Incorporation of diacids into the polyglycine II structure: model studies

A Folded Conformation around the Methylene Group in Simple Boc–NH–(CH2)3–NH–Boc: An X-ray Diffraction Study

Structural studies on model compounds Boc–NH–(CH2)2–NH–Boc (1) and Boc–NH–(CH2)3–NH–Boc (2) have shown the inherent tendency of the propylene group to adopt a folded conformation, which may help in peptide and peptide nucleic acid (PNA) design.

Anti-parallel sheet structures of side-chain-free γ-, δ-, and ε-dipeptides stabilized by benzene–pentafluorobenzene stacking

Benzene–pentafluorobenzene stacking can guide ω-amino acid dipeptides to arrange in an anti-parallel manner.

Flanking polyproline sequences inhibit beta-sheet structure in polyglutamine segments by inducing PPII-like helix structure

Polyglutamine (poly(Q)) expansion is associated with protein aggregation into beta-sheet amyloid fibrils and neuronal cytotoxicity. In the mutant poly(Q) protein huntingtin, associated with Huntington's disease, both aggregation and cytotoxicity may be abrogated by a polyproline (poly(P)) domain flanking the C terminus of the poly(Q) region. To understand structural changes that may occur with the addition of the poly(P) sequence, we synthesized poly(Q) peptides with 3-15 glutamine residues and a corresponding set of poly(Q) peptides flanked on the C terminus by 11 proline residues (poly(Q)-poly(P)), as occurs in the huntingtin sequence. The shorter soluble poly(Q) peptides (three or six glutamine residues) showed polyproline type II-like (PPII)-like helix conformation when examined by circular dichroism spectroscopy and were monomers as judged by size-exclusion chromatography (SEC), while the longer poly(Q) peptides (nine or 15 glutamine residues) showed a beta-sheet conformation by CD and defined oligomers by SEC. Soluble poly(Q)-poly(P) peptides showed PPII-like content but SEC showed poorly defined, overlapping oligomeric peaks, and as judged by CD these peptides retained significant PPII-like structure with increasing poly(Q) length. More importantly, addition of the poly(P) domain increased the threshold for fibril formation to approximately 15 glutamine residues. X-ray diffraction, electron microscopy, and film CD showed that, while poly(Q) peptides with >or=6 glutamine residues formed beta-sheet-rich fibrils, only the longest poly(Q)-poly(P) peptide (15 glutamine residues) did so. From these and other observations, we propose that poly(Q) domains exist in a "tug-of-war" between two conformations, a PPII-like helix and a beta-sheet, while the poly(P) domain is conformationally constrained into a proline type II helix (PPII). Addition of poly(P) to the C terminus of a poly(Q) domain induces a PPII-like structure, which opposes the aggregation-prone beta-sheet. These structural observations may shed light on the threshold phenomenon of poly(Q) aggregation, and support the hypothesized evolution of "protective" poly(P) tracts adjacent to poly(Q) aggregation domains.

Tautomeric and Conformational Properties of Malonamide, NH2C(O)−CH2−C(O)NH2: Electron Diffraction and Quantum Chemical Study

The geometric structure of malonamide, NH2C(O)-CH2-C(O)NH2, has been investigated by gas electron diffraction (GED) and quantum chemical calculations (B3LYP and MP2 approximations with 6-311++G(3df,pd) basis sets). Both GED and quantum chemistry result in the existence of a single diketo conformer in the gas phase. According to GED refinement this conformer possesses (sc,ac) conformation with one C=O bond in synclinal orientation (dihedral angle tau(O=C-C-C)=49.0(3.0) degrees) and the other C=O bond in anticlinal orientation (dihedral angle tau(O=C-C-C)=139.5(3.3) degrees). The experimental geometric parameters are reproduced very closely by the B3LYP method.

Systematic Evaluation of the Conformational Properties of Aliphatic ω-Methoxy Methyl Esters

[structure: see text] A systematic conformational study of omega-methoxy methyl esters, CH(3)O-(CH2)n-COO-CH3 with n = 3 and 4, has been performed using quantum mechanical calculations at the MP2 level. Calculations have been carried out in both gas phase and chloroform solution, a polarizable continuum solvation model being used to represent the latter. Results have been compared with those recently obtained for the analogues omega-hydroxy acids, HO-(CH2)n-COOH with n = 3 and 4. The compounds with n = 3 clearly favor coiled conformations, the population expected for extended and semiextended conformations being very low. However, for compounds with n = 4 the minimum energy extended and semiextended structures become considerably more stable. The overall results indicate that the conformational preferences of the central aliphatic segment of omega-methoxy methyl esters and omega-hydroxy acids are not influenced by the formation of intramolecular O-H...O hydrogen bonds.

Systematic Evaluation of the Conformational Properties of Aliphatic ω-Hydroxy Acids

A systematic conformational study of omega-hydroxy acids, HO-(CH(2))(n)()-COOH with n ranging from 2 to 5, has been performed using quantum mechanical calculations at the MP2 level. To distinguish between intrinsic and environmentally induced conformational preferences, calculations have been carried out in both gas phase and chloroform solution, a polarizable continuum solvation model being used to represent the latter. Results indicate a consistent conformational behavior, as reflects the feature that the lowest energy minimum for n = 2, 3, 4, and 5 corresponds to the g+g-t, g+g+g-t, g-g+g+g-t, and g+g-g+g+g-t conformations, respectively. Furthermore, the stability of the extended and semi-extended conformations increases systematically with the size of the central aliphatic segment. The relationship between the size of the aliphatic segment and the stability of folded conformations is analyzed and discussed.

Extended form of a retro-inverso peptide stabilized by beta-sheet unidirectional H-bonds: Crystallographic and NMR evidence

The crystallographic investigation of the retro-inverso peptide Bz-S-gAla-R-mAla-NHPh reveals an extended backbone conformation where the NH groups of the gem-diamino alkyl moiety and the CO groups of the malonyl residue face side by side. This extended conformation, presenting all carbonyls on opposite sides of the NH groups, is stabilized by interstrand H-bonds running in a single direction of the parallel beta-sheets that characterize the crystal packing. These sheets differ from the beta-sheets formed by native amino acids only. (1)H-NMR nuclear Overhauser effect spectroscopy (NOESY) experiments suggest that a conformation similar to that found in the crystal also prevails in dimethylsulfoxide solution. Previous potential energy calculations of gem-diamino alkyl (g) and malonyl (m) Ala residues predicted that extended forms were less stable than the helical ones because of strong electrostatic repulsions between the parallel polar groups. Similar arguments were invoked to give more weight to helical forms of the retro-peptide units in the proposal of packing models of some nylons in their crystalline polar regions. The present findings show that both g and m Ala residues can experience the extended conformation in the beta-sheet aggregation. The energy increase occurring in one strand, due to the parallel orientation of consecutive peptide dipoles, is more than compensated by favorable cooperative interactions among head-to-tail aligned peptide dipoles of facing strands, resulting in the formation of two C==O...H==N H-bonds per residue.

Spinalin, a new glycine- and histidine-rich protein in spines of Hydra nematocysts

Here we present the cloning, expression and immunocytochemical localization of a novel 24 kDa protein, designated spinalin, which is present in the spines and operculum of Hydra nematocysts. Spinalin cDNA clones were identified by in situ hybridization to differentiating nematocytes. Sequencing of a full-length clone revealed the presence of an N-terminal signal peptide, suggesting that the mature protein is sorted via the endoplasmic reticulum to the post-Golgi vacuole in which the nematocyst is formed. The N-terminal region of spinalin (154 residues) is very rich in glycines (48 residues) and histidines (33 residues). A central region of 35 residues contains 19 glycines, occurring mainly as pairs. For both regions a polyglycine-like structure is likely and this may be stabilized by hydrogen bond-mediated chain association. Similar sequences found in loricrins, cytokeratins and avian keratins are postulated to participate in formation of supramolecular structures. Spinalin is terminated by a basic region (6 lysines out of 15 residues) and an acidic region (9 glutamates and 9 aspartates out of 32 residues). Western blot analysis with a polyclonal antibody generated against a recombinant 19 kDa fragment of spinalin showed that spinalin is localized in nematocysts. Following dissociation of the nematocyst's capsule wall with DTT, spinalin was found in the insoluble fraction containing spines and the operculum. Immunocytochemical analysis of developing nematocysts revealed that spinalin first appears in the matrix but then is transferred through the capsule wall at the end of morphogenesis to form spines on the external surface of the inverted tubule and the operculum.

Chain conformation in polyretropeptides III: design of a 3(10) helix using alpha,alpha-dialkylated amino acids and retropeptide bonds

Computer simulations have been used to design a polypeptide with a 3(10) helix conformation. The study has been been performed taking advantage of the intrinsic helix forming tendency of alpha-Aminoisobutyric acid. In order to avoid the formation of the alpha helix, which is the other common helical conformation adopted by alpha-Aminoisobutyric acid-based peptides, retropeptide bonds have been included in the sequence. Thus, retropeptides are not able to form the intramolecular hydrogen bonding interactions characteristic of the alpha helix. The influences of both the peptide length and the solvent have been examined and compared with those of the polypeptide without retropeptide bonds.

Effect of the Folding of Methylene Units in the Conformational Preferences of Small Diesters

The conformational preferences of dimethyl succinate and ethylene glycol diacetate have been explored in the gas phase using ab initio quantum mechanical calculations at the HF/6-31G(d) and MP2/6-31G(d) levels. Furthermore, the effects of both aqueous and carbon tetrachloride solvents have been estimated using the self-consistent reaction-field model developed by Miertus, Scrocco, and Tomasi and adapted to semiempirical methods by Orozco and Luque. The results have been interpreted in terms of the so-called "folding of methylene units", which is the tendency of the methylene units to adopt a gauche conformations when a short aliphatic segment is placed between two carbonyls. For dimethyl succinate the lowest energy conformation corresponds to the TTGTT as expected from our previous studies on the folding of methylene units. On the other hand, for ethylene glycol diacetate the global minimum is the TGG&Smacr;T conformation, which is stabilized by the simultaneous combination of two stereoelectronic effects: (i) the folding of methylene units and (ii) the gauche oxygen effects.

Omega amino acids in peptide design: incorporation into helices

Incorporation of easily available achiral omega-amino acid residues into an oligopeptide results in substitution of amide bonds by polymethylene units of an aliphatic chain, thereby providing a convenient strategy for constructing a peptidomimetic. The central Gly-Gly segment of the helical octapeptide Boc-Leu-Aib-Val-Gly-Gly-Leu-Aib-Val-OMe(1) has been replaced by delta-amino-valeric acid (delta-Ava) residue in the newly designed peptide Boc-Leu-Aib-Val-delta-Ava-Leu-Aib-Val-OMe(2). 1H-nmr results clearly suggest that in the apolar solvent CDCl3, the delta-Ava residue is accommodated into a folded helical conformation, stabilized by successive hydrogen bonds involving the NH groups of Val(3), delta-Ava(4), and Leu(5). The delta-Ava residue must adopt a gauche-gauche-trans-gauche-gauche conformation along the central polymethylene unit of the aliphatic segment, a feature seen in an energy-minimized model conformation based on nmr parameters. The absence of hydrogen bonding functionalities, however, limits the elongation of the helix. In fact, in CDCl3, the folded conformation consists of an N-terminal helix spanning residues 1-4, followed by a Type II beta-turn at residues 5 and 6, whereas in strongly solvating media like (CD3)2SO, the unfolding of the N-terminal helix results in beta-turn conformations at Leu(1)-Aib(2). The Type II beta-turn at the Leu(5)-Aib(6) segment remains intact even in (CD3)2SO.CD comparisons of peptides 1 and 2 reveal a "nonhelical" spectrum for 2 in 2,2,2-trifluoroethanol.

Towards the understanding of the folding of methylene units in the glutamine residue

The conformational preferences of the methylenic sequence in the side chain of the glutamine residue were investigated by ab initio and semi-empirical quantum mechanical calculations and examination of both the Brookhaven Protein Databank and Cambridge Structural Data Base. The results were analysed on the basis of our previous findings about the folding of methylene groups in aliphatic segments. Both energy calculations and the crystallographic structure of small peptides indicate that methylene units of the glutamine residue tend to fold in a gauche conformation. In contrast, such groups usually adopt an all-trans conformation in proteins due basically to the entropic and solvent contributions. These results have been demonstrated by computing the entropic correction to the free energy and evaluating the solvent effects through SCRF calculations.