Structural and thermodynamical properties of saliva proteins - a public health perspective

SNIC 2018/1-3


SNIC Large Compute

Principal Investigator:

Marie Skepö


Lunds universitet

Start Date:


End Date:


Primary Classification:

10407: Theoretical Chemistry

Secondary Classification:

10402: Physical Chemistry




A prerequisite for oral health is well-functioning saliva. Human saliva has several important functions and it is an important part of the immune system. Saliva consists mainly of water but also smaller amounts of proteins, salts, fats and enzymes. Despite the low content of protein, only 0.2% (!), they have an important function. The goal of the project is to understand how the lack of structure of intrinsically disordered proteins (IDPs) in solution relates to their function when adsorbed to surfaces with focus on saliva and the oral cavity. The aims of the project can be divided into two categories, where the first aim is related to general research and a basic understanding of the structural and thermodynamical properties of IDPs, with focus on protein-protein, protein-surface, and protein-membrane interactions. The second and the third aim have a medical perspective, where the mechanism of the salivary protein, Histatin 5 anti-microbial activity, as well as the underlying physics of the remineralization, the tissue coating, and the lubrication mechanism of the proline rich proteins, are in focus. To achieve the best understanding of these systems, and to obtain a molecular understanding of the macroscopic properties, atomistic molecular dynamics- and coarse-grained Monte Carlo simulations will be used, in combination with experimental methods such as scattering (light, neutron, x-ray) as well as osmometry, CD-spectroscopy, ellipsometry, and QCM-D. I am applying for computer time from SNIC to continue my research about salivary proteins and its structural and thermodynamic properties. The objective is that the obtained knowledge shall serve as basics to develop new drugs, saliva substitutes and dental care products to relieve and prevent these problems. Currently there are four PhD-students as well as master students related to this project. In all projects we use a combined theoretical and experimental approach, where computer simulations play a major role. In May 2018 a new PhD-student will start in my group, Eric Fagerberg, and his project is directed into dynamics of intrinsically disordered proteins (combination of atomistic simulations, QENS and ToF neutron spectroscopy. This will increase our need of computational forces dramatically. Last round we were approved 200 hour/months and that has been in the lower limit, if possible I would very much appreciate if we could increase the allocation to 500 hours/months. We are using three different softwares for the simulations; two-inhouse developed programs for the coarse-grained modelling (Molsim and Faunus) and Monte Carlo simulations, as well as Gromacs for the MD simulations. During the last five years, we have solely been using LUNARC resources as Alarik and Aurora, without any problems. The Monte Carlo simulations are running in serial mode whereas for the MD-simulations we need more computer power. Every property of interest is simulated in five replicas, hence the computer need is increasing very fast. The requirements in our field of interest regarding the simulation length are on the micro-scale and up.