5mfd | pdb_00005mfd
Designed armadillo repeat protein YIIIM6AII in complex with pD_(KR)5
Structural highlights
FunctionDECO_LAMBD Stabilizes the expansion of the capsid head shell after genome packaging. The packaging of viral genome in the procapsid triggers a dramatic reconfiguration of the capsid shell, expanding from roughly 50nm to 60nm while the capsid thickness decreases. 415 capsid decoration protein molecules cooperatively bind the expanded capsid, thereby stabilizing the mature capsid shell.[1] [2] [3] Publication Abstract from PubMedDesigned armadillo repeat proteins (dArmRP) are alpha-helical solenoid repeat proteins with an extended peptide binding groove that were engineered to develop a generic modular technology for peptide recognition. In this context, the term "peptide" not only denotes a short unstructured chain of amino acids, but also an unstructured region of a protein, as they occur in termini, loops, or linkers between folded domains. Here we report two crystal structures of dArmRPs, in complex with peptides fused either to the N-terminus of Green Fluorescent Protein or to the C-terminus of a phage lambda protein D. These structures demonstrate that dArmRPs bind unfolded peptides in the intended conformation also when they constitute unstructured parts of folded proteins, which greatly expands possible applications of the dArmRP technology. Nonetheless, the structures do not fully reflect the binding behavior in solution, that is, some binding sites remain unoccupied in the crystal and even unexpected peptide residues appear to be bound. We show how these differences can be explained by restrictions of the crystal lattice or the composition of the crystallization solution. This illustrates that crystal structures have to be interpreted with caution when protein-peptide interactions are characterized, and should always be correlated with measurements in solution. Structures of designed armadillo repeat proteins binding to peptides fused to globular domains.,Hansen S, Kiefer JD, Madhurantakam C, Mittl PRE, Pluckthun A Protein Sci. 2017 Oct;26(10):1942-1952. doi: 10.1002/pro.3229. Epub 2017 Jul 25. PMID:28691351[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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