High-Resolution Magic Angle Spinning NMR Study of Resin-Bound Polyalanine Peptides

Amyloid fibril formation kinetics of low-pH denatured bovine PI3K-SH3 monitored by three different NMR techniques

Introduction: Misfolding of amyloidogenic proteins is a molecular hallmark of neurodegenerative diseases in humans. A detailed understanding of the underlying molecular mechanisms is mandatory for developing innovative therapeutic approaches. The bovine PI3K-SH3 domain has been a model system for aggregation and fibril formation. Methods: We monitored the fibril formation kinetics of low pH-denatured recombinantly expressed [U-13C, 15N] labeled bovine PI3K-SH3 by a combination of solution NMR, high-resolution magic angle spinning (HR-MAS) NMR and solid-state NMR spectra. Solution NMR offers the highest sensitivity and, therefore, allows for the recording of two-dimensional NMR spectra with residue-specific resolution for individual time points of the time series. However, it can only follow the decay of the aggregating monomeric species. In solution NMR, aggregation occurs under quiescent experimental conditions. Solid-state NMR has lower sensitivity and allows only for the recording of one-dimensional spectra during the time series. Conversely, solid-state NMR is the only technique to detect disappearing monomers and aggregated species in the same sample by alternatingly recoding scalar coupling and dipolar coupling (CP)-based spectra. HR-MAS NMR is used here as a hybrid method bridging solution and solid-state NMR. In solid-state NMR and HR-MAS NMR the sample is agitated due to magic angle spinning. Results: Good agreement of the decay rate constants of monomeric SH3, measured by the three different NMR methods, is observed. Moderate MAS up to 8 kHz seems to influence the aggregation kinetics of seeded fibril formation only slightly. Therefore, under sufficient seeding (1% seeds used here), quiescent conditions (solution NMR), and agitated conditions deliver similar results, arguing against primary nucleation induced by MAS as a major contributor. Using solid-state NMR, we find that the amount of disappeared monomer corresponds approximately to the amount of aggregated species under the applied experimental conditions (250 µM PI3K-SH3, pH 2.5, 298 K, 1% seeds) and within the experimental error range. Data can be fitted by simple mono-exponential conversion kinetics, with lifetimes τ in the 14-38 h range. Atomic force microscopy confirms that fibrils substantially grew in length during the aggregation experiment. This argues for fibril elongation as the dominant growth mechanism in fibril mass (followed by the CP-based solid-state NMR signal). Conclusion: We suggest a combined approach employing both solution NMR and solid-state NMR, back-to-back, on two aliquots of the same sample under seeding conditions as an additional approach to follow monomer depletion and growth of fibril mass simultaneously. Atomic force microscopy images confirm fibril elongation as a major contributor to the increase in fibril mass.

Site-Specific Isotopic Labeling (SSIL): Access to High-Resolution Structural and Dynamic Information in Low-Complexity Proteins

Remarkable technical progress in the area of structural biology has paved the way to study previously inaccessible targets. For example, large protein complexes can now be easily investigated by cryo-electron microscopy, and modern high-field NMR magnets have challenged the limits of high-resolution characterization of proteins in solution. However, the structural and dynamic characteristics of certain proteins with important functions still cannot be probed by conventional methods. These proteins in question contain low-complexity regions (LCRs), compositionally biased sequences where only a limited number of amino acids is repeated multiple times, which hamper their characterization. This Concept article describes a site-specific isotopic labeling (SSIL) strategy, which combines nonsense suppression and cell-free protein synthesis to overcome these limitations. An overview on how poly-glutamine tracts were made amenable to high-resolution structural studies is used to illustrate the usefulness of SSIL. Furthermore, we discuss the potential of this methodology to give further insights into the roles of LCRs in human pathologies and liquid-liquid phase separation, as well as the challenges that must be addressed in the future for the popularization of SSIL.

Real-time monitoring of solid-phase peptide synthesis using a variable bed flow reactor

On-resin aggregation and incomplete amide bond formation are major challenges for solid-phase peptide synthesis that are difficult to be monitored in real-time. Incorporation of a pressure-based variable bed flow reactor into an automated solid-phase peptide synthesizer permitted real-time monitoring of resin swelling to determine amino acid coupling efficiency and on-resin aggregation.

Naphthalene amine support for G-quadruplex isolation

The selective isolation of G-quadruplex (G4) using affinity ligands that bind tightly and selectively is a valuable strategy for discovering new G4 binders for the separation of G4 from duplexes or the discrimination of G4 structures.

Enhanced Solvation of Peptides Attached to "Solid-Phase" Resins: Straightforward Syntheses of the Elastin Sequence Pro-Gly-Val-Gly-Val-Pro-Gly-Val-Gly-Val

The solubility-enhancing power of covalent attachment to solvent-swollen cross-linked resin supports was illustrated by syntheses of the highly aggregating elastin-derived 10-residue peptide sequence Pro-Gly-Val-Gly-Val-Pro-Gly-Val-Gly-Val using standard protocols for both Boc and Fmoc chemistry SPPS.

Automated synthesis of backbone protected peptides

The automated introduction of removable substitution along a peptide backbone prevents chain-association and synthesis failure.

The synthesis of peptides rich in aggregation prone sequences can be improved with backbone protection. We report the automated introduction of backbone protection to a peptide. This new method was applied in a fully-automated synthesis, giving improved handling, quality and yield of several challenging target sequences.

Piperazine and DBU: a safer alternative for rapid and efficient Fmoc deprotection in solid phase peptide synthesis

We demonstrate PolyAla synthesis using 5% piperazine + 2% DBU, which significantly reduces deletion products arising due to incomplete Fmoc-deprotection and can be used for deletion-free assembly of aggregation prone difficult peptides.

Revealing protein structures in solid-phase peptide synthesis by 13C solid-state NMR: evidence of excessive misfolding for Alzheimer's β

Solid-phase peptide synthesis (SPPS) is a widely used technique in biology and chemistry. However, the synthesis yield in SPPS often drops drastically for longer amino acid sequences, presumably because of the occurrence of incomplete coupling reactions. The underlying cause for this problem is hypothesized to be a sequence-dependent propensity to form secondary structures through protein aggregation. However, few methods are available to study the site-specific structure of proteins or long peptides that are anchored to the solid support used in SPPS. This study presents a novel solid-state NMR (SSNMR) approach to examine protein structure in the course of SPPS. As a useful benchmark, we describe the site-specific SSNMR structural characterization of the 40-residue Alzheimer's β-amyloid (Aβ) peptide during SPPS. Our 2D (13)C/(13)C correlation SSNMR data on Aβ(1-40) bound to a resin support demonstrated that Aβ underwent excessive misfolding into a highly ordered β-strand structure across the entire amino acid sequence during SPPS. This approach is likely to be applicable to a wide range of peptides/proteins bound to the solid support that are synthesized through SPPS.

Length-dependent aggregation of uninterrupted polyalanine peptides

Polyalanine (polyA) is the third-most prevalent homopeptide repeat in eukaryotes, behind polyglutamine and polyasparagine. Abnormal expansion of the polyA repeat is linked to at least nine human diseases, and the disease mechanism likely involves enhanced length-dependent aggregation. Because of the simplicity of its side chain, polyA has been a favorite target of computational studies, and because of their tendency to fold into α-helix, peptides containing polyA-rich domains have been a popular experimental subject. However, experimental studies on uninterrupted polyA are very limited. We synthesized polyA peptides containing uninterrupted sequences of 7 to 25 alanines (A7 to A25) and characterized their length-dependent conformation and aggregation properties. The peptides were primarily disordered, with a modest component of α-helix that increased with increasing length. From measurements of mean distance spanned by the polyA segment, we concluded that physiological buffers are neutral solvents for shorter polyA peptides and poor solvents for longer peptides. At moderate concentration and near-physiological temperature, polyA assembled into soluble oligomers, with a sharp transition in oligomer physical properties between A19 and A25. With A19, oligomers were large, contained only a small fraction of the total peptide mass, and slowly grew into loose clusters, while A25 rapidly and completely assembled into small stable oligomers of ~7 nm radius. At high temperatures, A19 assembled into fibrils, but A25 precipitated as dense, micrometer-sized particles. A comparison of these results to those obtained with polyglutamine peptides of similar design sheds light on the role of the side chain in regulating conformation and aggregation.

Monitoring the allyl ester deprotection by HR MAS NMR in BAL-solid phase peptide synthesis

The backbone amide linker strategy, in which the growing peptide chain is anchored to a solid support via a backbone amide nitrogen, has proven to be successful for the synthesis of cyclic peptides. Optimisation of the reaction conditions for the synthesis of c(Gly-Trp-βAla-Phe) could be accomplished by the help of high resolution magic angle spinning (HR MAS) NMR and the results are presented here. Signal vanishing of HR MAS NMR resonances were encountered and proven to be originated from interchain aggregations of peptide chains.

Analytical strategies for characterizing the surface chemistry of nanoparticles

Chemical modifications of nanoparticle (NP) surfaces are likely to regulate their activities, remove their toxic effects, and enable them to perform desired functions. It is urgent to develop analytical strategies for acquiring structural and quantitative information about small molecules linked to the surface of NP. Recent progress in characterizing the surface chemistry of NPs using nuclear magnetic resonance (NMR) spectroscopy, Fourier-transform infrared (FTIR) spectroscopy, liquid chromatography-mass spectroscopy (LC-MS), X-ray photoelectron spectroscopy (XPS), and combustion elemental analysis are reviewed.

Real time HR-MAS NMR: application in reaction optimization, mechanism elucidation and kinetic analysis for heterogeneous reagent catalyzed small molecule chemistry

A novel application of in situ (1)H high-resolution magic angle spinning (HR-MAS) NMR technique for real-time monitoring of H(2)SO(4)-silica promoted formation of 2, 2-disubstituted quinozolin-4(3H)-ones is reported. The detailed NMR spectroscopic data led to elucidation of the mechanism, reaction optimization, kinetics and quantitative analysis of the product accurately and efficiently. The translation of the optimized parameters obtained by (1)H HR-MAS NMR in the wet laboratory provided similar results. It is proposed that (1)H HR-MAS has a potential utility for optimization of various organic transformations in solid supported catalyzed reactions.

Interpretation of the dissolution of insoluble peptide sequences based on the acid-base properties of the solvent

The dissolution process of model insoluble peptide sequences was investigated in view of the electron acceptor (AN) and electron donor (DN) solvent properties. The Alzheimer's disease-inducing (1-42) Abeta-amyloid peptide and its (1-21) fragment, the (66-97) transmembrane bradykinin B2 receptor sequence, and the strongly aggregated VVLGAAIV were selected as models of insoluble peptides. Solvents presenting similar AN and DN values failed, despite their polarities, to dissociate peptide chains (free in solution or bound to a polymer). The maximum solubility of these aggregated sequences was attained in solvents presenting the highest possible (AN-DN) values (in positive or negative mode). The AN-DN values ranged from approximately -20 to +80 and, notably, the lowest dissociation power was ascribed to solvents presenting values of approximately +40. The strong hydrogen bond donor water is located in this region, indicating that, for dissociation of specific insoluble segments, the solvent should appropriately combine its acid/base strength with the potential for van der Waals interactions. We also observed a sequence-dependent pH effect on peptide solubility confirmed through circular dichroism spectroscopy. This approach also revealed a complex but, in many cases, consistent influence of peptide conformation on its solubility degree, even when structure-inducing solvents were added. In conclusion, the random method of selecting solvents to dissolve insoluble and intractable peptide sequences, still in use by some, could be partially supplanted by the strategy described herein, which may be also applicable to other solute dissociation processes.

Spontaneous fibril formation by polyalanines; discontinuous molecular dynamics simulations

Fibrillary protein aggregates rich in beta-sheet structure have been implicated in the pathology of several neurodegenerative diseases. In this work, we investigate the formation of fibrils by performing discontinuous molecular dynamics simulations on systems containing 12 to 96 model Ac-KA(14)K-NH(2) peptides using our newly developed off-lattice, implicit-solvent, intermediate-resolution model, PRIME. We find that, at a low concentration, random-coil peptides assemble into alpha-helices at low temperatures. At intermediate concentrations, random-coil peptides assemble into alpha-helices at low temperatures and large beta-sheet structures at high temperatures. At high concentrations, the system forms beta-sheets over a wide range of temperatures. These assemble into fibrils above a critical temperature which decreases with concentration and exceeds the isolated peptide's folding temperature. At very high temperatures and all concentrations, the system is in a random-coil state. All of these results are in good qualitative agreement with those by Blondelle and co-workers on Ac-KA(14)K-NH(2) peptides. The fibrils observed in our simulations mimic the structural characteristics observed in experiments in terms of the number of sheets formed, the values of the intra- and intersheet separations, and the parallel peptide arrangement within each beta-sheet. Finally, we find that when the strength of the hydrophobic interaction between nonpolar side chains is high compared to the strength of hydrogen bonding, amorphous aggregates, rather than fibrillar aggregates, are formed.

Study of the effect of the peptide loading and solvent system in SPPS by HRMAS-NMR

The SPPS methodology has continuously been investigated as a valuable model to monitor the solvation properties of polymeric materials. In this connection, the present work applied HRMAS-NMR spectroscopy to examine the dynamics of an aggregating peptide sequence attached to a resin core with varying peptide loading (up to 80%) and solvent system. Low and high substituted BHAR were used for assembling the VQAAIDYING sequence and some of its minor fragments. The HRMAS-NMR results were in agreement with the swelling of each resin, i.e. there was an improved resolution of resonance peaks in the better solvated conditions. Moreover, the peptide loading and the attached peptide sequence also affected the spectra. Strong peptide chain aggregation was observed mainly in highly peptide loaded resins when solvated in CDCl3. Conversely, due to the better swelling of these highly loaded resins in DMSO, improved NMR spectra were acquired in this polar aprotic solvent, thus enabling the detection of relevant sequence-dependent conformational alterations. The more prominent aggregation was displayed by the VQAAIDYING segment and not by any of its intermediary fragments and these findings were also corroborated by EPR studies of these peptide-resins labelled properly with an amino acid-type spin probe.

Solvent effects on the conformational transition of a model polyalanine peptide

We have investigated the folding of polyalanine by combining discontinuous molecular dynamics simulation with our newly developed off-lattice intermediate-resolution protein model. The thermodynamics of a system containing a single Ac-KA(14)K-NH(2) molecule has been explored by using the replica exchange simulation method to map out the conformational transitions as a function of temperature. We have also explored the influence of solvent type on the folding process by varying the relative strength of the side-chain's hydrophobic interactions and backbone hydrogen bonding interactions. The peptide in our simulations tends to mimic real polyalanine in that it can exist in three distinct structural states: alpha-helix, beta-structures (including beta-hairpin and beta-sheet-like structures), and random coil, depending upon the solvent conditions. At low values of the hydrophobic interaction strength between nonpolar side-chains, the polyalanine peptide undergoes a relatively sharp transition between an alpha-helical conformation at low temperatures and a random-coil conformation at high temperatures. As the hydrophobic interaction strength increases, this transition shifts to higher temperatures. Increasing the hydrophobic interaction strength even further induces a second transition to a beta-hairpin, resulting in an alpha-helical conformation at low temperatures, a beta-hairpin at intermediate temperatures, and a random coil at high temperatures. At very high values of the hydrophobic interaction strength, polyalanines become beta-hairpins and beta-sheet-like structures at low temperatures and random coils at high temperatures. This study of the folding of a single polyalanine-based peptide sets the stage for a study of polyalanine aggregation in a forthcoming paper.

Determination of Site−Site Distance and Site Concentration within Polymer Beads: A Combined Swelling-Electron Paramagnetic Resonance Study

This work proposes a combined swelling-electron paramagnetic resonance (EPR) approach aiming at determining some unusual polymer solvation parameters relevant for chemical processes occurring inside beads. Batches of benzhydrylamine-resin (BHAR), a copolymer of styrene-1% divinylbenzene containing phenylmethylamine groups were, labeled with the paramagnetic amino acid 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amine-4-carboxylic acid (TOAC), and their swelling properties and EPR spectra were examined in DCM and DMF. By taking into account the BHARs labeling degrees, the corresponding swelling values, and some polymer structural characteristics, it was possible to calculate polymer swelling parameters, among them, the volume and the number of sites per bead, site-site distances and site concentration. The latter values ranged from 17 to 170 A and from 0.4 to 550 mM, respectively. EPR spectroscopy was applied to validate the multistep calculation strategy of these swelling parameters. Spin-spin interaction was detected in the labeled resins at site-site distances less than approximately 60 A or probe concentrations higher than approximately 1 x 10(-2) M, in close agreement with the values obtained for the spin probe free in solution. Complementarily, the yield of coupling reactions in different resins indicated that the greater the inter-site distance or the lower the site concentration, the faster the reaction. The results suggested that the model and the experimental measurements developed for the determination of solvation parameters represent a relevant step forward for the deeper understanding and improvement of polymer-related processes.

Conformational Studies of Resin-Bound Vancomycin and the Complex of Vancomycin and Ac2-l-Lys-d-Ala-d-Ala

The molecular target of vancomycin, a commonly used glycopeptide antibiotic, is the D-Ala-D-Ala dipeptide subunit on the bacterial cell wall. The molecular basis of interaction between vancomycin and D-Ala-D-Ala in solution is well-known. However, there is no structural data on vancomycin, and its interaction with D-Ala-D-Ala when the drug is tethered to a solid support. In this Article, vancomycin was directly coupled onto TentaGel or PEGA resin through its C terminus. High-resolution magic angle spinning NMR studies indicated that conformation of PEGA bead-bound vancomycin is identical to that of the free drug. Broadening and shifts of the same proton resonances were observed in solution-phase vancomycin or PEGA-bound vancomycin when complexed with Ac(2)-L-Lys-D-Ala-D-Ala. This study demonstrates that bead-bound molecules can behave the same as solution-phase molecules in terms of molecular interaction with its target molecule, thus validating the on-bead screening approach of the "one-bead-one-compound" combinatorial library method.

1H high-resolution magic-angle spinning (HR-MAS) NMR analysis of ligand density on resins using a resin internal standard

We recently attempted to generate an affinity chromatography adsorbent to purify cytochrome P450 4A1 by coupling 11-(1'-imidazolyl)-3,6,9-trioxaundecanoic acid to Toyopearl AF-Amino 650 M resin. Variations in ligand density for several resin batches were quantified by high-resolution magic-angle spinning (HR-MAS) NMR spectroscopy using a novel resin internal standard. The uniquely designed ImQ internal resin standard yields its signature resonance in a transparent region of the analyte spectrum making suppression of the polymer background unnecessary. This method enabled us to target a reasonable ligand density for enzyme purification and provides an advantageous alternative to quantitation against soluble standards or protonated solvent.

PFG-assisted selection and suppression of 1H NMR signals in the solid state under fast MAS

Under fast MAS conditions, techniques for 1H signal selection and suppression, which have originally been developed for solution-state NMR, become applicable to solids. In this work, we describe how WATERGATE and DANTE pulse sequences can be used under MAS to selectively excite or suppress peaks in 1H solid-state spectra. As known from the liquid-state analogues, signal selection and/or suppression is supported by pulsed-field gradients which selectively dephase and rephase transverse magnetisation. Under MAS, the required field gradients are provided by a simple pair of coils which have been built into a standard fast-MAS probe. PFG-assisted techniques enable efficient selection or suppression of 1H peaks in a single transient of the pulse sequence without the need for phase cycles. Therefore, these tools can readily be incorporated into solid-state MAS NMR experiments, which is demonstrated here for 1H-1H double-quantum NMR spectra of supramolecular systems. In the examples presented here, the 1H signals of interest are relatively weak and need to be observed despite the presence of the strong 1H signal of long alkyl sidechains. PFG-assisted suppression of this strong perturbing signal is shown to be particularly useful for obtaining unambiguous results.

Determination of long-range distances and dynamic order parameters by dipolar recoupling in high-resolution magic-angle spinning NMR spectroscopy

By introducing dipolar recoupling methods to high-resolution magic-angle spinning (HRMAS) NMR spectroscopy, a class of experiments has been delevoped that allows the measurement of residual dipole-dipole couplings of approximately 1 Hz in weakly immobilized molecules. Using homonuclear 1H-1H recoupling, distances of up to approximately 8 A can be selectively determined, while heteronuclear 1H-13C recoupling provides access to dynamic order parameters of individual molecular segments on the order of approximately 10-3. The experiments are demonstrated on functionalized oligopeptides that are attached to polymer resins.

Physicochemical and chromatographic evaluation of benzhydrylamine-resin as an anion exchanger solid support

Benzhydrylamine-resin (BHAR), a copolymer of styrene-divinylbenzene containing phenylmethylamine groups, used as solid support for peptide synthesis, was examined regarding physicochemical and anion exchanger chromatographic properties. The greater the ionic strength of the medium the poorer the solvation of beads. This effect is less pronounced the higher the amino group content of BHAR. The BHAR chromatographic behavior was compared with commercial cationic resins in columns of constant cation binding capacity. Three negatively charged heparan sulfate disaccharides were successfully purified in a 2.4 mmol/g BHAR that showed as good or better anion exchange performance than classical tertiary or quaternary amino group-containing resins. The BHAR chromatographic resin exclusion limit was estimated to be 30 kDa based on purification experiments of heparins of different molecular weight.

Conformational analysis by HRMAS NMR spectroscopy of resin-bound homo-peptides from C(alpha)-methyl-leucine

A series of [L-(alphaMe)Leu]n (n = 1-5) homo-peptides have been covalently linked to Tentagel and POEPOP resins and submitted to a conformational study using HRMAS NMR spectroscopy. Whereas the mono- and dipeptide are mainly fully-extended, stable 3(10)-helical structures are formed beginning from the trimer.

HRMAS NMR observation of beta-sheet secondary structure on a water swollen solid support

In this paper HRMAS NMR was used to investigate whether peptides on a peptidyl resin swollen in aqueous solution can adopt an intramolecular beta-sheet structure. A model peptide YQNPDGSQA, that was previously shown to adopt such a secondary structure in solution, (Blanco et al, J. Am. Chem. Soc., 1993) was grafted onto three different solid supports that swell in aqueous solution to examine the influence of the resin on the structure. Both parameters of resin loading and pH inside the swollen peptidyl resin proved to be important for the physicochemical behaviour of the peptide on the support.

Dipolar recoupling in NOESY-type 1H-1H NMR experiments under HRMAS conditions

[structure: see text]. The concept of dipolar recoupling is introduced to 1H-1H NOESY experiments performed under HRMAS conditions. Dipole-dipole couplings are selectively recoupled during the mixing period, while MAS ensures high resolution in the spectral dimensions. Incoherent dipolar exchange is replaced by amplified coherent processes, such that time scales for polarization transfer are shortened, and dipolar double-quantum techniques become applicable. In this way, dipole-dipole couplings, as well as J-couplings, can be individually measured.

Solid-phase enolate chemistry investigated using HR-MAS NMR spectroscopy

Supported P4-t-Bu enolate chemistry of phenylacetyloxymethyl polystyrene (PS) resin was investigated using high-resolution magic angle spinning (HR-MAS) NMR spectroscopy. Direct analysis of the crude reaction suspensions through the use of a diffusion filter (DF) allowed a rapid selection of the optimal experimental conditions, but also the characterization of the enolate on the solid phase. Comparison with solution experiments and literature data allowed us to address partially the structure of the enolate. HR-MAS NMR spectra of the enolate revealed also a tight interaction of P4-t-Bu base with the polymer matrix.

Rotor synchronization of radiofrequency and gradient pulses in high-resolution magic angle spinning NMR

We have investigated the extent to which rotor synchronization of radiofrequency pulses leads to spectral improvement in high-resolution magic angle spinning NMR experiments. Several pulse sequences were tested, and the effect was found to be maximal in homonuclear TOCSY spectra. The physicochemical nature of the sample plays a role in the phenomenon, as rotor synchronization allows the refocusing of residual anisotropic interactions. However, even in a liquid sample the effects were visible. Radial inhomogeneities of the radiofrequency field were identified as an important source of the problem.

Evidence of secondary structure by high-resolution magic angle spinning NMR spectroscopy of a bioactive peptide bound to different solid supports

The structure of the 19-amino acid peptide epitope, corresponding to the 141-159 sequence of capsid viral protein VP1 of foot-and-mouth disease virus (FMDV), bound to three different resins, namely, polystyrene-MBHA, PEGA, and POEPOP, has been determined by high-resolution magic angle spinning (HRMAS) NMR spectroscopy. A combination of homonuclear and heteronuclear bidimensional experiments was used for the complete peptide resonance assignment and the qualitative characterization of the peptide folding. The influence of the chemicophysical nature of the different polymers on the secondary structure of the covalently attached FMDV peptide was studied in detail. In the case of polystyrene-MBHA and polyacrylamide-PEGA resins, the analysis of the 2D spectra was hampered by missing signals and extensive overlaps, and only a propensity toward a peptide secondary structure could be derived from the assigned NOE correlations. When the FMDV peptide was linked to the polyoxyethylene-based POEPOP resin, it was found to adopt in dimethylformamide a helical conformation encompassing the C-terminal domain from residues 152 to 159. This conformation is very close to that of the free peptide previously analyzed in 2,2,2-trifluoroethanol. Our study clearly demonstrates that a regular helical structure can be adopted by a resin-bound bioactive peptide. Moreover, a change in the folding was observed when the same peptide-POEPOP conjugate was swollen in aqueous solution, displaying the same conformational features as the free peptide in water. The possibility of studying solid-supported ordered secondary structures by the HRMAS NMR technique in a wide range of solvents can be extended either to other biologically relevant peptides and proteins or to new synthetic oligomers.

Structure and conformational behavior of biopolymers by density functional calculations employing periodic boundary conditions. I. The case of polyglycine, polyalanine, and poly-alpha-aminoisobutyric acid in vacuo

Fully quantum mechanical calculations exploiting periodic boundary conditions (PBC) have been applied to the study of four different regular structures (alpha- and 3(10)-helix, fully extended and repeated gamma-turns) of the infinite polypeptides of glycine, alanine, and alpha-aminoisobutyric acid (Aib) in vacuo. alpha-Helix is predicted to be the most stable conformer for polyalanine and polyglycine, being stabilized over the 3(10)-helix mainly by more favorable dipole-dipole interactions. Contrary to previous suggestions, steric effects and hydrogen-bond strengths are comparable for both helix structures. 3(10)-Helix is preferred for poly-Aib, since in this case alpha-helix is strongly distorted due to unfavorable intrachain repulsions. Extended structures and repeated gamma-turns are much less stable than helix structures for all of the polypeptides examined, mainly due to the absence of favorable long-range interactions. The optimized geometries are in good agreement with the available experimental data and reveal a remarkable dependence on the nature of the residue forming the polypeptides; at the same time the electronic and structural parameters of each residue strongly depend on the secondary structure of the polypeptides.

Solvent effects on the energy landscapes and folding kinetics of polyalanine

The effect of a solvation on the thermodynamics and kinetics of polyalanine (Ala(12)) is explored on the basis of its energy landscapes in vacuum and in an aqueous solution. Both energy landscapes are characterized by two basins, one associated with alpha-helical structures and the other with coil and beta-structures of the peptide. In both environments, the basin that corresponds to the alpha-helical structure is considerably narrower than the basin corresponding to the beta-state, reflecting their different contributions to the entropy of the peptide. In vacuum, the alpha-helical state of Ala(12) constitutes the native state, in agreement with common helical propensity scales, whereas in the aqueous medium, the alpha-helical state is destabilized, and the beta-state becomes the native state. Thus solvation has a dramatic effect on the energy landscape of this peptide, resulting in an inverted stability of the two states. Different folding and unfolding time scales for Ala(12) in hydrophilic and hydrophobic chemical environments are caused by the higher entropy of the native state in water relative to vacuum. The concept of a helical propensity has to be extended to incorporate environmental solvent effects.

The Chemical Shift Index method applied to resin-bound peptides

The Chemical Shift Index (CSI) method proposed by Wishart et al. [Biochemistry (1992) 31, 1647-1651] to evaluate the secondary structure of peptides in aqueous solution uses as its reference the chemical shift values of each of the 20 natural amino acids (X) in a typical nonstructured sequence GGXAGG (17-20). In order to apply the CSI method to protected resin-bound peptides, we established a new database of chemical shift values for the same GGXAGG sequences in their protected form and anchored to a polystyrene resin swollen in DMF-d7. The predictive value of this new reference set in the CSI protocol was tested on different resin-bound peptides that were previously characterized by a full NOE analysis.

Multistep synthesis of 2,5-diketopiperazines on different solid supports monitored by high resolution magic angle spinning NMR spectroscopy

The solid-phase synthesis of 2,5-diketopiperazines containing the trans-4-hydroxy-L-proline amino acid residue (Hyp) was performed on Ellman polystyrene, polyoxyethylene-polyoxypropylene (POEPOP), polystyrene-polyoxyethylene NovaSyn, and Wang resins, respectively. The reaction pathway allowed the introduction of different functional groups around the bicyclic scaffold in a combinatorial approach, and it generated mixtures of isomers. A detailed characterization of the single reaction steps by high resolution magic angle spinning (HRMAS) NMR spectroscopy was performed. The NMR spectral resolution of the resin-bound intermediates and final products was greatly influenced by the polymer matrix. The POEPOP resin permitted to obtain HRMAS NMR spectra with a resolution comparable with that of the spectra of the molecules in solution. Moreover, configurational and conformational isomers formed during the solid-phase reaction steps could be detected and easily assigned. Therefore, the combination of the HRMAS NMR technique with the use of nonaromatic resins may become an extremely powerful tool in solid-phase organic synthesis. This approach will allow the monitoring of multistep reactions and the conception of on-bead structural studies either on small molecules or on natural and/or synthetic oligomers.