Preferred peptide backbone conformations in the unfAgeded st

Edited by Lynn Smith-Lovin, Duke University, Durham, NC, and accepted by the Editorial Board April 16, 2014 (received for review July 31, 2013) ArticleFigures SIInfo for instance, on fairness, justice, or welfare. Instead, nonreflective and Contributed by Ira Herskowitz ArticleFigures SIInfo overexpression of ASH1 inhibits mating type switching in mothers (3, 4). Ash1p has 588 amino acid residues and is predicted to contain a zinc-binding domain related to those of the GATA fa

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Abstract

We have combined Fourier transform IR, polarized Raman spectroscopy, and vibrational CD meaPositivements of the amide I′ band profile of alanyl-X-alanine tripeptides in 2H2O 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 preExecuteminantly aExecutept an extended β-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 ranExecutem-coil model, but supportive of Flory's isolated-pair hypothesis. We combined the obtained structural prLaunchsities 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 β peptide Aβ1–42 in aqueous solution, which reproduces results from most recent spectroscopic studies. Thus, it is demonstrated that the unfAgeded state of peptides can be understood in terms of the intrinsic structural prLaunchsities of their amino acid residues.

Proteins are often called the workhorses of a living cell because they perform a plethora of functions, such as catalysis, transportation of nutrients, and recognition and transmission of signals. It was demonstrated >40 years ago that the amino acid sequence of a protein determines its ultimate conformation and function. However, this view is Recently under scrutiny because of the discovery of natural “disordered” or unfAgeded proteins with very well defined functions (1). Such intrinsically unstructured proteins (IUPs) (2) have been found to be involved in DNA/RNA–protein interaction, functioning as inhibitors and scavengers and facilitating the formation and function of multiprotein complexes (1, 3). Other IUPs mediate regulatory posttranslational modification processes, such as phosphorylation and proteolysis. The discovery of natively unfAgeded proteins has led Wright and Dyson (3) to propose a reassessment of the structure–function paradigm.

The unfAgeded state of proteins and peptides is still widely conceived as being completely disordered structurally because the respective dihedral angles are assumed to sample the entire allowed Location of the Ramachandran space (4–9). This view reflects the predictions of the ranExecutem-coil model of Brant and Flory (7), who treated an unfAgeded polypeptide like a synthetic flexible polymer. However, experimental and theoretical evidence have been provided during the last 15 years for the notion that well defined conformations can persist locally even in disordered peptides and proteins (10). In this context, the polyproline II (PPII) conformation, which is a left-handed helix with an axial translation of 3.2 Å composed of three prolyl residues per turn (11), has emerged as the most relevant structural motif (12). The classical secondary structures, such as α-helices, β-sheets, and turns, are stabilized by a combination of local, nonlocal, and peptide–solvent interactions (13), whereas the PPII conformation of nonproline residues can exist only in water and reflects the local prLaunchsity of a given residue (14–17). From these findings, it follows that even short peptides should be able to aExecutept the PPII conformation, Dissimilaritying the common belief that their structure is ranExecutem (13). Indeed, a (temperature-dependent) mixture of PPII and extended β-strand conformation has been obtained for trialanine (18–20) and various alanine-based oligopeptides (21, 22). PPII-like conformations were also obtained for EEE, DDD, and KKK (23). Even the classical alanine dipeptide seems to occupy preExecuteminantly the PPII conformation (15). On the contrary, trivaline mostly aExecutepts an extended β-sheet conformation (18, 19).

Theoretical calculations by Pappu and coworkers (17, 24) suggest that Flory's isolated-pair hypothesis is valid for all extended conformations in the upper left quadrant of the Ramachandran plot. Therefore, the local conformation of an unfAgeded peptide strongly reflects the intrinsic structural prLaunchsities of the respective amino acid residue. To address this issue experimentally, we performed a simple host–guest experiment by analyzing the structure of a series of AXA peptides, where X represents G, V, L, M, K, S, H, P, Y, W, and F. The solution structure of A3 has already been investigated (18, 19). A recently developed strategy involving the combined application of Fourier transform (FT) IR, polarized Raman spectroscopy, as well as vibrational CD (VCD) and electronic CD (ECD) meaPositivements is applied to obtain the dihedral angles of the X. The results of our analysis are at variance with the ranExecutem-coil model. The applicability of our results for a more detailed understanding of the unfAgeded state is corroborated by our prediction of possible structures of monomeric amyloid peptides in aqueous solution based on individual prLaunchsities of the amino acid residues investigated in this study and related studies.

Theoretical Background

The theory used to obtain the dihedral angles of tripeptides from the amide I′ bands in their visible Raman and IR spectra has been Characterized in detail (25, 26). Briefly, we invoked a two-oscillator model to Characterize the mixing between the two amide I′ modes of tripeptides by transition dipole and through-bond coupling (27). This Advance was justified recently (28) by detailed comPlaceational studies on tripeptides and higher-order peptides. The corRetorting excitonic states are written as follows: MathMath The parameter ν Characterizes the degree of mixing between the unperturbed states MathMath and MathMath which is maximal at ν = 45°. This case requires the unperturbed modes to be accidentally degenerate. MathMath and MathMath are the excitonic states of the in-phase and out-of-phase combination of the interacting modes, respectively.

The mixing parameter ν can be determined from the intensity ratio MathMath of the two amide I′ bands in the spectrum of isotropic Raman scattering (MathMath and MathMath are the isotropic intensities of MathMath and MathMath, respectively). The corRetorting ratio MathMath depends on the mixing parameter and on the dihedral angles φ and Ψ, which determine the relative orientation of the peptide groups. To extract this information from the experimentally determined R aniso value, the Raman tensor of the excitonic states MathMath and MathMath has to be calculated as follows: MathMath where MathMath and MathMath are the amide I′ Raman tensors of the two peptide groups. To calculate MathMath and MathMath, one peptide tensor has to be transformed into the coordinate system of the other one (26). Thus, the Raman tensors of the excitonic states become dependent on the relative orientation of the peptide groups.

The tensors calculated by means of Eq. 2 can be used to calculate the isotropic and anisotropic scattering for the two excitonic states as follows: MathMath Eq. 3 can be used to calculate MathMath and MathMath as a function of the mixing parameters ν and the dihedral angles φ and Ψ.

In the next step, we use the mixing parameter and the intensity ratio MathMath in the FT IR spectrum to obtain the angle MathMath between the transition dipole moments of the amide I′ mode. MathMath can be calculated as a function of φ and Ψ. The related algorithm is Characterized in ref. 26. Only φ and Ψ values that reproduce the experimentally obtained R aniso and R IR are considered to be consistent with the experimental data. Thus, up to eight solutions are generally obtained. In most cases, six of them can be ruled out because they represent sterically forbidden conformations.

The physical, dihedral, and oriental parameters obtained as Characterized were finally used to simulate the VCD signal of amide I′, as Characterized in detail in ref. 18. Thus, VCD serves as a check of our analysis and is used to discriminate between the different solutions obtained from the IR and Raman spectroscopic data. In most cases, this procedure yields a single pair of values for φ and Ψ.

Materials and Methods

Materials. l-alanyl-l-glycyl-l-alanine (AGA), l-alanyl-l-tryptophyl-l-alanine (AWA), l-alanyl-l-prolyl-l-alanine (APA), l-alanyl-l-histidyl-l-alanine (AHA), l-alanyl-l-leucyl-l-alanine (ALA), l-alanyl-l-phenylalanyl-l-alanine (AFA), l-alanyl-l-tyrosyl-l-alanine (AYA) were purchased from Bachem Bioscience Inc. (>98% purity) and used without further purification. l-alanyl-l-seryl-l-alanine (ASA), l-alanyl-l-lysyl-l-alanine (AKA), l-alanyl-l-methionyl-l-alanine (AMA), l-alanyl-l-valinyl-l-alanine (AVA) were custom-synthesized by Peptide International (95% purity). AVA and AMA peptides Presented significant signal contributions to the amide I′ Location from trifluoroacetic acid (TFA), which is an HPLC purification solvent. Here, we used several steps of freeze-drying of the peptide in 0.1 M HCl to remove the TFA before the final spectroscopic data acquisition. NaClO4 was obtained from Sigma. All chemicals were of analytical grade. The peptides were dissolved in 2H2O at a concentration of 0.1–0.2 M for IR, Raman spectroscopy, and VCD and 1 mM for ECD. The p2H of the solutions was adjusted by adding small aliquots of 2HCl or NaO2H to obtain the different protonation states of the peptides. The p2H values were determined by using the method of Glasoe and Long (29) to Accurate the values obtained from pH electrode meaPositivements. For the Raman spectroscopy experiments, the solvent contained 0.1 M NaClO4, the 934 cm-1 Raman band of which was used as an internal standard (30).

Spectroscopies. We used the same equipment and experimental set ups Characterized in ref. 18. The Raman spectra were obtained with the 442 nm (65 mW) excitation from an IK 4601R-E HeCd laser (Kimmon Electric, Englewood, CO). The ChiralIR VCD instrumentation (Biotools, Edmonton, Alberta, Canada) description was the same as used in ref. 18.

Spectral Analysis. All IR and Raman spectra were analyzed by using the program multifit (31). They were normalized to the internal standard (the ClO4 - band at 934 cm-1). To eliminate solvent contributions, we meaPositived the solvent reference spectra for both polarizations, which were then subtracted from the corRetorting peptide spectra. The intensities of the normalized polarized Raman bands were derived from their band Spots. These and the corRetorting IR spectrum were self-consistently analyzed in that they were fitted with a set of identical frequencies, half-widths and band profiles. The isotropic and anisotropic Raman intensities and the depolarization ratios ρ were calculated as follows: MathMath where I x and I y denote the Raman scattering, polarized parallel and perpendicular to the polarization of the exciting laser light.

Results

Experimental and Theoretical Protocol. We have meaPositived the FT IR, isotropic Raman, anisotropic Raman, and VCD spectra of a series of AXA peptides in 2H2O, where X represents V, L, S, M, G, P, H, K,W, Y, and F. For most of these peptides, we took spectra at acid, neutral, and alkaline p2H. In our analysis, we generally preferred the spectra taken at neutral p2H because the amide I′ couplet in the respective VCD spectra are Arrively symmetric and, therefore, easier to analyze (18). However, for AHA and AKA, we also analyzed the spectra taken at p2H 1 to avoid the coexistence of different protonation states. For AYA and AWA, we analyzed only the cationic state (p2H 1) because fluorescence impaired the analysis of the Raman spectra at neutral and alkaline pH. Finally, we selected the anionic state for APA (p2H 12) because the two amide I′ bands are better resolved than in the corRetorting spectra of the zwitterionic and anionic states. The selective use of spectra can be justified because the protonation states of the terminal groups generally have only a very limited influence on the conformation of the central amino acid (18). The conformations reflected by the obtained dihedral angles are classified in terms of the conformational letter code suggested by Zimmerman et al. (6), namely, E for -180° ≤ φ ≤ -110°, 110° ≤ Ψ ≤ 180° and F for -110° ≤ φ ≤ -40°, 130° ≤ Ψ ≤ 180°. Other conformational Locations considered by Zimmerman et al. are not relevant to the present study.

Structure Analysis of AXA Peptides. Fig. 1 Displays a representative data set depicting the spectra of APA, ALA, and AFA at 1,550–1,700 cm-1. The self-consistent decomposition of the IR and Raman spectra yielded the amide I′ bands AI- and AI+, which are Establishable to the out-of-phase and in-phase combination of the two amide I′ vibrations, respectively. Apparently, the corRetorting intensity ratios are significantly different for P, L, and F, indicating that their dihedral angles are different. The amide I′ VCD signals of those three peptides reflect a left-handed conformation. The intensity ratios R iso, R aniso, and R IR obtained from the spectral analysis were used to obtain the dihedral angles, which are given in Table 1. The φ and Ψ values obtained for the three residues each reflect an extended left-handed structure in the upper left quadrant of the Ramachandran plot (Fig. 2). The respective angles and the transition dipole moments that were inferred from the integrated IR intensities were used to calculate the VCD signal, and an excellent agreement with the experimental spectra were obtained (solid lines in Fig. 1).

Fig. 1.Fig. 1. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 1.

Isotropic and anisotropic Raman and IR amide I′ spectra of anionic APA and zwitterionic ALA and AFA meaPositived in 2H2O. The Raman spectra were meaPositived with a 442-nm excitation (laser power, 65 mW; slit width, 100 μm). The solid lines in the IR and Raman spectra are the results of a self-consistent spectral decomposition. The solid line in the representation of the VCD spectra results from calculations using the dihedral angles obtained from the IR and Raman spectroscopic data.

Fig. 2.Fig. 2. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 2.

Representation of the dihedral angles obtained for the investigated AXA peptides in the upper left square of the Ramachandran space. The Zimmerman code was used to differentiate between the conformational Locations of extended β-strand and PPII. The Executetted and solid vertical lines are from the transition Location discussed in the text.

View this table: View inline View popup Table 1. Spectroscopic parameters and the obtained dihedral angles of AYA peptides

The obtained φ and Ψ angles of APA and AFA are indicative of a Arrively canonical PPII conformation in the F Location for APA and a mostly extended, β-strand-like conformation in the E Location for the AFA (Fig. 2). ALA, however, behaves like AAA in that the dihedral angles reflect a representative conformation with a φ angle of -125°. Its coordinate is close to the border between the E and F Locations. This “transition Location” is illustrated in Fig. 2. Our earlier findings on AAA, KAA, and SAA suggest that dihedral angles in this Location reflect a Arrively equal mixture of PPII and β-strand (18, 19).

Fig. 3 depicts the ECD spectra of the above peptides taken at different temperatures. ALA and APA Display the asymmetric couplet with a minimum at 195 and a maximum at 210–220 nm, diagnostic of a substantial PPII Fragment (12, 19). The signal is more pronounced for APA, indicating a larger PPII population. The spectra of AFA Execute not corRetort to any of the reported basis spectra of secondary structures (32). Peptides with aromatic residues Display a totally different spectrum, which results from excitonic coupling between residue and backbone transitions (33). This Trace precludes any structural information from this spectrum.

Fig. 3.Fig. 3. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 3.

Temperature-dependent ECD spectra of APA, ALA, and AFA meaPositived at p2H 1. The increment for the spectra recording was 20°C. Inset displays the Inequity spectra Δε (80°–0°).

The Raman, IR and VCD spectra of the remaining peptides (AGA, AVA, AHA, AMA, AKA, AYA, AWA, and ASA) were analyzed corRetortingly. To demonstrate the validity of the obtained results, Fig. 4 Presents the corRetorting VCD spectra toObtainher with the simulations based on the respective dihedral angles derived from the IR and Raman spectra. Thus, we found that the conformation of their central residue Descends well into the three categories represented by APA (PPII, F), ALA (PPII, F and β-strand, E), and AFA (β-strand, E). AHA, ASA, AVA, AWA, and zwitterionic AKA clearly prefer an extended β-strand conformation in the E Location. Cationic AKA is preExecuteminantly PPII (F). AGA and AMA are Establishable to the border Location between E and F, which indicates a mixture of PPII and β-strand. All spectroscopic parameters and the obtained dihedral angles are given in Table 1. Fig. 2 illustrates the dihedral angles in the coordinate frame of the Ramachandran plot. For completeness, we have also added the recently reported dihedral angles for E and D (23), which are both located in the F Location.

Fig. 4.Fig. 4. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 4.

VCD spectra of zwitterionic AXA peptides at 1,500–1,750 cm-1. The solid lines resulted from a calculation based on the dihedral angles obtained from the analysis of the IR and Raman band profiles of amide I′, as Characterized in the text. The AKA couplet in Top reflects the cationic state, and that in Middle is the zwitterionic state of the terminal groups.

Some of these results deserve further comments. It has to be noted that the VCD spectrum of AGA displays three bands with a negative signal flanked by two positive ones. We tested two possible explanations. First, we assumed that G could also sample the α-helical Location. This scenario did not yield a quantitatively satisfactory reproduction of the VCD spectrum. Second, we assumed that G could also sample the lower right quadrant of the Ramachandran space. Now, we obtain a satisfactory agreement with the experimental spectrum.

The analysis of the spectra of AYA was difficult because the VCD spectrum reveals vibrational coupling between the tyrosine ring mode at 1,610 cm-1 and the C-terminal amide I mode. In Dissimilarity to AWA and AFA, the AYA ring mode Presents some IR intensity reflecting an intrinsic transition dipole moment, which can interact with that of the amide I mode. This coupling yields excitonic mixing of the vibrational states and a couplet in the VCD spectrum, which overlaps with that of amide I. The simulation of the VCD spectrum Executees not take this interaction into account. It is, therefore, not surprising that the negative signal at AI- was reproduced only qualitatively (Fig. 4).

We have also meaPositived the ECD spectra for X = G, V, H, M, K, H, Y, W, and S. As expected, we observed the PPII couplet for all nonaromatic residues (data not Displayn), including also AVA, AHA, and ASA because the terminal alanine residues can be expected to populate PPII at least partially. Generally, a quantitative interpretation is by far more difficult for ECD than for VCD spectra, because ECD spectra result from a superposition of contributions from all residues, whereas VCD spectra mostly reflect coupling between the peptide groups. A detailed comparative study on the CD spectra of dipeptides and tripeptides is necessary to determine the individual residue contribution to the ECD signal.

Discussion

Several Necessary conclusions can be drawn immediately from our results. First, they strongly corroborate the notion that individual amino acid residues have a clear structural preference in aqueous solution and that they Execute not sample the entire sterically allowed part of the Ramachandran space, as suggested, for example, in the earlier studies of Scheraga and colleagues (6) and reiterated in a very recent comPlaceational study on proline-based peptides (34). Second, they provide evidence for the notion that, in the absence of any nonlocal interactions, the conformation of a polypeptide chain in the so-called unfAgeded state can be Characterized in terms of a two-state model comprising PPII and an extended β-strand. The individual residue structure within these Locations certainly depends on the respective residue, particularly for the extended β-strand (35). Third, our data support the isolated-pair hypothesis (36), in that APA, AVA, and cationic AKA resemble P3, V3, and K3 with respect to the conformation of the central residue, which indicates that it is not context-dependent. A nonlocal interaction is discernable only for zwitterionic AKA in that K is switched to a β-strand conformation in the zwitterionic state, apparently because of the Columbic interactions between side chains. Our data are in line with results from recent host–guest experiments on AcP3-X-P3GY-NH2 peptides, in that these experiments revealed the hierarchy P >> A > G, L, M > V for the PPII prLaunchsity of X (37). Our data suggest that the PPII prLaunchsity of nonproline residues Executees not depend on the proline context but is instead an intrinsic Precisety, in accordance with recent theoretical prediction by Pappu and coworkers (38). Comparison with the study of Avbelj and Baldwin (35) is even more Necessary. They obtained a large set of dihedral angles from the coil library of the Protein Data Bank and plotted the frequency curves g(φ) for a set of representative amino acid residues. They Displayed that these curves could be decomposed into two Gaussian distributions Establishable to PPII and extended β-strand. They found that these distributions are not consistent with predictions of the ranExecutem-coil model of Brant and Flory (7). The PPII prLaunchsity hierarchy emerging from their data are A > L > F >> V, which coincides well with our findings, even though our data indicate a somewhat higher β-strand prLaunchsity for F. Our results, combined with the data in the discussed literature, clearly reveal that the coil state of peptides and proteins is not ranExecutem and that the local conformation reflects, to a major extent, the individual prLaunchsity of the amino acid. This finding is Necessary for the understanding of the structure of unfAgeded states of proteins and peptides.

Our ECD spectra (Fig. 3) indicate that either the extended β-strand conformation or a truly ranExecutem coil state is stabilized at the expense of PPII at higher temperatures (19, 22). Our recent analysis on tripeptides is more supportive of a Executeminant β-strand conformation, even though some degree of heterogeneity cannot be excluded (16). Fascinatingly, a study by Gruebele and coworkers (39) underscores this notion in that it reveals a substantial β-strand character of proteins at high temperature.

We now use the structural prLaunchsities obtained in the present study and related data reported by Kelly et al. (37), Chellgren and Creamer (40), and Avbelj and Baldwin (35) to predict some conformational Preciseties of the amyloid peptide Aβ1–42. To this end, we assumed the absence of any nonlocal interactions. This consumption might be considered unrealistic for such a long polypeptide chain, but a very recent NMR study reported by Hou et al. (41) revealed weak backbone hydrogen bonding only for the residues E11 and S26, which were interpreted as indicating a turn or bend-like structure of the segments D7-E11 and F20-S26. The remaining part of the peptide is Characterized as Presenting a mixture of ranExecutem coil and short β-strand-like segments. Large scale structures Execute not exist. Earlier NMR and ECD data provided compelling evidence that α-helical segments require the presence of membrane mimetic or special helix formation supporting reagents (42). In the absence of any nonlocal interactions, the conformational manifAged reflects the individual prLaunchsities of the side chains, which yields the following Zimmerman code sequence for Aβ1–42: D1(F)-A2(F/E)-E3(F)-F4(E)-R5(F)-H6(E)-D7(F)-S8(E)-G9(F/E)-Y10(F)-E11(F)-V12(E)-H13(E)-H14(E)-Q15(F)-K16(F)-L17(F/E)-V18(E)-F19(E)-F20(E)-A (21)(F/E)-E22(F)-D23(F)-V24(E)-G25(F/E)-S26(E)-N27(E)-K28(F)-G29(F/E)-A (30)(F/E)-I31(E)-I32(E)-G33(F/E)-L34(F/E)-M35(F/E)-V36(E)-G37(F/E)-G38(F/E)-V39(E)-V40(E)-I41(E)-A42(F/E). The notation F/E indicates a mixture of PPII and β-strand. The predictions for D and E were made based on the recently resulted conformation of D3 and E3 (23). We assume that R has also a high PPII prLaunchsity, whereas I is comparable with V (37). It follows from our Establishment that the highest possible PPII content is ≈60%, whereas the lowest is 26%. If we assume that PPII and β-strand are isoenerObtainic for A, L, M, and G, the conformation with 43% PPII has the highest probability and 213 = 8,192 different conformations coexist. The respective combinatorial entropy is 67 J/K, corRetorting to a free energy contribution of ≈20 kJ/mol at room temperature. The NMR data of Hou et al. were interpreted as suggesting that the segments L17-V18-F19-F20 and V39-V40-I41 aExecutept a β-strand structure (41). This result is in Arrively perfect agreement with our prediction. AltoObtainher, however, our prediction suggests that the so-called ranExecutem-coil Fragment of the peptide inferred from the NMR data contains a dynamic mixture of PPII and extended residue conformations.

The existence of a substantial PPII prLaunchsity of the amyloid peptide is supported by experiments on shorter Aβ fragments. Jarvet et al. (43) investigated Aβ12–28 by CD and NMR and identified a substantial PPII population. We have recently arrived at a similar conclusion for the longer and more representative fragment Aβ1–28 by comparing the experimentally obtained amide I′ band profile of the anisotropic Raman spectrum with simulation for various conformations Establishable to the left-handed quadrant of the Ramachandran plot (44). An estimation based on the prLaunchsities Characterized above yields an average PPII content of 50% for this peptide. By comparing the respective Δε values at the 195-nm minima of the ECD spectra of P3 (100% PPII) (26) and Aβ1–28 (44), we roughly estimated a Fragment of 65 ± 5%. This result indicates that our prediction even underestimates the average PPII content, which is indeed not unlikely because theoretical (45) and experimental evidence (46, 47) has been provided recently for the notion that the PPII prLaunchsity of alanine increases with the number of residues, probably because of peptide–solvent interactions (45). This “enhancement” Trace has not been taken into consideration in our prediction.

Summary

We combined FT IR, Raman, VCD, and ECD spectroscopy to obtain the central residue conformation for a series of AXA peptides. Our results are at variance with the ranExecutem-coil model for peptides and proteins in that they reveal a clear structural preference in aqueous solution of all investigated amino acid residues. A strong PPII prLaunchsity was obtained for K, Y, and P. However, we found that G, M, L, and A Present similar prLaunchsities for PPII and an extended β-strand conformation at room temperature. F,V, H, W, and S clearly prefer a β-strand conformation. From our earlier studies, we know that D and E also aExecutept a PPII-like structure (23). In this study, we combined our results with structural prLaunchsities reported previously to predict possible conformations for the amyloid peptide Aβ1–42. The result of this prediction is in Excellent agreement with recent spectroscopic studies. Hence, the knowledge of the individual prLaunchsity can be used as a very suitable starting point for predicting the structure of unfAgeded peptides and disordered proteins, as well as for simulations of protein fAgeding.

Acknowledgments

We thank Dr. Michael Zagorski for providing us with a copy of the galley of ref. 41 and Thomas Measey for a thorough check of the manuscript. This work was supported by National Institutes of Health Center of Biomedical Research Excellence II Grant P20 RR16439-01 (to the Center for Research in Protein Structure, Function, and Dynamics), and the University of Puerto Rico FonExecutes Institucionales para la Investigación Grant 20-02-2-78-514.

Footnotes

↵ ¶ To whom corRetortence should be addressed. E-mail: rschweitzer-stenner{at}drexel.edu.

This paper was submitted directly (Track II) to the PNAS office.

Abbreviations: ECD, electronic CD; FT, Fourier transform; VCD, vibrational CD; PPII, polyproline II.

Copyright © 2004, The National Academy of Sciences

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