Atomistic and Coarse-grained Analysis of Double Spectrin Repeat Units: The Molecular Origins of Flexibility

Journal of Molecular Biology

Volumn 365, Issue 2, 2007, Pages 523-534

  Mirijanian, Dina T ^a   Chu, Jhih Wei ^a   Ayton, Gary S ^a   Voth, Gregory A ^a  

^a UNIVERSITY OF UTAH   (United States)

Author keywords

cytoskeleton; erythrocyte; flexibility; molecular dynamics; spectrin family

Indexed keywords

BRAIN PROTEIN; FODRIN; SPECTRIN; SPECTRIN BETA SUBUNIT; TRYPTOPHAN;

ALPHA HELIX; ARTICLE; ATOM; CELL STRUCTURE; CHICKEN; CONFORMATIONAL TRANSITION; CYTOSKELETON; ERYTHROCYTE; HUMAN; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE; SIMULATION;

METAZOA;

EID: 33751514898     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.10.003     Document Type: Article

References (36)

1. Broderick M.J.F., and Winder S.J. Spectrin, α-Actinin, and Dystrophin. Adv. Protein Chem. 70 (2005) 203-246
2. Bennett V., and Baines A.J. Spectrin and Ankrin-based pathways: metazoan inventions for integrating cells into tissues. Physiol. Rev. 81 (2001) 1353-1392
3. Berghs S., Ferracci F., Maksimova E., Gleason S., Leszczynski N., Butler M., et al. Autoimmunity of βIV spectrin in paraneoplastic lower motor neuron syndrom. Proc. Natl Acad. Sci. USA 98 (2001) 6945-6950
4. Stankewich M.C., Tse W.T., Peters L.L., Ch'ng Y., John K.M., Stabach P.R., et al. A widely expressed βIII spectrin associated with Golgi and cytoplasmic vesicles. Proc. Natl Acad. Sci. USA 95 (1998) 14158-14163
5. Lenormand G., Hénon S., Richert A., Siméon J., and Gallet F. Elasticity of the human red blood cell skeleton. Biorheology 40 (2003) 247-251
6. Hansen J.C., Skalak R., Chiem S., and Hoger A. Spectrin properties and the elasticity of the elasticity of the red blood cell membrane skeleton. Biorheology 34 (1997) 327-348
7. Marko J.F., and Siggia E.D. Stretching DNA. Macromolecules 28 (1995) 8750-8770
8. McGough A.M., and Josephs R. On the structure of erythrocyte spectrin in partially expanded membrane skeletons. Proc. Natl Acad. Sci. USA 87 (1990) 5208-5212
9. Discher D.E., and Carl P. New insight into red cell network structure, elasticity, and spectrin unfolding-A current review. Cell Mol. Biol. Letters 6 (2001) 593-606
10. Speicher D.W., and Marchesi V.T. Erythrocyte spectrin is comprised of many homologous triple helical segments. Nature 311 (1984) 177-180
11. Grum V.L., Li D., MacDonald R.I., and Mondragón A. Structures of two repeats of spectrin suggest models of flexibility. Cell 98 (1999) 523-535
12. Kusunoki H., MacDonald R.I., and Mondragón A. Structural insight into the stability and the flexibility of unusual erythroid spectrin repeats. Structure 12 (2004) 645-656
13. Ylanne J., Scheffzek K., Young P., and Saraste M. Crystal structures of the α-actinin rod reveals an extensive torsional twist. Structure 9 (2001) 597-604
14. Ortiz V., Nielsen S.O., Klein M.L., and Discher D.E. Unfolding a linker between helical repeats. J. Mol. Biol. 349 (2005) 638-647
15. Altmann S.M., Grünberg R.G., Pierre-François L., Ylänne J., Raae A., Herbert K., et al. Pathways and intermediates in forced unfolding of spectrin repeats. Structure 10 (2002) 1085-1096
16. Paci E., and Karplus M. Unfolding proteins by external forces and temperature: the importance of topology and energetics. Proc. Natl Acad. Sci. USA 97 (2000) 6521-6526
17. Paramore S., Ayton G.S., Mirijanian D.T., and Voth G.A. Extending a spectrin repeat unit. I: Linear force-extension response. Biophys. J. 90 (2006) 92-100
18. Paramore S., Ayton G.S., and Voth G.A. Extending a spectrin repeat unit. II: rupture behavior. Biophys. J. 90 (2006) 101-111
19. Pantazatos D.P., and MacDonald R.I. Site-directed mutagenesis of either the highly conserved Trp-22 or the moderately conserved Trp-95 to a large, hydrophobic residue reduces the thermodynamic stability of a spectrin repeating unit. J. Biol. Chem. 272 (1997) 21052-21059
20. MacDonald R.I., Musacchio A., Holmgren R.A., and Saraste S. Invariant tryptophan at a shielded site promotes folding of the conformational unit of spectrin. Proc. Natl Acad. Sci. USA 91 (1994) 1299-1303
21. MacDonald R.I., and Cummings J.A. Stability of folding of clustered, two repeat fragments of spectrin reveal a potential hinge in the human erythroid spectrin tetramer. Proc. Natl Acad. Sci. USA 101 (2004) 1502-1507
22. Chu J.W., and Voth G.A. Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis. Proc. Natl Acad. Sci. USA 102 (2005) 13111-13116
23. Chu J.W., and Voth G.A. Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. Biophys. J. 90 (2006) 1572-1582
24. Zubay G.L. Biochemistry. 4th edit. (1998), Wm. C. Brown Publishers, Dubuque, IA
25. De Loof H., Nilsson L., and Rigler R. Molecular dynamics simulation of galanin in aqueous and non-aqueous solution. J. Am. Chem. Soc. 114 (1992) 4028-4035
26. Parry D.A.D., Dixon T.W., and Cohen C. Analysis of the three α-helix motif in the spectrin superfamily of proteins. Biophys. J. 61 (1992) 858-867
27. Lankaš F., Šponer J., Langowski J., and Cheatham T.E.I. DNA base-pair step deformability inferred from molecular dynamics simulations. Biophys. J. 85 (2003) 2872-2883
28. Coleman T.R., Fishkind D.J., Mooseker M.S., and Morrow J.S. Contributions of the β-spectrin to spectrin structure and function. Cell Motil. Cytoskel. 12 (1989) 248-263
29. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., and Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4 (1983) 187-217
30. Jorgensen W.L., Chandrasekhar J., and Madura J.D. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79 (1983) 926-935
31. Grubmuller H. SOLVATE. The Enzymes. 1.0 edit (1996), Institut fur Medizinische Optik, Ludwig-Maximilians-Universitat Munchen, Munchen, Germany
32. Nelson M.T., Humphrey W., Gursoy A., Dalke A., Kale L.V., Skeel R.D., and Schulten K. NAMD: a parallel, object oriented molecular dynamics program. Int. J. Supercomput. Appl. High Perform. Comput. 10 (1996) 251-268
33. MacKerell A.D., Bashford D., Bellott M., Dunbrack R.L., Evanseck J.D., Field M.J., et al. All-atom emipical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. ser. B 102 (1998) 3586-3616
34. Allen M.P., and Tildesley D.J. Computer Simulation of Liquids (1987), Clarendon, Oxford, UK
35. Darden T., York D., and Pederson L. Particle Mesh Ewald: an N*LOG(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
36. Brooks B.R., Janezic D., and Karpulus M. Harmonic analysis of large systems. I. Methodology. J. Comput. Chem. 16 (1995) 1522-1542