The d鈥?-d--d鈥?Vertical Triad Is Less Discriminating Than the a鈥?-a--a鈥?Vertical Triad in the Antiparallel Coiled-Coil Dimer Motif

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• 作者：Jay D. Steinkruger ; Gail J. Bartlett ; Erik B. Hadley ; Lindsay Fay ; Derek N. Woolfson ; Samuel H. Gellman
• 刊名：The Journal of the American Chemical Society
• 出版年：2012
• 出版时间：February 8, 2012
• 年：2012
• 卷：134
• 期：5
• 页码：2626-2633
• 全文大小：434K
• 年卷期：v.134,no.5(February 8, 2012)
• ISSN：1520-5126

文摘

Elucidating relationships between the amino-acid sequences of proteins and their three-dimensional structures, and uncovering non-covalent interactions that underlie polypeptide folding, are major goals in protein science. One approach toward these goals is to study interactions between selected residues, or among constellations of residues, in small folding motifs. The 伪-helical coiled coil has served as a platform for such studies because this folding unit is relatively simple in terms of both sequence and structure. Amino acid side chains at the helix鈥揾elix interface of a coiled coil participate in so-called 鈥渒nobs-into-holes鈥?(KIH) packing whereby a side chain (the knob) on one helix inserts into a space (the hole) generated by four side chains on a partner helix. The vast majority of sequence鈥搒tability studies on coiled-coil dimers have focused on lateral interactions within these KIH arrangements, for example, between an a position on one helix and an a鈥?position of the partner in a parallel coiled-coil dimer, or between a--d鈥?pairs in an antiparallel dimer. More recently, it has been shown that vertical triads (specifically, a鈥?-a--a鈥?triads) in antiparallel dimers exert a significant impact on pairing preferences. This observation provides impetus for analysis of other complex networks of side-chain interactions at the helix鈥揾elix interface. Here, we describe a combination of experimental and bioinformatics studies that show that d鈥?-d--d鈥?triads have much less impact on pairing preference than do a鈥?-a--a鈥?triads in a small, designed antiparallel coiled-coil dimer. However, the influence of the d鈥?-d--d鈥?triad depends on the lateral a鈥?-d interaction. Taken together, these results strengthen the emerging understanding that simple pairwise interactions are not sufficient to describe side-chain interactions and overall stability in antiparallel coiled-coil dimers; higher-order interactions must be considered as well.