Mondal, J. — Page 4 | bioRxiv Science

bioRxiv2018

An Atomistic view of Short-chain Antimicrobial Biomimetic peptides in Action

Amphiphilic {beta}-peptides, which are rationally designed synthetic oligomers, are established biomimetic alternatives of natural antimicrobial peptides. The ability of these biomimetic peptides to form helical amphiphilic conformation using small number of residues provides a greater synthetic advantage over the naturally occurring antimicrobial peptides, which is reflected in more potent antimicrobial activity of {beta}-peptides than its naturally occurring counterparts. Here we address whether the distinct molecular architecture of short-chain and rigid synthetic peptides compared to relatively long and flexible natural antimicrobial peptides translates to a distinct mechanistic action with membrane. By simulating the interaction of membrane with antimicrobial 10-residue {beta}-peptides at diverse range of concentrations we reveal spontaneous insertion of {beta}-peptides in the membrane interface at a low concentration and occurrence of partial water leakage in the membrane at a high concentration. Intriguingly, unlike prototypical natural antimicrobial peptides, the water molecules leaked inside the membrane by these biomimetic peptides do not span entire membrane, as supported by free energy analysis. As a major advancement, this work brings into lights the key distinction in the membrane-activity of short synthetic biomimetic oligomers relative to the natural long-chain antimicrobial peptides.

biochemistry↗

bioRxiv2018

Atomic Resolution Mechanism of Ligand Binding to a Solvent Inaccessible Cavity in T4 Lysozyme

Ligand binding sites in proteins are often localized to deeply buried cavities, inaccessible to bulk solvent. Yet, in many cases binding of cognate ligands occurs rapidly. An intriguing system is presented by the L99A cavity mutant of T4 Lysozyme (L99A T4L) that rapidly binds benzene (~106 M-1 s-1). Although the protein has long served as a model system for protein thermodynamics and crystal structures of both free and benzene-bound L99A T4L are available, the kinetic pathways by which benzene reaches its solvent-inaccessible binding cavity remain elusive. The current work, using extensive molecular dynamics simulation, achieves this by capturing the complete process of spontaneous recognition of benzene by L99A T4L at atomistic resolution. A series of multi-microsecond unbiased molecular dynamics simulation trajectories unequivocally reveal how benzene, starting in bulk solvent, diffuses to the protein and spontaneously reaches the solvent inaccessible cavity of L99A T4L. The simulated and high-resolution X-ray derived bound structures are in excellent agreement. A robust four-state Markov model, developed using cumulative 60 {micro}s trajectories, identifies and quantifies multiple ligand binding pathways with low activation barriers. Interestingly, none of these identified binding pathways required large conformational changes for ligand access to the buried cavity. Rather, these involve transient but crucial opening of a channel to the cavity via subtle displacements in the positions of key helices (helix4/helix6, helix7/helix9) leading to rapid binding. Free energy simulations further elucidate that these channel-opening events would have been unfavorable in otherwise ligand-inactive wild type T4L. Taken together, by integrating experiments, these simulations provide unprecedented mechanistic insights into complete ligand recognition process in a buried cavity. By illustrating the power of subtle helix movements in opening up multiple pathways for ligand access, this work offers an alternate view of ligand recognition mechanism in a solvent-inaccessible cavity, contrary to common perception of single dominant pathway for ligand binding.

biophysics↗