Predicting protein crystallizability and nucleation

Protein and Peptide Letters

Volumn 19, Issue 7, 2012, Pages 725-731

  Sánchez Puig, Nuria ^a   Sauter, Claude ^b   Lorber, Bernard ^b   Giegé, Richard ^a   Moreno, Abel ^a  

^a UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

^b UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

Crystal growth; Crystallization feasibility; Nucleation; Proteins; Surface energy; X ray diffraction

Indexed keywords

POLYPEPTIDE;

ARTICLE; CRYSTALLIZATION; HYDROPHOBICITY; PREDICTION; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN CRYSTALLIZATION; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; X RAY CRYSTALLOGRAPHY;

COMPUTATIONAL BIOLOGY; CRYSTALLIZATION; PROTEINS; X-RAY DIFFRACTION;

EID: 84863729700     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/092986612800793127     Document Type: Article

References (50)

1. Fox, B. G.; Goulding, C.; Malkowski, M. G.; Stewart, L.; Deacon, A. Structural genomics: from genes to structures with valuable materials and many questions in between. Nat. Methods, 2008, 5(2), 129-132.
2. Dale, G. E.; Oefner, C.; D'Arcy, A. The protein as a variable in protein crystallization. J. Struct., Biol., 2003, 142(1), 88-97.
3. Malawski, G. A.; Hillig, R. C.; Monteclaro, F.; Eberspaecher, U.; Schmitz, A. A.; Crusius, K.; Huber, M.; Egner, U.; Donner, P.; Muller-Tiemann, B. Identifying protein construct variants with increased crystallization propensity-a case study. Protein Sci., 2006, 15(12), 2718-2728.
4. Moon, A. F.; Mueller, G. A.; Zhong, X.; Pedersen, L. C. A synergistic approach to protein crystallization: combination of a fixed-arm carrier with surface entropy reduction. Protein Sci, 2010, 19(5), 901-913.
5. Dyson, H. J.; Wright, P. E. Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell. Biol., 2005, 6(3), 197-208.
6. Chen, K.; Kurgan, L.; Rahbari, M. Prediction of protein crystallization using collocation of amino acid pairs. Biochem. Biophys. Res. Commun., 2007, 355(3), 764-769.
7. Kandaswamy, K. K.; Pugalenthi, G.; Suganthan, P. N.; Gangal, R. SVMCRYS: an SVM approach for the prediction of protein crystallization propensity from protein sequence. Protein Pept. Lett., 2010, 17(4), 423-430.
8. Kurgan, L.; Razib, A. A.; Aghakhani, S.; Dick, S.; Mizianty, M.; Jahandideh, S. CRYSTALP2: sequence-based protein crystallization propensity prediction. BMC Struct. Biol., 2009, 9, 50.
9. Mizianty, M. J.; Kurgan, L. Meta prediction of protein crystallization propensity. Biochem. Biophys. Res. Commun., 2009, 390(1), 10-15.
10. Overton, I. M.; Barton, G. J. A normalised scale for structural genomics target ranking: the OB-Score. FEBS Lett., 2006, 580(16), 4005-4009.
11. Overton, I. M.; Padovani, G.; Girolami, M. A.; Barton, G. J. ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction. Bioinformatics, 2008, 24(7), 901-907.
12. Overton, I. M.; van Niekerk, C. A.; Barton, G. J. XANNpred: neural nets that predict the propensity of a protein to yield diffractionquality crystals. Proteins, 2006, 79(4), 1027-1033.
13. Slabinski, L.; Jaroszewski, L.; Rychlewski, L.; Wilson, I. A.; Lesley, S. A.; Godzik, A. XtalPred: a web server for prediction of protein crystallizability. Bioinformatics, 2007, 23(24), 3403-3405.
14. Smialowski, P.; Schmidt, T.; Cox, J.; Kirschner, A.; Frishman, D. Will my protein crystallize? A sequence-based predictor. Proteins, 2006, 62(2), 343-355.
15. Kyte, J.; Doolittle, R. F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 1982, 157(1), 105-132.
16. Guruprasad, K.; Reddy, B. V.; Pandit, M. W. Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng., 1990, 4(2), 155-161.
17. Plewczynski, D.; Slabinski, L.; Tkacz, A.; Kajan, L.; Holm, L.; Ginalski, K.; Rychlewski, L. The RPSP: Web server for prediction of signal peptides. Polymer, 2007, 48(19), 5493-5496.
18. Krogh, A.; Larsson, B.; von Heijne, G.; Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 2001, 305(3), 567-580.
19. Lupas, A.; Van Dyke, M.; Stock, J. Predicting coiled coils from protein sequences. Science, 1991, 252(5010), 1162-1164.
20. Kurgan, L.; Mizianty, M. Sequence-based protein crystallization propensity prediction for structural genomics: review and comparative analysis. Nat. Sci., 2009, 1, 93-106.
21. Dosztanyi, Z.; Csizmok, V.; Tompa, P.; Simon, I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 2005, 21(16), 3433-3434.
22. Garbuzynskiy, S. O.; Lobanov, M. Y.; Galzitskaya, O. V. To be folded or to be unfolded? Protein Sci., 2004, 13(11), 2871-2877.
23. Linding, R.; Jensen, L. J.; Diella, F.; Bork, P.; Gibson, T. J.; Russell, R. B. Protein disorder prediction: implications for structural proteomics. Structure, 2003, 11(11), 1453-1459.
24. Linding, R.; Russell, R. B.; Neduva, V.; Gibson, T. J. GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res., 2003, 31(13), 3701-3708.
25. Obradovic, Z.; Peng, K.; Vucetic, S.; Radivojac, P.; Brown, C. J.; Dunker, A. K. Predicting intrinsic disorder from amino acid sequence. Proteins, 2003, 53 Suppl 6, 566-572.
26. Prilusky, J.; Felder, C. E.; Zeev-Ben-Mordehai, T.; Rydberg, E. H.; Man, O.; Beckmann, J. S.; Silman, I.; Sussman, J. L. FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics, 2005, 21(16), 3435-3438.
27. Romero, P.; Obradovic, Z.; Li, X.; Garner, E. C.; Brown, C. J.; Dunker, A. K. Sequence complexity of disordered protein. Proteins, 2001, 42(1), 38-48.
28. Vullo, A.; Bortolami, O.; Pollastri, G.; Tosatto, S. C. Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. Nucleic Acids Res., 2006, 34, W164-168.
29. Ward, J. J.; Sodhi, J. S.; McGuffin, L. J.; Buxton, B. F.; Jones, D. T. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J. Mol. Biol., 2004, 337(3), 635-645.
30. Xue, B.; Dunbrack, R. L.; Williams, R. W.; Dunker, A. K.; Uversky, V. N. PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochim. Biophys. Acta, 2010, 1804(4), 996-1010.
31. Yang, Z. R.; Thomson, R.; McNeil, P.; Esnouf, R. M. RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics, 2005, 21(16), 3369-3376.
32. Williams, R. M.; Obradovic, Z.; Mathura, V.; Braun, W.; Garner, E. C.; Young, J.; Takayama, S.; Brown, C. J.; Dunker, A. K. The protein non-folding problem: amino acid determinants of intrinsic order and disorder. Pac. Symp. Biocomput., 2001, 89-100.
33. Uversky, V. N. Cracking the folding code. Why do some proteins adopt partially folded conformations, whereas other don't? FEBS Lett., 2002, 514(2-3), 181-183.
34. Uversky, V. N.; Gillespie, J. R.; Fink, A. L. Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins, 2000, 41(3), 415-427.
35. Brocca, S.; Samalikova, M.; Uversky, V. N.; Lotti, M.; Vanoni, M.; Alberghina, L.; Grandori, R. Order propensity of an intrinsically disordered protein, the cyclin-dependent-kinase inhibitor Sic1. Proteins, 2009, 76(3), 731-746.
36. Sanchez-Puig, N.; Veprintsev, D. B.; Fersht, A. R. Binding of natively unfolded HIF-1alpha ODD domain to p53. Mol. Cell, 2005, 17(1), 11-21.
37. Dames, S. A.; Martinez-Yamout, M.; De Guzman, R. N.; Dyson, H. J.; Wright, P. E. Structural basis for Hif-1 alpha/CBP recognition in the cellular hypoxic response. Proc. Natl. Acad. Sci. USA, 2002, 99(8), 5271-5276.
38. Hewitson, K. S.; McNeill, L. A.; Riordan, M. V.; Tian, Y. M.; Bullock, A. N.; Welford, R. W.; Elkins, J. M.; Oldham, N. J.; Bhattacharya, S.; Gleadle, J. M.; Ratcliffe, P. J.; Pugh, C. W.; Schofield, C. J. Hypoxia-inducible factor (HIF) asparagine hydroxylase is identical to factor inhibiting HIF (FIH) and is related to the cupin structural family. J. Biol. Chem., 2002, 277(29), 26351-26355.
39. De Sancho, D.; Best, R. B. What is the time scale for alpha-helix nucleation? J. Am. Chem. Soc., 2011, 133(17), 6809-6816.
40. Vekilov, P. G. What determines the rate of growth of crystals from solution? Cryst. Growth Des., 2007, 7(12), 2796-2810.
41. Durbin, S. D.; Feher, G. Studies of crystal growth mechanisms of proteins by electron microscopy. J. Mol. Biol., 1990, 212(4), 763-774.
42. DeMattei, R. C.; Feigelson, R. S. Controlling Nucleation In Protein Solutions. J. Cryst. Growth, 1992, 122(1-4), 21-30.
43. George, A.; Wilson, W. W. Predicting protein crystallization from a dilute solution property. Acta Crystallogr. Sect D Biol. Crystallogr., 1994, 50(Pt 4), 361-365.
44. Kashchiev, D.; van Rosmalen, G. M. Review: Nucleation in solutions revisited. Cryst. Res. Technol., 2003, 38(7-8), 555-574.
45. Juárez-Martínez, G.; Garza, C.; Castillo, R.; Moreno, A. A dynamic light scattering investigation of the nucleation and growth of thaumatin crystals. J. Cryst. Growth, 2001, 232, 119-131.
46. Baird, J. K.; Scott, S. C.; Kim, Y. W. Theory of the effect of pH and ionic strength on the nucleation of protein crystals. J. Cryst. Growth, 2001, 232(1-4), 50-62.
47. Michinomae, M.; Mochizuki, M.; Ataka, M. Electron microscopic studies on the initial process of lysozyme crystal growth. J. Cryst. Growth, 1999, 197(1-2), 257-262.
48. Tanaka, S.; Ito, K.; Hayakawa, R.; Ataka, M. Size and number density of precrystalline aggregates in lysozyme crystallization process. J. Chem. Phys., 1999, 111(22), 10330-10337.
49. Georgalis, Y.; Schuler, J.; Frank, J.; Soumpasis, M. D.; Saenger, W. Protein crysatllization screening through scattering techniques. Adv. Colloid Interface Sci., 1995, 58(1), 57-86.
50. Niimura, N.; Minezaki, Y.; Ataka, M.; Katsura, T. Aggregation in supersaturated lysozyme solutions studied by time-resolved smallangle neutron scattering. J. Cryst. Growth, 1995, 154(1-2), 136-144.