Opening Lecture

TBA (David A. Leigh)

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Theory and practice of coarse graining (Adam Liwo)

Coarse-grained approaches, in which several atoms are merged into extended interaction sites, are widely used in simulating large systems, including biological macromolecules. Such reduction of representation offers a tremendous benefit of extending the accessible time- and size-scales by orders of magnitude. However, designing the pertinent force fields poses problems and simple translation of all-atom energy terms to coarse-grained representation does not give satisfactory result. The fundamental physical principle behind the coarse-grained force field is Boltzmann averaging over the degrees of freedom that are lost when passing from the all-atom to the coarse-grained representation; consequently, an effective coarse-grained energy function is a potential of mean force (PMF). Approximation of the PMF is, however, necessary, for tractability and transferability. This can be done by (1) defining the components of the PMF as statistical potentials extracted from structural databases (e.g., the ROSETTA or CABS force fields), (2) fitting neo-classical expression from all-atom force fields to thermodynamic and structural quantities (e.g., the MARTINI force field), (3) iterative Boltzmann inversion, (3) force matching, and (iv) factor expansion of the PMF into Kubo's cluster cumulants (e.g., the UNRES force field). The factor expansion approach enables aggressive coarse graining with retaining the ability to models the structural features without knowledge-based restraints. In this talk, these approaches will be described and examples to illustrate the ability of coarse-grained models to treat large systems at long time scales will be presented.

TBA (Antti J Niemi)

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TBA (Franco Ferrari)

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Dynamics of intrinsically disordered proteins and their droplet-like aggregates (Marek Cieplak)

Functioning of any biological cell involves proteins of two kinds: natively structured and intrinsically disordered. The disordered proteins may aggregate and form multiprotein droplets that act as membraneless organelles. Theoretical understanding of the formation and dynamics of such droplets requires using coarse-grained models. We'll describe our own coarse-grained model (constructed with Dr. Lukasz Mioduszewski) that is a generalization of the so-called Go-like model, designed for the structured proteins and based on the concept of contact interactions between amino acids. In the case of the intrinsically disordered proteins, the contacts are derived from an instantaneous shape of the backbone and not from the geometry of a single reference state (such as the native state). As an illustration, we discuss an example of a system of 100 proteins HCPEB3 S6 of 100 residues each. This system is currently investigated in the context of fighting toxicity in fish aquacultures (within the European Project PathoGelTrap). The toxins are supposed to be removerd by droplets built of chimeric proteins in which the hCPEB3 S6 molecules are connected covalently with molecules that have an ability to bind to the viral and bacterial toxins. The metastable proteinaceous droplets may arise within the coexistence region between the binodal and spinodal lines - hence a necessity to find theoretical methods to determine the phase diagrams of the solutions with proteins.

Deciphering 3D genome organization with probabilistic models (Noam Kaplan)

The spatial organization of the genome is closely linked with its function. Recent genomic technologies allow interrogating 3D genome organization by measuring spatial interaction frequencies of all pairs of loci in the genome. Investigation and interpretation of the resulting interaction matrices, which represent an average representation of highly stochastic genomic structures across a cell population, poses a major challenge. In my talk I will show how probabilistic models provide an excellent framework to accomplish this goal. These models allow to capture explicit mechanistic hypotheses, while simultaneously utilizing the large amounts of available data to infer genome-wide biological meaningful parameters. Modelling specific patterns of genomic structure such as topologically associating domains and genomic compartments, I will show how these models can be used to methodically ask biological questions about 3D genome organization.

TBA (Pietro Faccioli)

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TBA (Roumen Anguelov)

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TBA (Sarah Harris)

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Registered Participants

For the Workshop are registered 20 participants from 14 institutions in 9 countries.