Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions

Abstract

Turns are irregular secondary structure elements with a hydrogen bond or a specific Calpha-Calpha distance between the first and the last residue. They are up to six residues in length. Here, we present a uniform classification for all normal (CO(i) - NH(i+n) hydrogen bond), open (a Calpha(i)-Calpha(i+n) distance up to 10 A), and reverse (NH(i) - CO(i+i) hydrogen bond) turn families based on current structural data. Considering the large amount of data evaluated, this classification likely covers quite comprehensively most of the possible conformations of turns. All turn structures of a nonredundant dataset of 1903 protein chains were retrieved using Relibase and clustered using emergent self-organizing maps. This leads to three normal, four open, and five reverse turn families with several new turn-types. Based on the amino acid propensities, the achieved separation into normal, open, and reverse turn families seems convincing. In combination with beta-sheet and helix classification on average 96% of the given protein chain can now be successfully classified.

Conserved Properties of Polypeptide Transport-associated (POTRA) Domains Derived from Cyanobacterial Omp85

“…The L1-loop contains conserved ␤-turns (Fig. 6), and these secondary structures are documented protein-protein interaction motifs (49). However, the POTRA domains in FhaC are involved in crystal packing, and the superposition may thus not reflect the state in solution, if the POTRA domains are able to rotate.…”

“…The secondary structure of a ␤-turn is four amino acids in length and (usually) requires a glycine at the fourth position (49). Sequence conservation suggests that two ␤-turns are common to long L1-loops; short L1-loops may still contain one ␤-turn (see sequence logos in Fig.…”

Identifying Protein β-Turns with Vibrational Raman Optical Activity

“…However, for practical applications this is only of minor importance, as several turn types such as I' or II' occur only very seldom. On the other hand, turn type I is by far the most important one in the sense that it occurs most often (in the original data set used by Hutchinson and Thornton, [22] about one third of all turns belonged to type I, while in a larger data set used by Koch and Klebe, [23] over 80 % of all turns belonged to this class). Thus, identifying spectral features common to type I b-turns would already be very helpful.…”

“…Note that this scheme agrees with the one proposed in ref. [23] for all turn types considered herein. Furthermore, we will only concern ourselves with turns belonging to types I, I', II, II', or VIII as type IV is a miscellaneous category and types VIa1, VIa2, and VIb occur only seldom and have to fulfill special requirements.…”

“…If these two additional criteria are not fulfilled, the distance between the C a i and the C a iþ3 atoms is bigger than 7 . [21] Even though improved classification schemes have been developed recently, [23] we will adopt the well-known classification scheme by Hutchinson and Thornton as presented in Table 2. Note that this scheme agrees with the one proposed in ref.…”