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• W1995526603 abstract "In this study a molecular dynamics simulation of ribonuclease T1 in complex with its product 3‘GMP has been performed for a time span of 1.2 ns. By increasing the simulation time, the dynamic properties of the protein could be analyzed in more detail. Water has been included in an 18 Å radius sphere around the active site. We find that in this system 600 ps of simulation is needed before a stable conformation is reached as measured by the RMS (root mean square) difference from the starting structure, which was adapted from the crystallographic structure of ribonuclease T1 (RNT1)−2‘GMP. The increased length of the simulation gives new opportunities to study the behavior of protein motion. Several parameters such as the temperature factors and correlation functions change noticeably during the simulation. A possible mechanism for the diffusion of guanine from or to the active site was detected. This involves a two-step procedure, in which Tyr45 first opens the binding pocket, whereupon the phosphate rearranges its contacts with the catalytic residues. The motion of Tyr45 is different from what has been proposed from the structure of nucleotide-free RNT1. The binding site closes again during the simulation. We suggest that this mechanism is used to remove the product after catalysis, but not necessarily for the association of the substrate. These rearrangements are much slower than could have been detected in a shorter simulation." @default.
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• W1995526603 date "1996-01-01" @default.
• W1995526603 modified "2023-10-02" @default.
• W1995526603 title "A 1.2 ns Molecular Dynamics Simulation of the Ribonuclease T₁−3‘-Guanosine Monophosphate Complex" @default.
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• W1995526603 doi "https://doi.org/10.1021/jp952517g" @default.
• W1995526603 hasPublicationYear "1996" @default.
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