Solution structure of a calmodulin-target peptide complex by multidimensional NMR

TLDR

Peptides that bind calmodulin with high affinity commonly contain aromatic or long‑chain hydrophobic residues separated by 12 residues, implying a shared binding mode. The 3‑D solution structure of the Ca²⁺‑bound calmodulin–26‑residue peptide complex was determined by multidimensional heteronuclear NMR. The complex is globular, with CaM domains unchanged, a disrupted central helix forming two helices linked by a flexible loop, and a helical peptide that sits in a hydrophobic channel, stabilized mainly by methionine‑rich hydrophobic contacts and anchored by Trp4 and Phe17.

Abstract

The three-dimensional solution structure of the complex between calcium-bound calmodulin (Ca 2+ -CaM) and a 26-residue synthetic peptide comprising the CaM binding domain (residues 577 to 602) of skeletal muscle myosin light chain kinase, has been determined using multidimensional heteronuclear filtered and separated nuclear magnetic resonance spectroscopy. The two domains of CaM (residues 6 to 73 and 83 to 146) remain essentially unchanged upon complexation. The long central helix (residues 65 to 93), however, which connects the two domains in the crystal structure of Ca 2+ -CaM, is disrupted into two helices connected by a long flexible loop (residues 74 to 82), thereby enabling the two domains to clamp residues 3 to 21 of the bound peptide, which adopt a helical conformation. The overall structure of the complex is globular, approximating an ellipsoid of dimensions 47 by 32 by 30 angstroms. The helical peptide is located in a hydrophobic channel that passes through the center of the ellipsoid at an angle of ∼45° with its long axis. The complex is mainly stabilized by hydrophobic interactions which, from the CaM side, involve an unusually large number of methionines. Key residues of the peptide are Trp 4 and Phe 17 , which serve to anchor the amino- and carboxyl-terminal halves of the peptide to the carboxyl- and amino-terminal domains of CaM, respectively. Sequence comparisons indicate that a number of peptides that bind CaM with high affinity share this common feature containing either aromatic residues or long-chain hydrophobic ones separated by a stretch of 12 residues, suggesting that they interact with CaM in a similar manner.