1. Structural and sequence features of beta-turns in beta-hairpins
Bharat Madan, and Sun-Gu Lee*
Department of Chemical and Biochemical Engineering, Pusan National University, Busan , Republic of Korea
TEL: , FAX:
Abstract
Beta-turns in beta-hairpins have been implicated as important sites in protein folding. In particular, two residue β-turns, the most abundant connecting elements in beta-hairpins, have been a major target for engineering protein stability and folding. In this study, we attempted to investigate and update the structural and sequence properties of two residue turns in beta-hairpins with a large data set. For this, 3977 beta-turns were extracted from 2394 non-homologous protein chains and analyzed. First, the distribution, dihedral angles and twists of two residue turn types were determined, and compared with previous data. The trend of turn type occurrence and most structural features of the turn types were similar to previous results, but for the first time Type II turns in beta-hairpins were identified. Second, sequence motifs for the turn types were devised based on amino acid positional potentials of two-residue turns, and their distributions were examined. From this study, we could identify code-like sequence motifs for the two residue beta-turn types. Finally, structural and sequence properties of beta-strands in the beta-hairpins were analyzed, which revealed that the beta-strands showed no specific sequence and structural patterns for turn types. The analytical results in this study are expected to be a reference in the engineering or design of beta-hairpin turn structures and sequences.
Background
Beta-turns account for nearly 25% of the protein architecture.
They are found at regions of chain reversal in proteins and are an integral
part of beta-hairpin.
They consists of 4 residues (i to i+3) and are characterized into various
types based on phi/psi angles of residues at i+1 and i+2 positions.
Four main types commonly found in proteins are types – I, II, I’ and II’.
Figure 1. Four most common types of beta-turns found in proteins
Objective
Why beta-hairpin beta-turns ?
PDB (Protein Data Bank)
Structural and sequence characterization of two residue β-hairpin turns
Two beta-strands + turn = beta-hairpin.
Turns are an integral part of beta-hairpins.
Turns help in bringing the two strands of a hairpin
farther in primary sequence, closer in 3-D structure.
Thus, help in folding of a beta-hairpin.
Therefore, turns can act as nucleation sites of
protein folding.
Amino acid code identification for turns
Turn Type distribution
Positional Preferences of amino-acids in turns
Dihedral angle distribution
Sheet-twist
distribution
Beta-turn twist distribution
Extract structures containing two-residue beta-hairpins
Figure 2. Overview of the entire study.
Results
Turn type distribution in beta-hairpins
Turn twist distribution of beta-turns
Sheet twist distribution
Figure 3.. Turn type distribution in β-hairpins.
Dihedral angle preference of beta-turns
Position i+1
Type I’
Position i+2
Figure 5. Turn twist distribution of beta-turns.
Amino acid preferences in beta-turns
Type-I’
Type-II’
Type II’
Figure 7.Sheet twist distribution of β-hairpins.
Conclusion
Types I’ and II’ beta-turns are found predominantly in
β- hairpins.
Type I’ is evolutionarily more conserved than the
other turn types.
Each turn type has distinct residue preference.
This suggests that turn sequences do not occur
randomly in nature.
The higher occurrence of type I’ turns , with defined
residue preference suggests they could be efficient
in protein folding.
The results presented in this study can be used in
the efficient design of beta-hairpin β-turns.
Type-I
Type-II
Type I
Figure 6.Positional potentials of amino acids in beta-turns.
Amino acid codes for beta-turns
References
Type II
Based on the most preferred amino acids at positions i+1 and i+2, amino acid codes were defined for each beta-turn type .
33. Chou PY, Fasman GD. β-turns in proteins. J Mol Biol 1977;115:
28. Gunasekaran K, Ramakrishnan C, Balaram P. Beta-hairpins in proteins revisited: lessons for de novo design. Protein Eng 1997;10:
25. de Alba E, Rico M, Jimenez MA. The turn sequence directs beta-strand alignment in designed beta-hairpins. Protein Sci 1999;8:
8. Hutchinson EG, Thornton JM. A revised set of potentials for beta-turn formation in proteins. 1994;3:
Madan B, Seo SY, Lee SG. Structural and sequence features of two residue turns in beta-hairpins. Proteins 2014.
( doi/ /prot.24526)
Table 1. Amino acid codes for beta-turns
Type I’
Type II’
Type I
Type II
X-XP,G-G-XG
X-G-XG-XG
X-XP,G-XG-G
X-P-XG-G
X-P-G-XG
X= all 20 amino acids except the superscripted ones.
Figure 4. Ramachandran plots of Φ/Ψ preference for beta-turn residues i+1 and i+2.