Handedness preference and switching of peptide helices. Part I: Helices based on protein amino acids

Screw sense and screw sensibility: communicating information by conformational switching in helical oligomers

Biological systems have evolved a number of different strategies to communicate information on the molecular scale. Among these, the propagation of conformational change is among the most important, being the means by which G-protein coupled receptors (GPCRs) use extracellular signals to modulate intracellular processes, and the way that opsin proteins translate light signals into nerve impulses. The developing field of foldamer chemistry has allowed chemists to employ conformationally well-defined synthetic structures likewise to mediate information transfer, making use of mechanisms that are not found in biological contexts. In this review, we discuss the use of switchable screw-sense preference as a communication mechanism. We discuss the requirements for functional communication devices, and show how dynamic helical foldamers derived from the achiral monomers such as α-aminoisobutyric acid (Aib) and meso-cyclohexane-1,2-diamine fulfil them by communicating information in the form of switchable screw-sense preference. We describe the various stimuli that can be used to switch screw sense, and explore the way that propagation of the resulting conformational preference in a well-defined helical molecule allows screw sense to control chemical events remote from a source of information. We describe the operation of these conformational switches in the membrane phase, and outline the progress that has been made towards using conformational switching to communicate between the exterior and interior of a phospholipid vesicle.

Direct determination of the π-helix structure and helix transition behavior of poly(β-phenethyl l-aspartate) via synchrotron X-ray diffraction

The helix-sense inversions of poly(β-phenethyl l-aspartate) (2P) and diblock copolymers (2P-3P), with 2P and poly(β-phenylpropyl l-aspartate) (3P) blocks, were studied in their solid states using synchrotron wide-angle X-ray diffraction and small-angle X-ray scattering. The characteristic parameters of the π-helix structure of 2P were directly determined in situ after the helix transition at a high temperature. In the 2P-3P block copolymers, the main chains of the 3P blocks initially convert from right- to left-handed α-helices, and then the 2P blocks convert irreversibly from right-handed α-helices to left-handed π-helices. The chemical structures of the side chains of poly(l-aspartic acid ester)s significantly affect their helix transition behaviors.

Light-Controlled Lyotropic Liquid Crystallinity of Polyaspartates Exploited as Photo-Switchable Alignment Medium

Two polyaspartates bearing ortho-fluorinated azobenzenes (pFAB) as photo-responsive groups in the side chain were synthesized: PpFABLA (1) and co-polyaspartate PpFABLA-co-PBLA [11, 75%(n/n) PpFABLA content]. As a consequence of the E/Z-isomerization of the side chain, PpFABLA (1) undergoes a visible-light-induced reversible coil-helix transition in solution: Green light (525 nm) affords the coil, and violet light (400 nm) affords the helix. pFAB significantly increases the thermal stability of the Z-isomer at 20 °C (t_1/2 = 66 d for the Z-isomer) and effectively counters the favored back formation of the helix. At 20%(w/w) polymer concentration, the helical polymer forms a lyotropic liquid crystal (LLC) that further orients unidirectionally inside a magnetic field, while the coil polymer results in an isotropic solution. The high viscosity of the polymer solution stabilizes the coexistence of liquid crystalline and isotropic domains, which were obtained with spatial control by partial light irradiation. When used as an alignment medium, PpFABLA (1) enables (i) the measurement of dipolar couplings without the need for a separate isotropic reference and (ii) the differentiation of enantiomers. PpFABLA-co-PBLA (11) preserves the helical structure, by intention, independently of the E/Z-isomerization of the side chain: Both photo-isomers of PpFABLA-co-PBLA (11) form a helix that─at a concentration of 16%(w/w)─form an LLC. Despite the absence of a change in the secondary structure, the E/Z-isomerization of the side chain changes the morphology of the liquid crystal and leads to different sets of dipolar coupling for the same probe molecule.

Secondary Structures in Synthetic Poly(Amino Acids): Homo- and Copolymers of Poly(Aib), Poly(Glu), and Poly(Asp)

The secondary structure of poly(amino acids) is an excellent tool for controlling and understanding the functionality and properties of proteins. In this perspective article the secondary structures of the homopolymers of oligo- and poly-glutamic acid (Glu), aspartic acid (Asp), and α-aminoisobutyric acid (Aib) are discussed. Information on external and internal factors, such as the nature of side groups, interactions with solvents and interactions between chains is reviewed. A special focus is directed on the folding in hybrid-polymers consisting of oligo(amino acids) and synthetic polymers. Being part of the SFB TRR 102 "Polymers under multiple constraints: restricted and controlled molecular order and mobility" this overview is embedded into the cross section of protein fibrillation and supramolecular polymers. As polymer- and amino acid folding is an important step for the utilization and design of future biomolecules these principles guide to a deeper understanding of amyloid fibrillation.

A Unique and Stable Polyproline I Helix Sorted out from Conformational Equilibrium by Solvent Polarity

Polyproline I helical structures are often considered as the hidden face of their most famous geminal sibling, Polyproline II, as PPI is generally spotted only within a conformational equilibrium. We designed and synthesized a stable Polyproline I structure exploiting the striking tendency of (S)-indoline-2-carboxylic acid to drive the peptide bond conformation toward the cis amide isomer, when dissolved in polar solvents. The cooperative effect of only four amino acidic units is sufficient to form a preferential structure in solution. We shed light on this rare secondary structure with a thorough analysis of the spectroscopic and chiroptical properties of the tetramer, supported by X-ray crystallography and computational studies.

Capacity for increased surface area in the hydrophobic core of β-sheet peptide bilayer nanoribbons

Amphipathic peptides with amino acids arranged in alternating patterns of hydrophobic and hydrophilic residues efficiently self‐assemble into β‐sheet bilayer nanoribbons. Hydrophobic side chain functionality is effectively buried in the interior of the putative bilayer of these nanoribbons. This study investigates consequences on self‐assembly of increasing the surface area of aromatic side chain groups that reside in the hydrophobic core of nanoribbons derived from Ac‐(XKXE)₂‐NH₂ peptides (X = hydrophobic residue). A series of Ac‐(XKXE)₂‐NH₂ peptides incorporating aromatic amino acids of increasing molecular volume and steric profile (X = phenylalanine [Phe], homophenylalanine [Hph], tryptophan [Trp], 1‐naphthylalanine [1‐Nal], 2‐naphthylalanine [2‐Nal], or biphenylalanine [Bip]) were assessed to determine substitution effects on self‐assembly propensity and on morphology of the resulting nanoribbon structures. Additional studies were conducted to determine the effects of incorporating amino acids of differing steric profile in the hydrophobic core (Ac‐X₁KFEFKFE‐NH₂ and Ac‐(X_1,5KFE)‐NH₂ peptides, X = Trp or Bip). Spectroscopic analysis by circular dichroism (CD) and Fourier transform infrared (FT‐IR) spectroscopy indicated β‐sheet formation for all variants. Self‐assembly rate increased with peptide hydrophobicity; increased molecular volume of the hydrophobic side chain groups did not appear to induce kinetic penalties on self‐assembly rates. Transmission electron microscopy (TEM) imaging indicated variation in fibril morphology as a function of amino acid in the X positions. This study confirms that hydrophobicity of amphipathic Ac‐(XKXE)₂‐NH₂ peptides correlates to self‐assembly propensity and that the hydrophobic core of the resulting nanoribbon bilayers has a significant capacity to accommodate sterically demanding functional groups. These findings provide insight that may be used to guide the exploitation of self‐assembled amphipathic peptides as functional biomaterials.

Treating anisotropic artefacts in circular dichroism spectroscopy enables investigation of lyotropic liquid crystalline polyaspartate solutions

Circular dichroism (CD) spectroscopy is commonly used for investigation of the secondary structure of biomolecular compounds as well as polymers in isotropic solution. In anisotropic solution, the usage of the apparent CD is prone to misinterpretations due to artefacts from contributions of e.g. linear dichroism (LD). Herein, a method for the complete cancelation of anisotropic artefacts in the apparent CD is developed and its validity proven. The approach is further used for investigation of the conformation and the lyotropic liquid crystalline (LLC) structure of a copolyaspartate. For this system, a temperature-dependent change of the polymer's helical conformation (helix reversal) is known. Furthermore, a rotation of the aligned polymer helices inside a magnetic field (helix realignment) is independently present, occurring at a lower temperature compared to the helix reversal. In the current study, the helix reversal is confirmed and found to be accompanied by a change of the LLC structure. A cholesteric structure is detected and revealed to change its sense (cholesteric reversal) at the temperature at which the helix realigns in the magnetic field. The determination of the cholesteric sense is enabled by measuring the induced CD of an achiral dye, dissolved in the anisotropic polymer solution. Investigation of the anisotropic polymer solution is, thus, only made possible by cancellation of the aforementioned anisotropic artefacts. This allows the observation of changes of the liquid crystal structure from right-handed cholesteric, through left-handed cholesteric, to nematic with increasing temperature.

Oligodimethylsiloxane-Oligoproline Block Co-Oligomers: the Interplay between Aggregation and Phase Segregation in Bulk and Solution

Discrete block co-oligomers (BCOs) assemble into highly ordered nanostructures, which adopt a variety of morphologies depending on their environment. Here, we present a series of discrete oligodimethylsiloxane-oligoproline (oDMS-oPro) BCOs with varying oligomer lengths and proline end-groups, and study the nanostructures formed in both bulk and solution. The conjugation of oligoprolines to apolar siloxanes permits a study of the aggregation behavior of oligoproline moieties in a variety of solvents, including a highly apolar solvent like methylcyclohexane. The apolar solvent is more reminiscent of the polarity of the siloxane bulk, which gives insights into the supramolecular interactions that govern both bulk and solution assembly processes of the oligoproline. This extensive structural characterization allows the bridging of the gap between solution and bulk assembly. The interplay between the aggregation of the oligoproline block and the phase segregation induced by the siloxane drives the assembly. This gives rise to disordered, micellar microstructures in apolar solution and crystallization-driven lamellar nanostructures in the bulk. While most di- and triblock co-oligomers adopt predictable morphological features, one of them, oDMS15-oPro6-NH2, exhibits pathway complexity leading to gel formation. The pathway selection in the complex interplay between aggregation and phase segregation gives rise to interesting material properties.

Direct determination of helix structures involved in the screw-sense reversal of poly(β-phenylpropyl l-aspartate) by synchrotron X-ray diffraction

The helix-sense reversal of poly(β-phenylpropyl l-aspartate) (3PLA) in the solid state was studied by synchrotron wide-angle X-ray diffraction and small-angle X-ray scattering. The direct determination of the characteristic helical pitch before and after the transition revealed that the transition takes place reversibly between the two α-helices having opposite screw-sense during the heating and cooling cycle. While the hexagonal packing remains unaltered, the helix-sense inversion causes discontinuous changes in the molecular arrangement and, by extension, the crystalline dimension. In this study, another transition was detected at a higher temperature from the left-handed α-helix to the π-helix, the molecular chirality being unaffected.

Peptide-Metal Frameworks with Metal Strings Guided by Dispersion Interactions

Despite impressive advances in the construction of metal-organic frameworks (MOFs), the formation of networks from peptidic ligands is difficult, though they are sought after for their modularity and biocompatibility. Herein we present a peptide-metal framework that consists of helical oligoproline ligands and Zn/K (or Zn/Rb). The crystalline network contains pleated nanosheets with the metal ions aligned in strings. This unprecedented architecture derives from under-appreciated London dispersion interactions between the oligoproline ligands that play in concert with the metal coordination to create the network. Hence, the secondary structure of the peptidic ligand represents an additional control element for the creation of new MOF architectures. We anticipate that our results will instruct the design of further peptidic MOFs and enable the generation of versatile biocompatible materials.

Conformation and Morphology of 4-(NH2/OH)-Substituted l/d-Prolyl Polypeptides: Effect of Homo- and Heterochiral Backbones on Formation of β-Structures and Nanofibers

The relative stereochemistry of C2 and C4 in 4-substituted prolyl polypeptides plays an important role in defining the derived conformation in solution. cis-(2S,4S)-Amino/hydroxy-l-prolyl polypeptide (lC-Amp 9/lC-Hyp 9) shows a PPII conformation in phosphate buffer and a β-structure in a relatively hydrophobic solvent, trifluoroethanol (TFE). It is now demonstrated that the homochiral enantiomeric cis-substituted d-prolyl polypeptide (dC-Amp 9/dC-Hyp 9) exhibits mirror image β-structures in TFE. In the case of alternating heterochiral prolyl peptides, it is the trans-substituted [lT(2S,4R)-dT(2R,4S)] n prolyl polypeptide that shows β-structures in TFE, while the cis-substituted [lC(2S,4S)-dC(2R,4R)] n prolyl polypeptide is disordered in both phosphate buffer and TFE. The results highlight the important chirality-specific structural requirements for β-structure formation. The observed conformation in solution (circular dichroism (CD)) is also correlated with the morphology of the self-assemblies (field emission scanning electron microscopy (FESEM)), with the PPII form leading to spherical nanoparticles and β-structures leading to nanofiber formation. The results shed light on the role of relative stereochemistry at C2 and C4 in defining the polyproline peptide conformation in solution and how different conformations drive self-assemblies of peptides toward specific nanostructures.

Protease-Catalyzed l-Aspartate Oligomerization: Substrate Selectivity and Computational Modeling

Poly(aspartic acid) (PAA) is a biodegradable water-soluble anionic polymer that can potentially replace poly(acrylic acid) for industrial applications and has shown promise for regenerative medicine and drug delivery. This paper describes an efficient and sustainable route that uses protease catalysis to convert l-aspartate diethyl ester (Et2-Asp) to oligo(β-ethyl-α-aspartate), oligo(β-Et-α-Asp). Comparative studies of protease activity for oligo(β-Et-α-Asp) synthesis revealed α-chymotrypsin to be the most efficient. Papain, which is highly active for l-glutamic acid diethyl ester (Et2-Glu) oligomerization, is inactive for Et2-Asp oligomerization. The assignment of α-linkages between aspartate repeat units formed by α-chymotrypsin catalysis is based on nuclear magnetic resonance (NMR) trifluoacetic acid titration, circular dichroism, and NMR structural analysis. The influence of reaction conditions (pH, temperature, reaction time, and buffer/monomer/α-chymotrypsin concentrations) on oligopeptide yield and average degree of polymerization (DPavg) was determined. Under preferred reaction conditions (pH 8.5, 40 °C, 0.5 M Et2-Asp, 3 mg/mL α-chymotrypsin), Et2-Asp oligomerizations reached maximum oligo(β-Et-α-Asp) yields of ∼60% with a DPavg of ∼12 (M n 1762) in just 5 min. Computational modeling using Rosetta software gave relative energies of substrate docking to papain and α-chymotrypsin active sites. The substrate preference calculated by Rosetta modeling of α-chymotrypsin and papain for Et2-Asp and Et2-Glu oligomerizations, respectively, is consistent with experimental results.

Crystal structure of N-{N-[N-(tert-but-oxy-carbon-yl)-l-α-aspart-yl]-l-α-aspart-yl}-l-α-aspartic acid 14,24,34-trimethyl ester 31-2-oxo-2-phenyl-ethyl ester {Boc-[Asp(OMe)]3-OPac}

In the title homotripeptide {Boc-[Asp(OMe)]3-OPac}, C28H37N3O13, all peptide bonds adopt an s-trans conformation with respect to the N-H and C=O groups. In the crystal, N-H⋯O hydrogen bonds result in an infinite parallel β-sheet structure running along the b-axis direction. The Boc protecting group at the N-terminus of the peptide is disordered over two sites with occupancy factors of 0.504 (5) and 0.496 (5).

Real-Time Monitoring of Hierarchical Self-Assembly and Induction of Circularly Polarized Luminescence from Achiral Luminogens

Constructing artificial helical structures through hierarchical self-assembly and exploring the underlying mechanism are important, and they help gain insight from the structures, processes, and functions from the biological helices and facilitate the development of material science and nanotechnology. Herein, the two enantiomers of chiral Au(I) complexes ( S)-1 and ( R)-1 were synthesized, and they exhibited impressive spontaneous hierarchical self-assembly transitions from vesicles to helical fibers. An impressive chirality inversion and amplification was accompanied by the assembly transition, as elucidated by the results of in situ and time-dependent circular dichroism spectroscopy and scanning electron microscope imaging. The two enantiomers could serve as ideal chiral templates to co-assemble with other achiral luminogens to efficiently induce the resulting co-assembly systems to show circularly polarized luminescence (CPL). Our work has provided a simple but efficient way to explore the sophisticated self-assembly process and presented a facile and effective strategy to fabricate architectures with CPL properties.

α-Methyl phenylglycines by asymmetric α-arylation of alanine and their effect on the conformational preference of helical Aib foldamers

α-Arylated alanine derivatives were made enantioselectively by migratory rearrangement of a urea derivative using (R,R)-pseudoephedrine as a chiral auxiliary. Incorporation of a single residue of the product α-methyl phenylglycine into an otherwise achiral oligomer of aminoisobutyric acid oligomer induced a preferred screw sense, detectable by a NMR reporter located at the remote terminus of the oligomer. The magnitude of the screw sense induction was greater when the chiral residue was located at the N-terminus of the foldamer, and in some cases the sense of induction was opposite to that of related α-methylated amino acids with α-substituents other than aryl.

Helicity adaptation within a quadruply stranded helicate by encapsulation

The helicity of a quadruply stranded M2L4 helicate consisting of an aromatic amide bidendate ligand is flexible due to the twisting of the amide moieties and can be tuned by the encapsulated anions. This study reveals the multiple interplays and complementarities between the anions as well as between the anions and the helicate, which are synthetically responsive to the ultimate conformation of the helicate.

Amino acid modifications for conformationally constraining naturally occurring and engineered peptide backbones: Insights from the Protein Data Bank

Extensive efforts invested in understanding the rules of protein folding are now being applied, with good effect, in de novo design of proteins/peptides. For proteins containing standard α-amino acids alone, knowledge derived from experimentally determined three-dimensional (3D) structures of proteins and biologically active peptides are available from the Protein Data Bank (PDB), and the Cambridge Structural Database (CSD). These help predict and design protein structures, with reasonable confidence. However, our knowledge of 3D structures of biomolecules containing backbone modified amino acids is still evolving. A major challenge in de novo protein/peptide design concerns the engineering of conformationally constrained molecules with specific structural elements and chemical groups appropriately positioned for biological activity. This review explores four classes of amino acid modifications that constrain protein/peptide backbone structure. Systematic analysis of peptidic molecule structures (eg, bioactive peptides, inhibitors, antibiotics, and designed molecules), containing these backbone-modified amino acids, found in the PDB and CSD are discussed. The review aims to provide structure-function insights that will guide future design of proteins/peptides.

Thermoresponsive Alignment Media in NMR Spectroscopy: Helix Reversal of a Copolyaspartate at Ambient Temperatures

Poly(aspartic acid esters) are known to form either right-or left-handed α-helices depending on the ester group in the side chain, on solvent and/or on temperature. Polyphenethyl-l-aspartates (PPLA) exhibit a helix reversal from the right- to the left-handed form with increasing temperature. We have recently reported the application of polyphenethylaspartates as helically chiral alignment media. The thermoresponsivity observed for these polymers offers the possibility to measure different orientations of analytes before and after helix reversal of the alignment medium at 373 K. Herein we present a synthesized copolymer of phenethyl- and benzylaspartate as a new alignment medium undergoing this helix reversal at 303-313 K. Thus, the measurement of residual dipolar couplings (RDC) before and after the helix reversal is allowed for at ambient temperatures. A complete sign change of all ¹ H-¹³ C RDCs was observed, which is close to the highest possible difference in NMR spectra.

The Cooperative Effect of Both Molecular and Supramolecular Chirality on Cell Adhesion

Although helical nanofibrous structures have great influence on cell adhesion, the role played by chiral molecules in these structures on cells behavior has usually been ignored. The chirality of helical nanofibers is inverted by the odd-even effect of methylene units from homochiral l-phenylalanine derivative during assembly. An increase in cell adhesion on left-handed nanofibers and weak influence of cell behaviors on right-handed nanofibers are observed, even though both were derived from l-phenylalanine derivatives. Weak and negative influences on cell behavior was also observed for left- and right-handed nanofibers derived from d-phenylalanine, respectively. The effect on cell adhesion of single chiral molecules and helical nanofibers may be mutually offset.

Insights into the helix-sense inversion of poly(β-phenethyl-L-aspartate) by two-dimensional Raman correlation spectroscopy

In this study, the transition process of the helix-sense inversion of poly(β-phenethyl-L-aspartate) was investigated by Raman scattering and 2-dimensional correlation spectroscopy. Temperature-dependent Raman spectra were obtained during the helix-sense inversion. The results of 2-dimensional correlation analysis in the spectral regions of 1600-1800 and 3200-3400 cm^-1 showed that the intensity changes of the side-chain ester C═O stretching bands occurred prior to those of amide A and amide I bands in the unwinding process of αR-helix on heating. The sequential order of the intensity changes for amide A, amide I, and the side-chain ester C═O stretching bands during the inversion process was determined. It was found that the conformation change of the side chain occurred prior to that of the main chain for the αR-helix on heating. Thus, we concluded that the transformation of the backbone chain from right-handed to left-handed is triggered by the conformational change of the side chains.

CAL-B catalyzed regioselective bulk polymerization of l-aspartic acid diethyl ester to α-linked polypeptides

This paper reports that the bulk polymerization of l-aspartic acid diethyl ester catalyzed by immobilized CAL-B at 80 °C for 24 h gives primarily (∼95%) α-linked poly(l-aspartate) in 70% yield with DP_avg = 50 and regioselectivity (α/β) = 94 : 6. Plots of log{[M]₀/[M]_t} vs. time and DP_avgvs. conversion indicate that this polymerization proceeds in a controlled manner by a chain-growth mechanism up to 90% conversion. Thereafter, competition occurs between chain growth and step mechanisms.

Oligoprolines as Molecular Entities for Controlling Distance in Biological and Material Sciences

Nature utilizes large biomolecules to fulfill tasks that require spatially well-defined arrangements at the molecular level such as electron transfer, ligand-receptor interactions, or catalysis. The creation of synthetic molecules that enable precise control over spacing and functionalization provides opportunities across diverse disciplines. Key requirements of functionalizable oligomeric scaffolds include the specific control of their molecular properties where the correct balance of flexibility and rigidity must be maintained in addition to the prerequisite of defined length. These molecules must ideally be equally applicable in aqueous and organic environments, they must be easy to synthesize in a controlled stepwise fashion, and they must be easily modified with a palette of chemical appendages having diverse functionalities. Oligoproline, a peptidic polymer comprised of repeating units of the amino acid proline, is an ideal platform to meet such challenges. Oligoproline derives its characteristic rigidity and well-defined secondary structure from the innate features of proline. It is the only naturally occurring amino acid that has its side-chain cyclized to its α-amino group, generating often-populated trans and cis conformers around the tertiary amide bonds formed in proline oligomers. Oligoprolines are widely applied to define distance on the molecular level as they are capable of serving as both a "molecular ruler" with a defined length and as a "molecular scaffold" with precisely located and predictably oriented substitutions along the polymeric backbone. Our investigations focus on the use of oligoproline as a molecular scaffold. Toward this end, we have investigated the role of solvent upon helical structure of oligoproline, and the effect that substituents on the pyrrolidine ring and the oligomer termini have on the stability of the helix. We have also further explored the molecular characteristics of oligoproline through spectroscopic and crystallographic methods. All of these structural insights laid the basis for implementation of oligoproline in materials science and chemical biology. Within this Account, we highlight the value of oligoprolines for applications in distinctly different research areas. Toward materials chemistry, we have utilized oligoprolines for the size-controlled generation of noble metal nanoparticles, and to probe the role of spatial preorganization of π-systems for molecular self-assembly. Within the biological realm, we have applied oligoprolines to probe the role of distance on G-protein coupled receptor-mediated ligand uptake by cancerous cells and to investigate the effects of charge preorganization on the efficacy of cationic cell-penetrating peptides.

Stimuli-Directed Helical Chirality Inversion and Bio-Applications

Helical structure is a sophisticated ubiquitous motif found in nature, in artificial polymers, and in supramolecular assemblies from microscopic to macroscopic points of view. Significant progress has been made in the synthesis and structural elucidation of helical polymers, nevertheless, a new direction for helical polymeric materials, is how to design smart systems with controllable helical chirality, and further use them to develop chiral functional materials and promote their applications in biology, biochemistry, medicine, and nanotechnology fields. This review summarizes the recent progress in the development of high-performance systems with tunable helical chirality on receiving external stimuli and discusses advances in their applications as drug delivery vesicles, sensors, molecular switches, and liquid crystals. Challenges and opportunities in this emerging area are also presented in the conclusion.

Helical screw-sense preferences of peptides based on chiral, Cα-tetrasubstituted α-amino acids

The preferred helical screw senses of chiral α-amino acids with a C(α)-tetrasubstituted α-carbon atom, as determined in the crystal state by X-ray diffraction analyses on derivatives and peptides, are reviewed. This survey covers C(α)-methylated and C(α)-ethylated α-amino acids, as well as α-amino acids cyclized on the α-carbon, including those characterized by the combination of lack of chirality at the α-carbon with either side-chain or axial chirality. Although, in general, chiral C(α)-tetrasubstituted α-amino acids show a less pronounced bias toward a single helical screw sense than their proteinogenic (C(α)-trisubstituted) counterparts, our analysis highlights significant differences in terms of magnitude and direction of such a bias among the various sub-families of residues, and between individual amino acids within each sub-family as well. The experimental findings can be rationalized, at least in part, on the basis of steric considerations.

Importance of dipole moments and ambient polarity for the conformation of Xaa-Pro moieties - a combined experimental and theoretical study

NMR spectroscopic studies with a series of proline derivatives revealed that the polarity of the environment has a significant effect on the trans : cis isomer ratio of Xaa-Pro bonds. Computational studies showed that this effect is due to differences in the overall dipole moments of trans and cis conformers. Comparisons between the conformational properties of amide and ester derivatives revealed an intricate balance between polarity effects and n → π* interactions of adjacent carbonyl groups. The findings have important implications for protein folding and signaling as well as the performance of proline-based stereoselective catalysts.

Origin of Helical Screw Sense Selectivity Induced by Chiral Constrained Cα-Tetrasubstituted α-Amino Acids in Aib-based Peptides

The mechanisms behind the propensity of chiral constrained Cα-tetrasubstituted amino acids (cCTAAs) to induce one particular helical screw sense, when included in the Ac-Aib2-cCTAA-Aib2-NHMe peptide model, were studied through replica exchange molecular dynamics, potential of mean force, and quantum theory of atoms in molecules calculations. We observed that cCTAAs exert their effect on helical screw sense selectivity through the positioning of the side chain to generate steric hindrance in either the (-x, +y, +z) or (+x, +y, -z) sectors of a right-handed 3D Cartesian space, where the z axis corresponds to the axis of the helix and the Cα lies on the +y semiaxis (0, +y, 0). The different strengthening of the noncovalent interactions, also comprising C-H···O interactions, exerted by the cCTAA in the right-handed or left-handed helix was also found important to define the preference of a cCTAA for a particular helix screw sense.

Peptide δ-Turn: Literature Survey and Recent Progress

Among the various types of α-peptide folding motifs, δ-turn, which requires a central cis-amide disposition, has been one of the least extensively investigated. In particular, this main-chain reversal topology has been studied in-depth neither in linear/cyclic peptides nor in proteins. This Minireview article assembles and critically analyzes relevant data from a literature survey on the δ-turn conformation in those compounds. Unpublished results from recent conformational energy calculations and a preliminary solution-state analysis on a small model peptide, currently ongoing in our laboratories, are also briefly outlined.

Rapid Filament Supramolecular Chirality Reversal of HET-s (218-289) Prion Fibrils Driven by pH Elevation

Amyloid fibril polymorphism is not well understood despite its potential importance for biological activity and associated toxicity. Controlling the polymorphism of mature fibrils including their morphology and supramolecular chirality by postfibrillation changes in the local environment is the subject of this study. Specifically, the effect of pH on the stability and dynamics of HET-s (218-289) prion fibrils has been determined through the use of vibrational circular dichroism (VCD), deep UV resonance Raman, and fluorescence spectroscopies. It was found that a change in solution pH causes deprotonation of Asp and Glu amino acid residues on the surface of HET-s (218-289) prion fibrils and triggers rapid transformation of one supramolecular chiral polymorph into another. This process involves changes in higher order arrangements like lateral filament and fibril association and their supramolecular chirality, while the fibril cross-β core remains intact. This work suggests a hypothetical mechanism for HET-s (218-289) prion fibril refolding and proposes that the interconversion between fibril polymorphs driven by the solution environment change is a general property of amyloid fibrils.

Shape Persistence of Polyproline II Helical Oligoprolines

Oligoprolines are commonly used as molecular scaffolds. Past studies on the persistence length of their secondary structure, the polyproline II (PPII) helix, and on the fraction of backbone cis amide bonds have provided conflicting results. We resolved this debate by studying a series of spin-labeled proline octadecamers with EPR spectroscopy. Distance distributions between an N-terminal Gd(III) -DOTA (DOTA=1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) label and a nitroxide label at one of five evenly spaced backbone sites allowed us to discriminate between the flexibility of the PPII helix and the cis amide contributions. An upper limit of 2 % cis amide bonds per residue was found in a 7:3 (v/v) water/glycerol mixture, whereas cis amides were not observed in trifluoroethanol. Extrapolation of Monte Carlo models from the glass transition to ambient temperature predicts a persistence length of ≈3-3.5 nm in both solvents. The method is generally applicable to any type of oligomer for which the persistence length is of interest.

Experimental and theoretical evaluation on the conformational behavior of l-aspartic acid dimethyl ester and its N-acetylated derivative

The AspOMe and AcAspOMe conformational preferences and their corresponding intramolecular interactions were studied through spectroscopic and theoretical methodologies.