Structure and dynamics of human vimentin intermediate filament dimer and tetramer in explicit and implicit solvent models

Journal of Molecular Modeling

Volumn 17, Issue 1, 2011, Pages 37-48

  Qin, Zhao ^a   Buehler, Markus J ^a  

^a Massachusetts Institute of Technology   (United States)

Author keywords

Bending stiffness; Biopolymer; Dimer; Explicit solvent; Implicit solvent; Intermediate filaments; Materiomics; Molecular dynamics; Molecular structure; Persistence length; Structural optimization; Tetramer; Vimentin

Indexed keywords

DIMER; INTERMEDIATE FILAMENT PROTEIN; SOLVENT; TETRAMER; VIMENTIN;

ARTICLE; CHEMICAL STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; SIMULATION; STRUCTURAL BIOINFORMATICS; STRUCTURE ACTIVITY RELATION;

HUMANS; MODELS, MOLECULAR; POLYMERS; PROTEIN STRUCTURE, TERTIARY; SOLVENTS; VIMENTIN;

EUKARYOTA;

EID: 78651420058     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-010-0696-6     Document Type: Article

References (39)

1. Alberts B, Johnson A, Lewis J, Raff M, Roberts K et al. (2002) Molecular biology of the cell. Taylor & Francis, New York
2. H Herrmann H Bar L Kreplak SV Strelkov U Aebi 2007 Intermediate filaments: from cell architecture to nanomechanics Nat Rev Mol Cell Biol 8 7 562 573 1:CAS:528:DC%2BD2sXmvVaktLg%3D 10.1038/nrm2197 (Pubitemid 46985377)
3. N Wang JP Butler DE Ingber 1993 Mechanotransduction across the cell surface and through the cytoskeleton Science 260 5111 1124 1127 1:STN:280:DyaK3s3mt1Clsw%D%3D 10.1126/science.7684161
4. N Wang D Stamenovic 2002 Mechanics of vimentin intermediate filaments J Muscle Res Cell Motil 23 5-6 535 540 10.1023/A:1023470709071 (Pubitemid 36583670)
5. D Fudge D Russell D Beriault W Moore EB Lane, et al. 2008 The intermediate filament network in cultured human keratinocytes is remarkably extensible and resilient PLoS ONE 3 6 e2327 10.1371/journal.pone.0002327
6. Z Qin MJ Buehler L Kreplak 2010 A multi-scale approach to understand the mechanobiology of intermediate filaments J Biomech 43 1 15 22 10.1016/j.jbiomech.2009.09.004
7. MK Lewis PC Nahirney V Chen BB Adhikari J Wright, et al. 2003 Concentric intermediate filament lattice links to specialized Z-band junctional complexes in sonic muscle fibers of the type I male midshipman fish J Struct Biol 143 1 56 71 1:CAS:528:DC%2BD3sXlvVGqt7o%3D 10.1016/S1047-8477(03)00121-7 (Pubitemid 36918492)
8. L Kreplak H Herrmann U Aebi 2008 Tensile properties of single desmin intermediate filaments Biophys J 94 7 2790 2799 1:CAS:528:DC%2BD1cXjslCjsrY%3D 10.1529/biophysj.107.119826
9. Z Qin L Kreplak MJ Buehler 2009 Hierarchical structure controls nanomechanical properties of vimentin intermediate filaments PLoS ONE 4 10 e7294 10.1371/journal.pone.0007294
10. KN Dahl SM Kahn KL Wilson DE Discher 2004 The nuclear envelope lamina network has elasticity and a compressibility limit suggestive of a molecular shock absorber J Cell Sci 117 20 4779 4786 1:CAS:528:DC%2BD2cXptVygurs%3D 10.1242/jcs.01357 (Pubitemid 39433444)
11. KL Wilson MS Zastrow KK Lee 2001 Lamins and disease: Insights into nuclear infrastructure Cell 104 5 647 650 1:CAS:528:DC%2BD3MXitFaktbs%3D
12. U Aebi J Cohn L Buhle L Gerace 1986 The Nuclear Lamina is a Meshwork of Intermediate-Type Filaments Nature 323 6088 560 564 1:CAS:528: DyaL2sXhsVygsQ%3D%3D 10.1038/323560a0
13. M Brenner AB Johnson O Boespflug-Tanguy D Rodriguez JE Goldman, et al. 2001 Mutations in GFAP, encoding glial fibrillary acidic protein, are associated with Alexander disease Nat Genet 27 1 117 120 1:CAS:528:DC%2BD3MXis1yrtQ%3D%3D 10.1038/83679 (Pubitemid 32044531)
14. CA Brown RW Lanning KQ McKinney AR Salvino E Cherniske, et al. 2001 Novel and recurrent mutations in lamin A/C in patients with Emery-Dreifuss muscular dystrophy Am J Med Genet 102 4 359 367 1:STN:280:DC%2BD3Mvls1KgtA%3D%3D 10.1002/ajmg.1463 (Pubitemid 32778022)
15. G Bonne E Mercuri A Muchir A Urtizberea HM Becane, et al. 2000 Clinical and molecular genetic spectrum of autosomal dominant Emery-Dreifuss muscular dystrophy due to mutations of the lamin A/C gene Ann Neurol 48 2 170 180 1:CAS:528:DC%2BD3cXlvFKhtb8%3D 10.1002/1531-8249(200008)48:2<170::AID- ANA6>3.0.CO;2-J (Pubitemid 30617035)
16. JLV Broers CJ Hutchison FCS Ramaekers 2004 Laminopathies J Pathol 204 4 478 488 1:CAS:528:DC%2BD2cXhtVCgsrjJ 10.1002/path.1655 (Pubitemid 39468159)
17. MB Omary PA Coulombe WH McLean 2004 Intermediate filament proteins and their associated diseases N Engl J Med 351 20 2087 2100 1:CAS:528: DC%2BD2cXpslegs7g%3D 10.1056/NEJMra040319 (Pubitemid 39482502)
18. DAD Parry SV Strelkov P Burkhard U Aebi H Herrmann 2007 Towards a molecular description of intermediate filament structure and assembly Exp Cell Res 313 10 2204 2216 1:CAS:528:DC%2BD2sXmtFOitL4%3D 10.1016/j.yexcr.2007.04.009 (Pubitemid 46842987)
19. AV Sokolova L Kreplak T Wedig N Mucke DI Svergun, et al. 2006 Monitoring intermediate filament assembly by small-angle x-ray scattering reveals the molecular architecture of assembly intermediates Proc Natl Acad Sci USA 103 44 16206 16211 1:CAS:528:DC%2BD28Xht1WmsLzE 10.1073/pnas.0603629103 (Pubitemid 44715175)
20. SV Strelkov H Herrmann N Geisler A Lustig S Ivaninskii, et al. 2001 Divide-and-conquer crystallographic approach towards an atomic structure of intermediate filaments J Mol Biol 306 4 773 781 1:CAS:528:DC%2BD3MXhslSnsrg%3D 10.1006/jmbi.2001.4442 (Pubitemid 33027699)
21. DAD Parry 2006 Hendecad repeat in segment 2A and linker L2 of intermediate filament chains implies the possibility of a right-handed coiled-coil structure J Struct Biol 155 2 370 374 1:CAS:528:DC%2BD28XovVWqtb8%3D 10.1016/j.jsb.2006.03.017 (Pubitemid 44278651)
22. SV Strelkov H Herrmann N Geisler T Wedig R Zimbelmann, et al. 2002 Conserved segments 1A and 2B of the intermediate filament dimer: their atomic structures and role in filament assembly EMBO J 21 6 1255 1266 1:CAS:528:DC%2BD38XisVKntLo%3D 10.1093/emboj/21.6.1255 (Pubitemid 34246505)
23. ME Rafik J Doucet F Briki 2004 The intermediate filament architecture as determined by X-ray diffraction modeling of hard alpha-keratin Biophys J 86 6 3893 3904 10.1529/biophysj.103.034694 (Pubitemid 38780266)
24. S Luca WM Yau R Leapman R Tycko 2007 Peptide conformation and supramolecular organization in amylin fibrils: Constraints from solid-state NMR Biochemistry 46 47 13505 13522 1:CAS:528:DC%2BD2sXht1CktbzK 10.1021/bi701427q (Pubitemid 350209947)
25. KN Goldie T Wedig AK Mitra U Aebi H Herrmann, et al. 2007 Dissecting the 3-D structure of vimentin intermediate filaments by cryo-electron tomography J Struct Biol 158 3 378 385 1:CAS:528:DC%2BD2sXls1Wrsbs%3D 10.1016/j.jsb.2006.12. 007 (Pubitemid 46764567)
26. A Huang CM Stultz 2007 Conformational sampling with implicit solvent models: Application to the PHF6 peptide in tau protein Biophys J 92 1 34 45 1:CAS:528:DC%2BD28XhtlCmsr%2FL 10.1529/biophysj.106.091207 (Pubitemid 46048414)
27. RH Zhou BJ Berne 2002 Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water? Proc Natl Acad Sci USA 99 20 12777 12782 1:CAS:528:DC%2BD38XnvFGhsLg%3D 10.1073/pnas.142430099
28. H Nymeyer AE Garcia 2003 Simulation of the folding equilibrium of alpha-helical peptides: a comparison of the generalized Born approximation with explicit solvent Proc Natl Acad Sci USA 100 24 13934 13939 1:CAS:528: DC%2BD3sXpsFGisb0%3D 10.1073/pnas.2232868100 (Pubitemid 37499169)
29. T Lazaridis M Karplus 1999 Effective energy function for proteins in solution Protein Struct Funct Genet 35 2 133 152 1:CAS:528:DyaK1MXitlagsbk%3D 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N (Pubitemid 29165128)
30. T Lazaridis M Karplus 1997 "New view" of protein folding reconciled with the old through multiple unfolding simulations Science 278 5345 1928 1931 1:CAS:528:DyaK2sXotVCntb0%3D 10.1126/science.278.5345.1928 (Pubitemid 28013230)
31. RB Best KA Merchant IV Gopich B Schuler A Bax, et al. 2007 Effect of flexibility and cis residues in single-molecule FRET studies of polyproline Proc Natl Acad Sci USA 104 48 18964 18969 1:CAS:528:DC%2BD2sXhsVSru7nJ 10.1073/pnas.0709567104
32. E Paci M Karplus 2000 Unfolding proteins by external forces and temperature: the importance of topology and energetics Proc Natl Acad Sci USA 97 12 6521 6526 1:CAS:528:DC%2BD3cXktFajtL8%3D 10.1073/pnas.100124597 (Pubitemid 30412746)
33. E Paci M Karplus 1999 Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations J Mol Biol 288 3 441 459 1:CAS:528:DyaK1MXislWrs7k%3D 10.1006/jmbi.1999.2670 (Pubitemid 29221813)
34. AD MacKerell D Bashford M Bellott RL Dunbrack JD Evanseck, et al. 1998 All-atom empirical potential for molecular modeling and dynamics studies of proteins J Phys Chem B 102 18 3586 3616 1:CAS:528:DyaK1cXivVOlsb4%3D 10.1021/jp973084f
35. MT Nelson W Humphrey A Gursoy A Dalke LV Kale, et al. 1996 NAMD: A parallel, object oriented molecular dynamics program Int J Supercomput Appl 10 4 251 268 10.1177/109434209601000401
36. N Mucke T Wedig A Burer LN Marekov PM Steinert, et al. 2004 Molecular and biophysical characterization of assembly-starter units of human vimentin J Mol Biol 340 1 97 114 1:CAS:528:DC%2BD2cXks1eks7g%3D 10.1016/j.jmb.2004.04.039 (Pubitemid 38739440)
37. S Keten MJ Buehler 2008 Geometric confinement governs the rupture strength of H-bond assemblies at a critical length scale Nano Lett 8 2 743 748 1:CAS:528:DC%2BD1cXhslKgsLk%3D 10.1021/nl0731670 (Pubitemid 351346050)
38. GN Ramachandran C Ramakrishnan V Sasisekharan 1963 Stereochemistry of polypeptide chain configurations J Mol Biol 7 95 99 1:CAS:528:DyaF3sXks1arsLk%3D 10.1016/S0022-2836(63)80023-6
39. C Guzman S Jeney L Kreplak S Kasas AJ Kulik, et al. 2006 Exploring the mechanical properties of single vimentin intermediate filaments by atomic force microscopy J Mol Biol 360 3 623 630 1:CAS:528:DC%2BD28Xms1anu74%3D 10.1016/j.jmb.2006.05.030 (Pubitemid 43975111)