Theoretical Studies of β-Peptide Models

Modulating the Structural Properties of α,γ-Hybrid Peptides by α-Amino Acid Residues: Uniform 12-Helix Versus "Mixed" 12/10-Helix

The most important natural α- and 3₁₀ -helices are stabilized by unidirectional intramolecular hydrogen bonds along the helical cylinder. In contrast, we report here on 12/10-helical conformations with alternately changing hydrogen-bond directionality in sequences of α,γ-hybrid peptides P1-P5 [P1: Boc-Ala-Aic-Ala-Aic-COOH; P2: Boc-Leu-Aic-Leu-Aic-OEt; P3: Boc-Leu-Aic-Leu-Aic-Leu-Aic-Aib-OMe; P4: Boc-Ala-Aic-Ala-Aic-Ala-Aic-Ala-OMe; P5: Boc-Leu-Aic-Leu-Aic-Leu-Aic-Leu-Aic-Aib-OMe; Aic=4-aminoisocaproic acid, Aib=2-aminoisobutyric acid] composed of natural α-amino acids and the achiral γ^4,4 -dimethyl substituted γ-amino acid Aic in solution and in single crystals. The helical conformations are stabilized by alternating i→i+3 and i→i-1 intramolecular hydrogen bonds. The experimental data are supported by ab initio MO calculations. Surprisingly, replacing the natural α-amino acids of the sequence by the achiral dialkyl amino acid Ac₆ c [P6: Boc-Ac₆ c-Aic-Ac₆ c-Aic-Ac₆ c-Aic-Ac₆ c-Aic-Ac₆ c-CONHMe; Ac₆ c = 1-aminocyclohexane-1-carboxylic acid] led to a 12-helix with unidirectional hydrogen bonds showing an entirely different backbone conformation. The results presented here emphasize the influence of the structure of the α-amino acid residues in dictating the helix types in α,γ-hybrid peptide foldamers and demonstrate the consequences for folding of small structural variations in the monomers.

Self-Assembly of Ultralong Aligned Dipeptide Single Crystals

Oriented arrangement of single crystals plays a key role in improving the performance of their functional devices. Herein we describe a method for the exceptionally fast fabrication (mm/min) of ultralong aligned dipeptide single crystals (several centimeters). It combines an induced nucleation step with a continuous withdrawal of substrate, leading to specific evaporation/composition conditions at a three-phase contact line, which makes the growth process controllable. These aligned dipeptide fibers possess a uniform cross section with active optical waveguiding properties that can be used as waveguiding materials. The approach provides guidance for the controlled arrangement of organic single crystals, a family of materials with considerable potential applications in large-scale functional devices.

Synthesis of a new β-amino acid with a 3-deoxy-L-ara furnaoside side chain: the influence of the side chain on the conformation of α/β-peptides

The important role of side chains in the stabilization of helical folds in peptidic foldamers containing C-linked carbo-β-amino acids (β-Caa), an interesting class of β-amino acids, with carbohydrate side chains has been extensively elaborated. As a pragmatic approach to alleviate the interference of substituents in the side chains on the folding propensities of the peptides, they are often modified or removed. The present study reports the synthesis of a new β-Caa with a 3-deoxy-L-ara furanoside side chain, [(R)-β-Caa(da)], from D-glucose, and its use in the synthesis of α/β-peptides in 1 : 1 alternation with D-Ala. The synthesis of peptides using (R)-β-Caa(da), was facile unlike those from (R)-β-Caa(a) having the L-ara furanoside side chain. The detailed NMR, molecular dynamics (MD) and CD studies on the new α/β-peptides showed the presence of robust left-handed 11/9-mixed helices. The study demonstrates that the new (R)-β-Caa(da), behaves differently compared to the other two related monomers, (R)-β-Caa(x) with the D-xylo furanoside side chain and (R)-β-Caa(a).

Going clean: structure and dynamics of peptides in the gas phase and paths to solvation

The gas phase is an artificial environment for biomolecules that has gained much attention both experimentally and theoretically due to its unique characteristic of providing a clean room environment for the comparison between theory and experiment. In this review we give an overview mainly on first-principles simulations of isolated peptides and the initial steps of their interactions with ions and solvent molecules: a bottom up approach to the complexity of biological environments. We focus on the accuracy of different methods to explore the conformational space, the connections between theory and experiment regarding collision cross section evaluations and (anharmonic) vibrational spectra, and the challenges faced in this field.

Conformational properties of 1,4- and 1,5-substituted 1,2,3-triazole amino acids – building units for peptidic foldamers

Peptidic foldamers have recently emerged as a novel class of artificial oligomers with properties and structural diversity similar to that of natural peptides, but possessing additional interesting features granting them great potential for applications in fields from nanotechnology to pharmaceuticals. Among these, foldamers containing 1,4- and 1,5-substitued triazole amino acids are easily prepared via the Cu- and Ru-catalyzed click reactions and may offer increased side chain variation, but their structural capabilities have not yet been widely explored. We here describe a systematic analysis of the conformational space of the two most important basic units, the 1,4-substitued (4Tzl) and the 1,5-substitued (5Tzl) 1,2,3-triazole amino acids, using quantum chemical calculations and NMR spectroscopy. Possible conformations of the two triazoles were scanned and their potential minima were located using several theoretical approaches (B3LYP/6-311++G(2d,2p), ωB97X-D/6-311++G(2d,2p), M06-2X/6-311++G(2d,2p) and MP2/6-311++G(2d,2p)) in different solvents. BOC-protected versions of 4Tzl and 5Tzl were also prepared via one step transformations and analyzed by 2D NOESY NMR. Theoretical results show 9 conformers for 5Tzl derivatives with relative energies lying close to each other, which may lead to a great structural diversity. NMR analysis also indicates that conformers preferring turn, helix and zig-zag secondary structures may coexist in solution. In contrast, 4Tzl has a much lower number of conformers, only 4, and these lack strong intraresidual interactions. This is again supported by NMR suggesting the presence of both extended and bent conformers. The structural information provided on these building units could be employed in future design of triazole foldamers.

Self-assembly of β-alanine homotetramer: formation of nanovesicles for drug delivery

The present paper describes the fabrication of nanovesicles using the stirring induced self-assembly of a β-alanine homotetramer (H₂N–βAla–βAla–βAla–βAla–CONH₂) in an aqueous medium.

Helix stability of oligoglycine, oligoalanine, and oligo-β-alanine dodecamers reflected by hydrogen-bond persistence

Helices are important structural/recognition elements in proteins and peptides. Stability and conformational differences between helices composed of α- and β-amino acids as scaffolds for mimicry of helix recognition has become a theme in medicinal chemistry. Furthermore, helices formed by β-amino acids are experimentally more stable than those formed by α-amino acids. This is paradoxical because the larger sizes of the hydrogen-bonding rings required by the extra methylene groups should lead to entropic destabilization. In this study, molecular dynamics simulations using the second-generation force field, AMOEBA (Ponder, J.W., et al., Current status of the AMOEBA polarizable force field. J Phys Chem B, 2010. 114(8): p. 2549-64.) explored the stability and hydrogen-bonding patterns of capped oligo-β-alanine, oligoalanine, and oligoglycine dodecamers in water. The MD simulations showed that oligo-β-alanine has strong acceptor+2 hydrogen bonds, but surprisingly did not contain a large content of 3(12) -helical structures, possibly due to the sparse distribution of the 3(12) -helical structure and other structures with acceptor+2 hydrogen bonds. On the other hand, despite its backbone flexibility, the β-alanine dodecamer had more stable and persistent <3.0 Å hydrogen bonds. Its structure was dominated more by multicentered hydrogen bonds than either oligoglycine or oligoalanine helices. The 3(1) (PII) helical structure, prevalent in oligoglycine and oligoalanine, does not appear to be stable in oligo-β-alanine indicating its competition with other structures (stacking structure as indicated by MD analyses). These differences are among the factors that shape helical structural preferences and the relative stabilities of these three oligopeptides.

Unusual folding propensity of an unsubstituted β,γ-hybrid model peptide: importance of the C-H⋅⋅⋅O intramolecular hydrogen bond

The single-crystal X-ray diffraction analysis of a β,γ-hybrid model peptide Boc-β-Ala-γ-Abu-NH2 revealed the existence of four crystallographically independent molecules (A, B, C and D conformers) in the asymmetric unit. The analysis revealed that unusual β-turn-like folded structures predominate, wherein the conformational space of non-proteinogenic β-Ala and γ-Abu residues are restricted to gauche-gauche-skew and skew-gauche-trans-skew orientations, respectively. Interestingly, the U-shaped conformers are seemingly stabilised by an effective unconventional C-H⋅⋅⋅O intramolecular hydrogen bond, encompassing a non-covalent 14-membered ring-motif. Taking into account the signs of torsion angles, these conformers could be grouped into two distinct categories, A/B and C/D, establishing the incidence of non-superimposable stereogeometrical features across a non-chiral one-component peptide model system, that is, "mirror-image-like" relationships. The natural occurrence of β-Ala and γ-Abu entities in various pharmacologically important molecules, coupled with their biocompatibilities, highlight how the non-functionalised β,γ-hybrid segment may offer unique advantages for introducing and/or manipulating a wide spectrum of biologically relevant hydrogen bonded secondary structural mimics in short synthetic peptides.

ESTIMATION ON THE INTRAMOLECULAR 8- AND 12-MEMBERED RING N–H…O=C HYDROGEN BONDING ENERGIES IN β-PEPTIDES

Computation of accurate hydrogen bonding energies in peptides is of great importance in understanding the conformational stabilities of peptides. In this paper, the intramolecular 8- and 12-membered ring N – H … O = C hydrogen bonding energies in β-peptide structures were evaluated. The optimal structures of the β-peptide conformers were obtained using MP2/6-31G(d) method. The MP2/6-311++G(d,p) calculations were then carried out to evaluate the single-point energies. The results show that the intramolecular 8-membered ring N – H … O = C hydrogen bonding energies in the five β-dipeptide structures β-di, β-di-R1, β-di-R2, β-di-R3, and β-di-R4 are -5.50, -5.40, -7.28, -4.94, and -6.84 kcal/mol with BSSE correction, respectively; the intramolecular 12-membered ring N – H … O = C hydrogen bonding energies in the nine β-tripeptide structures β-tri, β-tri-R1, β-tri-R2, β-tri-R3, β-tri-R4, β-tri-R1', β-tri-R2', β-tri-R3' and β-tri-R4' are -10.23, -10.32, -9.53, -10.30, -10.32, -10.55, -10.09, -10.51, and -9.60 kcal/mol with BSSE correction, respectively. Our calculation results further indicate that for the intramolecular 8-membered ring hydrogen bondings, the structures where the orientation of the side chain methyl group is "a–a" have stronger intramolecular hydrogen bondings than those where the orientation of the side chain methyl group is "e–e", while for the intramolecular 12-membered ring hydrogen bondings, the structures where the orientation of the side chain methyl group is "e–e" have stronger intramolecular hydrogen bondings than those where the orientation of the side chain methyl group is "a–a". The method is also applied to estimate the individual intermolecular hydrogen bonding energies in the dimers of amino-acetaldehyde, 2-amino-acetamide, 2-oxo-acetamide, and oxalamide, each dimer having two identical intermolecular hydrogen bonds. According to our method, the individual intermolecular hydrogen bonding energies in the four dimers are calculated to be -1.71, -1.50, -4.67, and -3.22 kcal/mol at the MP2/6-311++G(d,p) level, which are in good agreement with the values of -1.84, -1.72, -4.93, and -3.26 kcal/mol predicted by the supermolecular method.

Establishing effective simulation protocols for beta- and alpha/beta-peptides. III. Molecular mechanical model for acyclic beta-amino acids

All-atom molecular mechanics (MM) force field parameters are developed for the backbone of acyclic beta-amino acid using an improved version of the multiobjective evolutionary algorithm (MOEA). The MM model is benchmarked using beta(3)-homo-Alanine (beta(3)-hAla) diamide in water with SCC-DFTB/MM simulations as the reference. Satisfactory agreements are found between the MM and SCC-DFTB/MM results regarding the distribution of key dihedral angles for the beta(3)-hAla diamide in water. The MM model is further applied to a beta-hepta-peptide in methanol solution. The calculated NOE values and (3)J coupling constants averaged over different trajectories are consistent with experimental data. By contrast, simulations using parameters directly transferred from the CHARMM22 force field for proteins lead to much worse agreement, which highlights the importance of careful parameterization for non-natural peptides, for which the improved MOEA is particularly useful. Finally, as an initial application of the new force field parameters, the behaviors of a short random copolymer consisting of beta amino acids in bulk solution and membrane/water interface are studied using a generalized Born implicit solvent model (GBSW). Results for four selected sequences show that segregation of hydrophobic and cationic groups occur easily at the membrane/solution interface for all sequences. The sequence that features alternating short blocks exhibits signs of lower stability at the interface compared to other sequences. These results confirm the hypothesis in recent experimental studies that beta-amino-acid based random copolymers can develop a high degree of amphiphilicity without regular three-dimensional structure.

Theoretical analysis of secondary structures of beta-peptides

Unlike alpha-amino acids, peptides formed from beta-amino acids (beta-peptides) display stability toward enzymatic degradation and may form turns and helices with as few as four residues. Because both the C alpha and C beta of the beta-amino acid may bear substituents, a large number of beta-amino acids can be synthesized. Beta-peptides form various well-defined secondary structures, including 14-helix, 12-helix, 10/12-helix, 10-helix, 8-helix, turn structures, sheets, and hairpins. For all of these reasons, beta-amino acids have been increasingly used as building blocks for molecular design and pharmaceutical applications. To explain the conformational features of beta-peptides, several quantum mechanics and molecular dynamics studies that rationalize the observed conformational features have been reported. However, a systematic account that unifies various factors critical to the conformational features is still lacking. In this Account, we present a detailed analysis of the conformational features of various beta-peptides. We start by studying the basic local conformational features of beta-peptides using di- and tripeptide models. Then, various secondary structures of unsubstituted beta-peptides with differing numbers of residues are investigated using a repeating unit approach to derive the intrinsic backbone conformational features. We find that the 10/12-helix is intrinsically most stable for the beta-peptide backbone. The 14-helix, 12-helix, and 10-helix structures have similar stabilities for beta-peptide backbones of four to six residues. The substituent effects on the stabilities of beta-peptide secondary structures are then analyzed. Combined with the substituent effect and the intrinsic backbone preferences, all experimental observations of secondary structure formation can be understood. For example, the 10/12-helix is favored for like-beta(2)/beta(3)-peptides, unlike-beta(3)/beta(3)-peptides, and beta(3)/beta-hGly-peptides because these substitution patterns do not cause steric problems for the 10/12-helix. Beta(3)-peptides, beta(2)-peptides, and beta (2,3)-peptides favor the 14-helix because the substituents in these peptides benefit the 14-helix the most but significantly destabilize the 10/12-helix. Because the 10/12-helix is intrinsically favored and has two favorable positions in each residue for substituents, many more hybrid beta-peptides are predicted to exist in this secondary structure, which suggests the need for further experiments. These results are valuable for determining the best use of these building blocks in the design of well-structured molecules with desirable chemical functions.

Conformations of beta-amino acid residues in peptides: X-ray diffraction studies of peptides containing the achiral residue 1-aminocyclohexaneacetic acid, beta3,3Ac6c

The conformational preferences of the 3,3-disubstituted beta-amino acid residue, 1-aminocyclohexaneacetic acid (beta3,3Ac6c) have been investigated by determining the crystal structures of the parent amino acid, the hydrochloride derivative, 10 protected derivatives and di and tripeptides. The symmetrical cyclohexyl substituent at the beta-position restricts the values of the torsion angles phi (N--C(beta)) and theta (C(beta)--C(alpha)) to approximately gauche values (+/-60 degrees ). Relatively few intramolecularly hydrogen bonded conformations are observed. In the dipeptide Boc-beta(3,3)Ac6c-beta(3,3)Ac6c-NHMe a C6 hydrogen bond is observed. In Piv-Pro-beta(3,3)Ac6c-NHMe a C11 hydrogen bonded hybrid alphabeta turn is characterized. In a majority of cases the amino group occupies the axial position in the cyclohexane ring. The conformations observed are compared with crystallographically observed structures for other beta-residues, including beta(2,2)Ac6c.

Time-dependent density functional theory study on hydrogen-bonded intramolecular charge-transfer excited state of 4-dimethylamino-benzonitrile in methanol

The time-dependent density functional theory (TDDFT) method was carried out to investigate the hydrogen-bonded intramolecular charge-transfer (ICT) excited state of 4-dimethylaminobenzonitrile (DMABN) in methanol (MeOH) solvent. We demonstrated that the intermolecular hydrogen bond C[triple bond]N...H-O formed between DMABN and MeOH can induce the C[triple bond]N stretching mode shift to the blue in both the ground state and the twisted intramolecular charge-transfer (TICT) state of DMABN. Therefore, the two components at 2091 and 2109 cm(-1) observed in the time-resolved infrared (TRIR) absorption spectra of DMABN in MeOH solvent were reassigned in this work. The hydrogen-bonded TICT state should correspond to the blue-side component at 2109 cm(-1), whereas not the red-side component at 2091 cm(-1) designated in the previous study. It was also demonstrated that the intermolecular hydrogen bond C[triple bond]N...H-O is significantly strengthened in the TICT state. The intermolecular hydrogen bond strengthening in the TICT state can facilitate the deactivation of the excited state via internal conversion (IC), and thus account for the fluorescence quenching of DMABN in protic solvents. Furthermore, the dynamic equilibrium of these electronically excited states is explained by the hydrogen bond strengthening in the TICT state.

Testing β-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: A molecular dynamics study

The search for new building block templates useful for nanostructures design, targets protein motifs with a wide range of structures. Stabilizing these building blocks when extracted from their natural environment becomes a fundamental goal in order to successfully control their assembly. Targeted replacements of natural residues by conformationally constrained amino acids were shown to be a successful strategy to achieve such stabilization. In this work, the effect of replacing natural amino acids by non-proteogenic residues in a beta-helix building block has been evaluated using extensive molecular dynamics simulations. Here, we focus on systematic substitutions of valine residues present in beta-sheet segments of a beta-helical building block excised from Escherichia coli galactoside acetyltransferase, residues 131-165. Four different types of non-proteogenic amino acids have been considered for substitution: (i) one dehydroamino acid, (ii) two d-amino acids, (iii) one beta-amino acid and (iv) two alpha,alpha-dialkylamino acids. Our results indicate that the ability of non-proteogenic amino acids to stabilize small building block motifs is site-dependent. We conclude that if the replacement does not alter the energy balance between attractive non-covalent interactions and steric hindrance, synthetic residues are suitable candidates to nucleate beta-helix formation.

Thermodynamic stability of beta-peptide helices and the role of cyclic residues

Beta-peptides are emerging as an attractive class of peptidomimetic molecules. In contrast to naturally occurring alpha-peptides, short oligomers of beta-amino acids (comprising just 4-6 monomers) exhibit stable secondary structures that make them amenable for quantitative, concerted experimental and theoretical studies of the effects of particular chemical interactions on structure. In this work, molecular simulations are used to study the thermodynamic stability of helical conformations formed by beta-peptides containing varying proportions of acyclic (beta(3)) and cyclic (ACH) residues. More specifically, several beta-peptides differing only in their content of cyclic residues are considered in this work. Previous computational studies of beta-peptides have relied mostly on energy minimization of molecular dynamics simulations. In contrast, our study relies on density-of-states based Monte Carlo simulations to calculate the free energy and examine the stability of various folded structures of these molecules along a well-defined order parameter. By resorting to an expanded-ensemble formalism, we are able to determine the free energy required to unfold specific molecules, a quantity that could be measured directly through single-molecule force spectroscopy. Simulations in both implicit and explicit solvents have permitted a systematic study of the role of cyclic residues and electrostatics on the stability of secondary structures. The molecules considered in this work are shown to exhibit stable H-14 helical conformations and, in some cases, relatively stable H-12 conformations, thereby suggesting that solvent quality may be used to manipulate the hydrogen-bonding patterns and structure of these peptides.

Biomimetic facially amphiphilic antibacterial oligomers with conformationally stiff backbones

A foldamer has been designed with a conformationally stiff backbone that is facially amphiphilic. The oligomer has excellent antimicrobial activity and was found to be 18 times more active toward bacterial cells than human red blood cells. The oligomer is built from arylamide bonds around a central 4,6-dicarboxy pyrimidine ring. The conformation was studied by X-ray crystallography and solution NMR spectroscopy. Density-functional (DFT) calculations were performed to guide the design. These calculations accurately predicted the overall conformation as well as NMR chemical shifts. Antibacterial activity was demonstrated against E. coli, a gram-negative strain, and B. subtilis, a gram-positive strain. The minimal inhibitory concentration is 0.8 microg/ml.