Abstract
The upper and lower lip regions in lysozyme from bacteriophage lambda (λ-lysozyme) are flexible in solution and exhibit two different conformations in crystal structures of the protein. MD simulations have been used to characterize the structure and dynamics of these lip regions, which surround the active site. Ten different simulations have been run including those with restraining to experimental NOE distance and 1H-15N order parameter data. The simulations show that the lower lip region, although undergoing considerable backbone fluctuations, contains two persistent β-strands. In the upper lip region, a wide range of conformations are populated and it is not clear from the available data whether some helical secondary structure is present. The work provides a clear example of the advantages of combining MD simulations with experimental data to obtain a structural interpretation of the latter. In this case, time-averaged order parameter restraining has played an essential role in enabling convergence between two different starting structures and identifying the extent to which flexible regions in solution can contain persistent secondary structure.
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Abbreviations
- λ-lysozyme:
-
Lysozyme from bacteriophage lambda
- MD:
-
Molecular dynamics
- NMR:
-
Nuclear magnetic resonance
- NOE:
-
Nuclear Overhauser Effect
- PDB:
-
Protein data bank
- RMSD:
-
Root-mean-square difference
- RMSF:
-
Root-mean-square fluctuation
- SPC:
-
Simple point charge
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Acknowledgments
WFvG thanks the Swiss National Science Foundation, grant number 200020-137827 and its National Competence Center for Research (NCCR) in Structural Biology, and the European Research Council, grant number 228076, for financial support. NH thanks the German Research Foundation (DFG) for financial support within the Cluster of Excellence in Simulation Technology (EXC 310/1) at the University of Stuttgart. LJS acknowledges the use of the Advanced Research Computing resources at the University of Oxford in carrying out some of this work. We thank Christina Redfield and André Matagne for their help and advice regarding the experimental data for λ-lysozyme.
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Smith, L.J., van Gunsteren, W.F. & Hansen, N. Characterization of the flexible lip regions in bacteriophage lambda lysozyme using MD simulations. Eur Biophys J 44, 235–247 (2015). https://doi.org/10.1007/s00249-015-1018-9
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DOI: https://doi.org/10.1007/s00249-015-1018-9