Salt-bridging effects on short amphiphilic helical structure and introducing sequence-based short beta-turn motifs

Determining the minimal sequence necessary to induce protein folding is beneficial in understanding the role of protein–protein interactions in biological systems, as their three-dimensional structures often dictate their activity. Proteins are generally comprised of discrete secondary structures, from α-helices to β-turns and larger β-sheets, each of which is influenced by its primary structure. Manipulating the sequence of short, moderately helical peptides can help elucidate the influences on folding. We created two new scaffolds based on a modestly helical eight-residue peptide, PT3, we previously published. Using circular dichroism (CD) spectroscopy and changing the possible salt-bridging residues to new combinations of Lys, Arg, Glu, and Asp, we found that our most helical improvements came from the Arg–Glu combination, whereas the Lys–Asp was not significantly different from the Lys–Glu of the parent scaffold, PT3. The marked 3₁₀-helical contributions in PT3 were lessened in the Arg–Glu-containing peptide with the beginning of cooperative unfolding seen through a thermal denaturation. However, a unique and unexpected signature was seen for the denaturation of the Lys–Asp peptide which could help elucidate the stages of folding between the 3₁₀ and α-helix. In addition, we developed a short six-residue peptide with β-turn/sheet CD signature, again to help study minimal sequences needed for folding. Overall, the results indicate that improvements made to short peptide scaffolds by fine-tuning the salt-bridging residues can enhance scaffold structure. Likewise, with the results from the new, short β-turn motif, these can help impact future peptidomimetic designs in creating biologically useful, short, structured β-sheet-forming peptides.     

Studies on the peptidase activity of transthyretin (TTR)

Transthyretin (TTR) is a plasma protein transporter of thyroxine (T₄) and retinol and also has peptidase activity. In order to characterize TTR peptidase activity we used fluorescence resonance energy transfer (FRET) peptides derived from Abz-KLRSSK-Q-EDDnp and from two portion-mixing libraries as substrates. Most of the susceptible FRET peptides were cleaved at more than one peptide bond, without particular substrate specificity. The more relevant observation was that the peptides containing E or D were cleaved at only one peptide bond and TTR was competitively inhibited by glutathione analog peptide γ-E-A-G-OH that contains two free carboxyl groups. The dependence on ionic interactions of TTR hydrolytic activity was confirmed by the large inhibitory effects of salt and ionic surfactants. TTR was not inhibited by any usual peptidase inhibitors, except by ortho-phenanthroline and EDTA. The mechanism of TTR catalysis was explored by the pH-profile of TTR hydrolytic activity in different temperatures and by proton inventory. The obtained pK and heat of ionization values suggest that a carboxylate and an ammonium group, possibly from a lysine side chain are involved. These results support the recently proposed inducible metalloprotease mechanism for TTR based on its 3D structure in presence of Zn²⁺ and a series of point mutations [Liz et al., Biochem. J 443 (2012) 769–778].     

Computational modelling and molecular dynamics simulations of a cyclic peptide mimotope of the CD52 antigen complexed with CAMPATH-1H antibody

A peptide mimotope of the CD52 antigen with the sequence T₁SSPSAD₇ has been co-crystallised with the CAMPATH-1H antibody. Molecular dynamics (MD) simulations in explicit water of the T₁SSPSAD₇ peptide in both antibody free and bound states showed that the peptide's β-turn remained stable in the bound state but it was eliminated in the free state. Based on the observation that Thr₁ and Ala₆ residues made close contacts through their side chain, a new peptide mimotope is proposed: (S,S)-C₁SSPSCD₇. Thr₁ and Ala₆ residues have been mutated in Cys residues and a disulphide bond has been imposed. The new analogue has been simulated in both antibody bound and free states with MD in explicit water. It was found that the peptide remained in the stable β-turn conformation, both in complexed and free states. The difference in configurational entropy was estimated to be 0.15 kJ/K/mol. However, despite the structural similarity, the cyclic analogue lost more than 25% of its buried surface area contact with the antibody and a couple of critical hydrogen bond interactions were broken. It is concluded that design of cyclic analogues that mimic the bound conformation of peptides should be carefully performed and conformational ‘freezing’ does not necessarily guarantee better binding.     

Manipulation of peptide conformations by fine-tuning of the environment and/or the primary sequence

The widely observed phenomenon that peptides are capable of adopting multiple conformations in different environments suggests that secondary structure formation in a peptide segment is a process involving not only the peptide itself hut also the surrounding solvent media. The influence of the primary sequence and the molecular environment on peptide conformations are now investigated using synthetic peptides of amino acid sequence H₂N-(Ser-Lys)₂-Ala-X-Gly-Ala-X-Gly-Trp-Ala-X-Gly-(Lys-Ser)₃-OH, where X = Ile or Val. These two peptides, namely 3I (X = Ile) and 3V (X = Val), are found to lack defined secondary structure in aqueous buffer. However, discrete conformational states, e.g., α-helices and β-sheets, are readily generated and interconverted for both peptides when the buffer is modulated with the addition of methanol, sodium dodecyl sulfate (SDS) micelles, or phospholipid vesicles. The role of the primary sequence in affecting peptide conformations is manifested in that peptides 3I and 3V, which differ respectively in their content of β-branched Ile or Val residues, differ in their secondary structures at monomeric concentrations in 2 mM SDS and in mixed lipid vesicles of phosphatidic acid and phosphatidylcholine. The overall results suggest that peptide segments can be conformationally flexible entities poised to react to minor modulations in cither the molecular environment or the primary sequence, a circumstance that may he relevant to protein functioning and folding. © 1995 John Wiley & Sons, Inc.     

Type II β-turn conformation of pivaloyl-L-prolyl-α-aminoisobutyryl-N-methylamide: Theoretical,spectroscopic, and X-ray studies

Pivaloyl-L -Pro-Aib-N-methylamide has been shown to possess one intramolecular hydrogen bond in (CD₃)₂SO solution, by ¹H-nmr methods, suggesting the existence of β-turns, with Pro-Aib as the corner residues. Theoretical conformational analysis suggests that Type II β-turn conformations are about 2 kcal mol^?1 more stable than Type III structures. A crystallographic study has established the Type II β-turn in the solid state. The molecule crystallizes in the space group P2₁ with a = 5.865 Å, b = 11.421 Å, c = 12.966 Å, β = 97.55°, and Z = 2. The structure has been refined to a final R value of 0.061. The Type II β-turn conformation is stabilized by an intramolecular 4 → 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are ?_Pro = ?57.8°, ψ_Pro = 139.3°, ?_Aib = 61.4°, and ψ_Aib = 25.1°. The Type II β-turn conformation for Pro-Aib in this peptide is compared with the Type III structures observed for the same segment in larger peptides.     

Conformational and antigenic properties of SRYD-containing peptide analogues of Leishmania gp63 adhesion site

Summary The antigenicity and conformational properties of the Ser-Arg-Tyr-Asp (SRYD) segment (252–255) of the major surface glycoprotein ofLeishmania, gp63, which plays a key role in the parasite-macrophage attachement, are presented. It was found that the antibody recognition, using anti-IASRYDQL antibodies, of the SRYD-containing analogues, Ac-SRYD-NH₂ (1), ANIASRYD-NH₂ (2), Ac-SRYD (3), SRYD (4) and ANIASRYD (5), is rather similar. The structure of the SRYD moiety in analogues 1 and 2 is characterized by the presence of a type I -turn, stabilized by the formation of a hydrogen bonding between the C-terminaltrans-carboxamide proton and the Arg-CO and an ionic bridge between arginine and aspartic acid side chains, while the conformation of compounds 3, 4 and 5 is stabilized by an ionic bridge between the arginine side chain and the C-terminal carboxylate group. A common structural motif involving the arginine side chain in an ionic interaction is identified in all the SRYD analogues, which may explain the observed similarities in the antibody recognition of the reported peptides.     

Membrane interactions of a self-assembling model peptide that mimics the self-association,structure and toxicity of Aβ(1–40)

β-amyloid peptide (Aβ) is a primary protein component of senile plaques in Alzheimer's disease (AD) and plays an important, but not fully understood role in neurotoxicity. Model peptides with the demonstrated ability to mimic the structural and toxicity behavior of Aβ could provide a means to evaluate the contributions to toxicity that are common to self-associating peptides from many disease states. In this work, we have studied the peptide–membrane interactions of a model β-sheet peptide, P_11-2 (CH₃CO-Gln-Gln-Arg-Phe-Gln-Trp-Gln-Phe-Glu-Gln-Gln-NH₂), by fluorescence, infrared spectroscopy, and hydrogen–deuterium exchange. Like Aβ(1–40), the peptide is toxic, and conditions which produce intermediate oligomers show higher toxicity against cells than either monomeric forms or higher aggregates of the peptide. Further, P_11-2 also binds to both zwitterionic (POPC) and negatively charged (POPC:POPG) liposomes, acquires a partial β-sheet conformation in presence of lipid, and is protected against deuterium exchange in the presence of lipids. The results show that a simple rationally designed model β-sheet peptide recapitulates many important features of Aβ peptide structure and function, reinforcing the idea that toxicity arises, at least in part, from a common mode of action on membranes that is independent of specific aspects of the amino acid sequence. Further studies of such well-behaved model peptide systems will facilitate the investigation of the general principles that govern the molecular interactions of aggregation-prone disease-associated peptides with cell and/or membrane surfaces.     

Conformational analysis of amyloid precursor protein fragment containing amino acids 667-676, and the effect of D-Asp and iso-Asp substitution at Asp₆₇₂ residue

Amyloid precursor protein (APP) fragment containing amino acids 667–676, (APP_667–676), is a substrate for β-secretase which is responsible for generating amyloid β peptides. Conformational analysis of APP_667–676 peptide [Ac-Ser-Glu-Val-Lys-Met-Asp-Ala-Glu-Phe-Arg-NH₂] and the effect of substitution of Asp₆₇₂ with d-Asp and iso-l-Asp, studied for the first time, demonstrate that the peptide backbone of APP_667–676 is flexible and adopts different conformations in different solvent environments (water, trifluoroethanol and dimethylsulfoxide). A major conformational difference was observed in trifluoroethanol solvent when Asp₆₇₂ is substituted with d-Asp and iso-Asp. These conformational changes involved in APP_667–676 may assist in understanding the interactions between β-secretase and APP_667–676, with relevance to Alzheimer’s disease.     

The role of hydroxyproline in collagen folding: conformational energy calculations on oligopeptides containing proline and hydroxyproline

We have observed that the rate of folding of the enzymatically hydroxylated form of poly(Gly-Pro-Pro) into the triple-helical conformation is considerably higher than that of the unhydroxylated polypeptide [R. K. Chopra and V. S. Ananthanarayanan (1982) Proc. Natl. Acad. Sci. USA 79 , 7180–7184]. In this study, we examine a plausible kinetic pathway for triple-helix formation by selecting peptide models for the unhydroxylated collagen molecule, and computing their conformational energies before and after proline hydroxylation. Starting with the available data on the preferred conformations of proline- and hydroxyproline-containing peptide sequences, energy minimization was carried out on the following pairs of peptides: Gly-Ala-Pro-Gly-Ala and Gly-Ala-Hyp-Gly-Ala; Gly-Pro-Pro-Gly-Ala and Gly-Pro-Hyp-Gly-Ala; Gly-Ala-Pro-Gly-Ala-Pro and Gly-Ala-Hyp-Gly-Ala-Hyp. It was found that, with each pair of peptides, the energetically most favorable conformation (I) has an extended structure at the Gly-Ala or Gly-Pro segment and a β-bend at the Pro-Gly or Hyp-Gly segment. In the Hyp-containing peptides, this conformation is further stabilized by a (Hyp_{i + 2})OH…OC(Gly_i) hydrogen bond. Conformation I is lower in energy by about 6–13 kcal/mol of the peptide than the fully extended conformations that resemble the single collagen polypeptide chain and contain no intramolecular hydrogen bond. In contrast to the proline counterpart, the hydroxyproline-containing peptides are found capable of adopting a partially extended conformation that does not contain the β-bend but retains the (Hyp)OH…OC(Gly) hydrogen bond. The energy of this conformation is intermediate between conformation I and the fully extended conformation. The continuation of the β-bend along the chain is restricted by stereochemical constraints that are more severe in the latter two pairs of peptides than in the first pair. Such a restriction may be considered to trigger the “unbending” of the minimum energy conformation leading to its straightening into the fully extended conformation; the latter, in turn, would lead to triple-helix formation through favorable interchain interactions. We propose that the partially extended conformation in the Hyp-containing peptides could serve as a kinetic intermediate on the way to forming the fully extended conformation. Because of the (Hyp_{i + 2})OH…OC(Gly_i) hydrogen bond, this conformation would also serve to lock the trans geometry at the Gly-Ala(Pro) and Ala(Pro)-Hyp peptide bonds, thereby enhancing the rate of their helix formation. A scheme for collagen folding in proposed on the basis of these results.     

Effect of conformation on the conversion of cyclo-(1,7)-Gly-Arg-Gly-Asp-Ser-Pro-Asp-Gly-OH to its cyclic imide degradation product.

The objective of this study was to explain the increased propensity for the conversion of cyclo-(1,7)-Gly-Arg-Gly-Asp-Ser-Pro-Asp-Gly-OH (1), a vitronectin-selective inhibitor, to its cyclic imide counterpart cyclo-(1,7)-Gly-Arg-Gly-Asu-Ser-Pro-Asp-Gly-OH (2). Therefore, we present the conformational analysis of peptides 1 and 2 by NMR and molecular dynamic simulations (MD). Several different NMR experiments, including COSY, COSY-Relay, HOHAHA, NOESY, ROESY, DQF-COSY and HMQC, were used to: (a) identify each proton in the peptides; (b) determine the sequential assignments; (c) determine the cis-trans isomerization of X-Pro peptide bond; and (d) measure the NH-HCalpha coupling constants. NOE- or ROE-constraints were used in the MD simulations and energy minimizations to determine the preferred conformations of cyclic peptides 1 and 2. Both cyclic peptides 1 and 2 have a stable solution conformation; MD simulations suggest that cyclic peptide 1 has a distorted type I beta-turn at Arg2-Gly3-Asp4-Ser5 and cyclic peptide 2 has a pseudo-type I beta-turn at Ser5-Pro6-Asp7-Gly1. A shift in position of the type I beta-turn at Arg2-Gly3-Asp4-Ser5 in peptide 1 to Ser5-Pro6-Asp7-Gly1 in peptide 2 occurs upon formation of the cyclic imide at the Asp4 residue. Although the secondary structure of cyclic peptide 1 is not conducive to succinimide formation, the reaction proceeds via neighbouring group catalysis by the Ser5 side chain. This mechanism is also supported by the intramolecular hydrogen bond network between the hydroxyl side chain and the backbone nitrogen of Ser5. Based on these results, the stability of Asp-containing peptides cannot be predicted by conformational analysis alone; the influence of anchimeric assistance by surrounding residues must also be considered.     

Long time molecular dynamic simulation on the agonist binding and activation of the β2-adrenergic receptor

β₂-Adrenergic receptor (β₂AR) plays a critical role in mediating the effects of catecholamine hormones. Due to the flexibility of the structure of its active state, study of agonist–β2AR is usually performed by molecular dynamic (MD) simulation. In this study we show the representative characteristics of agonist binding and activation on β₂AR by MD simulation. The binding site and the conformational changes in the specific regions of β2AR are reasonable which confirmed the conclusion that agonist–β2AR reached its active-like state. We have studied the disruption of non-covalent intramolecular interactions, including the conserved DRY motif, the rotamer toggle switch and the ionic lock, the cytoplasmic ends of transmembranes 5 and 6, and some water-mediated hydrogen bond network regions. We conclude that agonist induced β₂AR to its active conformation, or at least the active-like conformation.     

Nmr studies of the molecular conformations in the linear oligopeptides H-(L-Ala)n-L-Pro-OH

The molecular conformations of the linear oligopeptides H-(L -Ala)_n-L -Pro-OH, with n = 1,2 and 3, have been investigated. ¹³C nmr observation of the equilibrium between the cis and trans forms of the Ala-Pro peptide bond indicated the occurrence of nonrandom conformations in solutions of these flexible peptides. The formation of the nonrandom species containing the cis form of the Ala-Pro bond was found to depend on the deprotonation of the carboxylic acid group of proline, the solvent, and the ionic strength in aqueous solution. The influence of intramolecular hydrogen bonding on the relative conformational energies of the species containing the cis and trans Ala-Pro peptide bond was studied by comparison of the peptides H-(Ala)_n-Pro-OH with analogous molecules where hydrogen bond formation was excluded by the covalent structure. In earlier work a hydrogen bond between the protonated terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue had been suggested to stabilize conformations including trans proline. For the systems described here this hypothesis can be ruled out, since the cis:trans ratio is identical for molecules with methyl ester protected and free protonated terminal carboxylic acid groups of proline. Direct evidence for hydrogen bond formation between the deprotonated terminal carboxylic acid group and the amide proton of the penultimate amino acid residue in the molecular species containing cis proline was obtained from ¹H nmr studies. However, the cis:trans ratio of the Ala-Pro bond was not affected by N-methylation of the penultimate amino acid residue, which prevents formation of this hydrogen bond. Overall the experimental observations lead to the conclusion that the relative energies of the peptide conformations including cis or trans proline are mainly determined by intramolecular electrostatic interactions, whereas in the molecules considered, intramolecular hydrogen bonding is a consequence of specific peptide backbone conformations rather than a cause for the occurrence of energetically favored species. Independent support for this conclusion was obtained from model consideration which indicated that electrostatic interactions between the terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue could indeed account for the observed relative conformational energies of the species containing cis and trans proline, respectively.     

Complexation of Al(III) with reduced glutathione in acidic aqueous solutions

The complexation of reduced glutathione (GSH) in its free and Al(III)-bound species in acidic aqueous solutions was characterized by means of multi-analytical techniques: pH-potentiometry, multinuclear (¹H, ¹³C and ²⁷Al) and two-dimensional nuclear Overhauser enhancement NMR spectroscopy (¹H, ¹H-NOESY), electrospray mass spectroscopy (ESI-MS), and ab initio electronic structure calculations. The following results were found. In the 25 °C 0.1 M KCl and 37 °C 0.15 M NaCl ionic medium systems, Al³⁺ coordinates with the important biomolecule GSH through carboxylate groups to form various mononuclear 1:1 (AlHL, AlH₂L and AlH₋₁L), 1:2 (AlL₂) complexes, and dinuclear (Al₂H₅L₂) species, where H₄L⁺ denotes totally protonated GSH. Besides the monodentate complexes through carboxylate groups, the amino groups and the peptide bond imino and carbonyl groups may also be involved in binding with Al³⁺ in the bidentate and tridentate complexes. The present data reinforce that the glycine carboxylate group of GSH has a higher microscopic complex formation constant than γ-glutamyl carboxylate. Compared with simple amino acids, the tripeptide GSH displays a greater affinity for the Al³⁺ ion and thus may interfere with aluminum’s biological role more significantly.     

Contrasting solution conformations of peptides containing α,α-dialkylated residues with linear and cyclic side chains

The conformational properties of α,α-dialkylated amino acid residues possessing acyclic (diethylglycine, Deg: di-n-propylglycine, Dpg; di-n-butylglycine, Dbg) and cyclic (1-amino-cycloalkane-1-carboxylic acid, Ac_nc) side chains have been compared in solution. The five peptides studied by nmr and CD spectroscopy are Boc-Ala-Xxx-Ala-OMe, where Xxx = Deg(I). Dpg (II), Dbg (III), Ac₆c (IV), and Ac₇c (V). Delineation of solvent-shielded NH groups have been achieved by solvent and temperature dependence of NH chemical shifts in CDCl₃ and (CD₃)₂SO and by paramagnetic radical induced line broadening in pepiide III. In the Dxg peptides the order of solvent exposure of NH groups is Ala(1) > Ala(3) > Dxg(2), whereas in the Ac_nc peptides the order of solvent exposure of NH groups is Ala(1) > Ac_nc(2) > Ala(3). The nmr results suggest that Ac_nc peptides adopt folded β-turn conformations with Ala(1) and Ac_nc(2) occupying i + 1 and i + 2 positions. In contrast, the Dxg peptides favor extended C₅ conformations. The conformational differences in the two series are clearly borne out in CD studies. The solution conformations of peptides I-III are distinctly different from the β-turn structure observed in crystals. Low temperature nmr spectra recorded immediately after dissolution of crystals of peptide II provide evidence for a structural transition. Introduction of an additional hydrogen-bonding function in Boc-Ala-Dpg-Ala-NHMe (VI) results in a stabilization of a consecutive β-turn or incipient 3₁₀-helix in solution. © 1995 John Wiley & Sons, Inc.     

A three-step procedure for the isolation of peptides derived from adenine nucleotide binding sites of enzymes labeled with p-fluorosulfonyl [14C]benzoyl-5'-adenosine.

A simple three-step procedure is described for the purification of a labeled peptide from a tryptic digest of the β-subunit of the F₁-ATPase after the enzyme had been inactivated with p-fluorosulfonyl-[¹⁴C]benzoyl-5′-adenosine. The procedure involves: (1) anion-exchange chromatography of a tryptic digest of the labeled β-subunit on diethylaminoethyl-Sephadex; (2) treatment of the peptides in the radioactive peak from the first step with 0.1m NaOH under conditions in which the ester bond in the label is hydrolyzed; and (3) anion-exchange chromatography of the treated peptides under conditions identical to those of the first step after removal of the NaOH by gel filtration. Cleavage of the ester bond in the second step releases adenosine and specifically introduces an additional negative charge onto the labeled peptide. Thus, it is resolved from the peptides that contaminate it in the third step.     

Sequence-dependence of secondary structure formation: conformational studies of host-guest peptides in alpha-helix and beta-structure supporting media

A newly designed host–guest approach is introduced as a experimental tool to explore the relationship between the sequence of peptides and their secondary structure. From the CD spectra of the host–guest peptides studied, a tentative scale for the α-helix potential in 2,2,2-trifluorethanol of guest amino acids is delineated. The conformational preferences are also examined in β-structure supporting media (solid state, CH₂Cl₂, CH₃OH, H₂O) using ir-absorption and CD techniques. Scales for the β-forming tendency of guest amino acid residues in the different media are delineated. It is shown that the preferred conformation of the host–guest peptides is a function of the medium, the chain length, and the protecting groups. Given the fact that conformational effects are important in peptide synthesis, the tentative scales may serve as a guideline to predict secondary structures of side-chain-protected or -deprotected peptides in a given solvent, complementing the well-known empirical conformational prediction parameters.     

β-Turn conformations in crystal structures of model peptides containing α,α-Di-n-propylglycine and α,α-Di-n-butylglycine

The crystal state conformations of three peptides containing the α,α-dialkylated residues. α,α-di-n-propylglycine (Dpg) and α,α-di-n-butylglycine (Dbg), have been established by x-ray diffraction. Boc-Ala-Dpg-Alu-OMe (I) and Boc-Ala-Dbg-Ala-OMe (III) adopt distorted type II β-turn conformations with Ala (1) and Dpg/Dbg (2) as the corner residues. In both peptides the conformational angles at the Dxg residue (I: ? = 66.2°, ψ = 19.3°; III: ? = 66.5°. ψ = 21.1°) deviate appreciably from ideal values for the i + 2 residue in a type II β-turn. In both peptides the observed (N…O) distances between the Boc CO and Ala (3) NH groups are far too long (1: 3.44 Å: III: 3.63 Å) for an intramolecular 4 → 1 hydrogen bond. Boc-Ala-Dpg-Ata-NHMe (II) crystallizes with two independent molecules in the asymmetric unit. Both molecules HA and HB adopt consecutive β-turn (type III-III in HA and type III-I in IIB) or incipient 3₁₀-helical structures, stabilized by two intramolecular 4 → 1 hydrogen bonds. In all four molecules the bond angle N-C^α-C′ (τ) at the Dxg residues are ≥ 110°. The observation of conformational angles in the helical region of ?,ψ space at these residues is consistent with theoretical predictions. © 1995 John Wiley & Sons, Inc.     

Conformational properties of the disaccharide building units of hyaluronan

The conformational space of the disaccharide building units of hyaluronan, β-(1→4) and β-(1→3)-linked N-acetyl-β-d-glucosamine (GN) and β-d-glucuronic acid (GA), has been investigated by density functional theory calculations at the B3LYP/6-31G^** level. The study covered the anionic disaccharides, the neutral acids as well as the sodium salts in the isolated state and in aqueous solution using the PCM model approach. We elucidated the intramolecular hydrogen bonding interactions characterizing the most favoured conformers. The protonation and salt formation change these secondary interactions in the vicinity of the carboxyl group, resulting often in a considerable alteration of the conformational preferences. The Na⁺ ion in the salt is involved in multiple bonding in the most stable structures: beyond the primary ionic bond with the carboxylate group it forms slightly weaker interactions with neighbouring oxygens. The main effect of protonation and salt formation on the electron density distribution is restricted to the surroundings of the broken/formed interactions near the carboxylate group.     

Effect of side chain length on intrahelical interactions between carboxylate- and guanidinium-containing amino acids

The charge-containing hydrophilic functionalities of encoded charged amino acids are linked to the backbone via different numbers of hydrophobic methylenes, despite the apparent electrostatic nature of protein ion pairing interactions. To investigate the effect of side chain length of guanidinium- and carboxylate-containing residues on ion pairing interactions, α-helical peptides containing Zbb–Xaa (i, i + 3), (i, i + 4) and (i, i + 5) (Zbb = carboxylate-containing residues Aad, Glu, Asp in decreasing length; Xaa = guanidinium residues Agh, Arg, Agb, Agp in decreasing length) sequence patterns were studied by circular dichroism spectroscopy (CD). The helicity of Aad- and Glu-containing peptides was similar and mostly pH independent, whereas the helicity of Asp-containing peptides was mostly pH dependent. Furthermore, the Arg-containing peptides consistently exhibited higher helicity compared to the corresponding Agp-, Agb-, and Agh-containing peptides. Side chain conformational analysis by molecular mechanics calculations showed that the Zbb–Xaa (i, i + 3) and (i, i + 4) interactions mainly involved the χ ₁ dihedral combinations (g+, g+) and (g?, g+), respectively. These low energy conformations were also observed in intrahelical Asp–Arg and Glu–Arg salt bridges of natural proteins. Accordingly, Asp and Glu provides variation in helix characteristics associated with Arg, but Aad does not provide features beyond those already delivered by Glu. Importantly, nature may have chosen the side chain length of Arg to support helical conformations through inherent high helix propensity coupled with stabilizing intrahelical ion pairing interactions with the carboxylate-containing residues.     

Helicity of short E-R/K peptides

Understanding the secondary structure of peptides is important in protein folding, enzyme function, and peptide‐based drug design. Previous studies of synthetic Ala‐based peptides (>12 a.a.) have demonstrated the role for charged side chain interactions involving Glu/Lys or Glu/Arg spaced three (i, i + 3) or four (i, i + 4) residues apart. The secondary structure of short peptides (<9 a.a.), however, has not been investigated. In this study, the effect of repetitive Glu/Lys or Glu/Arg side chain interactions, giving rise to E‐R/K helices, on the helicity of short peptides was examined using circular dichroism. Short E‐R/K–based peptides show significant helix content. Peptides containing one or more E‐R interactions display greater helicity than those with similar E‐K interactions. Significant helicity is achieved in Arg‐based E‐R/K peptides eight, six, and five amino acids long. In these short peptides, each additional i + 3 and i + 4 salt bridge has substantial contribution to fractional helix content. The E‐R/K peptides exhibit a strongly linear melt curve indicative of noncooperative folding. The significant helicity of these short peptides with predictable dependence on number, position, and type of side chain interactions makes them an important consideration in peptide design.