Molecular dynamics simulations of forced conformational transitions in 1,6-linked polysaccharides

Biophysical Journal

Volumn 87, Issue 3, 2004, Pages 1456-1465

  Lee, Gwangrog ^a   Nowak, Wiesław ^a,c   Jaroniec, Justyna ^a   Zhang, Qingmin ^a   Marszalek, Piotr E ^a,b  

^a Duke University   (United States)

^b DUKE UNIVERSITY   (United States)

^c NICOLAUS COPERNICUS UNIVERSITY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

MONOSACCHARIDE; POLYMER; POLYSACCHARIDE;

ARTICLE; ATOMIC FORCE MICROSCOPY; CALCULATION; CHEMICAL BOND; CONFORMATIONAL TRANSITION; ELASTICITY; FORCE; MATHEMATICAL ANALYSIS; MEASUREMENT; MECHANICS; MOLECULAR DYNAMICS; NONHUMAN; ROTATION; SIMULATION;

EID: 4444317314     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.042879     Document Type: Article

References (44)

1. 3.Oboats, and skew-boat conformations. Carbohydr. Res. 339:537-551.
2. Barrows, S. E., F. J. Dulles, C. J. Cramer, A. D. French, and D. G. Truhlar. 1995. Relative stability of alternative chair forms and hydroxymethyl conformations of β-D-glucopyranose. Carbohydr. Res. 276:219-251.
3. Barton, D. H. R. 1970. The principles of conformational analysis. Science. 169:539-544.
4. Brant, D. A. 1999. Novel approaches to the analysis of polysaccharide structures. Curr. Opin. Struct. Biol. 9:556-562.
5. Brunger, A. 1992. X-PLOR, Version 3.1: A System for X-Ray Crystallography and NMR. Yale University, New Haven, CT.
6. Drickamer, K. 1997. Making a fitting choice: common aspects of sugar-binding sites in plant and animal lectins. Structure. 5:465-468.
7. Florin, E. L., M. Rief, H. Lehmann, M. Ludwig, C. Dornmair, V. T. Moy, and H. E. Gaub. 1995. Sensing specific molecular interactions with the atomic force microscope. Biosensors Biolelectr. 10:895-901.
8. Flory, P. J. 1953. Principles of Polymer Chemistry. Cornell University Press, Ithaca, NY .
9. French, A. D., R. S. Rowland, and N. L. Allinger. 1990. Modeling of glucopyranose. The flexible monomer of amylose. In Computer Modeling of Carbohydrate Molecules. A. D. French and J. W. Brady, editors. ACS Symposium series, American Chemical Society, Washington, DC. 121-140.
10. Gao, M., H. Lu, and K. Schulten. 2002. Unfolding of titin domains studied by molecular dynamics simulations. J. Muscle Res. Cell Motil. 23:513-521.
11. Grubmüller, H., B. Heymann, and P. Tavan. 1996. Ligand binding and molecular mechanics calculation of the streptavidin-biotin rupture force. Science. 271:997-999.
12. Hellerqvist, C. G., B. Lindberg, and K. Samuelsson. 1968. Methylation analysis of pustulan. Acta Chem. Scand. 22:2736-2737.
13. Humphrey, W., A. Dalke, and K. Schulten. 1996. VMD-visual molecular dynamics. J. Mol. Graph. 14:33-38.
14. Izrailev, S., S. Stepaniants, M. Balsera, Y. Oono, and K. Schulten. 1997. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys. J. 72:1568-1581.
15. Isralewitz, B., M. Gao, and K. Schulten. 2001. Steered molecular dynamics and mechanical functions of proteins. Curr. Op. Struct. Biol. 11:224-230.
16. Kale, L., R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Rrawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten. 1999. NAMD2: greater scalability for parallel molecular dynamics. J. Comput. Phys. 151:283-312.
17. Kirschner, K. N., and R. I. Woods. 2001. Solvent interaction determine carbohydrate conformation. Proc. Natl. Acad. Sci. USA. 98:10541-10545.
18. Krammer, A., H. Lu, B. Isralewitz, K. Schulten, and V. Vogel. 1999. Forced unfolding of the fibronectin type HI module reveals a tensile molecular recognition switch. Proc. Natl. Acad. Sci. USA. 96:1351-1356.
19. Kuttel, M., J. W. Brady, and K. J. Naidoo. 2002. Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. J. Comput. Chem. 23:1236-1243.
20. Lee, G., W. Nowak, J. Jaroniec, Q. Zhang, and P. E. Marszalek. 2004. Nanomechanical control of glucopyranose rotamers. J. Am. Chem. Soc. 126:6218-6219.
21. Li, H., M. Rief, F. Oesterhelt, and H. E. Gaub. 1998. Single-molecular force spectroscopy on xanthan by AFM. Adv. Mater. 10:316-319.
22. Li, H., M. Rief, F. Oesterhelt, H. E. Gaub, X. Zhang, and J. Shen. 1999. Single-molecule force spectroscopy on polysaccharides by AFM-nanomechanical fingerprint of α-(1,4)-linked polysaccharides. Chem. Phys. Lett. 305:197-201.
23. Lindberg, B., and J. McPherson. 1954. Studies on the chemistry of lichens. VI. The structure of pustulan. Acta Chem. Scand. 8:985-988.
24. Lu, H., B. Isralewitz, A. Krammer, V. Vogel, and K. Schulten. 1998. Unfolding of titin immunoglobulin domains by steered molecular dynamics. Biophys. J. 75:662-671.
25. Lu, H., and K. Schulten. 1999a. Steered molecular dynamics simulations of force-induced protein domain unfolding. Proteins Struct. Funct. Gen. 35:453-463.
26. Lu, H., and K. Schulten. 1999b. Steered molecular dynamics simulation of conformational changes of immunoglobulin domain 127 interpret atomic force microscopy observations. Chem. Phys. 247:141-153.
27. Marszalek, P. E., A. F. Oberhauser, Y.-P. Pang, and J. M. Fernandez. 1998. Polysaccharide elasticity governed by chair-boat transitions of the glucopyranose ring. Nature. 396:661-664.
28. Marszalek, P. E., Y. P. Pang, H. Li, J. E. Yazal, A. F. Oberhauser, and J. M. Fernandez. 1999a. Atomic levers control pyranose ring conformations. Proc. Natl. Acad. Sci. USA. 96:7894-7898.
29. Marszalek, P. E., H. Lu, H. Li, M. Camon-Vazquez, A. F. Oberhauser, K. Schulten, and J. M. Fernandez. 1999b. Mechanical unfolding intermediates in titin modules. Nature. 402:100-103.
30. Marszalek, P. E., A. F. Oberhauser, H. Li, and J. M. Fernandez. 2003. The force-driven conformations of heparin studied with single molecule force microscopy. Biophys. J. 85:2696-2704.
31. Marszalek, P. E., H. Li, A. F. Oberhauser, and J. M. Fernandez. 2002. Chair-boat transitions in single polysaccharide molecules observed with force-ramp AFM. Proc. Natl. Acad. Sci. USA. 99:4278-4283.
32. Marszalek, P. E., H. Li, and J. M. Fernandez. 2001. Fingerprinting polysaccharides with single molecule AFM. Nat. Biotech. 19:258-262.
33. Momany, F. A., and J. L. Wilett. 2000. Computational studies on carbohydrates: solvation studies on maltose and cyclomaltooligosaccharides (cyclodextrins) using a DFT/ab initio-derived empirical force field, AMB99C. Carbohydr. Res. 326:210-226.
34. Oberhauser, A. F., P. E. Marszalek, H. P. Erickson, and J. M. Fernandez. 1998. The molecular elasticity of the extracellular matrix protein tenascin. Nature. 393:181-185.
35. O'Donoghue, P., and Z. A. Luthey-Schulten. 2000. Barriers to forced transitions in polysaccharides. J. Phys. Chem. B. 104:10398-10405.
36. 1 distances. Carbohydr. Res. 87:1-10.
37. Pickett, H. M., and H. L. Strauss. 1970. Conformational structure, energy, and inversion rates of cyclohexane and some related oxanes. J. Am. Chem. Soc. 92:7281-7290.
38. Puri, K. D., S. Chen, and T. A. Springer. 1998. Modifying the mechanical property and shear threshold of L-selectin adhesion independently of equilibrium properties. Nature. 392:930-933.
39. Rao, V. S. R., P. K. Qasba, P. V. Balaji, and R. Chandrasekaran. 1998. Conformation of Carbohydrates. Harwood Academic Publishers, Amsterdam, The Netherlands.
40. Rief, M., F. Oesterhelt, B. Heymann, and H. E. Gaub. 1997. Single molecule force spectroscopy on polysaccharides by atomic force microscopy. Science. 275:1295-1297.
41. Stenger, J., M. C. Cowman, F. Eggers, E. M. Eyring, U. Kaatze, and S. Petrucci. 2000. Molecular dynamics and kinetics of monosaccharides in solution. A broadband ultrasonic relaxation study. J. Phys. Chem. B. 104:4782-4790.
42. Tvaroška, I., F. R. Taravel, J. P. Utille, and J. P. Carver. 2002. Quantum mechanical and NMR spectroscopy studies on the conformations of the hydroxymethyl groups in aldohexosides. Carbohydr. Res. 337:353-367.
43. Weimar, T., U. C. Kreis, J. S. Andrews, and B. M. Pinto. 1999. Conformational analysis of maltoside heteroanalogues using high-quality NOE data and molecular mechanics calculations. Flexibility as a function of the interglycosidic chacogen atom. Carbohydr. Res. 315:222-233.
44. Whistler, R. L., and J. N. BeMiller. 1993. Industrial Gums. Polysaccharides and their Derivatives. Academic Press, San Diego, CA.