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1.
The polyproline type II (PPII) helix is a prevalent conformation in both folded and unfolded proteins, and is known to play important roles in a wide variety of biological processes. Polyproline itself can also form a type I (PPI) helix, which has a disparate conformation. Here, we use derivatives of polyproline, (Pro)10, (Hyp)10, (Flp)10, and (flp)10, where Hyp is (2S,4R)-4-hydroxyproline, Flp is (2S,4R)-4-fluoroproline, and flp is (2S,4S)-4-fluoroproline, to probe for a stereoelectronic effect on the conformation of polyproline. Circular dichroism spectral analyses show that 4R electron-with-drawing substituents stabilize a PPII helix relative to a PPI helix, even in a solvent that favors the PPI conformation, such as n-propanol. The stereochemistry at C4 ordains the relative stability of PPI and PPII helices, as (flp)10 forms a mixture of PPI and PPII helices in water and a PPI helix in n-propanol. The conformational preferences of (Pro)10 are intermediate between those of (Hyp)10/(Flp)10 and (flp)10. Interestingly, PPI helices of (flp)10 exhibit cold denaturation in n-propanol with a value of T(s) near 70 degrees C. Together, these data show that stereoelectronic effects can have a substantial impact on polyproline conformation and provide a rational means to stabilize a PPI or PPII helix. 相似文献
2.
The pyrrolidine side chain makes proline play a unique role in protein structure and function. The Cγ ring pucker preference and the cis– trans peptidyl bond ratio can be mediated via stereoelectronic effects. Here we used a compact triple‐stranded antiparallel β‐sheet protein, the human Pin1 WW domain, to study the consequences of implanting a preorganized Cγ ring pucker on protein structure and function. The conserved Pro37 is a key residue involved in one hydrophobic core, plays an important role in the WW domain, and adopts a Cγ‐endo ring pucker in the native structure. Pro37 was replaced with Cγ‐exo biased pucker derivatives: (2S,4R)‐4‐hydroxyproline (4R‐Hyp), (2S,4R)‐4‐fluoroproline (4R‐Flp), (2S,4R)‐4‐methoxyproline (4R‐Mop), and Cγ‐endo biased pucker derivatives: (2S,4S)‐4‐hydroxyproline (4S‐hyp), (2S,4S)‐4‐fluoroproline (4S‐flp), (2S,4S)‐4‐methoxyproline (4S‐mop) to examine how a preorganized pucker affects the folding stability and ligand‐binding affinity. Circular dichroism measurements indicate that among the variants, only the one with 4S‐flp substitution (P37flp) is more stable than the wild type, suggesting that the stabilization effects originated from preorganization of the backbone conformation and the hydrophobicity of C? F group. Analysis of ligand‐binding affinity using isothermal titration calorimetry revealed that only P37flp has a stronger ligand affinity than the wild type, showing that 4S‐flp can stabilize the WW domain and increase its ligand affinity. Together we have used 4‐substituted proline derivatives and the WW domain to demonstrate that proline ring puckering can be a key factor in determining the folding stability of a protein but the choice of the derivative groups is also critical. Proteins 2014; 82:67–76. © 2013 Wiley Periodicals, Inc. 相似文献
3.
Hinderaker MP Raines RT 《Protein science : a publication of the Protein Society》2003,12(6):1188-1194
The well-known preference of the peptide bond for the trans conformation has been attributed to steric effects. Here, we show that a proline residue with an N-formyl group (H(i-1)-C'(i-1)=O(i-1)), in which H(i-1) presents less steric hindrance than does O(i-1), likewise prefers a trans conformation. Thus, the preference of the peptide bond for the trans conformation cannot be explained by steric effects alone. Rather, an n --> pi* interaction between the oxygen of the peptide bond (O(i-1)), and the subsequent carbonyl carbon in the polypeptide chain (C'(i)) also contributes to this preference. The O(i-1) and C'(i) distance and O(i-1).C'(i)=O(i) angle are especially favorable for such an n --> pi* interaction in a polyproline II helix. We propose that this electronic effect provides substantial stabilization to this and other elements of protein structure. 相似文献
4.
Researchers have recently questioned the role hydroxylated prolines play in stabilizing the collagen triple helix. To address these issues, we have developed new molecular mechanics parameters for the simulation of peptides containing 4(R)-fluoroproline (Flp), 4(R)-hydroxyproline (Hyp), and 4(R)-aminoproline (Amp). Simulations of peptides based on these parameters can be used to determine the components that stabilize hydroxyproline over proline in the triple helix. The dihedrals F-C-C-N, O-C-C-N, and N-C-C-N were built using a N-beta-ethyl amide model. One nanosecond simulations were performed on the trimers [(Pro-Pro-Gly)(10)](3), [(Pro-Hyp-Gly)(10)](3), [(Pro-Amp-Gly)(10)](3), [(Pro-Amp(1+)-Gly)(10)](3), and [(Pro-Flp-Gly)(10)](3) in explicit solvent. The results of our simulations suggest that pyrrolidine ring conformation is mediated by the strength of the gauche effect and classical electrostatic interactions. 相似文献
5.
The molecular conformation of oligo‐proline peptides composed of two oligo‐proline block sequences and a non‐proline linker residue, designated as (Pro) m‐Gly/Ala‐(Pro) n peptides, was analyzed by circular dichroism (CD) spectroscopy. The CD spectra in water and trifluoroethanol indicated that the two oligo‐proline blocks were separated by an inserted residue independent of polyproline‐II (PP‐II). In addition, the stability of the (Pro) m‐Gly/Ala‐(Pro) n peptides was analyzed using a conformational transition system, during transition from PP‐II to polyproline‐I (PP‐I) in aliphatic alcohols, methanol (MeOH), and 1‐propanol (1‐PrOH). Interestingly, the PP‐II/PP‐I transition was inhibited after a Gly/Ala was inserted at the center of the oligo‐proline; the inhibitory effect of Ala was stronger than that of Gly. When the position of the inserted Ala moved towards the C‐terminal, the (Pro) m‐Gly/Ala‐(Pro) n peptides displayed a PP‐II/PP‐I transition in 1‐PrOH. Our results confirmed that (Pro) m‐Gly/Ala‐(Pro) n peptides prefer to form PP‐II hairpin conformations even in MeOH and 1‐PrOH. Thus, our findings suggest that the insertion of Gly/Ala acts as a stabilizer in PP‐II in proline‐rich peptides. 相似文献
6.
Paolo Ruzza Giuliano Siligardi Arianna Donella-Deana Andrea Calderan Rohanah Hussain Chiara Rubini Luca Cesaro Alessio Osler Andrea Guiotto Lorenzo A Pinna Gianfranco Borin 《Journal of peptide science》2006,12(7):462-471
Eukaryotic signal transduction involves the assembly of transient protein-protein complexes mediated by modular interaction domains. Specific Pro-rich sequences with the consensus core motif PxxP adopt the PPII helix conformation upon binding to SH3 domains. For short Pro-rich peptides, little or no ordered secondary structure is usually observed before binding interactions. The association of a Pro-rich peptide with the SH3 domain involves unfavorable binding entropy due to the loss of rotational freedom on forming the PPII helix. With the aim of stabilizing the PPII helix conformation in the Pro-rich HPK1 decapeptide PPPLPPKPKF (P2), a series of P2 analogues was prepared, in which specific Pro positions were alternatively occupied by 4(S)- or 4(R)-4-fluoro-L-proline. The interactions of these peptides with the SH3 domain of the HPK1-binding partner HS1 were quantitatively analyzed by the NILIA-CD approach. A CD thermal analysis of the P2 analogues was performed to assess their propensity to adopt the PPII helix conformation. Contrary to our expectations, the K(d) values of the analogues were lower than that of the parent peptide P2. These results clearly show that the induction of a stable PPII helix conformation in short Pro-rich peptides is not sufficient to increase their affinity toward the SH3 domain and that the effect of 4-fluoroproline strongly depends on the position of this residue in the sequence and the chirality of the substituent in the pyrrolidine ring. 相似文献
7.
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. 相似文献
8.
Recent studies have indicated that the unfolded states of polypeptides contain a substantial amount of polyproline type II (P(II)) structure. This energetically and structurally preorganized state may contribute to the reduction of the folding search, as well as to the recognition of intrinsically unstructured proteins and polyproline ligands. Using Monte Carlo simulations of natively unfolded peptides in the presence of explicit aqueous solvation, we observe that residue-specific P(II) conformational propensity is the result of the modulation of polypeptide backbone hydration by a proximal side-chain. Such a mechanism may be unique among those that contribute to the modulation of secondary structures in proteins. The calculated conformational propensities should prove useful for the development of a configurational P(II) scale necessary for the prediction and design of natural-like polypeptides. 相似文献
9.
A simultaneous estimation of the chiral discrimination abilities of several chiral hosts was demonstrated on the basis of one mass spectrum. The chiral host mixture, including H(1), H(2), H(3) ..., and H(m) (m: number of hosts) was prepared by etherification of several chiral alcohols with bistosylate of diethylene glycol. An equimolar mixture of a deuterium-labeled (S)- and unlabeled (R)-enantiomer of an amino acid isopropyl ester hydrochloride (G(S-dn) (+)Cl(-) and G(R) (+)Cl(-), n: number of deuterium atoms) was added to the chiral host mixture, and the FAB mass spectrum was measured to evaluate the chiral discrimination ability of each host in the mixture without isolation. The chiral discrimination ability of each host toward the guest is represented by the relative peak intensity of the diastereomeric complex ion pair, I(H(m) + G(R)((+)/I(H(m) + G(S-dn))(+) (=I(R)/I(S-dn) value). Several new hosts showed good chiral discrimination toward the guest. 相似文献
10.
The polyproline‐II helix is the most extended naturally occurring helical structure and is widely present in polar, exposed stretches and “unstructured” denatured regions of polypeptides. Can it be hydrophobic? In this study, we address this question using oligomeric peptides formed by a hydrophobic proline analogue, (2S,3aS,7aS)‐octahydroindole‐2‐carboxylic acid (Oic). Previously, we found the molecular principles underlying the structural stability of the polyproline‐II conformation in these oligomers, whereas the hydrophobicity of the peptide constructs remains to be examined. Therefore, we investigated the octan‐1‐ol/water partitioning and inclusion in detergent micelles of the oligo‐Oic peptides. The results showed that the hydrophobicity is remarkably enhanced in longer oligomeric sequences, and the oligo‐Oic peptides with 3 to 4 residues and higher are specific towards hydrophobic environments. This contrasts significantly to the parent oligoproline peptides, which were moderately hydrophilic. With these findings, we have demonstrated that the polyproline‐II structure is compatible with nonpolar media, whereas additional manipulations of the terminal functionalities feature solubility in extremely nonpolar solvents such as hexane. 相似文献
11.
Gloria Uccello‐Barretta Volker Schurig Federica Balzano Letizia Vanni Federica Aiello Mattia Mori Francesca Ghirga 《Chirality》2015,27(2):95-103
Nuclear magnetic resonance (NMR) investigations on mixtures containing octakis(3‐O‐butanoyl‐2,6‐di‐O‐pentyl)‐γ‐cyclodextrin (Lipodex E) and each enantiomer of methyl‐2‐chloropropionate (MCP) ascertained the role of trace amounts of water in the enantiodiscrimination processes. Water is deeply included into the cyclodextrin and favors the formation of the inclusion complex with (S)‐MCP, whereas (R)‐MCP is only slightly affected, thus causing a significant increase of NMR differentiation. Molecular dynamics simulations were performed to shed light on the possible behavior of Lipodex E in different conditions (i.e., solvent, inclusion complexes), providing energetic and atomistic details that are in agreement with NMR observations. Chirality 27:95–103, 2014. © 2014 Wiley Periodicals, Inc. 相似文献
12.
Chiral monoaza-15-crown-5 ethers (1, 2) were prepared from (R)-(-)-2-amino-1-butanol in high yield. The chiral monoaza-15-crown-5 ethers were purified directly as NaClO(4) complexes. Molecular recognition by these chiral monoaza-crown ethers of (R)- and (S)-PhEtHClO(4) and (R)- and (S)-NapEtHClO(4) as characterized by UV-vis spectroscopy. The order of enantiomeric selectivity is (R)- > (S)- PhEtHClO(4) and (S)- > (R)-NapEtHClO(4) for 1. In the case of 2 it was (R)- > (S)-PhEtHClO(4) and (R)- > (S)- NapEtHClO(4). The cavity of macrocycle and steric hindrance of the benzene units appears to play an important role in recognition. 相似文献
13.
Despite prolonged scientific efforts to elucidate the intrinsic peptide backbone preferences of amino-acids based on understanding of intermolecular forces, many open questions remain, particularly concerning neighboring peptide interaction effects on the backbone conformational distribution of short peptides and unfolded proteins. Here, we show that spectroscopic studies of a complete library of 400 dipeptides reveal that, irrespective of side-chain properties, the backbone conformation distribution is narrow and they adopt polyproline II and β-strand, indicating the importance of backbone peptide solvation and electronic effects. By directly comparing the dipeptide circular dichroism and NMR results with those of unfolded proteins, the comprehensive dipeptides form a complete set of structural motifs of unfolded proteins. We thus anticipate that the present dipeptide library with spectroscopic data can serve as a useful database for understanding the nature of unfolded protein structures and for further refinements of molecular mechanical parameters. 相似文献
14.
An overview on the use of bile acid‐based compounds able to catalyze transformations, control the stereochemical course of a given reaction, recognize and bind other molecules, is presented. The recent developments in inclusion discrimination of chiral and achiral guests and enantioselective recognition achieved by bile acid are described with suitable examples. Chirality 2010. © 2009 Wiley‐Liss, Inc. 相似文献
15.
Ivana Cacciatore Antonio Di Stefano Grazia Luisi Francesco Pinnen Piera Sozio 《Journal of peptide science》2004,10(2):109-114
The fully deprotected glutathione analogue containing the aminomethylene unit as transition state isostere of the gamma-Glu-Cys peptide bond was synthesized for the first time and characterized in both the reduced and oxidized forms. 相似文献
16.
The application of (S)‐1,1′‐binaphthyl‐2,2′‐diol as NMR chiral solvating agent (CSA) for omeprazole, and three of its analogs (lanso‐, panto‐, and rabe‐prazole) was investigated. The formation of diastereomeric host–guest complexes in solution between the CSA and the racemic substrates produced sufficient NMR signal splitting for the determination of enantiomeric excesses by 1H‐ or 19F‐NMR spectroscopy. Using of hydrophobic deuterated solvents was mandatory for obtaining good enantiodiscrimination, thus suggesting the importance of intermolecular hydrogen bonds in the stabilization of the complexes. The method was applied to the fast quantification of the enantiomeric purity of in‐process samples of S‐omeprazole. Chirality, 2010. © 2009 Wiley‐Liss, Inc. 相似文献
17.
Reinhard Schweitzer‐Stenner Fatma Eker Alejandro Perez Kai Griebenow Xiaolin Cao Laurence A. Nafie 《Peptide Science》2003,71(5):558-568
Tripeptidesserve as model systems for understanding the so‐called random‐coil state of peptides and proteins. While it is well known that polyproline or proline‐rich polypeptides adopt the very regular polyproline‐II (PPII) or left‐handed 31‐helix conformation, it was thus far not clear whether this is also the predominant structure adopted by proline‐containing tripeptides. To clarify this issue, we have investigated the amide I′ band profile in the ir, isotropic, and anisotropic Raman, and vibrational circular dichroism (VCD) spectrum of cationic and zwitterionic tri‐proline in D2O. The data were analyzed by modifying a recently developed algorithm, which allows one to obtain the central dihedral angles of tripeptides from the amide I′ band intensities (R. Schweitzer‐Stenner, Biophysical Journal, 2002, Vol. 83, pp. 523–532). Our analysis revealed that the peptide adopts a nearly canonical PPII structure in water with ψ and ϕ values in the range of 175°–165° and −70°–(−80°), respectively. This is fully confirmed by the respective electronic ultraviolet‐CD spectra. Our result indicates that the strong PPII propensity of trans proline results from local interactions between the pyrrolidine ring and the backbone and is not due to any long‐range interactions. © 2003 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 71: 558–568, 2003 相似文献
18.
19.
Aline Schmitt Bastien Chatelet Solène Collin Jean‐Pierre Dutasta Alexandre Martinez 《Chirality》2013,25(8):475-479
Enantiopure hemicryptophanes efficiently discriminate chiral ammonium neurotransmitters. The ephedrine and norephedrine molecules associate with hemicryptophane hosts to form 1:1 and 1:2 host‐guest complexes. Binding constants are determined by fitting the 1H nuclear magnetic resonance (NMR) titration curves to give β1 and β2 values, which are used to characterize the diastereomeric and enantiomeric discriminating potentials of the hosts. Chirality 25:47–479, 2013. © 2013 Wiley Periodicals, Inc. 相似文献
20.
Artificial proteins potentially barrier-free in the folding kinetics are approached computationally under the guidance of protein-folding theories. The smallest and fastest folding globular protein triple-helix-bundle (THB) is so modified as to minimize or eliminate its presumed barriers in folding speed. As the barriers may reside in the ordering of either secondary or tertiary structure, the elements of both secondary and tertiary structure in the protein are targeted for prenucleation with suitable stereochemically constrained amino acid residues. The required elements of topology and sequence for the THB are optimized independently; first the topology is optimized with simulated annealing in polypeptides of highly simplified alphabet; next, the sequence in side chains is optimized using the standard inverse design methods. The resultant three best-adapted THBs, variable in topology and distinctive in sequences, are assessed by comparing them with a few benchmark proteins. The results of mainly molecular dynamics (MD) comparisons, undertaken in explicit water at different temperatures, show that the designed sequences are favorably placed against the chosen benchmarks as THB proteins potentially thermostable in the native folds. Folding simulation experiments with MD establish that the designed sequences are rapid in the folding of individual helices, but not in the evolution of tertiary structure; energetic cum topological frustrations remain but could be the artifacts of the starting conformations that were chosen in the THBs in the folding simulations. Overall, a practical high-throughput approach for de novo protein design has been developed that may have fruitful application for any type of tertiary structure. 相似文献