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Abstract:
Four novel structural motifs were found and characterized in alpha-helical proteins. One of them consists of three alpha helices and can be represented as a combination of an alpha-alpha corner and an L-shaped structure. Its second alpha helix is a part of both one of the two alpha helices of the alpha-alpha corner and one of the two L-structure helices. The second structural motif, named the ABCD unit, consists of four alpha helices A, B, C, and D. These are consecutive in sequence and arranged in space in such a manner that the helices B, C, and D form a left-handed superhelix and the helix A is located between the helices B and D and is approximately antiparallel to them. The third motif, alpha helix-loop-alpha helix, consists of two alpha helices and a long connection. Its alpha helices are arranged in an approximately parallel manner and together with the long connection, form a left-handed alpha-1-alpha superhelix in space. The fourth structural motif considered is formed by four consecutive alpha helices. It is named the phi motif, because its overall shape is reminiscent of the Greek letter phi. Various variants of these motifs are analyzed on numerous examples of proteins with the known spatial structures.