Structural features and chaperone activity of the NudC protein family

Journal of Molecular Biology

Volumn 409, Issue 5, 2011, Pages 722-741

  Zheng, Meiying ^a,d   Cierpicki, Tomasz ^a,e   Burdette, Alexander J ^b,c   Utepbergenov, Darkhan ^a   Janczyk, Paweł Ł ^a   Derewenda, Urszula ^a   Stukenberg, P Todd ^a   Caldwell, Kim A ^b,c   Derewenda, Zygmunt S ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

^b UNIVERSITY OF ALABAMA   (United States)

^c University of Alabama at Birmingham   (United States)

^d MONSANTO COMPANY   (United States)

^e UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

chaperones; crystallography; nuclear migration; protein structure; protein protein interactions

Indexed keywords

CHAPERONE; HEAT SHOCK PROTEIN 90; PROTEIN; PROTEIN NUDC; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; DIMERIZATION; HUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STRUCTURE; STRUCTURAL GENOMICS; X RAY CRYSTALLOGRAPHY;

EMERICELLA NIDULANS; EUKARYOTA; VERTEBRATA;

EID: 79958032911     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.04.018     Document Type: Article

References (101)

1. Morris N.R. Mitotic mutants of Aspergillus nidulans Genet. Res. 26 1975 237 254
2. Xiang X., Beckwith S.M., and Morris N.R. Cytoplasmic dynein is involved in nuclear migration in Aspergillus nidulans Proc. Natl Acad. Sci. USA 91 1994 2100 2104 (Pubitemid 24092050)
3. Xiang X., Osmani A.H., Osmani S.A., Xin M., and Morris N.R. NudF, a nuclear migration gene in Aspergillus nidulans is similar to the human LIS-1 gene required for neuronal migration Mol. Biol. Cell. 6 1995 297 310
4. Willins D.A., Xiang X., and Morris N.R. An alpha tubulin mutation suppresses nuclear migration mutations in Aspergillus nidulans Genetics 141 1995 1287 1298
5. Morris N.R., Xiang X., and Beckwith S.M. Nuclear migration advances in fungi Trends Cell. Biol. 5 1995 278 282
6. Beckwith S.M., Roghi C.H., and Morris N.R. The genetics of nuclear migration in fungi Genet. Eng. (NY) 17 1995 165 180
7. Jones K.L., Gilbert E.F., Kaveggia E.G., and Opitz J.M. The Miller-Dieker syndrome Pediatrics 66 1980 277 281 (Pubitemid 10046535)
8. Reiner O., Carrozzon R., Shen Y., Wehnert M., Faustinella F., and Dobyns W.B. Isolation of a Miller-Dieker lissencephaly gene containing G-protein β-subunits-like repeats Nature (London) 364 1993 717 721 (Pubitemid 23273124)
9. Hattori M., Adachi H., Tsujimoto M., Arai H., and Inoue K. Miller-Dieker lissencephaly gene encodes a subunit of brain platelet-activating factor acetylhydrolase Nature (London) 370 1994 216 218
10. Morris N.R. Nuclear migration. From fungi to the mammalian brain J. Cell Biol. 148 2000 1097 1101
11. Tarricone C., Perrina F., Monzani S., Massimiliano L., Kim M.H., and Derewenda Z.S. Coupling PAF signaling to dynein regulation: structure of LIS1 in complex with PAF-acetylhydrolase Neuron 44 2004 809 821 (Pubitemid 39575634)
12. Kardon J.R., and Vale R.D. Regulators of the cytoplasmic dynein motor Nat. Rev. Mol. Cell Biol. 10 2009 854 865
13. Niethammer M., Smith D.S., Ayala R., Peng J., Ko J., and Lee M. NUDEL is a novel Cdk5 substrate that associates with LIS1 and cytoplasmic dynein Neuron 28 2000 697 711 (Pubitemid 32038065)
14. Feng Y., Olson E.C., Stukenberg P.T., Flanagan L.A., Kirschner M.W., and Walsh C.A. LIS1 regulates CNS lamination by interacting with mNudE, a central component of the centrosome Neuron 28 2000 665 679 (Pubitemid 32038063)
15. Yan X., Li F., Liang Y., Shen Y., Zhao X., Huang Q., and Zhu X. Human Nudel and NudE as regulators of cytoplasmic dynein in poleward protein transport along the mitotic spindle Mol. Cell. Biol. 23 2003 1239 1250 (Pubitemid 36177034)
16. Derewenda U., Tarricone C., Choi W.C., Cooper D.R., Lukasik S., and Perrina F. The structure of the coiled-coil domain of Ndel1 and the basis of its interaction with Lis1, the causal protein of Miller-Dieker lissencephaly Structure 15 2007 1467 1481 (Pubitemid 350064493)
17. McKenney R.J., Vershinin M., Kunwar A., Vallee R.B., and Gross S.P. LIS1 and NudE induce a persistent dynein force-producing state Cell 141 2010 304 314
18. Chiu Y.H., Xiang X., Dawe A.L., and Morris N.R. Deletion of nudC, a nuclear migration gene of Aspergillus nidulans, causes morphological and cell wall abnormalities and is lethal Mol. Biol. Cell 8 1997 1735 1749 (Pubitemid 27411138)
19. Helmstaedt K., Laubinger K., Vosskuhl K., Bayram O., Busch S., and Hoppert M. The nuclear migration protein NUDF/LIS1 forms a complex with NUDC and BNFA at spindle pole bodies Eukaryotic Cell 7 2008 1041 1052 (Pubitemid 351961583)
20. Dawe A.L., Caldwell K.A., Harris P.M., Morris N.R., and Caldwell G.A. Evolutionarily conserved nuclear migration genes required for early embryonic development in Caenorhabditis elegans Dev. Genes Evol. 211 2001 434 441 (Pubitemid 32927040)
21. Cunniff J., Chiu Y.H., Morris N.R., and Warrior R. Characterization of DnudC, the Drosophila homolog of an Aspergillus gene that functions in nuclear motility Mech. Dev. 66 1997 55 68 (Pubitemid 27376642)
22. Moreau N., Aumais J.P., Prudhomme C., Morris S.M., and Yu-Lee L.Y. NUDC expression during amphibian development Int. J. Dev. Biol. 45 2001 839 843 (Pubitemid 33095474)
23. Miller B.A., Zhang M.Y., Gocke C.D., De Souza C., Osmani A.H., and Lynch C. A homolog of the fungal nuclear migration gene nudC is involved in normal and malignant human hematopoiesis Exp. Hematol. 27 1999 742 750 (Pubitemid 29181450)
24. Matsumoto N., and Ledbetter D.H. Molecular cloning and characterization of the human NUDC gene Hum. Genet. 104 1999 498 504 (Pubitemid 29370926)
25. Zhou T., Zimmerman W., Liu X., and Erikson R.L. A mammalian NudC-like protein essential for dynein stability and cell viability Proc. Natl Acad. Sci. USA 103 2006 9039 9044 (Pubitemid 43902529)
26. Yang Y., Yan X., Cai Y., Lu Y., Si J., and Zhou T. NudC-like protein 2 regulates the LIS1/dynein pathway by stabilizing LIS1 with Hsp90 Proc. Natl Acad. Sci. USA 107 2010 3499 3504
27. Garcia-Ranea J.A., Mirey G., Camonis J., and Valencia A. p23 and HSP20/alpha-crystallin proteins define a conserved sequence domain present in other eukaryotic protein families FEBS Lett. 529 2002 162 167
28. Wang Q., Li M., Wang Y., Zhang Y., Jin S., and Xie G. RNA interference targeting CML66, a novel tumor antigen, inhibits proliferation, invasion and metastasis of HeLa cells Cancer Lett. 269 2008 127 138
29. Yang X.F., Wu C.J., McLaughlin S., Chillemi A., Wang K.S., and Canning C. CML66, a broadly immunogenic tumor antigen, elicits a humoral immune response associated with remission of chronic myelogenous leukemia Proc. Natl Acad. Sci. USA 98 2001 7492 7497 (Pubitemid 32567976)
30. Gocke C.D., Osmani S.A., and Miller B.A. The human homologue of the Aspergillus nuclear migration gene nudC is preferentially expressed in dividing cells and ciliated epithelia Histochem. Cell. Biol. 114 2000 293 301
31. Zhang M.Y., Huang N.N., Clawson G.A., Osmani S.A., Pan W., and Xin P. Involvement of the fungal nuclear migration gene nudC human homolog in cell proliferation and mitotic spindle formation Exp. Cell Res. 273 2002 73 84
32. Zhou T., Aumais J.P., Liu X., Yu-Lee L.Y., and Erikson R.L. A role for Plk1 phosphorylation of NudC in cytokinesis Dev. Cell 5 2003 127 138 (Pubitemid 36827347)
33. Aumais J.P., Williams S.N., Luo W., Nishino M., Caldwell K.A., and Caldwell G.A. Role for NudC, a dynein-associated nuclear movement protein, in mitosis and cytokinesis J. Cell Sci. 116 2003 1991 2003 (Pubitemid 36622297)
34. Nishino M., Kurasawa Y., Evans R., Lin S.H., Brinkley B.R., and Yu-Lee L.Y. NudC is required for Plk1 targeting to the kinetochore and chromosome congression Curr. Biol. 16 2006 1414 1421 (Pubitemid 44066771)
35. Hatakeyama H., Kondo T., Fujii K., Nakanishi Y., Kato H., Fukuda S., and Hirohashi S. Protein clusters associated with carcinogenesis, histological differentiation and nodal metastasis in esophageal cancer Proteomics 6 2006 6300 6316 (Pubitemid 44935516)
36. Lin S.H., Nishino M., Luo W., Aumais J.P., Galfione M., Kuang J., and Yu-Lee L.Y. Inhibition of prostate tumor growth by overexpression of NudC, a microtubule motor-associated protein Oncogene 23 2004 2499 2506 (Pubitemid 38520747)
37. Hartmann T.B., Mattern E., Wiedemann N., van Doorn R., Willemze R., and Niikura T. Identification of selectively expressed genes and antigens in CTCL Exp. Dermatol. 17 2008 324 334 (Pubitemid 351338676)
38. Suzuki S.O., McKenney R.J., Mawatari S., Mizuguchi M., Mikami A., and Iwaki T. Expression patterns of LIS1, dynein and their interaction partners dynactin, NudE, NudEL and NudC in human gliomas suggest roles in invasion and proliferation Acta Neuropathol. 113 2007 591 599 (Pubitemid 46672606)
39. Morris S.M., Albrecht U., Reiner O., Eichele G., and Yu-Lee L.Y. The lissencephaly gene product Lis1, a protein involved in neuronal migration, interacts with a nuclear movement protein, NudC Curr. Biol. 8 1998 603 606 (Pubitemid 28222897)
40. Zhu X.J., Liu X., Jin Q., Cai Y., Yang Y., and Zhou T. The L279P mutation of nuclear distribution gene C (NudC) influences its chaperone activity and lissencephaly protein 1 (LIS1) stability J. Biol. Chem. 285 2010 29903 29910
41. Aumais J.P., Tunstead J.R., McNeil R.S., Schaar B.T., McConnell S.K., and Lin S.H. NudC associates with Lis1 and the dynein motor at the leading pole of neurons J. Neurosci. 21 2001 RC187
42. Riera J., Rodriguez R., Carcedo M.T., Campa V.M., Ramos S., and Lazo P.S. Isolation and characterization of nudC from mouse macrophages, a gene implicated in the inflammatory response through the regulation of PAF-AH(I) activity FEBS Lett. 581 2007 3057 3062 (Pubitemid 46899047)
43. Yamada M., Toba S., Takitoh T., Yoshida Y., Mori D., and Nakamura T. mNUDC is required for plus-end-directed transport of cytoplasmic dynein and dynactins by kinesin-1 EMBO J. 29 2010 517 531
44. Faircloth L.M., Churchill P.F., Caldwell G.A., and Caldwell K.A. The microtubule-associated protein, NUD-1, exhibits chaperone activity in vitro Cell Stress Chaperones 14 2009 95 103
45. Chen W.M., Yu B., Zhang Q., and Xu P. Identification of the residues in the extracellular domain of thrombopoietin receptor involved in the binding of thrombopoietin and a nuclear distribution protein (human NUDC) J. Biol. Chem. 285 2010 26697 26709
46. Pang S.F., Li X.K., Zhang Q., Yang F., and Xu P. Interference RNA (RNAi)-based silencing of endogenous thrombopoietin receptor (Mpl) in Dami cells resulted in decreased hNUDC-mediated megakaryocyte proliferation and differentiation Exp. Cell Res. 315 2009 3563 3573
47. Tang Y.S., Zhang Y.P., and Xu P. hNUDC promotes the cell proliferation and differentiation in a leukemic cell line via activation of the thrombopoietin receptor (Mpl) Leukemia 22 2008 1018 1025 (Pubitemid 351689884)
48. Zhang Y.P., Tang Y.S., Chen X.S., and Xu P. Regulation of cell differentiation by hNUDC via a Mpl-dependent mechanism in NIH 3T3 cells Exp. Cell Res. 313 2007 3210 3221 (Pubitemid 47284056)
49. Wei M.X., Yang Y., Ge Y.C., and Xu P. Functional characterization of hNUDC as a novel accumulator that specifically acts on in vitro megakaryocytopoiesis and in vivo platelet production J. Cell. Biochem. 98 2006 429 439
50. Pan R.M., Yang Y., Wei M.X., Yu X.B., Ge Y.C., and Xu P. A microtubule associated protein (hNUDC) binds to the extracellular domain of thrombopoietin receptor (Mpl) J. Cell. Biochem. 96 2005 741 750 (Pubitemid 41567545)
51. Riera J., and Lazo P.S. The mammalian NudC-like genes: a family with functions other than regulating nuclear distribution Cell. Mol. Life Sci. 66 2009 2383 2390
52. Lupas A., Van Dyke M., and Stock J. Predicting coiled coils from protein sequences Science 252 1991 1162 1164 (Pubitemid 21917026)
53. Srivastava M., Begovic E., Chapman J., Putnam N.H., Hellsten U., and Kawashima T. The Trichoplax genome and the nature of placozoans Nature 454 2008 955 960
54. Kajan L., and Rychlewski L. Evaluation of 3D-Jury on CASP7 models BMC Bioinf. 8 2007 304
55. Ginalski K., Elofsson A., Fischer D., and Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions Bioinformatics 19 2003 1015 1018 (Pubitemid 36675823)
56. Cooper D.R., Boczek T., Grelewska K., Pinkowska M., Sikorska M., Zawadzki M., and Derewenda Z. Protein crystallization by surface entropy reduction: optimization of the SER strategy Acta Crystallogr. Sect. D 63 2007 636 645 (Pubitemid 46661535)
57. Goldschmidt L., Cooper D.R., Derewenda Z.S., and Eisenberg D. Toward rational protein crystallization: a Web server for the design of crystallizable protein variants Protein Sci. 16 2007 1569 1576 (Pubitemid 47195684)
58. Derewenda Z.S., and Vekilov P.G. Entropy and surface engineering in protein crystallization Acta Crystallogr. Sect. D 62 2006 116 124
59. Derewenda Z.S. Rational protein crystallization by mutational surface engineering Structure 12 2004 529 535 (Pubitemid 38447156)
60. Weaver A.J., Sullivan W.P., Felts S.J., Owen B.A., and Toft D.O. Crystal structure and activity of human p23, a heat shock protein 90 co-chaperone J. Biol. Chem. 275 2000 23045 23052 (Pubitemid 30646194)
61. Bagneris C., Bateman O.A., Naylor C.E., Cronin N., Boelens W.C., Keep N.H., and Slingsby C. Crystal structures of alpha-crystallin domain dimers of alphaB-crystallin and Hsp20 J. Mol. Biol. 392 2009 1242 1252
62. Holm L., Kaariainen S., Rosenstrom P., and Schenkel A. Searching protein structure databases with DaliLite v.3 Bioinformatics 24 2008 2780 2781 (Pubitemid 352722625)
63. Holm L., Kaariainen S., Wilton C., and Plewczynski D. Using Dali for structural comparison of proteins Curr. Protoc. Bioinf. 2006 Chapter 5, Unit 5.5
64. Zhang M., Kadota Y., Prodromou C., Shirasu K., and Pearl L.H. Structural basis for assembly of Hsp90-Sgt1-CHORD protein complexes: implications for chaperoning of NLR innate immunity receptors Mol. Cell 39 2010 269 281
65. Kadota Y., Shirasu K., and Guerois R. NLR sensors meet at the SGT1-HSP90 crossroad Trends Biochem. Sci. 35 2010 199 207
66. Ali M.M., Roe S.M., Vaughan C.K., Meyer P., Panaretou B., and Piper P.W. Crystal structure of an Hsp90-nucleotide-p23/Sba1 closed chaperone complex Nature 440 2006 1013 1017
67. Singh M., Gonzales F.A., Cascio D., Heckmann N., Chanfreau G., and Feigon J. Structure and functional studies of the CS domain of the essential H/ACA ribonucleoparticle assembly protein SHQ1 J. Biol. Chem. 284 2009 1906 1916
68. Finn R.D., Tate J., Mistry J., Coggill P.C., Sammut S.J., and Hotz H.R. The Pfam protein families database Nucleic Acids Res. 36 2008 D281 D288
69. Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., and Eddy S.R. The Pfam protein families database Nucleic Acids Res. 30 2002 276 280 (Pubitemid 34679563)
70. Bhattacharya S., Lee Y.T., Michowski W., Jastrzebska B., Filipek A., Kuznicki J., and Chazin W.J. The modular structure of SIP facilitates its role in stabilizing multiprotein assemblies Biochemistry 44 2005 9462 9471 (Pubitemid 40962045)
71. Santelli E., Leone M., Li C., Fukushima T., Preece N.E., and Olson A.J. Structural analysis of Siah1-Siah-interacting protein interactions and insights into the assembly of an E3 ligase multiprotein complex J. Biol. Chem. 280 2005 34278 34287 (Pubitemid 41443153)
72. Clark J.I., and Muchowski P.J. Small heat-shock proteins and their potential role in human disease Curr. Opin. Struct. Biol. 10 2000 52 59 (Pubitemid 30099327)
73. Lupas A. Predicting coiled-coil regions in proteins Curr. Opin. Struct. Biol. 7 1997 388 393 (Pubitemid 27281409)
74. Zhu H., Domingues F.S., Sommer I., and Lengauer T. NOXclass: prediction of protein-protein interaction types BMC Bioinf. 7 2006 27
75. Perez D.E., Hoyer J.S., Johnson A.I., Moody Z.R., Lopez J., and Kaplinsky N.J. BOBBER1 is a noncanonical Arabidopsis small heat shock protein required for both development and thermotolerance Plant Physiol. 151 2009 241 252
76. Burdette A.J., Churchill P.F., Caldwell G.A., and Caldwell K.A. The early-onset torsion dystonia-associated protein, torsinA, displays molecular chaperone activity in vitro Cell Stress Chaperones 15 2010 605 617
77. Cherepkova O.A., Lyutova E.M., Eronina T.B., and Gurvits B.Y. Chaperone-like activity of macrophage migration inhibitory factor Int. J. Biochem. Cell Biol. 38 2006 43 55 (Pubitemid 41540716)
78. Saibil H.R. Chaperone machines in action Curr. Opin. Struct. Biol. 18 2008 35 42
79. McHaourab H.S., Godar J.A., and Stewart P.L. Structure and mechanism of protein stability sensors: chaperone activity of small heat shock proteins Biochemistry 48 2009 3828 3837
80. Horwitz J. Alpha-crystallin can function as a molecular chaperone Proc. Natl Acad. Sci. USA 89 1992 10449 10453
81. Jakob U., Gaestel M., Engel K., and Buchner J. Small heat shock proteins are molecular chaperones J. Biol. Chem. 268 1993 1517 1520 (Pubitemid 23033534)
82. Lee G.J., Roseman A.M., Saibil H.R., and Vierling E. A small heat shock protein stably binds heat-denatured model substrates and can maintain a substrate in a folding-competent state EMBO J. 16 1997 659 671 (Pubitemid 27067794)
83. Jakob U., Lilie H., Meyer I., and Buchner J. Transient interaction of Hsp90 with early unfolding intermediates of citrate synthase. Implications for heat shock in vivo J. Biol. Chem. 270 1995 7288 7294
84. Holaska J.M., Black B.E., Love D.C., Hanover J.A., Leszyk J., and Paschal B.M. Calreticulin is a receptor for nuclear export J. Cell Biol. 152 2001 127 140 (Pubitemid 32102442)
85. Guo L., Groenendyk J., Papp S., Dabrowska M., Knoblach B., and Kay C. Identification of an N-domain histidine essential for chaperone function in calreticulin J. Biol. Chem. 278 2003 50645 50653 (Pubitemid 37548913)
86. Galigniana M.D., Harrell J.M., O'Hagen H.M., Ljungman M., and Pratt W.B. Hsp90-binding immunophilins link p53 to dynein during p53 transport to the nucleus J. Biol. Chem. 279 2004 22483 22489 (Pubitemid 38679447)
87. Nery F.C., Zeng J., Niland B.P., Hewett J., Farley J., and Irimia D. TorsinA binds the KASH domain of nesprins and participates in linkage between nuclear envelope and cytoskeleton J. Cell Sci. 121 2008 3476 3486
88. Longenecker K., Read P., Derewenda U., Dauter Z., Liu X., and Garrard S. How RhoGDI binds Rho Acta Crystallogr. Sect. D 55 1999 1503 1515 (Pubitemid 29449859)
89. Hoffman G.R., Nassar N., and Cerione R.A. Structure of the Rho family GTP-binding protein Cdc42 in complex with the multifunctional regulator RhoGDI Cell 100 2000 345 356 (Pubitemid 30353090)
90. Sheffield P., Garrard S., and Derewenda Z. Overcoming expression and purification problems of RhoGDI using a family of "Parallel" expression vectors Protein Expression Purif. 15 1999 34 39 (Pubitemid 29321466)
91. Schneider T.R., and Sheldrick G.M. Substructure solution with SHELXD Acta Crystallogr. Sect. D 58 2002 1772 1779 (Pubitemid 35169744)
92. Sheldrick G.M. Macromolecular phasing with SHELXE Z. Kristallogr. 217 2002 644 650
93. Morris R.J., Perrakis A., and Lamzin V.S. ARP/wARP and automatic interpretation of protein electron density maps Methods Enzymol. 374 2003 229 244 (Pubitemid 37531812)
94. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallogr. Sect. D 53 1997 240 255 (Pubitemid 27235885)
95. Adams P.D., Afonine P.V., Bunkoczi G., Chen V.B., Davis I.W., and Echols N. PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr. Sect. D 66 2010 213 221
96. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for binding protein models in electron density maps and the location of errors in these models Acta Crystallogr. Sect. A 47 1991 110 119
97. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics Acta Crystallogr. Sect. D 60 2004 2126 2132 (Pubitemid 41742764)
98. Davis I.W., Leaver-Fay A., Chen V.B., Block J.N., Kapral G.J., and Wang X. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Nucleic Acids Res. 35 2007 W375 W383
99. Laskowski R.A., McArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26 1993 282 291
100. Ashkenazy H., Erez E., Martz E., Pupko T., and Ben-Tal N. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids Nucleic Acids Res. 38 2010 W529 W533
101. Landau M., Mayrose I., Rosenberg Y., Glaser F., Martz E., Pupko T., and Ben-Tal N. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures Nucleic Acids Res. 33 2005 W299 W302