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On the importance of backbone loop and peptide flip in the Walker sequence in F-1-ATPase action

Ramasarma, T and Ramakrishnan, C (2002) On the importance of backbone loop and peptide flip in the Walker sequence in F-1-ATPase action. In: Indian Journal of Biochemistry & Biophysics, 39 (1). pp. 5-15.

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The Walker sequence, GXXXXGKT, present in all the six subunits of F-1-ATPase exists in a folded form, known as phosphate-binding loop (P-loop). Analysis of the Ramachandran angles showed only small RMS deviation between the nucleotide-bound and nucleotide-free forms. This indicated a good overlap of the backbone loops. The catalytic beta-subunits (chains D, E and F) showed significant changes in the Ramachandran angles and the side chain torsion angles, but not the structural alpha-subunits (chains A, B and C). Most striking among these are the changes associated with Val160 and Gly161 corresponding to a flip in the peptide unit between them when a nucleotide is bound (chains D or F compared to nucleotide-free chain E). The conformational analysis further revealed a hitherto unnoticed hydrogen bond between amide-N of the flipped Gly161 and terminal phosphate-O of the nucleotide. This assigns a role for this conserved amino acid, otherwise ignored, of making an unusual direct interaction between the peptide backbone of the enzyme protein and the incoming nucleotide substrate. Significance of this interaction is enhanced, as it is limited only to the catalytic subunits, and also likely to involve a mechanical rotation of bonds of the peptide unit. Hopefully this is part of the overall events that link the chemical hydrolysis of ATP with the mechanical rotation of this molecule, now famous as tiny molecular motor.

Item Type: Journal Article
Publication: Indian Journal of Biochemistry & Biophysics
Publisher: National Institute of Science Communication and Information Resources
Additional Information: Copyright of this article belongs to National Institute of Science Communication and Information Resources.
Department/Centre: Division of Biological Sciences > Biochemistry
Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 21 Jul 2011 06:28
Last Modified: 21 Jul 2011 06:28
URI: http://eprints.iisc.ac.in/id/eprint/39316

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