Molecular dynamics simulation of conformational heterogeneity in transportin 1

Proteins: Structure, Function and Bioinformatics

Volumn 80, Issue 2, 2012, Pages 382-397

  Wang, Xia ^a   Xu, Xue ^a   Zhu, Shanna ^a   Xiao, Zhengtao ^a   Ma, Zhi ^a   Li, Yan ^b   Wang, Yonghua ^a  

^a NORTHWEST A F UNIVERSITY   (China)

^b DALIAN UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Conformational heterogeneity; Intrinsically disordered region; Molecular dynamics; Transportin 1

Indexed keywords

KARYOPHERIN BETA; LIGAND; PROTEIN TRANSPORTIN 1; UNCLASSIFIED DRUG; NUCLEAR LOCALIZATION SIGNAL; RAN PROTEIN; TNPO1 PROTEIN, HUMAN;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; ENZYME SUBSTRATE; MOLECULAR DYNAMICS; MOLECULAR PROBE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN POLYMORPHISM; PROTEIN STRUCTURE; PROTEIN TRANSPORT; SIMULATION; ACTIVE TRANSPORT; CHEMISTRY; HYDROGEN BOND; HYDROLYSIS; METABOLISM; NUCLEAR LOCALIZATION SIGNAL; PRINCIPAL COMPONENT ANALYSIS; PROTEIN STABILITY;

ACTIVE TRANSPORT, CELL NUCLEUS; BETA KARYOPHERINS; HYDROGEN BONDING; HYDROLYSIS; MOLECULAR DYNAMICS SIMULATION; NUCLEAR LOCALIZATION SIGNALS; PRINCIPAL COMPONENT ANALYSIS; PROTEIN CONFORMATION; PROTEIN STABILITY; RAN GTP-BINDING PROTEIN;

EID: 84855664641     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23193     Document Type: Article

References (41)

1. Weis K. Regulating access to the genome: nucleocytoplasmic transport throughout the cell cycle. Cell 2003; 112: 441-451.
2. Conti E, Müller CW, Stewart M. Karyopherin flexibility in nucleocytoplasmic transport. Curr Opin Struct Biol 2006; 16: 237-244.
3. Chook YM, Blobel G. Karyopherins and nuclear import. Curr Opin Struct Biol 2001; 11: 703-715.
4. Quimby BB, Dasso M. The small GTPase Ran: interpreting the signs. Curr Opin Cell Biol 2003; 15: 338-344.
5. Conti E, Uy M, Leighton L, Blobel G, Kuriyan J. Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin alpha. Cell 1998; 94: 193-204.
6. Guttinger S, Muhlhausser P, Koller-Eichhorn R, Brennecke J, Kutay U. Transportin2 functions as importin and mediates nuclear import of HuR. Proc Natl Acad Sci U S A 2004; 101: 2918-2923.
7. Rebane A, Aab A, Steitz JA. Transportins 1 and 2 are redundant nuclear import factors for hnRNP A1 and HuR. RNA 2004; 10: 590-599.
8. Suzuki M, Iijima M, Nishimura A, Tomozoe Y, Kamei D, Yamada M. Two separate regions essential for nuclear import of the hnRNP D nucleocytoplasmic shuttling sequence. FEBS J 2005; 272: 3975-3987.
9. Siomi H, Dreyfuss G. A nuclear localization domain in the hnRNP A1 protein. J Cell Biol 1995; 129: 551-560.
10. Lee BJ, Cansizoglu AE, Süel KE, Louis TH, Zhang Z, Chook YM. Rules for nuclear localization sequence recognition by karyopherinβ2. Cell 2006; 126: 543-558.
11. Imasaki T, Shimizu T, Hashimoto H, Hidaka Y, Kose S, Imamoto N, Yamada M, Sato M. Structural basis for substrate recognition and dissociation by human transportin 1. Mol Cell 2007; 28: 57-67.
12. Andrade MA, Bork P. HEAT repeats in the Huntington's disease protein. Nat Genet 1995; 11: 115-116.
13. Cansizoglu AE, Chook YM. Conformational heterogeneity of karyopherinβ2 is segmental. Structure 2007; 15: 1431-1441.
14. Sotomayor M, Schulten K. Single molecule experiments in vitro and in silico. Science 2007; 316: 1144-1148.
15. Chook YM, Jung A, Rosen MK, Blobel G. Uncoupling Kapβ2 substrate dissociation and Ran binding. Biochemistry 2002; 41: 6955-6966.
16. Cansizoglu AE, Lee BJ, Zhang ZC, Fontoura BM, Chook YM. Structure-based design of a pathway-specific nuclear import inhibitor. Nat Struct Mol Biol 2007; 14: 452-454.
17. Wang Y, Li Y, Ma Z, Yang W, Ai C. Mechanism of microRNA-target interaction: molecular dynamics simulations and thermodynamics analysis. PLoS Comput Biol 2010; 6:e1000866.
18. Xu X, Yang W, Wang X, Li Y, Wang Y, Ai C. Dynamic communication between androgen and coactivator: mutually induced conformational perturbations in androgen receptor ligand-binding domain. Proteins 2011; 79: 1154-1171.
19. Xu X, Wang X, Xiao Z, Li Y, Wang Y. Two TPX2-dependent switches control the activity of Aurora A. PLoS One 2011; 6:e16757.
20. Wang X, Xu X, Ma Z, Huo Y, Xiao Z, Li Y, Wang Y. Dynamic mechanisms for pre-miRNA binding and export by Exportin-5. RNA 2011; 17: 1511-1528.
21. Li L, Uversky VN, Dunker AK, Meroueh SO. A computational investigation of allostery in the catabolite activator protein. J Am Chem Soc 2007; 129: 15668-15676.
22. Chook Y, Blobel G. Structure of the nuclear transport complex karyopherin-beta2-Ran·GppNHp. Nature 1999; 399: 230-237.
23. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 1983; 22: 2577-2637.
24. Sickmeier M, Hamilton JA, LeGall T, Vacic V, Cortese MS, Tantos A, Szabo B, Tompa P, Chen J, Uversky VN, Obradovic Z, Dunker AK. DisProt: the database of disordered proteins. Nucleic Acids Res 2007; 35: 786-793.
25. Uversky VN. Natively unfolded proteins: a point where biology waits for physics. Protein Sci 2002; 11: 739-756.
26. Macara IG. Transport into and out of the nucleus. Microbiol Mol Biol Rev 2001; 65: 570-594.
27. Kutay U, Izaurralde E, Bischoff FR, Mattaj IW, Gorlich D. Dominant-negative mutants of important-beta block multiple pathways of import and export through the nuclear pore complex. EMBO J 1997; 16: 1153-1163.
28. Kose S, Imamoto N, Tachibana T, Shimamoto T, Yoneda Y. Ran-unassisted nuclear migration of a 97-kD component of nuclear pore-targeting complex. J Cell Biol 1997; 139: 841-849.
29. Chi NC, Adam EJH, Adam SA. Different binding domains for Ran-GTP and Ran-GDP/RanBP1 on nuclear import factor p 9 7. J Biol Chem 1997; 272: 6818-6822.
30. Chaillan-Huntington C, Braslavsky CV, Kuhlmann J, Stewart M. Dissecting the interactions between NTF2, RanGDP, and the nucleoporin XFXFG repeats. J Biol Chem 2000; 275: 5874-5879.
31. Gorlich D, Seewald MJ, Ribbeck K. Characterization of Ran-driven cargo transport and the RanGTPase system by kinetic measurements and computer simulation. EMBO J 2003; 22: 1088-1100.
32. Vriend G. WHAT IF: a molecular modeling and drug design program. J Mol Graph 1990; 8: 52-56.
33. Hess B, Kutzner C, Van Der Spoel D, Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 2008; 4: 435-447.
34. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comp Chem 2003; 24: 1999-2012.
35. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983; 79: 79926-79935.
36. Berendsen HJC, Postma JPM, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984; 81: 3684-3690.
37. Hess B, Bekker H, Berendsen HJC, Fraaije JGEM. LINCS: a linear constraint solver for molecular simulations. J Comput Chem 1997; 18: 1463-1472.
38. 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.
39. Swaminathan S, Harte WE, Jr, Beveridge DL. Investigation of domain structure in proteins via molecular dynamics simulation: application to HIV-1 protease dimer. J Am Chem Soc 1991; 113: 2717-2721.
40. Sherer EC, Harris SA, Soliva R, Orozco M, Laughton CA. Molecular dynamics studies of DNA A-tract structure and flexibility. J Am Chem Soc 1999; 121: 5981-5991.
41. Hayward S, Berendsen HJ. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins 1998; 30: 144-154.