Beta-turn new classification and its some features in proteins.
An inspection of the phi-psi angle distribution strongly suggests that protein folding is highly constrained. A number of researchers have even suggested that a relatively small set of discrete phi-psi regions might be sufficient to describe most protein conformation. The total of 541 tight turns from 101 non-identical proteins were extracted form Brookhaven DataBank. The dihedral values of tight turns were scattered into the seven regions on the Ramachandran plot. These seven regions were called A1, A2, B1, B2, B22, T1 and T2. A1 and A2 are the traditional alpha-helix regions, B1, B2 and B22 the beta-strand regions, T1 and T2 the beta-turn regions. The A2 and T2 regions were not defined as "discrete" or single points but rather as one dimensional extended states. Based on the geometry of the two central residues of the tight turns, the new classification of beta-turn was defined. This classification of the majority of beta-turns fell into only six of the possible forty nine region combinations and were identifiable with the traditional nomenclature of Venkatachalam(1), but much simpler. The function of beta-turn in the conformation of proteins was studied. The hydrophobicity for different type turns was discussed. It shows that beta-turns have very strong hydrophilic property, so they are usually situated at the folding protein surface. The features of beta-turn and its amino acid distribution in this 541 beta-turn group and different type beta-turn were given.
Zhu
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Department of Computer Science, Institute of Basic Medical Science, CAMS & PUMC, Beijing 100005.
Vajda
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Smith
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TF
D000595:Amino Acid Sequence; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D011506:Proteins