The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins
While reliable procedures for determining the conformations of proteins are available, methods for generating ensembles of structures that also reflect their flexibility are much less well established. Here we present a systematic assessment of the ability of ensemble-averaged molecular dynamics simulations with ensemble-averaged NMR restraints to simultaneously reproduce the average structure of proteins and their associated dynamics. We discuss the effects that under-restraining (overfitting) and over-restraining (underfitting) have on the structures generated in ensemble-averaged molecular simulations. We then introduce the MUMO (minimal under-restraining minimal over-restraining) method, a procedure in which different observables are averaged over a different number of molecules. As both over-restraining and under-restraining are significantly reduced in the MUMO method, it is possible to generate ensembles of conformations that accurately characterize both the structure and the dynamics of native states of proteins. The application of the MUMO method to the protein ubiquitin yields a high-resolution structural ensemble with an RDC Q-factor of 0.19.
KeywordsStructure determination Molecular dynamics simulations Nuclear magnetic resonance Structural ensembles Over-restraining Under-restraining
This research was supported by the NSF, the Leverhulme Trust and by the Royal Society.
- Carlson HA (2002) Protein flexibility and drug design: How to hit a moving target. Curr Opin Cell Biol 6:447–452Google Scholar
- Carlson HA, McCammon JA (2000) Accomodating protein flexibility in computational drug design. Mol Pharmacol 57:213–218Google Scholar
- Cordier F, Grzesiek S (1999) Direct observation of hydrogen bonds in proteins by interresidue 3hJNC’ scalar couplings. J Am Chem Soc 117:5179–5197Google Scholar
- Grunberg R, Leckner J, Nilges M (2004) Complementarity of structure ensembles in protein–protein binding. Science 12:2125–2136Google Scholar
- MacKerell Jr AD, Bashford D, Bellot M, Dunbrack RLJ, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Ha S, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich B, Smith JC, Stote RH, Straub J, Wiórkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586–3616CrossRefGoogle Scholar
- Neuhaus D, Williamson MP (2000) The nuclear Overhauser effect in structural and conformational analysis. New York, WileyGoogle Scholar
- Wüthrich K (1986) NMR of proteins and nucleic acids. New York, WileyGoogle Scholar