Using Molecular Dynamics Simulations To Provide New Insights into Protein Structure on the Nanosecond Timescale: Comparison with Experimental Data and Biological Inferences for the Hyaluronan-Binding
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- 作者：Andrew Almond ; Charles D. Blundell ; Victoria A. Higman ; Alexander D. MacKerell ; Jr. ; Anthony J. Day
- 刊名：Journal of Chemical Theory and Computation
- 出版年：2007
- 出版时间：January 2007
- 年：2007
- 卷：3
- 期：1
- 页码：1 - 16
- 全文大小：1386K
- 年卷期：v.3,no.1(January 2007)
- ISSN：1549-9626
文摘
Link module domains play an essential role in extracellular matrix assembly andremodeling by binding to the flexible glycosaminoglycan hyaluronan. A high-resolution NMR-structure of the Link module from the protein product of tumor necrosis factor-stimulated gene-6(Link_TSG6) has been determined, but a fuller appreciation of protein dynamics may benecessary to understand its hyaluronan-binding. Therefore, we have performed a 0.25 
s MDsimulation, starting from the lowest-energy NMR-derived solution structure of Link_TSG6, withexplicit water and ions, using the CHARMM22 protein force field. The simulation was as gooda fit to the NMR data as the ensemble from simulated annealing, except in the 
5-6 loop.Furthermore, analysis revealed that secondary structure elements extended further thanpreviously reported and underwent fast picosecond time scale dynamics, whereas nanoseconddynamics was found in certain loops. In particular, surface side chains proposed to interactwith glycosaminoglycans were predicted to be highly mobile and be directed away from theprotein surface. Furthermore, the hyaluronan-binding 4-5 loop remained in a closedconformation, favoring an allosteric interaction mechanism. This enhanced view of the Linkmodule provides general insight into protein dynamics and may be helpful for understandingthe dynamic molecular basis of tissue assembly, remodeling, and disease processes.
s MDsimulation, starting from the lowest-energy NMR-derived solution structure of Link_TSG6, withexplicit water and ions, using the CHARMM22 protein force field. The simulation was as gooda fit to the NMR data as the ensemble from simulated annealing, except in the 5-6 loop.Furthermore, analysis revealed that secondary structure elements extended further thanpreviously reported and underwent fast picosecond time scale dynamics, whereas nanoseconddynamics was found in certain loops. In particular, surface side chains proposed to interactwith glycosaminoglycans were predicted to be highly mobile and be directed away from theprotein surface. Furthermore, the hyaluronan-binding 4-5 loop remained in a closedconformation, favoring an allosteric interaction mechanism. This enhanced view of the Linkmodule provides general insight into protein dynamics and may be helpful for understandingthe dynamic molecular basis of tissue assembly, remodeling, and disease processes.