Enhancement of peptide binding to MHC class I molecules by small compounds - a combined biochemical and computational investigation

• Applicants: Professor Dr. Sebastian Springer; Professor Dr. Martin Zacharias
• Subject Area: Biochemistry
• Term: from 2010 to 2015
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 161303304

• Final Report Year: 2014

Final Report Abstract

The aim of this project was the detailed investigation of peptide binding to major histocompatibility complex (MHC) class I molecules, which play a central role in antiviral immune defense by presenting viral peptides to cytotoxic T lymphocytes. We thoroughly examined the mechanisms that govern peptide binding and identified compounds that could influence it using a multi disciplinary approach, which involved biochemical, biophysical, and computational methods. We first regarded the phenomenon that class I molecules are highly unstable without a bound peptide (usually a nonamer) and therefore thought to be incapable to attain a native conformation. The lack of available crystal structures of “empty” class I molecules devoid of any peptide supports that hypothesis. However, we could clearly demonstrate by thermal stability measurements that in vitro synthesized class I can indeed fold in the absence of a peptide ligand, though with reduced thermal stability of the resulting molecule compared to a peptidebound class I complex. We next wanted to virtually and then experimentally identify the minimal requirements of a class I-binding peptide and found out that several dipeptides were sufficient to confer folding and stability to class I. Furthermore, the binding of high-affinity peptides was strongly enhanced when the molecules had been pre-bound to the dipeptides. We also showed that those dipeptides were able to mediate the exchange of high-affinity peptides on class I molecules by keeping the peptide binding region “open”, an effect that holds the potential for medical utilization and commercial exploitation. Our expertise in performing MD simulations enabled us to approach further issues concerning class I peptide binding and dynamics apart from the central questions of this project. For instance, we virtually examined the peptide editing effect of the class I-specialized chaperone tapasin, which aids the class I molecules to bind high-affinity peptides, and found out that its method of action may be very similar to the peptide exchange effect of the small dipeptides, namely, modulation and control of the folding and flexibility of the peptide binding region. In the future, the methodical and scientific achievements of this project will help to realize subsequent projects and publications of scientific, economic, and medical importance as well as the possibility of generating a starbust, which still is, however, dependent on further funding.

Publications

• Method for producing an examination reagent and kit for analyzing a T-cell frequency. WO 2013/102458 A1. July 11, 2013
  S. K. Saini and S. Springer
  
• “Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins.” Biochim. et Biophys. Acta. (BBA)-Prot. Proteom., 2013. 1834:847-853
  Ostermeir, K., Zacharias, M.
  
• “Dipeptides promote folding and peptide binding of MHC class I molecules.” Proc Natl Acad Sci USA, 2013. 110(38): p.15383-8
  Saini, S.K., Ostermair, K., Ramnarayan, V.R., Schuster, H., Zacharias, M., Springer, S.
  
• “Not all MHC class I molecules are molten globules: Tryptophan fluorescence revelas a two-step mechanism of thermal denaturation.” Mol Immunol, 2013. 54(3-4): p.386-96
  Saini, S.K., Abualrous, E.T., Tigan, A.S., Covella, K., Wellbrock, U., Springer, S.,
  
• “Allosteric coupling between side chain interactions and binding pocket flexibility in HLA-B*44:02 molecules investigated by Molecular Dynamics simulations.” Mol Immunology, 2014
  Ostermeir, K., Springer, S., Zacharias, M.
  
• “Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic Molecular Dynamics Simulations.“ Proteins: Structure, Function and Bioinfo, 82,12, December 2014, Pages 3410-3419
  Ostermeir, K., Zacharias, M.
  
• “Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles.” J Comput Chem, 2014. 35:150-158
  Ostermeir, K., Zacharias, M.
  
• “Rapid alchemical free energy calculation employing a Generalized Born implicit solvent model.” J Phys Chem, 2014
  Ostermeir, K., Zacharias, M.
  
• “Dipeptides catalyze rapid peptide exchange on MHC class I molecules”, PNAS January 6, 2015 112 (1) 202-207
  Saini, S.K., Schuster, H., Ramnarayan, V.R., Rammensee, H.G., Stevanovic, S., Springer, S.