Tag: molecular dynamics

Featured publication: Long and large simulation of a megadalton peptide cage – implications for design.

Posted on by debshoemark

Our manuscript entitled, “The dynamical interplay between a megadalton peptide nanocage and solutes probed by microsecond atomistic MD; implications for design”  has been accepted for publication in Physical Chemistry Chemical Physics (PCCP), (2018), DOI: 10.1039/c8cp06282j. Deborah K. Shoemark, Amaurys Avila Ibarra, James F. Ross, Joseph L. Beesley, Harriet E.V. Bray, Majid Mosayebi, Noah Linden, Tanniemola B. Liverpool, Simon N. McIntosh-Smith, Derek N. Woolfson and Richard B. Sessions.

Here we present the lessons learnt from performing atomistic simulations of 0.6 – 1 microseconds of three ~42 million atom peptide nanocage (SAGE) systems, with and without protein and small molecule solutes. Using GROMACS and the UK supercomputer Archer, data were collected over 2 years. Detailed analysis reveals the structural integrity/helical stability of the SAGEs themselves, how SAGEs interact with the proteins and small molecule species in the systems, whether contact with SAGE influences the native fold of solute proteins and how frequently solutes or ions pass through pores in the SAGEs. Knowing how and where to elaborate and/or modify the SAGE building blocks is important to inform the design process for this synthetic biological approach to diverse applications.  As a vaccine delivery platform, SAGEs that are modular and reproducible, could be tailored to respond to emerging infectious threats more rapidly than conventional methods. For targeted drug delivery, adding peptides that bind SAGEs packed with drug, to specific cell types could reduce dosage demand and side-effects. As nanoreactors for complex chemistry, encapsulating enzyme pathways may allow for more efficient and environmentally friendly catalysis.

 

Featured publication: Specific cardiolipin–SecY interactions are required for proton-motive force stimulation of protein secretion

Posted on by ChrisWellsWood

In a recent publication in PNAS, Corey et al (Collinson Group,  School of Biochemistry, University of Bristol) work on the bacterial form of the general secretion system – aka the SecY machinery. This complex carries out the bulk of pre-protein secretion at the bacterial plasma membrane, powered by both ATP and the proton-motive force (PMF). They were interested in the interaction of SecY with the energetically-important cardiolipin (CL) molecule. CL is thought to be involved in many different bioenergetics processes, and has been previously implicated in SecY activity.

To approach this problem, they coupled the high predictive power of coarse-grained (CG) molecular dynamics (MD) with experimental analyses. Considerable speed up on atomistic simulation can be achieved using CG force fields, such as the Martini force field for biomolecules. By reducing the degrees of freedom of a system, it is possible to achieve sampling orders of magnitude faster than atomistic simulation – driven primarily by an increase in permissible MD step size, a reduction in interactions to compute per step and a smoothing of the energy landscape.

The CG data revealed two distinct CL binding sites on the SecY surface, which they were able to validate using native mass spectrometry (nMS), with Dr Argyris Politis at King’s College London, and FRET-based analysis on carefully designed variants of SecY.

Cardiolipin bound to SecY.

They then used these knockout variants to more deeply understand the importance of the SecY-CL interactions. Using a range of biochemical assays, they reveal that the specific interaction of CL at these sites is responsible for the previously-recorded heightened activity of SecY. Moreover, they establish a hitherto unknown role for CL in the PMF-driven activity of SecY. This is the first direct evidence of CL acting directly with the PMF in any bioenergetic system.