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Paircoil2: improved prediction of coiled coils from sequence
TLDR
A new version of the Paircoil program, which uses pairwise residue probabilities to detect coiled-coil motifs in protein sequence data, achieves 98% sensitivity and 97% specificity on known coiled coils in leave-family-out cross-validation. Expand
The structure of VibH represents nonribosomal peptide synthetase condensation, cyclization and epimerization domains
TLDR
The crystal structure of the free-standing NRPS condensation (C) domain VibH, which catalyzes amide bond formation in the synthesis of vibriobactin, a Vibrio cholerae siderophore, is reported. Expand
Comprehensive Identification of Human bZIP Interactions with Coiled-Coil Arrays
TLDR
Protein arrays used to test pairings of a nearly complete set of coiled-coil strands from human basic-region leucine zipper transcription factors find considerable partnering selectivity despite the bZIPs' homologous sequences. Expand
Networks of bZIP Protein-Protein Interactions Diversified Over a Billion Years of Evolution
TLDR
The results reveal differences within bZIP interactive networks that have accumulated over time and identify plasticity among interactions and changes in binding specificity that relate to specific amino acid residue changes. Expand
Design of protein-interaction specificity affords selective bZIP-binding peptides
TLDR
A computational framework for designing protein-interaction specificity is presented and used to identify specific peptide partners for human basic-region leucine zipper (bZIP) transcription factors and may prove broadly useful as a tool for protein design. Expand
The MCL-1 BH3 Helix is an Exclusive MCL-1 inhibitor and Apoptosis Sensitizer
TLDR
X-ray crystallography and mutagenesis studies defined key binding and specificity determinants, including the capacity to harness the hydrocarbon staple to optimize affinity while preserving selectivity, and generated an MCL-1-specific agent that defines the structural and functional features of targeted M CL-1 inhibition. Expand
Structural specificity in coiled-coil interactions.
TLDR
Experimental and computational methods for dealing with the near-degeneracy of many coiled-coil structures appear promising for future design applications. Expand
A synthetic coiled-coil interactome provides heterospecific modules for molecular engineering.
TLDR
The coiled-coil toolkit is greatly expanded by measuring the complete pairwise interactions of 48 synthetic coiled coils and 7 human bZIP coiled coil using peptide microarrays, resulting in a 55-member protein "interactome" that includes 27 pairs of interacting peptides that preferentially heteroassociate. Expand
Predicting specificity in bZIP coiled-coil protein interactions
TLDR
This work presents a method for predicting protein-protein interactions mediated by the coiled-coil motif that identifies 70% of strong interactions while maintaining that 92% of predictions are correct. Expand
Multicoil2: Predicting Coiled Coils and Their Oligomerization States from Sequence in the Twilight Zone
TLDR
Multicoil2 is presented, an algorithm that predicts both the location and oligomerization state (two versus three helices) of coiled coils in protein sequences and significantly improves both coiled-coil detection and dimer versus trimer state prediction over the original Multicoil algorithm retrained on a newly-constructed database of coil sequences. Expand
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