Jaakko J. Uusitalo

The power of coarse graining in biomolecular simulations

Computational modeling of biological systems is challenging because of the multitude of spatial and temporal scales involved. Replacing atomistic detail with lower resolution, coarse grained (CG), beads has opened the way to simulate large‐scale biomolecular processes on time scales inaccessible to all‐atom models. We provide an overview of some of the more popular CG models used in biomolecular applications to date, focusing on models that retain chemical specificity. A few state‐of‐the‐art examples of protein folding, membrane protein gating and self‐assembly, DNA hybridization, and modeling of carbohydrate fibers are used to illustrate the power and diversity of current CG modeling.

Martini Coarse-Grained Force Field: Extension to DNA

We systematically parameterized a coarse-grained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to seven CG beads and is parameterized following the Martini philosophy. The CG nonbonded interactions are based on partitioning of the nucleobases between polar and nonpolar solvents as well as base-base potential of mean force calculations. The bonded interactions are fit to single-stranded DNA (ssDNA) atomistic simulations and an elastic network is used to retain double-stranded DNA (dsDNA) and other specific DNA conformations. We present the implementation of the Martini DNA model and demonstrate the properties of individual bases, ssDNA as well as dsDNA, and DNA-protein complexes. The model opens up large-scale simulations of DNA interacting with a wide range of other (bio)molecules that are available within the Martini framework.

Stability and dynamics of membrane-spanning DNA nanopores

Recently developed DNA-based analogues of membrane proteins have advanced synthetic biology. A fundamental question is how hydrophilic nanostructures reside in the hydrophobic environment of the membrane. Here, we use multiscale molecular dynamics (MD) simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube. Steered simulations along the bilayer normal establish the metastable nature of the inserted pore, yielding a force profile with barriers for membrane exit due to the membrane anchors. Atomistic, equilibrium simulations at two salt concentrations confirm the close packing of lipid around of the stably inserted DNA pore and its cation selectivity, while revealing localized structural fluctuations. The wide-ranging and detailed insight informs the design of next-generation DNA pores for synthetic biology or biomedicine.

Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations

Control over the morphology of the active layer of bulk heterojunction (BHJ) organic solar cells is paramount to achieve high-efficiency devices. However, no method currently available can predict morphologies for a novel donor–acceptor blend. An approach which allows reaching relevant length scales, retaining chemical specificity, and mimicking experimental fabrication conditions, and which is suited for high-throughput schemes has been proven challenging to find. Here, we propose a method to generate atom-resolved morphologies of BHJs which conforms to these requirements. Coarse-grain (CG) molecular dynamics simulations are employed to simulate the large-scale morphological organization during solution-processing. The use of CG models which retain chemical specificity translates into a direct path to the rational design of donor and acceptor compounds which differ only slightly in chemical nature. Finally, the direct retrieval of fully atomistic detail is possible through backmapping, opening the way for improved quantum mechanical calculations addressing the charge separation mechanism. The method is illustrated for the poly(3-hexyl-thiophene) (P3HT)–phenyl-C61-butyric acid methyl ester (PCBM) mixture, and found to predict morphologies in agreement with experimental data. The effect of drying rate, P3HT molecular weight, and thermal annealing are investigated extensively, resulting in trends mimicking experimental findings. The proposed methodology can help reduce the parameter space which has to be explored before obtaining optimal morphologies not only for BHJ solar cells but also for any other solution-processed soft matter device.

Glucose limitation in Lactococcus shapes a single-peaked fitness landscape exposing membrane occupancy as a constraint

A central theme in biology is to understand the molecular basis of fitness: which strategies succeed under which conditions; how are they mechanistically implemented; and which constraints shape trade-offs between alternative strategies. We approached these questions with parallel bacterial evolution experiments in chemostats. Chemostats provide a constant environment with a defined resource limitation (glucose), in which the growth rate can be controlled. Using Lactococcus lactis, we found a single mutation in a global regulator of carbon metabolism, CcpA, to confer predictable fitness improvements across multiple growth rates. In silico protein structural analysis complemented with biochemical and phenotypic assays, show that the mutation reprograms the CcpA regulon, specifically targeting transporters. This supports that membrane occupancy, rather than biosynthetic capacity, is the dominant constraint for the observed fitness enhancement. It also demonstrates that cells can modulate a pleiotropic regulator to work around limiting constraints.