A theoretical study of the stability of disulfide bridges in various β-sheet structures of protein segment models

Electron structure calculations are used to explore stabilization effects of disulfide bridges in a (Ala–Cys–Ala–Cys–Ala)2 β-sheet model both in the parallel and the anti-parallel (103142 and 143102) arrangements. Stabilities were calculated using a redox reaction involving a weak oxidizing agent (1,4-benzoquinone). The results show that both inter- and intra-strand disulfide SS-bridges stabilize the β-sheet backbone fold. However, inter-strand SS-bridges give more stability than their intra-strand counterparts. For both single and double disulfide linked conformations, stabilization was larger for the parallel than for the anti-parallel β-sheet arrangements

Impairment of a model peptide by oxidative stress: Thermodynamic stabilities of asparagine diamide C(alpha)-radical foldamers

Electron structure calculations on N-acetyl asparagine N-methylamide were performed to identify the global minimum from which radicals were formed after H-abstraction by the OH radical. It was found that the radical generated by breaking the C–H bond of the alpha-carbon was thermodynamically the most stable one in the gas- and aqueous phases. The extended ((beta)L and (beta)D) backbone conformations are the most stable, but syn–syn or inverse gamma-turn ((gamma)L) and gamma-turn ((gamma)D) have substantial stability too. The highest energy conformers are the degenerate eL and eD foldamers. Clearly, the most stable beta foldamer is the most likely intermediate for racemization

Влияние семантики локализованности на текстовую внешнетемпоральную транспозицию

Языковая временная семантика в лингвистических исследованиях последних лет рассматривается как широкая сфера языковых/речевых отношений различных категорий (грамматических, функционально- семантических, текстовых), т.е. как область пересечения, иногда концентрации аспектуального, собственно темпорального, таксисного и другого аналогичного содержания, где центральное место принадлежит глагольной единице, потенциальные функциональные возможности которой и определяют указанные грамматические отношения

Helix compactness and stability: Electron structure calculations of conformer dependent thermodynamic functions

Structure, stability, cooperativity and molecular packing of two major backbone forms: 310-helix and β-strand are investigated. Long models HCO-(Xxx)n-NH2 Xxx = Gly and (l-)Ala, n ⩽ 34, are studied at two levels of theory including the effect of dispersion forces. Structure and folding preferences are established, the length modulated cooperativity and side-chain determined fold compactness is quantified. By monitoring ΔG°β→α rather than the electronic energy, ΔEβ→α, it appears that Ala is a much better helix forming residue than Gly. The achiral Gly forms a more compact 310-helix than any chiral amino acid residue probed here for l-Ala

Atropisomerism of the Asn α Radicals Revealed by Ramachandran Surface Topology

C radicals are typically trigonal planar and thus achiral, regardless of whether they originate from a chiral or an achiral C-atom (e.g., C−H + •OH → C• + H2O). Oxidative stress could initiate radical formation in proteins when, for example, the H-atom is abstracted from the Cα-carbon of an amino acid residue. Electronic structure calculations show that such a radical remains achiral when formed from the achiral Gly,or the chiral but small Ala residues. However, when longer side-chain containing proteogenic amino acid residues are studied (e.g., Asn), they provide radicals of axis chirality, which in turn leads to atropisomerism observed for the first time for peptides. The two enantiomeric extended backbone structures, •βL and •βD, interconvert via a pair of enantiotopic reaction paths, monitored on a 4D Ramachandran surface, with two distinct transition states of very different Gibbs-free energies: 37.4 and 67.7 kJ/mol, respectively. This discovery requires the reassessment of our understanding on radical formation and their conformational and stereochemical behavior. Furthermore, the atropisomerism of proteogenic amino acid residues should affect our understanding on radicals in biological systems and, thus, reframes the role of the D-residues as markers of molecular aging