Peptide Bond In subject area: Biochemistry, Genetics and Molecular Biology Proteins are made by the formation of peptide bonds between the amino group of one amino acid and the carboxyl group of another. From: Quantitative Human Physiology (Second Edition), 2017 About this pageSet alert ...
Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. Therefore, the variability of peptide bond geometry in proteins is remarkably reproduced by extremely simplified systems since local factors ...
Several statistical and quantum chemical investigations performed in the last two decades have unveiled a strong correlation between protein backbone geometry (bond angles, dihedral angles and pyramidalization) and the local conformation (Berkholz et al. 2012 ; Berkholz et al. 2009 ; Esposito et al....
β-sheet structures stabilized by 2–4 disulfide bridges; (2) unstructured peptides that fold into α-helices upon contact with membranes; (3) peptides with predominance of certain amino-acids adopting extended helices; (4) peptides with loop structures formed by a single disulfide bond. Despite...
we then attribute this energy to the encoded conformation. In optimizing over positions of atoms side chain atoms, we restricted these to live on the lattice, though this is not strictly necessary. Finally, atomic bond distances were always fixed to 1.5 Å. This corresponds in order of mag...
From the “transition state” the system evolves toward thebona fidethioether bond, see Fig.3D. The chlorine atom leaves and diffuses into solvent (in a form of chloride anion). At the end of the Trxnperiod the force field terms corresponding to the old covalent geometry are reduced to ni...
Two distance constraints were set per hydrogen bond; 1.9 Å (O-HN) and 2.9 Å (O-N). The structure calculation was performed with the program X-PLOR version 3.1 51, 52) using standard protocols for simulated annealing [53]. For the final calculation a total of 802 NOE distance ...
“Stapling,”“hydrocarbon-stapling” as used herein introduces into a peptide at least two moieties capable of undergoing reaction to promote carbon-carbon bond formation that can be contacted with a reagent to generate at least one cross-linker between the at least two moieties. Stapling provides...
proteins/ molecular structure stabilitycovalent bondThe present study focuses on important questions associated with modeling of peptide and protein stability. Computing at different levels of theory (RHF, B3LYP) for a representative ensemble of conformers of di- and tripeptides of alanine, we found ...
by a (CH2NH) reduced bond, a (NHCO) retro-inverso bond, a (CH2-O) methylene-oxy bond, a (CH2-S) thiomethylene bond, a (CH2CH2) carba bond, a (CO—CH2) cetomethylene bond, a (CHOH—CH2) hydroxyethylene bond), a (N—N) bound, a E-alcene bond or also a —CH═CH-bond...