The origin of β-strand bending in globular proteins.
BACKGROUND
Many β-strands are not flat but bend and/or twist. However, although almost all β-strands have a twist, not all have a bend, suggesting that the underlying force(s) driving β-strand bending is distinct from that for the twist. We, therefore, investigated the physical origin(s) of β-strand bends.


METHODS
We calculated rotation, twist and bend angles for a four-residue short frame. Fixed-length fragments consisting of six residues found in three consecutive short frames were used to evaluate the twist and bend angles of full-length β-strands.


RESULTS
We calculated and statistically analyzed the twist and bend angles of β-strands found in globular proteins with known three-dimensional structures. The results show that full-length β-strand bend angles are related to the nearby aromatic residue content, whereas local bend angles are related to the nearby aliphatic residue content. Furthermore, it appears that β-strands bend to maximize their hydrophobic contacts with an abutting hydrophobic surface or to form a hydrophobic side-chain cluster when an abutting hydrophobic surface is absent.


CONCLUSIONS
We conclude that the dominant driving force for full-length β-strand bends is the hydrophobic interaction involving aromatic residues, whereas that for local β-strand bends is the hydrophobic interaction involving aliphatic residues.
Department of Bioinformatics, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, 192-8577, Japan. fujiwara@soka.ac.jp.
Kazuo
K
Fujiwara
Department of Bioinformatics, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, 192-8577, Japan. sin_ebisawa@yahoo.co.jp.
Shinichi
S
Ebisawa
Department of Bioinformatics, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, 192-8577, Japan. bari-fuwa-chiffon@t.vodafone.ne.jp.
Yuka
Y
Watanabe
Department of Bioinformatics, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, 192-8577, Japan. todafone_hiro@yahoo.co.jp.
Hiromi
H
Fujiwara
Department of Bioinformatics, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, 192-8577, Japan. ikeguchi@soka.ac.jp.
Masamichi
M
Ikeguchi
D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins