Interactions of proteins with graphene and carbon nanotubes
Glucose oxidase (GOx) is an enzyme which catalyze oxidation of β-D-glucose by molecular oxygen. Since 60ties the medical industry is employing this enzyme for construction of glucose biosensors. By incorporating nanomaterials, it is possible to achieve enhanced sensitivity, improved response time and smaller size. The direct electrochemistry of enzyme refers to the direct electron communication between the electrode and the active center of the enzyme without the participation of mediators or other reagents. However, the realization of direct electrochemistry of redox enzymes on common electrodes is very difficult because the active centers of most redox enzymes are located deeply in a hydrophobic cavity of the molecule (e.g. FAD – flavin cofactor in case of GOx). It was experimentally confirmed that the modified electrode surfaces involving graphene or carbon nanotubes can increase electron-transfer-rate. Proteins can also be used for construction of nanoelectronics, photovoltaics and other chemical/biological sensors so determination of contacts of proteins with modified electrode materials is of great importance.
The latest news
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.