Abstract
Molecular dynamics simulations of Ribonuclease Sa yield properties that are compared to data extracted from crystallography and NMR. Similar distributions of static/average as well as dynamic properties are found. The pattern of fluctuations in the backbone torsions as revealed by order parameters is conserved between different techniques. The character of concerted displacements between the different techniques is qualitatively similar. The extent of variation of conformation during the simulations is much higher than is observed by any other technique and is confined to a subspace that differs from that describing the major variation in the observed structures. The functional motions deduced are composed of a highly mobile His85 coupled to a less mobile Glu54 as forming the catalytic diad, in concert with the motion of loops lining the active site. Two of these loops have been found to exist in three distinct conformational substates: the C-terminaI part of the alpha-beta2 loop from NMR and the beta2-beta3 loop in the simulations. The simulations present a view of the dynamics of Rnase Sa that is different but complementary to NMR and X-ray, and together the data reveal a more comprehensive picture of the protein's "real" dynamics than from any method alone.
Original language | English |
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Pages (from-to) | 6038-6048 |
Number of pages | 11 |
Journal | Journal of Physical Chemistry B |
Volume | 106 |
Issue number | 23 |
DOIs | |
Publication status | Published - 13 Jun 2002 |
Keywords
- ALPHA-LYTIC PROTEASE
- PHOTOACTIVE YELLOW PROTEIN
- MOLECULAR-DYNAMICS
- NORMAL-MODE
- CONFORMATIONAL-CHANGES
- ESCHERICHIA-COLI
- STREPTOMYCES-AUREOFACIENS
- DIHYDROFOLATE-REDUCTASE
- ENZYME SPECIFICITY
- ATOMIC-RESOLUTION