Crystallographic refinement by knowledge-based exploration of complex energy landscapes.
Although X-ray crystallography remains the most versatile method to determine the three-dimensional atomic structure of proteins and much progress has been made in model building and refinement techniques, it remains a challenge to elucidate accurately the structure of proteins in medium-resolution crystals. This is largely due to the difficulty of exploring an immense conformational space to identify the set of conformers that collectively best fits the experimental diffraction pattern. We show here that combining knowledge-based conformational sampling in RAPPER with molecular dynamics/simulated annealing (MD/SA) vastly improves the quality and power of refinement compared to MD/SA alone. The utility of this approach is highlighted by the automated determination of a lysozyme mutant from a molecular replacement solution that is in congruence with a model prepared independently by crystallographers. Finally, we discuss the implications of this work on structure determination in particular and conformational sampling and energy minimization in general.
Depristo
Mark A
MA
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom. mark_depristo@harvard.edu
de Bakker
Paul I W
PI
Johnson
Russell J K
RJ
Blundell
Tom L
TL
D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D006801:Humans; D007375:Interleukin-1 / Q000737:chemistry; D008840:Microfilament Proteins / Q000737:chemistry; D008969:Molecular Sequence Data; D009113:Muramidase / Q000737:chemistry / Q000235:genetics; D009154:Mutation; D011487:Protein Conformation; D011505:Protein-Tyrosine Kinases / Q000737:chemistry; D012984:Software; D013816:Thermodynamics
D007375:Interleukin-1; D008840:Microfilament Proteins; C485188:TWF1 protein, human; D011505:Protein-Tyrosine Kinases; D009113:Muramidase