An Experimental and Computational Investigation of Spontaneous Lasso Formation in Microcin J25

• Published in: Biophysical journal Vol. 99; no. 9; pp. 3056 - 3065
• Main Authors: Ferguson, Andrew L., Zhang, Siyan, Dikiy, Igor, Panagiotopoulos, Athanassios Z., Debenedetti, Pablo G., James Link, A.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 03.11.2010; Biophysical Society; Elsevier; The Biophysical Society
• Subjects: Amino Acid Sequence; Antimicrobial Cationic Peptides - chemistry; Antimicrobial Cationic Peptides - genetics; Antimicrobial Cationic Peptides - metabolism; Bacteriocins - chemistry; Bacteriocins - genetics; Bacteriocins - metabolism; Biophysical Phenomena; Biophysics; Chromatography, High Pressure Liquid; Computation; Computer simulation; Dynamical systems; Enzyme kinetics; Enzymes; Experiments; Maturation; Models, Molecular; Molecular Dynamics Simulation; Molecular Sequence Data; Molecular structure; Peptides; Protein; Protein Conformation; Protein Folding; Protein Processing, Post-Translational; Protein Stability; Spontaneous; Tandem Mass Spectrometry; Topology
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1016/j.bpj.2010.08.073

The antimicrobial peptide microcin J25 (MccJ25) is posttranslationally matured from a linear preprotein into its native lasso conformation by two enzymes. One of these enzymes cleaves the preprotein and the second enzyme installs the requisite isopeptide bond to establish the lasso structure. Analysis of a mimic of MccJ25 that can be cyclized without the influence of the maturation enzymes suggests that MccJ25 does not spontaneously adopt a near-lasso structure. In addition, we conducted atomistically detailed replica-exchange molecular dynamics simulations of pro-microcin J25 (pro-MccJ25), the 21-residue uncyclized analog of MccJ25, to determine the conformational ensemble explored in the absence of the leader sequence or maturation enzymes. We applied a nonlinear dimensionality reduction technique known as the diffusion map to the simulation trajectories to extract two global order parameters describing the fundamental dynamical motions of the system, and identify three distinct pathways. One path corresponds to the spontaneous adoption of a left-handed lasso, in which the N-terminus wraps around the C-terminus in the opposite sense to the right-handed topology of native MccJ25. Our computational and experimental results suggest a role for the MccJ25 leader sequence and/or its maturation enzymes in facilitating the adoption of the right-handed topology.