Capturing the Flexibility of a Protein-Ligand Complex: Binding Free Energies from Different Enhanced Sampling Techniques

التفاصيل البيبلوغرافية
العنوان: Capturing the Flexibility of a Protein-Ligand Complex: Binding Free Energies from Different Enhanced Sampling Techniques
المؤلفون: Sebastian Wingbermühle, Lars V. Schäfer
بيانات النشر: American Chemical Society (ACS), 2020.
سنة النشر: 2020
مصطلحات موضوعية: Flexibility (engineering), 010304 chemical physics, Chemistry, Metadynamics, Sampling (statistics), Molecular Dynamics Simulation, Ligand (biochemistry), Ligands, 01 natural sciences, Computer Science Applications, Maxima and minima, Molecular dynamics, 0103 physical sciences, Thermodynamics, Free energies, Amino Acid Sequence, Physical and Theoretical Chemistry, Umbrella sampling, HLA-B35 Antigen, Biological system, Peptides, Protein Binding
الوصف: Enhanced sampling techniques are a promising approach to obtain reliable binding free energy profiles for flexible protein-ligand complexes from molecular dynamics (MD) simulations. To put four popular enhanced sampling techniques to a biologically relevant and challenging test, we studied the partial dissociation of an antigenic peptide from the Major Histocompatibility Complex I (MHC I) HLA-B*35:01 to systematically investigate the performance of Umbrella Sampling (US), Replica Exchange with Solute Tempering 2 (REST2), Bias Exchange Umbrella Sampling (BEUS, or replica-exchange umbrella sampling), and well-tempered Metadynamics (MTD). With regard to the speed of sampling and convergence, the peptide-MHC I complex (pMHC I) under study showcases intrinsic strengths and weaknesses of the four enhanced sampling techniques used. We found that BEUS can handle best the sampling challenges that arise from the coexistence of an enthalpically and an entropically stabilized free energy minimum in the pMHC I under study. These findings might be relevant also for other flexible biomolecular systems with competing enthalpically and entropically stabilized minima.
DOI: 10.26434/chemrxiv.11106806.v3
URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::73bb96da1977f7102d2968dd45a79a12
https://doi.org/10.26434/chemrxiv.11106806.v3
Rights: OPEN
رقم الانضمام: edsair.doi.dedup.....73bb96da1977f7102d2968dd45a79a12
قاعدة البيانات: OpenAIRE
الوصف
DOI:10.26434/chemrxiv.11106806.v3