Crystallographic refinement by incorporation of molecular dynamics: thermostable serine protease thermitase complexed with eglin c.
In order to investigate the principles of protein thermostability, the crystal structure of thermitase from Thermoactinomyces vulgaris, a thermostable member of the subtilisin family of serine proteases, has been determined in a complex with eglin c. Eglin c is a serine protease inhibitor from the leech Hirudo medicinalis. After data collection with a television area-detector diffractometer and initial structure solution by molecular-replacement methods, crystallographic refinement proceeded with incorporation of molecular-dynamics techniques. It appeared that this refinement procedure has a large convergence radius with movements of more than 5 A for many atoms. Two procedures for the crystallographic molecular-dynamics refinement have been tested. They differed mainly in time span and weight on the X-ray 'energy'. The best results were obtained with a procedure which allowed the molecular-dynamics technique to search a large area in conformational space by having less weight on the X-ray restraints and allowing more time. The use of molecular-dynamics refinement considerably simplified the laborious and difficult task of fitting the model in its electron density during the refinement process. The final crystallographic R factor is 17.9% at 2.2 A resolution.
Gros
P
P
Department of Chemistry, University of Groningen, The Netherlands.
Fujinaga
M
M
Dijkstra
B W
BW
Kalk
K H
KH
Hol
W G
WG
D055598:Chemical Phenomena; D002627:Chemistry, Physical; D010450:Endopeptidases; D004795:Enzyme Stability; D006358:Hot Temperature; D011487:Protein Conformation; D011506:Proteins; D012697:Serine Endopeptidases; D015842:Serine Proteinase Inhibitors; D015843:Serpins; D014961:X-Ray Diffraction
D011506:Proteins; D015842:Serine Proteinase Inhibitors; D015843:Serpins; C028656:eglin proteinase inhibitors; D010450:Endopeptidases; D012697:Serine Endopeptidases; C022728:thermitase