Biomolecular mechanisms at functionalized solid surfaces

May 14, 2019 to May 17, 2019


  • Sophie Sacquin-Mora (Laboratoire de Biochimie Théorique, CNRS-UPR9080, France)
  • Marc Baaden (CNRS-Institute of Physico-Chemical Biology, Paris, France)
  • Florent Barbault (University Paris Diderot, France)




LabEx Dynamo


Practical information: In addition to invited talks, a number of slots for short contributed talks are available. A poster session is also planned. If you would like to present some results during the workshop, you can send an abstract mentioning your preferred format (contributed talk or poster) with your application.

The deadline for abstract submission is March 31st (with final answers given on April 7th)

The deadline for registration (without abstract submission) is April 14th.

The interaction of biomolecular systems with solid surfaces is of crucial importance in the field of biomaterials, since it plays a key role in numerous applications, such as tissue engineering and regenerative medicine (where we need to know the cellular response to implanted materials), the optimization of surfaces for biosensors, the development of bioactive nanoparticles, biocatalysts or bioanalytical systems.

This phenomenon has now been under scrutiny for several decades, but reaching a detailed understanding of the molecular mechanisms associated with biomolecular adsorption on functionalized surfaces is far from being achieved. For over ten years, molecular simulations approaches have been developed to address these issues and represent a promising tool for the biomaterials field.

Molecular simulation approaches can roughly be divided in three classes. Numerous works have been made using quantum mechanical (QM) computations at the solid interface but, due to inherent size limits of QM approaches, these works cannot encompass the complexity of biological systems. Therefore, researchers also resort to all-atom empirical force-fields and coarse-grain methods, which grant a compromise in accuracy in the description of the modeled system and thus feature decreased computational costs.

Some of the key issues that must be addressed when developing molecular simulations approaches are the following:

  • The quality of the empirical force-field parametrization. In particular, the force-field transferability is an important question, since most FF parameters for biomolecular systems such as proteins and nucleic acid were developed for molecules in solution and might not be suitable for the same molecules in a different environment (such a the vicinity of a solid surface). In addition one also has to develop specific FF parameters for the numerous possible solid surfaces, which can be metallic, silica or carbon-based, and bear various functionalizing chemical groups.
  • Solvation effects, which can be modeled using explicit or implicit representation, are essential, since solvant molecules are active components of the system, and likely to play a role in the molecular processes taking place on the surface.
  • Sampling is another critical aspect to take into account. In fact, events taking place on bio/solid interfaces happen on long time-scales, and their investigation requires the modeling of large systems with a rough energy surface, that are difficult to explore thouroughly for an accessible computational cost. In that perspective, multi-scale modeling approaches offer new perspectives for exploring a large range of time and length scales.

Regarding the solid surfaces under investigation, several aspects must be taken into account:

  • The large variety of surfaces that have to be modeled (metal and alloys, oxides, minerals, carbon-based etc…)
  • The surface treatment enabling its functionalization (such as SAMs deposition). In particular, how can we tune surface properties to interact specifically with a target biomolecular system ?
  • The various physico-chemical properties, such as ionization or hydration state, polarization, or surface topography, which will determine the behavior of biomolecules adsorbed on the surface.

Finally, we must investigate the wide range of biomolecules that might need to be immobilized on solid surfaces, such as peptides, proteins, nucleic acids or lipids. What is the specific impact of surface adsorption on the structure, dynamics, and eventually biological activity of these systems ? These questions are especially important for devices such as biosensors or biofuel cells, which use redox enzymes grafted on functionalized surfaces[1], and therefore rely on the conservation of biomolecular function out of the cellular environment.

In addition to addressing the concerns of experts in molecular simulation, the scientific discussions will also benefit from the contribution of experimentalist of various fields, since the availability of reliable experimental data is crucial for the parametrization of theoretical models. Numerous techniques such as X-ray diffraction, NMR spectroscopy, XPS, SPR or AFM microscopy can bring essential information regarding the solid surfaces structure, dynamics or composition, and the way they interact with biomolecular systems.


References :
1. Hitaishi, V., et al., Controlling Redox Enzyme Orientation at Planar Electrodes. Catalysts, 2018. 8(5): p. 192.
2. Latour, R.A., Molecular simulation of protein-surface interactions: benefits, problems, solutions, and future directions. Biointerphases, 2008. 3(3): p. FC2-12.
3. Martin, L., et al., Force fields for simulating the interaction of surfaces with biological molecules. Interface Focus, 2016. 6(1): p. 20150045.
4. Ozboyaci, M., et al., Modeling and simulation of protein-surface interactions: achievements and challenges. Q Rev Biophys, 2016. 49: p. e4.