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Modeling α‐helical coiled‐coil interactions: The axial and azimuthal alignment of 1B segments from vimentin intermediate filaments
Author(s) -
Smith Thomasin A.,
Hempstead Paul D.,
Palliser Christopher C.,
Parry David A.D.
Publication year - 2002
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.10254
Subject(s) - antiparallel (mathematics) , molecule , intermolecular force , chemical physics , coiled coil , azimuth , chemistry , ionic bonding , molecular physics , crystallography , physics , ion , optics , biochemistry , organic chemistry , quantum mechanics , magnetic field
Abstract Attempts at predicting the relative axial alignments of fibrous protein molecules in filamentous structures have relied upon representing the (multichain) molecular structure by a one‐dimensional sequence of amino acids. Potential intermolecular ionic and apolar interactions were counted and determined as a function of the relative axial stagger between the molecules. No attempts were made to consider the azimuthal aspect of the interacting molecules and neither were apolar or ionic energy terms used. Surprisingly, this simple approach proved remarkably informative and yielded accurate predictions of the axial periods present. However, a more comprehensive analysis involving the energetics of aggregation taking due regard for the relative azimuths of the molecules as well as their separation should decrease the noise level in the calculations and reveal other pertinent information. Toward that end, we have modeled the interaction between two α‐helical coiled‐coil segments in intermediate filament molecules (1B segments from human vimentin). The relative axial alignment and polarity of the molecules is already known from detailed crosslinking studies and this provides a criterion against which the success (or otherwise) of the modeling can be judged. The results confirm that an antiparallel alignment of two 1B segments is preferred over any of the parallel options (as observed experimentally). The calculated axial alignment, however, is not identical to that observed from detailed crosslinking studies indicating that other parts of the molecule (probably the head and tail domains as well as other coiled‐coil segments) have a crucial role in determining the precise mode of axial aggregation. The results also show that the apolar interactions seem to be significantly less important in the alignment process than the ionic ones. This is consistent with the observation of a well‐defined period in the linear disposition of the charged (but not apolar) residues along the length of the outer surface of the vimentin molecule. Proteins 2003;50:207–212. © 2002 Wiley‐Liss, Inc.