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According to one definition, a turn is a structural motif where the C α atoms of two residues separated by a few (usually 1 to 5) peptide bonds are close (less than 7 Å [0.70 nm]). [1] The proximity of the terminal C α atoms often correlates with formation of an inter main chain hydrogen bond between the corresponding residues.
The four types of beta turn are distinguished by the φ, ψ angles of residues i+1 and i+2 as shown in the table below giving the typical average values. Glycines are especially common as amino acids with positive φ angles; for prolines such a conformation is sterically impossible but they occur frequently at amino acid positions where φ is ...
In biochemistry and molecular genetics, an AP site (apurinic/apyrimidinic site), also known as an abasic site, is a location in DNA (also in RNA but much less likely) that has neither a purine nor a pyrimidine base, either spontaneously or due to DNA damage. It has been estimated that under physiological conditions 10,000 apurinic sites and 500 ...
The standard hydrogen-bond definition for secondary structure is that of DSSP, which is a purely electrostatic model. It assigns charges of ± q 1 ≈ 0.42 e to the carbonyl carbon and oxygen, respectively, and charges of ± q 2 ≈ 0.20 e to the amide hydrogen and nitrogen, respectively.
The model is used in a variety of biochemical situations other than enzyme-substrate interaction, including antigen–antibody binding, DNA–DNA hybridization, and protein–protein interaction. [ 17 ] [ 18 ] It can be used to characterize a generic biochemical reaction, in the same way that the Langmuir equation can be used to model generic ...
Inverse Warburg effect Another model has been described in tumor cells in an obesity model called Warburg effect inversion . Whereas in the reverse model, the stroma of the microenvironment produces energy-rich nutrients, in a context of obesity these nutrients already exist in the bloodstream and in the extracellular fluid (ECF).
In biochemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. [1] This process and its inverse, dephosphorylation , are common in biology . [ 2 ] Protein phosphorylation often activates (or deactivates) many enzymes .
Flow processes may also be important. This more complex behavior implies that a model with several parameters is required to describe the data; models with only either a single diffusion constant D or a single off rate constant, k off, are inadequate. There are models with both diffusion and reaction. [2]