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Molecular dynamics modeling of tubulin C‐terminal tail interactions with the microtubule surface
Author(s) -
Freedman Holly,
Luchko Tyler,
Luduena Richard F.,
Tuszynski Jack A.
Publication year - 2011
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.23155
Subject(s) - tubulin , microtubule , dimer , biophysics , molecular dynamics , helix (gastropod) , microtubule nucleation , chemistry , biology , microbiology and biotechnology , biochemistry , computational chemistry , centrosome , cell , ecology , organic chemistry , snail , cell cycle
Tubulin, an α/β heterodimer, has had most of its 3D structure analyzed; however, the carboxy (C)‐termini remain elusive. Importantly, the C‐termini play critical roles in regulating microtubule structure and function. They are sites of most of the post‐translational modifications of tubulin and interaction sites with molecular motors and microtubule‐associated proteins. Simulated annealing was used in our molecular dynamics modeling to predict the interactions of the C‐terminal tails with the tubulin dimer. We examined differences in their flexibility, interactions with the body of tubulin, and the existence of structural motifs. We found that the α‐tubulin tail interacts with the H11 helix of β‐tubulin, and the β‐tubulin tail interacts with the H11 helix of α‐tubulin. Tail domains and H10/B9 loops interact with each other and compete for interactions with positively‐charged residues of the H11 helix on the neighboring monomer. In a simulation in which α‐tubulin's H10/B9 loop switches on sub‐nanosecond intervals between interactions with the C‐terminal tail of α‐tubulin and the H11 helix of β‐tubulin, the intermediate domain of α‐tubulin showed more fluctuations compared to those in the other simulations, indicating that tail domains may cause shifts in the position of this domain. This suggests that C‐termini may affect the conformation of the tubulin dimer which may explain their essential function in microtubule formation and effects on ligand binding to microtubules. Our modeling also provides evidence for a disordered‐helical/helical double‐state system of the T3/H3 region of the microtubule, which could be linked to depolymerization following GTP hydrolysis. Proteins 2011; © 2011 Wiley‐Liss, Inc.