Generalized Crick equations for modeling noncanonical coiled coils.

@article{citeulike:2706564, abstract = {Crick envisaged the alpha-helical coiled coil to result from systematic bending of an alpha-helix such that every seventh residue was structurally equivalent, and he derived equations for the coordinates of the backbone atoms. Crick's predictions were vindicated experimentally and coiled-coil sequences were shown to have hydrophobic residues alternately spaced 3 and 4 residues apart. Nonetheless, in some coiled coils such canonical heptad repeats are interrupted by inserts of 3 or 4 residues generating decad and hendecad motifs. The supercoiling of the coiled coils varies with the sequence pattern, being left- or right-handed in purely heptad-based or hendecad-based motifs, respectively. To model coiled coils with a mixture of motifs, we describe how Crick's equations can be modified for cases where the pitch is not constant. Using the analogy of the bending of a beam, we took the tilt angle to change linearly with distance along the major helix and the pitch of a motif to be affected by neighboring motifs depending on the rigidity of the alpha-helical strands. We tested our approach by fitting the two-, three-, and four-stranded noncanonical coiled coils of GrpE, hemagglutinin, and tetrabrachion. The backbone atoms of the model and crystal structures agreed with root mean square deviations of <1.1 A.}, address = {Muscle Contraction Group, Department of Physiology, Medical School, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom. g.w.offer@bristol.ac.uk}, author = {Offer, G. and Hicks, M. R. and Woolfson, D. N. }, citeulike-article-id = {2706564}, doi = {10.1006/jsbi.2002.4448}, issn = {1047-8477}, journal = {Journal of structural biology}, keywords = {coile}, number = {1-2}, pages = {41--53}, posted-at = {2008-04-23 09:44:48}, priority = {2}, title = {Generalized Crick equations for modeling noncanonical coiled coils.}, url = {http://dx.doi.org/10.1006/jsbi.2002.4448}, volume = {137}, year = {2002} }

TY - JOUR ID - citeulike:2706564 L3 - citeulike-article-id:2706564 TI - Generalized Crick equations for modeling noncanonical coiled coils. JF - Journal of structural biology VL - 137 IS - 1-2 SP - 41 EP - 53 AD - Muscle Contraction Group, Department of Physiology, Medical School, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom. g.w.offer@bristol.ac.uk SN - 1047-8477 N2 - Crick envisaged the alpha-helical coiled coil to result from systematic bending of an alpha-helix such that every seventh residue was structurally equivalent, and he derived equations for the coordinates of the backbone atoms. Crick's predictions were vindicated experimentally and coiled-coil sequences were shown to have hydrophobic residues alternately spaced 3 and 4 residues apart. Nonetheless, in some coiled coils such canonical heptad repeats are interrupted by inserts of 3 or 4 residues generating decad and hendecad motifs. The supercoiling of the coiled coils varies with the sequence pattern, being left- or right-handed in purely heptad-based or hendecad-based motifs, respectively. To model coiled coils with a mixture of motifs, we describe how Crick's equations can be modified for cases where the pitch is not constant. Using the analogy of the bending of a beam, we took the tilt angle to change linearly with distance along the major helix and the pitch of a motif to be affected by neighboring motifs depending on the rigidity of the alpha-helical strands. We tested our approach by fitting the two-, three-, and four-stranded noncanonical coiled coils of GrpE, hemagglutinin, and tetrabrachion. The backbone atoms of the model and crystal structures agreed with root mean square deviations of <1.1 A. KW - coile AU - Offer, G AU - Hicks, MR AU - Woolfson, DN PY - 2002///b UR - http://dx.doi.org/10.1006/jsbi.2002.4448 ER -