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Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study.

Lee HS, Qi Y, Im W - Sci Rep (2015)

Bottom Line: There is considerable interest in developments of general approaches to predict the structural consequences of site-specific glycosylation and to understand how these effects can be exploited in protein design with advantageous properties.Our study reveals that N-glycosylation does not induce significant changes in protein structure, but decreases protein dynamics, likely leading to an increase in protein stability.Overall, these results suggest not only a common role of glycosylation in proteins, but also a need for certain proteins to be properly glycosylated to gain their intrinsic dynamic properties.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, United States.

ABSTRACT
N-linked glycosylation is one of the most important, chemically complex, and ubiquitous post-translational modifications in all eukaryotes. The N-glycans that are covalently linked to proteins are involved in numerous biological processes. There is considerable interest in developments of general approaches to predict the structural consequences of site-specific glycosylation and to understand how these effects can be exploited in protein design with advantageous properties. In this study, the impacts of N-glycans on protein structure and dynamics are systematically investigated using an integrated computational approach of the Protein Data Bank structure analysis and atomistic molecular dynamics simulations of glycosylated and deglycosylated proteins. Our study reveals that N-glycosylation does not induce significant changes in protein structure, but decreases protein dynamics, likely leading to an increase in protein stability. Overall, these results suggest not only a common role of glycosylation in proteins, but also a need for certain proteins to be properly glycosylated to gain their intrinsic dynamic properties.

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The RMSD time-series of glycosylated (GP, blue) and deglycosylated (P, red) proteins from 200-ns MD simulations.The RMSD was calculated with respect to the initial structure. Each line represents an independent run.
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f3: The RMSD time-series of glycosylated (GP, blue) and deglycosylated (P, red) proteins from 200-ns MD simulations.The RMSD was calculated with respect to the initial structure. Each line represents an independent run.

Mentions: The RMSD with respect to the initial structure is plotted as a function of simulation time in Figure 3 for each glycoprotein system. Figure 4A shows the means and standard errors of the average RMSDs from the last 50 ns for the three replicates. A comparison of the mean RMSDs between glycosylated and deglycosylated proteins indicates that glycosylation does not significantly affect proteins' global structures (P-value = 0.16), which is in agreement with the results from the PDB structure analysis. 1cxpC is the system showing the largest mean RMSD difference between the glycosylated and deglycosylated protein, but the magnitude is still around 1 Å.


Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study.

Lee HS, Qi Y, Im W - Sci Rep (2015)

The RMSD time-series of glycosylated (GP, blue) and deglycosylated (P, red) proteins from 200-ns MD simulations.The RMSD was calculated with respect to the initial structure. Each line represents an independent run.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4352867&req=5

f3: The RMSD time-series of glycosylated (GP, blue) and deglycosylated (P, red) proteins from 200-ns MD simulations.The RMSD was calculated with respect to the initial structure. Each line represents an independent run.
Mentions: The RMSD with respect to the initial structure is plotted as a function of simulation time in Figure 3 for each glycoprotein system. Figure 4A shows the means and standard errors of the average RMSDs from the last 50 ns for the three replicates. A comparison of the mean RMSDs between glycosylated and deglycosylated proteins indicates that glycosylation does not significantly affect proteins' global structures (P-value = 0.16), which is in agreement with the results from the PDB structure analysis. 1cxpC is the system showing the largest mean RMSD difference between the glycosylated and deglycosylated protein, but the magnitude is still around 1 Å.

Bottom Line: There is considerable interest in developments of general approaches to predict the structural consequences of site-specific glycosylation and to understand how these effects can be exploited in protein design with advantageous properties.Our study reveals that N-glycosylation does not induce significant changes in protein structure, but decreases protein dynamics, likely leading to an increase in protein stability.Overall, these results suggest not only a common role of glycosylation in proteins, but also a need for certain proteins to be properly glycosylated to gain their intrinsic dynamic properties.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, United States.

ABSTRACT
N-linked glycosylation is one of the most important, chemically complex, and ubiquitous post-translational modifications in all eukaryotes. The N-glycans that are covalently linked to proteins are involved in numerous biological processes. There is considerable interest in developments of general approaches to predict the structural consequences of site-specific glycosylation and to understand how these effects can be exploited in protein design with advantageous properties. In this study, the impacts of N-glycans on protein structure and dynamics are systematically investigated using an integrated computational approach of the Protein Data Bank structure analysis and atomistic molecular dynamics simulations of glycosylated and deglycosylated proteins. Our study reveals that N-glycosylation does not induce significant changes in protein structure, but decreases protein dynamics, likely leading to an increase in protein stability. Overall, these results suggest not only a common role of glycosylation in proteins, but also a need for certain proteins to be properly glycosylated to gain their intrinsic dynamic properties.

Show MeSH