Abstract
BackgroundCoiled-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.FindingsWe 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.ConclusionsThe 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.
Highlights
Coiled-coils are found in different proteins like transcription factors, myosin tail domain, tropomyosin, leucine zippers and kinesins
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
All the structures were parsed through SOCKET program [31] so that regions satisfying the knobs-into-holes interactions alone could be considered for further analysis
Summary
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. The alphahelical coiled-coils are simple structural units that consist of repeating blocks of seven residues which are commonly termed as 'heptads'. They are mostly seen as protein-protein interaction domains which mediate many vital functions in the system like oligomerization, cell division, transport of macromolecules, mobility and transcription. The set of interactions observed between ‘a,’ ‘d,’ ‘e’ and ‘g’ positions of the heptad repeat forms the basis for knobs-into-holes packing in coiled-coils [7]
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