Modeling of structure and dynamics of membrane proteins and their complexes with ligands and other proteins. Drug design. Development of new methods of coarse-grain dynamics. Studies of interactions of proteins with graphene, carbon nanotubes and other electrode materials for biosensor applications.
Exemplary titles of expected Master/Doctoral theses:
Modeling of action of agonist/antagonist sensor and molecular switches of formyl / opioid / cannabinoid / chemokine / etc. receptors from GPCR family using theoretical methods.
Studies of formation and dynamics of oligomers of membrane proteins.
Design of drugs preventing aggregation of beta-amyloid / activating or deactivating GPCRs / etc.
Interactions of modified graphene or other electrode nanomaterial with proteins.
Modelowanie struktury i dynamiki białek błonowych oraz ich kompleksów z ligandami oraz z innymi białkami. Projektowanie leków. Rozwój nowych metod symulacji gruboziarnistych. Badanie oddziaływań białek z grafenem, nanorurkami i innymi materiałami elektrodowymi do zastosowania w bioczujnikach.
Przykładowe przewidywane tematy prac magisterskich/doktorskich:
Modelowanie działania sensora agonista/antagonista oraz przełączników molekularnych receptorów formylowych / opioidowych / kanabinoidowych / chemokinowych i innych z rodziny GPCR metodami teoretycznymi.
Badanie powstawania i dynamiki oligomerów białek błonowych.
Projektowanie leków przeciwdziałających agregacji beta-amyloidu / aktywujących lub deaktywujących receptory GPCR i inne.
Oddziaływanie modyfikowanego grafenu lub innego nanomateriału elektrody z białkami.
The applicants interested in working in our group are welcomed to contact us
Minimal requirements for candidates:
Practical knowledge of at least one protein visualizing/modeling program (e.g. YASARA, VMD, PyMol, MolMol, SPDBviewer)
Knowledge of types of protein structures
Practical usage of biological web servers (e.g. UniProt, ExPASy, BLAST, Protein Data Bank)
Our service GPCRM is completely reshaped, much faster, and user friendly. Now, it contains 3 main routes: Quick path (default), Long path, and High similarity (the fastest) for homology modeling of GPCRs. Currently, the service contains over 90 template structures. The updated version was recently published in NAR 2018, W1.
A development of cryo-EM (cryo-electron microscopy) was the subject of the Nobel Prize in Chemistry 2017. Recently, this method became so precise that it is possible to obtain the structures of large biomolecular complexes with very high, atomic resolution. This article [»»»] describes in short the cryo-EM method and the Nobel laureates (including YouTube movie).
Currently, our group works on the γ-secretase, the very large complex of 4 membrane proteins. This complex produces β-amyloid being a hallmark of Alzheimer's disease. The determination of structure of this complex was possible only using the cryo-EM method.
We revealed how the hydrophobic ligands entry to and exit from CB1 cannabinoid receptor directly from the membrane, Published in J. Chem. Inf. Model. (2016) (DOI).
New papers linking the activation of GPCRs with water flows inside receptor: in Nature Communication (2014) (DOI) and in Angew. Chem. Int. Ed. (2015) (DOI).
The web server GPCRM, built by BIOmodeling group for construction of homology models of GPCRs based on multiple templates, proved to be one of the best among other services of this type so it was recently selected to be implemented into GPCRDB platform. Employing this service we participated in GPCR Dock competition for docking of ligands to unknown structures of serotonin receptors 5-HT1B and 5-HT2B where we obtained 2nd and 1st place, respectively.
The Nobel prize in Chemistry for 2013 was awarded to three computer scientists. They created foundations of methods for molecular modeling and molecular dynamics to study both small molecules and large systems composed of DNA and proteins enabling docking of ligands to molecular targets for drug design. They developed a concept of force-field and also combined these methods with quantum chemistry to simulate enzymatic reactions.