Abstract
The development of a method that accurately predicts protein folding nucleus is critical at least on two points. On one hand, they can participate to misfolded proteins and therefore they are related to several amyloid diseases. On the other hand, as they constitute structural anchors, their prediction from the sequence can be valuable to improve database screening algorithms. The concept of Most Interacting Residues (MIR) aims at predicting the amino acids more likely to initiate protein folding. An alternative approach describes a protein 3D structure as a series of Tightened End Fragments (TEF). Their spatially close ends have been shown to be mainly located in the folding nucleus. While the current sequence-driven approach seems to capture all MIR, the structure-driven method partially fails to predict known folding. We present a stability-based analysis of protein folding to increase the recall and precision of these two methods.
Results: Prediction of the folding nucleus by MIR algorithm is in agreement with mutation stability prediction.
Availability: The database is available at:
http://bioinformatics.eas.asu.edu/Stability/index.php . The MIR calculation program is available at:
http://bioserv.rpbs.univ-paris-diderot.fr/cgi-bin/MIR and the TEF program at:
http://bioserv.rpbs.univ-paris-diderot.fr/TEF .
Contact: jacques.chomilier@impmc.jussieu.fr
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Brockwell, D.J., Smith, D.A., Radford, S.E.: Protein folding mechanisms: new methods and emerging ideas. Curr. Opin. Struct. Biol. 10(1), 16–25 (2000)
Steward, R.E., MacArthur, M.W., Laskowski, R.A., Thornton, J.M.: Molecular basis of inherited diseases: a structural perspective. Trends Genet. 19(9), 505–513 (2003)
Mogensen, J.E., Ipsen, H., Holm, J., Otzen, D.E.: Elimination of a misfolded folding intermediate by a single point mutation. Biochemistry 43(12), 3357–3367 (2004)
Cerdà-Costa, N., Esteras-Chopo, A., Avilés, F.X., Serrano, L., Villegas, V.: Early kinetics of amyloid fibril formation reveals conformational reorganisation of initial aggregates. J. Mol. Biol. 366(4), 1351–1363 (2007)
Wetlaufer, D.B.: Nucleation, rapid folding, and globular intrachain regions in proteins. Proc. Natl. Acad. Sci. USA 70(3), 697–701 (1973)
Abkevich, V.I., Gutin, A.M., Shakhnovich, E.I.: Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry 33(33), 10026–10036 (1994)
Fersht, A.R.: Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications. Proc. Natl. Acad. Sci. USA 92(24), 10869–10873 (1995)
Shakhnovich, E., Abkevich, V., Ptitsyn, O.: Conserved residues and the mechanism of protein folding. Nature 379(6560), 96–98 (1996)
Fersht, A.R.: Nucleation mechanisms in protein folding. Curr. Opin. Struct. Biol. 7(1), 3–9 (1997)
Papandreou, N., Berezovsky, I.N., Lopes, A., Eliopoulos, E., Chomilier, J.: Universal positions in globular proteins. Eur. J. Biochem. 271(23-24), 4762–4768 (2004)
Sacile, R., Ruggiero, C.: Hunting for “key residues” in the modeling of globular protein folding: an artificial neural network-based approach. IEEE Trans Nanobioscience 1(2), 85–91 (2002)
Religa, T.L., Markson, J.S., Mayor, U., Freund, S.M.V., Fersht, A.R.: Solution structure of a protein denatured state and folding intermediate. Nature 437(7061), 1053–1056 (2005)
Alexander, P.A., He, Y., Chen, Y., Orban, J., Bryan, P.N.: The design and characterization of two proteins with 88% sequence identity but different structure and function. Proc. Natl. Acad. Sci. 104(29), 11961–11963 (1968)
Ittah, V., Haas, E.: Nonlocal interactions stabilize long range loops in the initial folding intermediates of reduced bovine pancreatic trypsin inhibitor. Biochemistry 34(13), 4493–4506 (1995)
Berezovsky, I.N., Grosberg, A.Y., Trifonov, E.N.: Closed loops of nearly standard size: common basic element of protein structure. FEBS 466(2-3), 283–286 (2000)
Berezovsky, I.N., Kirzhner, V.M., Kirzhner, A., Trifonov, E.N.: Protein folding: looping from hydrophobic nuclei. Proteins 45(4), 346–350 (2001)
Lamarine, M., Mornon, J.P., Berezovsky, N., Chomilier, J.: Distribution of tightened end fragments of globular proteins statistically matches that of topohydrophobic positions: towards an efficient punctuation of protein folding? Cell Mol. Life Sci. 58(3), 492–498 (2001)
Poupon, A., Mornon, J.P.: Predicting the protein folding nucleus from sequences [correction of a sequence]. FEBS Lett. 452(3), 283–289 (1999)
Baussand, J., Deremble, C., Carbone, A.: Periodic distributions of hydrophobic amino acids allows the definition of fundamental building blocks to align distantly related proteins. Proteins 67(3), 695–708 (2007)
Miyazawa, S., Jernigan, R.L.: Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 256(3), 623–644 (1996)
Chomilier, J., Lamarine, M., Mornon, J.P., Torres, J.H., Eliopoulos, E., Papandreou, N.: Analysis of fragments induced by simulated lattice protein folding. C. R. Biol. 327(5), 431–443 (2004)
Poupon, A., Mornon, J.P.: Populations of hydrophobic amino acids within protein globular domains: identification of conserved “topohydrophobic” positions. Proteins 33(3), 329–342 (1998)
Cheng, J., Randall, A., Baldi, P.: Prediction of protein stability changes for single-site mutations using support vector machines. Proteins 62(4), 1125–1132 (2006)
Capriotti, E., Fariselli, P., Casadio, R.: I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res. 33(Web Server issue), W306–W310 (2005)
Zhou, H., Zhou, Y.: Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci. 11(11), 2714–2726 (2002)
Gilis, D., Rooman, M.: PoPMuSiC, an algorithm for predicting protein mutant stability changes: application to prion proteins. Protein Eng. 13(12), 849–856 (2000)
Parthiban, V., Gromiha, M.M., Schomburg, D.: CUPSAT: prediction of protein stability upon point mutations. Nucleic Acids Res. 34(Web Server issue), W239–W242 (2006)
Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., Serrano, L.: The FoldX web server: an online force field. Nucleic Acids Res. 33(Web Server issue), W382–W388 (2005)
Kumar, M.D.S., Bava, K.A., Gromiha, M.M., Prabakaran, P., Kitajima, K., Uedaira, H., Sarai, A.: ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. Nucleic Acids Res. 34(Database issue), D204–D206 (2006)
Fersht, A.R., Daggett, V.: Protein folding and unfolding at atomic resolution. Cell 108(4), 573–582 (2002)
Shakhnovich, E.: Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet. Chem. Rev. 106(5), 1559–1588 (2006)
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Lonquety, M., Lacroix, Z., Chomilier, J. (2008). Evaluation of the Stability of Folding Nucleus upon Mutation. In: Chetty, M., Ngom, A., Ahmad, S. (eds) Pattern Recognition in Bioinformatics. PRIB 2008. Lecture Notes in Computer Science(), vol 5265. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88436-1_5
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