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Open Access Technical Note

Structural attributes for the recognition of weak and anomalous regions in coiled-coils of myosins and other motor proteins

Margaret S Sunitha1, Anu G Nair1, Amol Charya2, Kamalakar Jadhav2, Sami Mukhopadhyay2 and Ramanathan Sowdhamini1*

Author Affiliations

1 National Centre for Biological Sciences (TIFR), UAS-GKVK Campus, Bellary Road, Bangalore, 560 065, India

2 VLife Sciences Technologies Private Limited, Aundh, Pune, 411 007, India

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BMC Research Notes 2012, 5:530  doi:10.1186/1756-0500-5-530

Published: 25 September 2012

Abstract

Background

Coiled-coils are found in different proteins like transcription factors, myosin tail domain, tropomyosin, leucine zippers and kinesins. Analysis of various structures containing coiled-coils has revealed the importance of electrostatic and hydrophobic interactions. In such domains, regions of different strength of interactions need to be identified since they could be biologically relevant.

Findings

We have updated our coiled-coil validation webserver, now called COILCHECK+, where new features were added to efficiently identify the strength of interaction at the interface region and measure the density of charged residues and hydrophobic residues. We have examined charged residues and hydrophobic ladders, using a new algorithm called CHAHO, which is incorporated within COILCHECK + server. CHAHO permits the identification of spatial charged residue patches and the continuity of hydrophobic ladder which stabilizes and destabilizes the coiled-coil structure.

Conclusions

The availability of such computational tools should be useful to understand the importance of spatial clustering of charged residues and the continuity of hydrophobic residues at the interface region of coiled-coil dimers. COILCHECK + is a structure based tool to validate coiled-coil stability; it can be accessed at http://caps.ncbs.res.in/coilcheckplus webcite.

Keywords:
Coiled-coil; Charged-patch; Hydro ladder; Pseudoenergies; Charged clusters; Heptads; Knobs-into-holes packing