Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favorability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB)versus Thr(HB)-Asn(nHB). Significantly (p < or = 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi1 rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi1 conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi1 and chi2 conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favorability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http://www.rubic.rdg.ac.uk/betapairprefsparallel/).

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favourability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB) versus Thr(HB)-Asn(nHB). Significantly (p <= 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi(1) rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi(1) conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi(1) and chi(2) conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favourability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http:// www.rubic.rdg.ac.uk/betapairprefsparallel/). (c) 2005 Elsevier Ltd. All rights reserved.

Amino-acid cycling drives nitrogen fixation in the legume - Rhizobium symbiosis

The biological reduction of atmospheric N-2 to ammonium (nitrogen fixation) provides about 65% of the biosphere's available nitrogen. Most of this ammonium is contributed by legume rhizobia symbioses(1), which are initiated by the infection of legume hosts by bacteria (rhizobia), resulting in formation of root nodules. Within the nodules, rhizobia are found as bacteroids, which perform the nitrogen fixation: to do this, they obtain sources of carbon and energy from the plant, in the form of dicarboxylic acids(2,3). It has been thought that, in return, bacteroids simply provide the plant with ammonium. But here we show that a more complex amino-acid cycle is essential for symbiotic nitrogen fixation by Rhizobium in pea nodules. The plant provides amino acids to the bacteroids, enabling them to shut down their ammonium assimilation. In return, bacteroids act like plant organelles to cycle amino acids back to the plant for asparagine synthesis. The mutual dependence of this exchange prevents the symbiosis being dominated by the plant, and provides a selective pressure for the evolution of mutualism.

Amino terminal interaction in the prion protein identified using fusion to green fluorescent protein

In contrast to the well-characterized carboxyl domain, the amino terminal half of the mature cellular prion protein has no defined structure. Here, following fusion of mouse prion protein fragments to green fluorescence protein as a reporter of protein stability, we report extreme variability in fluorescence level that is dependent on the prion fragment expressed. In particular, exposure of the extreme amino terminus in the context of a truncated prion protein molecule led to rapid degradation, whereas the loss of only six amino terminal residues rescued high level fluorescence. Study of the precise endpoints and residue identity associated with high fluorescence suggested a domain within the amino terminal half of the molecule defined by a long-range intramolecular interaction between 23KKRPKP28 and 143DWED146 and dependent upon the anti-parallel beta-sheet ending at residue 169 and normally associated with the structurally defined carboxyl terminal domain. This previously unreported interaction may be significant for understanding prion bioactivity and for structural studies aimed at the complete prion structure.

1,3-Dipolar cycloadditions to unsymmetrical ketone-derived chiral stabilized azomethine ylides: strategies for the synthesis of highly substituted amino acids

We report herein, the first generation of unsymmetrical ketone-derived chiral stabilized azomethine ylides. Intrairiolecular and intermolecular cycloaddition strategies have been utilized to synthesize both an enantiornerically pure bicyclic proline derivative and an enantionierically pure beta-hydroxy-alpha-amino acid.

Amyloid-like fibril-forming supramolecular beta-sheets from a beta-turn forming tripeptide containing non-coded amino acids: the crystallographic signature

The crystal structure of a terminally protected tripeptide Boc-Leu-Aib-beta-Ala-OMe 1 containing non-coded amino acids reveals that it adopts a beta-turn structure, which sell-assembles to form a supramolecular beta-sheet via non-covalent interactions. The SEM image of peptide 1 exhibits amyloid-like fibrillar morphology in the solid state. (C) 2002 Elsevier Science Ltd. All rights reserved.

Supramolecular peptide helix from a novel double turn forming peptide containing a beta-amino acid

A single-crystal X-ray diffraction study of the terminally protected tetrapeptide Boc-beta-Ala-Aib-Leu-Aib-OMe 1 (Aib: alpha-aminoisobutyric acid; beta-Ala: beta-Alanine) reveals that it adopts a new type of double turn structure which self-associates to form a unique supramolecular helix through intermolecular hydrogen bonds. Scanning electron microscopic studies show that peptide 1 exhibits amyloid-like fibrillar morphology in the solid state. (C) 2003 Elsevier Science Ltd. All rights reserved.

Low molecular weight organogelators from self-assembling synthetic tripeptides with coded amino acids: morphological, structural, thermodynamic and spectroscopic investigations

A series of self-assembling terminally blocked tripeptides (containing coded amino acids) form gels in various aromatic solvents including benzene, toluene, xylenes at low concentrations. However these tripeptides do not form gels in aliphatic hydrocarbons like n-hexane, cyclohexane, n-decane etc. Morphological studies of the dried gel indicate the presence of an entangled fibrous network, which is responsible for gelation. Differential scanning calorimetric (DSC) studies of the gels produced by peptide 1 clearly demonstrates thermoreversible nature of the gel and tripeptide-solvent complex may be produced during gel formation. FT-IR and H-1 NMR studies of the gels demonstrate that an intermolecular hydrogen-bonding network is formed during gelation. Single crystal X-ray diffraction studies for peptides 1, 2 and 3 have been performed to investigate the molecular arrangement that might be responsible for forming the fibrous network of these self-assembling peptide gelators. It has been found that the morph responsible for gelation of peptides 1, 2 and 3 in benzene is somewhat different from that of its xerogel.

Stabilisation of two Cu(I)-amino N bonds in presence of imino N's

Two structurally characterised examples of air stable Cu-1 (amino N)(2)(imino N)(2) chromophores having a Cu(II/I) potential of 0.01-0.19 V vs SCE in CH2Cl2 are provided using two tetradentate N-donor ligands.

beta-Sheet mediated self-assembly of dipeptides of omega-amino acids and remarkable fibrillation in the solid state

Single crystal X-ray diffraction studies show that the extended structure of dipeptide I Boc-beta-Ala-m-ABA-OMe (m-ABA: meta-aminobenzoic acid) self-assembles in the solid state by intermolecular hydrogen bonding to create an infinite parallel P-sheet structure. In dipeptide II Boc-gamma-Abu-m-ABA-OMe (gamma-Abu: gamma-aminobutyric acid), two such parallel beta-sheets are further cross-linked by intermolecular hydrogen bonding through m-aminobenzoic acid moieties. SEM (scanning electron microscopy) studies reveal that both the peptides I and II form amyloid-like fibrils in the solid state. The fibrils are also found to be stained readily by Congo red, a characteristic feature of the amyloid fiber whose accumulation causes several fatal diseases such as Alzheimer's, prion-protein etc.

Conformational and self-assembly studies of helix forming hexapeptides containing two alpha-amino isobutyric acids

Single crystal X-ray diffraction studies reveal that three hexapeptides with general formula Boc-Ile-Aib-Xx-Ile-Aib-Yy-OMe, where Xx and Yy are Leu in peptide I, Len and Phe in peptide II, and Phe and Leu in peptide III, respectively, adopt equivalent conformations that can be described as mixed 3(10)/alpha-helice with two 4 -> 1 and two 5 -> 1 intramolecular N-H center dot center dot center dot O=C H-bonds. The peptides do not generate any helixterminating Schellman motif despite having Aib at the penultimate position from C-terminus. In the crystalline state, the helices are packed in head-to-tail fashion through intermolecular hydrogen bonds to create supramolecular helical structures. The CD Studies of the three hexapeptides in acetonitrile indicate that they are folded in well-developed 3(10)-helical structures. NMR studies of peptide I in CDCl3 also suggest the formation of a homogeneous 3 m-helical structure. The field emission scanning electron microscopic (FE-SEM) images of peptide 11 in the solid state reveal a non-twisted ribbon-like morphology, which is formed through lateral association of non-twisted filaments. (c) 2007 Elsevier Ltd. All rights reserved.

Stabilization of two smallest possible diastereomeric beta-hairpins in a water soluble tetrapeptide containing non-coded alpha-amino isobutyric acid (Aib) and m-amino benzoic acid

Single crystal X-ray diffraction study reveals that the water soluble tetrapeptide H2N-Ile-Aib-Leu-m-ABA-CO2H, containing non-coded Aib (alpha-amino isobutyric acid) and m-ABA (meta-amino benzoic acid), crystallizes with two smallest possible diastereomeric beta-hairpin molecules in the asymmetric unit. Although in both of the molecules the chiralities at Ile(1) and Leu(3) are S, a conformational reversal in the back bone chain is observed to produce the beta-hairpins with beta-turn conformations of type II and II'. Interestingly Aib which is known to adopt helical conformation, adopts unusual semi-extended conformation with phi: -49.5(5)degrees, psi: 135.2(5)degrees in type II and phi: 50.6(6)degrees. psi: -137.0(4)degrees in type II' for occupying the i + 1 position of the beta-turns. The two hairpin molecules are further interlocked through intermolecular hydrogen bonds and electrostatic interactions between CO2- and -+NH3 groups to form dimeric supramolecular beta-hairpin aggregate in the crystal state. The CD measurement and 2D NMR study of the peptide in aqueous medium support the existence of beta-hairpin structure in water. (C) 2009 Elsevier B.V. All rights reserved.

Design of a turn-linker-turn foldamer by incorporating meta-amino benzoic acid in the middle of a helix forming hexapeptide sequence: A helix breaking approach

Single crystal X-ray diffraction studies reveal that the incorporation of meta-amino benzoic acid in the middle of a helix forming hexapeptide sequence such as in peptide I Boc-Ile(1)-Aib(2)-Val(3)-m-ABA(4)-Ile(5)-Aib(6)-Leu(7)-OMe (Aib: alpha-amino isobutyric acid: m-ABA: meta-amino benzoic acid) breaks the helix propagation to produce a turn-linker-turn (T-L-T) foldamer in the solid state. In the crystalline state two conformational isomers of peptide I self-assemble in antiparallel fashion through intermolecular hydrogen bonds and aromatic pi-pi interactions to form a molecular duplex. The duplexes are further interconnected through intermolecular hydrogen bonds to form a layer of peptides. The layers are stacked one on top of the other through van der Waals interactions to form hydrophilic channels filled with solvent methanol. (C) 2009 Elsevier B.V. All rights reserved.

Novel charge transfer supramolecular assemblies with Keggin anions and 2-amino-5-nitropyridine

Several novel compounds with the non-linear optical chromophore 2-amino-5-nitropyridine (2A5NP) and Keggin polyoxoanions (alpha-isomers), having the general formula (2A5NP)(m)H-n[XM12O40]center dot xH(2)O, M = Mo, W, were synthesised. Compounds were obtained with X = P, n = 3, m = 3 and 4 and X = Si, n = m = 4 ( x = 2 - 6). Thus, for each of the anions [PMo12O40](3-) and [PW12O40](3-) two different compounds were obtained, with the same anion and organic counterpart but with a different stoichiometric ratio. These presented different charge transfer properties and thermal stability. All compounds were characterised by spectroscopic and analytical techniques. The single crystal X-ray diffraction structure of (2A5NP)(4)H-3[PMo12O40]center dot 2.5H(2)O center dot 0.5C(2)H(5)OH showed that the water solvent molecules and the organic chromophores are assembled via infinite one-dimensional chains of hydrogen bonds with formation of open channels, which accommodate [ PMo12O40] 3- and ethanol solvent molecules.