title: Structural attributes for the recognition of weak and anomalous regions in coiled-coils of myosins and other motor proteins.
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.
  
  
  RESULTS
  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.
authors.affiliation: National Centre for Biological Sciences (TIFR), UAS-GKVK Campus, Bellary Road, Bangalore 560 065, India.
authors.forename: Margaret S
authors.initials: MS
authors.lastname: Sunitha
authors.forename: Anu G
authors.initials: AG
authors.lastname: Nair
authors.forename: Amol
authors.initials: A
authors.lastname: Charya
authors.forename: Kamalakar
authors.initials: K
authors.lastname: Jadhav
authors.forename: Sami
authors.initials: S
authors.lastname: Mukhopadhyay
authors.forename: Ramanathan
authors.initials: R
authors.lastname: Sowdhamini
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000818:Animals; D030562:Databases, Protein; D006801:Humans; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D020407:Internet; D008958:Models, Molecular; D020409:Molecular Motor Proteins / Q000737:chemistry* / Q000378:metabolism; D018995:Myosin Heavy Chains / Q000737:chemistry* / Q000378:metabolism; D010363:Pattern Recognition, Automated; D011487:Protein Conformation; D055550:Protein Stability; D055672:Static Electricity; D040681:Structural Homology, Protein; D013329:Structure-Activity Relationship; D014335:Tropomyosin / Q000737:chemistry
chemical_list: D020409:Molecular Motor Proteins; D014335:Tropomyosin; C089785:myosin VI; D018995:Myosin Heavy Chains