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In biochemistry, a Ramachandran plot (also known as a Rama plot, a Ramachandran diagram or a [φ,ψ] plot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, [1] is a way to visualize energetically allowed regions for backbone dihedral angles ( also called as torsional angles , phi and psi angles ) ψ ...
Intramolecular transesterification, resulting in a branched polypeptide. In inteins, the new ester bond is broken by an intramolecular attack by the soon-to-be C-terminal asparagine. Intermolecular transesterification can transfer a whole segment from one polypeptide to another, as is seen in the Hedgehog protein autoprocessing.
Polypeptide direction, NH 2 and COOH termini Small arrows on one or both of the termini, or letters. For β-strands, the direction of the arrow is sufficient. Today, the direction of the polypeptide chain is often indicated by a colour ramp. Disulfide bonds Interlocked SS symbol or a zigzag, like a stylized lightning stroke.
Secondary structure refers to highly regular local sub-structures on the actual polypeptide backbone chain. Two main types of secondary structure, the α-helix and the β-strand or β-sheets, were suggested in 1951 by Linus Pauling. [5] These secondary structures are defined by patterns of hydrogen bonds between the
Three sequences, UAG, UGA, and UAA, known as stop codons, [note 1] do not code for an amino acid but instead signal the release of the nascent polypeptide from the ribosome. [7] In the standard code, the sequence AUG—read as methionine—can serve as a start codon and, along with sequences such as an initiation factor, initiates translation.
The principles applied in the 1950 paper to theoretical polypeptide structures, true of the 3 10 helix, included: [2] The chains are held together by hydrogen bonding between the hydrogen and oxygen atoms of different by nearby amide (peptide) links formed as the amino acids condense to form the polypeptide chain. These form helical ...
A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation. The supramolecular association of β-sheets has been implicated in the formation of the fibrils and protein aggregates observed in amyloidosis, Alzheimer's disease and other proteinopathies.
Topology of a transmembrane protein refers to locations of N- and C-termini of membrane-spanning polypeptide chain with respect to the inner or outer sides of the biological membrane occupied by the protein. [1] Group I and II transmembrane proteins have opposite final topologies.