We are developing methods to predict protein-protein interactions and how proteins bind to surfaces and membranes. These methods mostly rely on Brownian dynamics simulation with SDA and molecular dynamics simulation. SDA can be used to simulate the association of two solutes, e.g. two proteins, in implicit solvent. SDA can also be applied to simulate the diffusion of many solutes, e.g. a concentrated protein solution, to investigate oligomerization and diffusion in macromolecularly crowded environments, see Mereghetti et al, 2012. It can also be applied to simulate the adsorption of proteins on inorganic surfaces, see e.g. Romanowska et al., 2015, Reinhardt et al, 2021.
We apply these approaches to various biological problems. One example is the docking of an enzyme that contributes in the N-terminal processing of nascent polypeptide chains to the ribosome, see Sandikci et al, 2013. In another set of studies, we combined SDA docking with PIPSA analysis of protein electrostatic potentials to investigate the network of interactions of HSP40 J-protein co-chaperones that play an important role in driving protein disaggregation in eukaryotes, see Nillegoda et al, 2015, Nillegoda et al, 2017. Electrostatic interactions also play an important role in the formation of complexes between linker histone proteins and nucleosomes, for which we investigate the binding mechanism and the effects of variations in protein and DNA sequence (for review, see Öztürk et al, 2020). We adopt a multiresolution simulation approach, combining Brownian dynamics with coarse-grained and atomic detail molecular dynamics, to simulate the interaction of cytochrome P450 enzymes with phospholipid bilayers and to generate electron transfer competent structural ensembles of the complexes of membrane-bound cytochrome P450s with cytochrome P450 reductase, see e.g. Mukherjee et al, 2021.
This page is only available in English
We use cookies on our website. Some of them are essential, while others help us improve this site and your experience.
Here you will find an overview of all cookies used. You can give your consent to entire categories or have further information displayed and thus select only certain cookies.
Essential cookies enable basic functions and are necessary for the proper functioning of the website.
Name | |
---|---|
Provider | Eigentümer dieser Website |
Purpose | Speichert die Einstellungen der Besucher, die in der Cookie Box von Borlabs Cookie ausgewählt wurden. |
Cookie Name | borlabs-cookie |
Cookie Expiry | 1 Jahr |
Statistics Cookies collect information anonymously. This information helps us to understand how our visitors use our website.
Accept | |
---|---|
Name | |
Provider | HITS gGmbH |
Purpose | Cookie von Matomo für Website-Analysen. Erzeugt statistische Daten darüber, wie der Besucher die Website nutzt. |
Cookie Name | _pk_*.* |
Cookie Expiry | 13 Monate |
Content from video platforms and social media platforms is blocked by default. If cookies from external media are accepted, access to this content no longer requires manual consent.
Accept | |
---|---|
Name | |
Provider | |
Purpose | Wird verwendet, um Facebook-Inhalte zu entsperren. |
Privacy Policy | https://www.facebook.com/privacy/explanation |
Host(s) | .facebook.com |
Accept | |
---|---|
Name | |
Provider | |
Purpose | Wird zum Entsperren von Google Maps-Inhalten verwendet. |
Privacy Policy | https://policies.google.com/privacy |
Host(s) | .google.com |
Cookie Name | NID |
Cookie Expiry | 6 Monate |
Accept | |
---|---|
Name | |
Provider | |
Purpose | Wird verwendet, um Instagram-Inhalte zu entsperren. |
Privacy Policy | https://www.instagram.com/legal/privacy/ |
Host(s) | .instagram.com |
Cookie Name | pigeon_state |
Cookie Expiry | Sitzung |
Accept | |
---|---|
Name | |
Provider | OpenStreetMap Foundation |
Purpose | Wird verwendet, um OpenStreetMap-Inhalte zu entsperren. |
Privacy Policy | https://wiki.osmfoundation.org/wiki/Privacy_Policy |
Host(s) | .openstreetmap.org |
Cookie Name | _osm_location, _osm_session, _osm_totp_token, _osm_welcome, _pk_id., _pk_ref., _pk_ses., qos_token |
Cookie Expiry | 1-10 Jahre |
Accept | |
---|---|
Name | |
Provider | |
Purpose | Wird verwendet, um Twitter-Inhalte zu entsperren. |
Privacy Policy | https://twitter.com/privacy |
Host(s) | .twimg.com, .twitter.com |
Cookie Name | __widgetsettings, local_storage_support_test |
Cookie Expiry | Unbegrenzt |
Accept | |
---|---|
Name | |
Provider | Vimeo |
Purpose | Wird verwendet, um Vimeo-Inhalte zu entsperren. |
Privacy Policy | https://vimeo.com/privacy |
Host(s) | player.vimeo.com |
Cookie Name | vuid |
Cookie Expiry | 2 Jahre |
Accept | |
---|---|
Name | |
Provider | YouTube |
Purpose | Wird verwendet, um YouTube-Inhalte zu entsperren. |
Privacy Policy | https://policies.google.com/privacy |
Host(s) | google.com |
Cookie Name | NID |
Cookie Expiry | 6 Monate |