Effect Of Amino Acid Side Chain Research Articles

Quantitation of the nearest-neighbour effects of amino acid side-chains that restrict conformational freedom of the polypeptide chain using reversed-phase liquid chromatography of synthetic model peptides with l- and d-amino acid substitutions

Side-chain backbone interactions (or “effects”) between nearest neighbours may severely restrict the conformations accessible to a polypeptide chain and thus represent the first step in protein folding. We have quantified nearest-neighbour effects ( i to i + 1) in peptides through reversed-phase liquid chromatography (RP-HPLC) of model synthetic peptides, where l- and d-amino acids were substituted at the N-terminal end of the peptide sequence, adjacent to a l-Leu residue. These nearest-neighbour effects (expressed as the difference in retention times of l- and d-peptide diastereomers at pHs 2 and 7) were frequently dramatic, depending on the type of side-chain adjacent to the l-Leu residue, albeit such effects were independent of mobile phase conditions. No nearest-neighbour effects were observed when residue i is adjacent to a Gly residue. Calculation of minimum energy conformations of selected peptides supported the view that, whether a l- or d-amino acid is substituted adjacent to l-Leu, its orientation relative to this bulky Leu side-chain represents the most energetically favourable configuration. We believe that such energetically favourable, and different, configurations of l- and d-peptide diastereomers affect their respective interactions with a hydrophobic stationary phase, which are thus quantified by different RP-HPLC retention times. Side-chain hydrophilicity/hydrophobicity coefficients were generated in the presence of these nearest-neighbour effects and, despite the relative difference in such coefficients generated from peptides substituted with l- or d-amino acids, the relative difference in hydrophilicity/hydrophobicity between different amino acids in the l- or d-series is maintained. Overall, our results demonstrate that such nearest-neighbour effects can clearly restrict conformational space of an amino acid side-chain in a polypeptide chain.

Effect of amino acid side-chain on fragmentation of cyclic peptide ions: differences of ESI-MS/CID mass spectra of toxic heptapeptide microcystins containing ADMAdda instead of Adda

Characteristics of collision-induced decomposition (CID) spectra recorded following electrospray ionization (ESI) of toxic heptapeptide microcystins containing (2S,3S,8S,9S)-3-amino-9-acetoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid (ADMAdda) have been investigated in detail and compared with those from compounds containing (2S,3S,8S,9S)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid (Adda). A significant difference in their CID spectra was observed in the cleavage of cyclic structures in low-energy CID processes due to the effect of the amino acid side-chain on fragmentation. Microcystins containing ADMAdda produced mostly b-type ions. Fragment ions predicted on the basis of the known fragmentation of cyclic peptides and linear-peptide b-type ions, predicted by the Peptide Matching (PEPM) program, matched well with peaks in the CID spectra. A neutral loss of CH3COOH from the ADMAdda residues was observed in the CID spectra of doubly charged ions, [M + 2H]2+. The present study sugg...

Influence of amino acid and peptide counterions on the conformation of DNA

We describe fibre diffraction studies on the interaction of DNA with different amino acids and peptides. The B form of DNA, with ten base-pairs per turn, is always found at high levels of humidity. We suggest that this pitch is observed because the DNA molecules are maintained in a straight position. In solution, the DNA molecules are bent and may have a larger pitch. The A form of DNA is never found upon dehydration. Instead, the B form may be either stabilized by the counterions or altered so that the number of base-pairs per helical turn decreases upon dehydration. Alteration is favoured either by small counterions that have a single charge or by large basic polypeptides and proteins. Stabilization is favoured by small counterions that have several charged groups. A third type of behaviour is found with some amino acids that contain hydrophobic groups, which destabilize the secondary structure of DNA, probably due to a modification of its intramolecular interactions. We have not detected any specific effect of amino acid side-chains, although the amino acid sequence has a clear influence on the interaction. We think that these observations are of interest in the pursuit of more detailed crystallographic studies on protein-DNA interactions.