Molecular modeling of coiled-coil alpha-tropomyosin: analysis of staggered and in register helix-helix interactions.
In register and staggered models of tropomyosin coiled-coil were built from X-ray C alpha coordinates and refined via molecular dynamics. The two models show similar structural features with the X-ray structure of GCN4 leucine zipper. Empirical energetic methods used to compare the in register and staggered models indicate that both are equally probable. The two models have similar profiles of solvation free energy of folding for residues at positions a and d of the repeating heptad, indicating that residues at these positions are as well buried in an in register structure as in a staggered one. Neither the in register nor the 14 residues staggered structure can be ruled out based on hydrophobic or e-g' (g-e') electrostatic interactions which are not able to distinguish between the two models and are therefore not selective. However, the eg-b'c' electrostatic interactions, although smaller in magnitude, are in favor of the in register model. Furthermore, analysis of hydrophobic and electrostatic interactions along the tropomyosin sequence shows that bulky residues in positions a and d prevent the formation of inter-chain salt bridges.
Cregut
D
D
Centre CNRS-INSERM de Pharmacologie-Endocrinologie, Montpellier, France.
Liautard
J P
JP
Heitz
F
F
Chiche
L
L
D003198:Computer Simulation; D004268:DNA-Binding Proteins; D005656:Fungal Proteins / Q000737:chemistry; D008958:Models, Molecular; D017510:Protein Folding; D011494:Protein Kinases / Q000737:chemistry; D017434:Protein Structure, Tertiary; D029701:Saccharomyces cerevisiae Proteins; D012996:Solutions / Q000737:chemistry; D014157:Transcription Factors / Q000737:chemistry; D014335:Tropomyosin / Q000737:chemistry*; D014961:X-Ray Diffraction
D004268:DNA-Binding Proteins; D005656:Fungal Proteins; D029701:Saccharomyces cerevisiae Proteins; D012996:Solutions; D014157:Transcription Factors; D014335:Tropomyosin; D011494:Protein Kinases