UV-CD and H-NMR spectroscopy to determine the conformations of cationic trialanine in water, as well as in binary water/glycerol water/ethanol mixtures. All spectra were recorded as a function of temperature ranging between 0°C and 90°C. The resultant dichrosim at 216nm and 3J(HαHN) coupling constants were subjected to a simplified two state PPII↔β strand thermodynamic analysis. The experimental results indicate that both alcohol co-solvents substantially lower the PPII propensity of alanine in each respective binary mixture. Glycerol seems to be most effective in replacing water in the solvation shell, causing large enthalpic decreases between the two conformers; from ΔH=18.15 kJ/mol in water, to ΔH=12.42 kJ/mol with only a 0.012 mole fraction admixture of glycerol.

Conformational Characterization of Tachykinin Neuropeptides: Role of the Polyproline II Structure

Substance P (SP), Neurokinin A (NKA) and Scyliorhinin I (Scyl) peptides belong to the Tachykinin family and are agonists for Neurokinin1 (NK1) GPCR receptor with different potent activities. These Tachykinins are involved in several physiological processes and some neurodegenerative disorders, what make them relevant therapeutically agents. The characterization of the active peptide conformations of the Tachykinins is essential for the elucidation of the mechanism of action and for the design of drugs. To address the molecular basis for the peptide recognition by the NK1 receptor we studied the conformation of SP, NKA and Scyl in solution and membrane-mimic environments: micelles and liposomes, by using CD and FTIR spectroscopies. The analysis of CD data revealed that the three peptides form a partially α helical structure in the presence of the negatively charged micelles and vesicles, but not in zwitterionic DMPC. By performing CD spectra at increasing temperatures we demonstrated that in an aqueous environment SP, NKA and Scyl form extended polyproline II (PPII) helical structure. The same structure was found in the membrane mimics, which do not induce formation of α helical conformation of the peptides. FTIR experiments performed in D2O support the presence of PPII conformation. Further we questioned whether the formation of PPII needs peptide binding to the membrane or it is a peptide intrinsic property, by using fluorescence techniques. We propose that the peptide-membrane interaction is a two-step process involving first electrostatic interactions through PPII structure, followed by the folding and insertion of the alpha-helical segment.

Application of ring‐closing metathesis to Grb2 SH3 domain‐binding peptides

Molecular processes depending on protein–protein interactions can use consensus recognition sequences that possess defined secondary structures. Left-handed polyproline II (PPII) helices are a class of secondary structure commonly involved with cellular signal transduction. However, unlike -helices, for which a substantial body of work exists regarding applications of ring-closing metathesis (RCM), there are few reports on the stabilization of PPII helices by RCM methodologies. The current study examined the effects of RCM macrocyclization on left-handed PPII helices involved with the SH3 domain-mediated binding of Sos1–Grb2. Starting with the Sos1-derived peptide “Ac-V1-P2-P3-P4-V5-P6-P7-R8-R9-R10-amide,” RCM macrocyclizations were conducted using alkenyl chains of varying lengths originating from the pyrrolidine rings of the Pro4 and Pro7 residues. The resulting macrocyclic peptides showed increased helicity as indicated by circular dichroism and enhanced abilities to block Grb2–Sos1 interactions in cell lysate pull-down assays. The synthetic approach may be useful in RCM macrocyclizations, where maintenance of proline integrity at both ring junctures is desired.