Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 20, 2012, Pages 7759-7764

  Wereszczynski, Jeff ^a   McCammon, J Andrew ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Adaptive biasing force; Enhanced sampling

Indexed keywords

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; HOMODIMER; MEMBRANE PROTEIN; NUCLEOTIDE;

ARTICLE; CRYSTALLOGRAPHY; CYTOSOL; ENDOPLASMIC RETICULUM; ENERGY; HYDROLYSIS; MOLECULAR DYNAMICS; PRIORITY JOURNAL; SIMULATION; THERMODYNAMICS;

ADENOSINE TRIPHOSPHATASES; CRYSTALLOGRAPHY; GUANINE NUCLEOTIDE EXCHANGE FACTORS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; NUCLEOTIDES; PROTEIN CONFORMATION; PROTEIN TRANSPORT; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84861210523     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1117441109     Document Type: Article

References (54)

1. Wallin E, von Heijne G (1998) Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 7:1029-1038. (Pubitemid 28216544)
2. Keenan RJ, Freymann DM, Stroud RM, Walter P (2001) The signal recognition particle. Annu Rev Biochem 70:755-775. (Pubitemid 32662224)
3. Rapoport TA (2007) Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes. Nature 450:663-669.
4. Wattenberg B, Lithgow T (2001) Targeting of C-terminal (tail)-anchored proteins: Understanding how cytoplasmic activities are anchored to intracellular membranes. Traffic 2:66-71. (Pubitemid 32219858)
5. Kalbfleisch T, Cambon A, Wattenberg BW (2007) A bioinformatics approach to identifying tail-anchored proteins in the human genome. Traffic 8:1687-1694. (Pubitemid 350066681)
6. Kutay U, Hartmann E, Rapoport TA (1993) A class of membrane proteins with a C-terminal anchor. Trends Cell Biol 3:72-75. (Pubitemid 23072280)
7. Favaloro V, Spasic M, Schwappach B, Dobberstein B (2008) Distinct targeting pathways for the membrane insertion of tail-anchored (TA) proteins. J Cell Sci 121:1832-1840. (Pubitemid 351943376)
8. Schuldiner M, et al. (2008) The GET complex mediates insertion of tail-anchored proteins into the ER membrane. Cell 134:634-645.
9. Simpson PJ, Schwappach B, Dohlman HG, Isaacson RL (2010) Structures of Get3, Get4, and Get5 provide new models for TA membrane protein targeting. Structure 18:897-902.
10. Chang YW, et al. (2010) Crystal structure of Get4-Get5 complex and its interactions with Sgt2, Get3, and Ydj1. J Biol Chem 285:9962-9970.
11. Hegde RS, Keenan RJ (2011) Tail-anchored membrane protein insertion into the endoplasmic reticulum. Nat Rev Mol Cell Biol 12:787-798.
12. Chartron JW, Suloway CJ, Zaslaver M, Clemons WM (2010) Structural characterization of the Get4/Get5 complex and its interaction with Get3. Proc Natl Acad Sci USA 107:12127-12132.
13. Wang F, Brown EC, Mak G, Zhuang J, Denic V (2010) A chaperone cascade sorts proteins for posttranslational membrane insertion into the endoplasmic reticulum. Mol Cell 40:159-171.
14. Chartron JW, Suloway CJ, Zaslaver M, Clemons WM (2010) Structural characterization of the Get4/Get5 complex and its interaction with Get3. Proc Natl Acad Sci USA 107:12127-12132.
15. Wang F, Whynot A, Tung M, Denic V (2011) The Mechanism of tail-anchored protein insertion into the ER membrane. Mol Cell 43:738-750.
16. Auld KL, et al. (2006) The conserved ATPase Get3/Arr4 modulates the activity of membrane- associated proteins in Saccharomyces cerevisiae. Genetics 174:215-227. (Pubitemid 44427667)
17. Mariappan M, et al. (2011) The mechanism of membrane-associated steps in tail-anchored protein insertion. Nature 477:61-66.
18. Stefer S, et al. (2011) Structural basis for tail-anchored membrane protein biogenesis by the Get3-receptor complex. Science 333:758-762.
19. Stefanovic S, Hegde RS (2007) Identification of a targeting factor for posttranslational membrane protein insertion into the ER. Cell 128:1147-1159. (Pubitemid 46427870)
20. Kurdi-Haidar B, Heath D, Naredi P, Varki N, Howell SB (1998) Immunohistochemical analysis of the distribution of the human ATPase (hASNA-I) in normal tissues and its overexpression in breast adenomas and carcinomas. J Histochem Cytochem 46:1243-1248. (Pubitemid 28487744)
21. Hemmingsson O, Zhang Y, Still M, Naredi P (2009) ASNA1, an ATPase targeting tailanchored proteins, regulates melanoma cell growth and sensitivity to cisplatin and arsenite. Cancer Chemother Pharmacol 63:491-499.
22. Hemmingsson O, Nöjd M, Kao G, Naredi P (2009) Increased sensitivity to platinating agents and arsenite in human ovarian cancer by downregulation of ASNA1. Oncol Rep 22:869-875.
23. Mateja A, et al. (2009) The structural basis of tail-anchored membrane protein recognition by Get3. Nature 461:361-366.
24. Suloway CJ, Chartron JW, Zaslaver M, Clemons WM (2009) Model for eukaryotic tailanchored protein binding based on the structure of Get3. Proc Natl Acad Sci USA 106:14849-14854.
25. Bozkurt G, et al. (2009) Structural insights into tail-anchored protein binding and membrane insertion by Get3. Proc Natl Acad Sci USA 106:21131-21136.
26. Hu J, Li J, Qian X, Denic V, Sha B (2009) The crystal structures of yeast Get3 suggest a mechanism for tail-anchored protein membrane insertion. PLoS One 4:e8061.
27. Yamagata A, et al. (2010) Structural insight into the membrane insertion of tailanchored proteins by Get3. Genes Cells 15:29-41.
28. Lange O, Grubmüeller H (2008) Full correlation analysis of conformational protein dynamics. Proteins Struct Funct Bioinf 70:1294-1312. (Pubitemid 351304090)
29. Hamelberg D, Mongan J, McCammon JA (2004) Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules. J Chem Phys 120:11919-11929.
30. Hamelberg D, de Oliveira CA, McCammon JA (2007) Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. J Chem Phys 127:155102.
31. Darve E, Rodríguez-Gómez D, Pohorille A (2008) Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys 128:144120.
32. Hénin J, Fiorin G, Chipot C, Klein M (2010) Exploring multidimensional free energy landscapes using time-dependent biases on collective variables. J Chem Theory Comput 6:35-47.
33. Yoshimoto K, Arora K, Brooks CL (2010) Hexameric helicase deconstructed: Interplay of conformational changes and substrate coupling. Biophys J 98:1449-1457.
34. Grant BJ, Gorfe AA, McCammon JA (2010) Large conformational changes in proteins: Signaling and other functions. Curr Opin Struct Biol 20:142-147.
35. Jacobson MP, et al. (2004) A hierarchical approach to all-atom protein loop prediction. Proteins 55:351-367. (Pubitemid 38437493)
36. Hornak V, et al. (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65:712-725. (Pubitemid 44583220)
37. Meagher KL, Redman LT, Carlson HA (2003) Development of polyphosphate parameters for use with the AMBER force field. J Comput Chem 24:1016-1025.
38. Peters MB, et al. (2010) Structural survey of zinc containing proteins and the development of the zinc AMBER force field (ZAFF). J Chem Theory Comput 6:2935-2947.
39. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926-935.
40. Case DA, et al. (2005) The Amber biomolecular simulation programs. J Comput Chem 26:1668-1688. (Pubitemid 43076180)
41. Phillips JC, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781-1802. (Pubitemid 43078511)
42. Wang Y, Harrison CB, Schulten K, McCammon JA (2011) Implementation of accelerated molecular dynamics in NAMD. Comput Sci Discov 4:015002.
43. Darden T, York D, Pedersen L (1993) Particle mesh Ewald-an N·log(N) method for Ewald sums in large systems. J Chem Phys 98:10089-10092.
44. Martyna GJ, Tobias DJ, Klein ML (1994) Constant-pressure molecular-dynamics algorithms. J Chem Phys 101:4177-4189.
45. Feller SE, Zhang YH, Pastor RW, Brooks BR (1995) Constant-pressure moleculardynamics simulation-the langevin piston method. J Chem Phys 103:4613-4621.
46. Wereszczynski J, McCammon JA (2012) Computational Drug Discovery and Design, ed R Baron (Humana Press, Clifton, NJ), pp 515-524.
47. Trabuco LG, Villa E, Mitra K, Frank J, Schulten K (2008) Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 16:673-683. (Pubitemid 351615021)
48. Humphrey W, Dalke A, Schulten K (1996) VMD: Visual molecular dynamics. J Mol Graphics 14:33-38. (Pubitemid 26152973)
49. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435-447.
50. Oliphant T (2007) Python for scientific computing. Comp Sci Engin 9:10-20.
51. Jones E, et al. (2001) SciPy: Open source scientific tools for Python, http://www. scipy.org.
52. Hunter JD (2007) Matplotlib: A 2D graphics environment. Comput Sci Eng 9:90-95.
53. Young MA, Gonfloni S, Superti-Furga G, Roux B, Kuriyan J (2001) Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell 105:115-126. (Pubitemid 32323921)
54. Onufriev A, Bashford D, Case DA (2004) Exploring protein native states and largescale conformational changes with a modified generalized born model. Proteins 55:383-394. (Pubitemid 38437495)