Two structural scenarios for protein stabilization by PEG

Journal of Physical Chemistry B

Volumn 118, Issue 28, 2014, Pages 8388-8395

  Chao, Shu Han ^a   Matthews, Sam S ^b   Paxman, Ryan ^b   Aksimentiev, Aleksei ^a,d   Gruebele, Martin ^a,c,d   Price, Joshua L ^b  

^a University of Illinois at Urbana Champaign   (United States)

^b Brigham Young University   (United States)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^d UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CHAINS; MOLECULAR DYNAMICS; POLYETHYLENE GLYCOLS; SOLVENTS; STABILIZATION; STRUCTURAL DYNAMICS;

EXPLICIT SOLVENT MOLECULAR DYNAMICS; LOCAL SEQUENCES; PHARMACEUTICAL APPLICATIONS; POLY(ETHYLENE GLYCOL) CHAINS; PROTEIN STABILIZATION; PROTEIN SURFACE; SEQUENCE-DEPENDENT; STABILIZATION EFFECTS;

PROTEINS;

MACROGOL DERIVATIVE; PROTEIN;

CHEMISTRY; GENETICS; MOLECULAR DYNAMICS; MUTATION; PROTEIN CONFORMATION; PROTEIN STABILITY;

MOLECULAR DYNAMICS SIMULATION; MUTATION; POLYETHYLENE GLYCOLS; PROTEIN CONFORMATION; PROTEIN STABILITY; PROTEINS;

EID: 84904550902     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp502234s     Document Type: Article

References (29)

1. Rudd, P. M.; Elliott, T.; Cresswell, P.; Wilson, I. A.; Dwek, R. A. Glycosylation and the Immune System Science 2001, 291, 2370-2376
2. Harris, J. M.; Chess, R. B. Effect of Pegylation on Pharmaceuticals Nat. Rev. Drug Discovery 2003, 2, 214-221
3. Veronese, F. M.; Pasut, G. Pegylation, Successful Approach to Drug Delivery Drug Discovery Today 2005, 10, 1451-1458
4. Meng, W.; Guo, X.; Qin, M.; Pan, H.; Cao, Y.; Wang, W. Mechanistic Insights into the Stabilization of Srcsh3 by Pegylation Langmuir 2012, 28, 16133-16140
5. Hamed, E.; Xu, T.; Keten, S. Poly(Ethylene Glycol) Conjugation Stabilizes the Secondary Structure of A-Helices by Reducing Peptide Solvent Accessible Surface Area Biomacromolecules 2013, 14, 4053-4060
6. Pandey, B. K.; Smith, M. S.; Torgerson, C.; Lawrence, P. B.; Matthews, S. S.; Watkins, E.; Groves, M. L.; Prigozhin, M. B.; Price, J. L. Impact of Site-Specific Pegylation on the Conformational Stability and Folding Rate of the Pin Ww Domain Depends Strongly on Peg Oligomer Length Bioconjugate Chem. 2013, 24, 796-802
7. Shental-Bechor, D.; Levy, Y. Effect of Glycosylation on Protein Folding: A Close Look at Thermodynamic Stabilization Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 8256-8261
8. Chen, M. M.; Bartlett, A. I.; Nerenberg, P. S.; Friel, C. T.; Hackenberger, C. P. R.; Stultz, C. M.; Radford, S. E.; Imperiali, B. Perturbing the Folding Energy Landscape of the Bacterial Immunity Protein Im7 by Site-Specific N-Linked Glycosylation Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 22528-22533
9. Price, J. L.; Shental-Bechor, D.; Dhar, A.; Turner, M. J.; Powers, E. T.; Gruebele, M.; Levy, Y.; Kelly, J. W. Context-Dependent Effects of Asparagine Glycosylation on Pin Ww Folding Kinetics and Thermodynamics J. Am. Chem. Soc. 2010, 132, 15359-15367
10. Price, J. L.; Powers, E. T.; Kelly, J. W. N-Pegylation of a Reverse Turn Is Stabilizing in Multiple Sequence Contexts, Unlike N-Glcnacylation ACS Chem. Biol. 2011, 6, 1188-1192
11. Ellis, C. R.; Maiti, B.; Noid, W. G. Specific and Nonspecific Effects of Glycosylation J. Am. Chem. Soc. 2012, 134, 8184-8193
12. Price, J. L.; Powers, D. L.; Powers, E. T.; Kelly, J. W. Glycosylation of the Enhanced Aromatic Sequon Is Similarly Stabilizing in Three Distinct Reverse Turn Contexts Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 14127-14132
13. Culyba, E. K.; Price, J. L.; Hanson, S. R.; Dhar, A.; Wong, C.-H.; Gruebele, M.; Powers, E. T.; Kelly, J. W. Protein Native-State Stabilization by Placing Aromatic Side Chains in N-Glycosylated Reverse Turns Science 2011, 331, 571-575
14. Poly(Ethylene Glycol) Chemistry; Lim, K.; Herron, J. N., Eds.; Springer: New York, 1992.
15. Ranganathan, R.; Lu, K. P.; Hunter, T.; Noel, J. P. Structural and Functional Analysis of the Mitotic Rotamase Pin1 Suggests Substrate Recognition Is Phosphorylation Dependent Cell 1997, 89, 875-886
16. Humphrey, W.; Dalke, A.; Schulten, K. Vmd: Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 33-38
17. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. Scalable Molecular Dynamics with Namd J. Comput. Chem. 2005, 26, 1781-1802
18. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79, 926-935
19. Beglov, D.; Roux, B. Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations J. Chem. Phys. 1994, 100, 9050-9063
20. MacKerell, A. D.; Bashford, D.; Bellott; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-3616
21. MacKerell, A. D.; Feig, M.; Brooks, C. L. Improved Treatment of the Protein Backbone in Empirical Force Fields J. Am. Chem. Soc. 2004, 126, 698-699
22. Best, R. B.; Zhu, X.; Shim, J.; Lopes, P. E. M.; Mittal, J.; Feig, M.; MacKerell, J. A. D. Optimization of the Additive Charmm All-Atom Protein Force Field Targeting Improved Sampling of the Backbone Φ, Ψ and Side-Chain X 1and X 2dihedral Angles J. Chem. Theory Comput. 2012, 8, 3257-3273
23. Vorobyov, I.; Anisimov, V. M.; Greene, S. Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers J. Chem. Theory Comput. 2007, 3, 1120-1133
24. Lee, H.; Venable, R. M.; MacKerell, A. D.; Pastor, R. W. Molecular Dynamics Studies of Polyethylene Oxide and Polyethylene Glycol: Hydrodynamic Radius and Shape Anisotropy Biophys. J. 2008, 95, 1590-1599
25. Yoo, J.; Aksimentiev, A. Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems J. Phys. Chem. Lett. 2012, 3, 45-50
26. Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An N ̇ Log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-10092
27. Payne, M. C.; Teter, M. P.; Allan, D. C.; Arias, T. A.; Joannopoulos, J. D. Iterative Minimization Techniques for Ab Initio Total-Energy Calculations: Molecular Dynamics and Conjugate Gradients Rev. Mod. Phys. 1992, 64, 1045-1097
28. Martyna, G. J.; Tobias, D. J.; Klein, M. L. Constant Pressure Molecular Dynamics Algorithms J. Chem. Phys. 1994, 101, 4177-4189
29. Jäger, M.; Dendle, M.; Kelly, J. W. Sequence Determinants of Thermodynamic Stability in a WW Domain - an All-β-Sheet Protein Protein Sci. 2009, 18, 1806-1813