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• W2061638963 abstract "Reliable predictive rules that relate protein sequence to structure would facilitate postgenome predictive biology and the engineering and de novo design of peptides and proteins. Through a combination of experiment and analysis of the protein data bank (PDB), we have deciphered and rationalized new rules for helix-helix interfaces of a common protein-folding and association motif, the antiparallel dimeric coiled coil. These interfaces are defined by a specific pattern of interactions among largely hydrophobic side chains often referred to as knobs-into-holes (KIH) packing: a knob from one helix inserts into a hole formed by four residues on the partner. Previous work has focused on lateral interactions within the KIH motif, for example, between an a position on one helix and a d' position on the other in an antiparallel coiled coil. We show that vertical interactions within the KIH motif, such as a'-a-a', are energetically important as well. The experimental and database analyses concur regarding preferred vertical combinations, which can be rationalized as leading to favorable side-chain interactions that we call constellations. The findings presented here highlight an unanticipated level of complexity in coiled-coil interactions, and our analysis of a few specific constellations illustrates a general, multipronged approach to addressing this complexity." @default.
• W2061638963 created "2016-06-24" @default.
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• W2061638963 date "2008-01-15" @default.
• W2061638963 modified "2023-10-11" @default.
• W2061638963 title "Preferred side-chain constellations at antiparallel coiled-coil interfaces" @default.
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• W2061638963 doi "https://doi.org/10.1073/pnas.0709068105" @default.
• W2061638963 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2206570" @default.
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