Nejvíce citovaný článek - PubMed ID 31084902
Rotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteins
Side-chain rotamer prediction is one of the most critical late stages in protein 3D structure building. Highly advanced and specialized algorithms (e.g., FASPR, RASP, SCWRL4, and SCWRL4v) optimize this process by use of rotamer libraries, combinatorial searches, and scoring functions. We seek to identify the sources of key rotamer errors as a basis for correcting and improving the accuracy of protein modeling going forward. In order to evaluate the aforementioned programs, we process 2496 high-quality single-chained all-atom filtered 30% homology protein 3D structures and use discretized rotamer analysis to compare original with calculated structures. Among 513,024 filtered residue records, increased amino acid residue-dependent rotamer errors─associated in particular with polar and charged amino acid residues (ARG, LYS, and GLN)─clearly correlate with increased amino acid residue solvent accessibility and an increased residue tendency toward the adoption of non-canonical off rotamers which modeling programs struggle to predict accurately. Understanding the impact of solvent accessibility now appears key to improved side-chain prediction accuracies.
- MeSH
- algoritmy MeSH
- aminokyseliny * chemie MeSH
- konformace proteinů MeSH
- proteiny * chemie MeSH
- rozpouštědla MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- aminokyseliny * MeSH
- proteiny * MeSH
- rozpouštědla MeSH
Cancer cells can escape the effects of chemotherapy through mutations and upregulation of a tyrosine kinase protein called the epidermal growth factor receptor (EGFR). In the past two decades, four generations of tyrosine kinase inhibitors targeting EGFR have been developed. Using comparative structure analysis of 116 EGFR-drug complex crystal structures, cluster analysis produces two clans of 73 and 43 structures, respectively. The first clan of 73 structures is larger and is comprised mostly of the C-helix-IN conformation while the second clan of 43 structures correlates with the C-helix-OUT conformation. A deep rotamer analysis identifies 43 residues (18%) of the total of 237 residues spanning the kinase structures under investigation with significant rotamer variations between the C-helix-IN and C-helix-OUT clans. The locations of these rotamer variations take on the appearance of side chain conformational relays extending out from points of EGFR mutation to different regions of the EGFR kinase. Accordingly, we propose that key EGFR mutations act singly or together to induce drug resistant conformational changes in EGFR that are communicated via these side chain conformational relays. Accordingly, these side chain conformational relays appear to play a significant role in the development of tumour resistance. This phenomenon also suggests a new paradigm in protein conformational change that is mediated by supportive relays of rotamers on the protein surface, rather than through conventional backbone movements.
- Klíčová slova
- EGFR, NSCLC, Protein folding, Protein structure, Rotamer, Tumour resistance, Tyrosine kinase inhibitor,
- Publikační typ
- časopisecké články MeSH
Most of the available crystal structures of epidermal growth factor receptor (EGFR) kinase domain, bound to drug inhibitors, originated from ligand-based drug design studies. Here, we used variations in 110 crystal structures to assemble eight distinct families highlighting the C-helix orientation in the N-lobe of the EGFR kinase domain. The families shared similar mutational profiles and similarity in the ligand R-groups (chemical composition, geometry, and charge) facing the C-helix, mutation sites, and DFG domain. For structure-based drug design, we recommend a systematic decision-making process for choice of template, guided by appropriate pairwise fitting and clustering before the molecular docking step. Alternatively, the binding site shape/volume can be used to filter and select the compound libraries.
- MeSH
- erbB receptory antagonisté a inhibitory chemie genetika MeSH
- inhibitory proteinkinas farmakologie MeSH
- lidé MeSH
- ligandy MeSH
- mutace MeSH
- racionální návrh léčiv metody MeSH
- rozhodování MeSH
- simulace molekulového dockingu MeSH
- vazebná místa MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- Názvy látek
- EGFR protein, human MeSH Prohlížeč
- erbB receptory MeSH
- inhibitory proteinkinas MeSH
- ligandy MeSH