Abstract
In the protein universe, many proteins are composed of two or more polypeptide chains, generally referred to as subunits, which associate through noncovalent interactions and, occasionally, disulfide bonds to form protein quaternary structures. It has been known for long that the functions of proteins are closely related to their quaternary structure. With the number of protein sequences entering into data banks rapidly increasing, it is highly desirable to predict protein quaternary structures automatically from their primary sequences. Here, multi-scale energy of factor solution scores and feature combination were employed to form various input feature vectors, and the multi-class support vector machine (SVM) classifier modules were adopted for predicting protein quaternary structures. The rates of correct identification suggest that the individual primary sequence of an oligomeric protein do contain the information of its quaternary structure. The results of multi-scale energy of Factor 1 solution scores indirectly prove that biologically relevant complex formation is driven predominantly by the hydrophobic effect. The current approach is quite promising and may at least play a complimentary role to the existing methods.
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References
Terry, B.F., Richard, M.C.: Determination of protein–protein interactions by matrix-assisted laser desorption/ionization mass spectrometry. J. Mass Spectrom. 33, 697–704 (1998)
Klotz, I.M., Darnell, D.W., Langerman, N.R.: Quaternary structure of proteins. In: Neurath, H., Hill, R.L. (eds.) The proteins, 3rd edn., vol. 1, pp. 226–241. Academic Press, New York (1975)
Einstein, E., Schachman, H.K.: Determing the roles of subunits in protein function. In: Creighton, T.E. (ed.) Protein function: A practical approach, pp. 135–176. IRL Press, London (1989)
Price, N.C.: Assembly of multi-subunit structure. In: Pain, R.H. (ed.) Mechanisms of Protein Folding, pp. 160–193. Oxford University Press, New York (1994)
Garian, R.: Prediction of quaternary structure from primary structure. Bioinformatics 17, 551–556 (2001)
Zhang, S.W., Pan, Q., Zhang, H.C., Zhang, Y.L., Wang, H.Y.: Classification of protein quaternary structure with support vector machine. Bioinformatics 19, 2390–2396 (2003)
Zhang, S.W., Pan, Q., Zhang, H.C., Shao, Z.C., Shi, J.Y.: Prediction protein homo-oligomer types by pesudo amino acid composition: approached with an improved feature extraction and Naive Bayes feature fusion. Amino Acids 30, 461–468 (2006)
Chou, K.C., Cai, Y.D.: Predicting protein quaternary structure by pseudo amino acid composition. Protein: structure, function, and genetics 53, 282–289 (2003)
Atchley, W.R., Zhao, J.P., Fernandes, A.D., Druke, T.: Solving the protein sequence metric problem. PNAS 102, 6395–6400 (2005)
Pittner, S., Kamarthi, S.V.: Feature extraction from wavelet coeffi-cients for pattern recognition tasks. IEEE Trans Pattern Anal Mach Intell. 21, 83–88 (1999)
Shi, J.Y., Zhang, S.W., Pan, Q., Cheng, Y.M., Xie, J.: SVM-based Method for Subcellular Localization of Protein Using Multi-Scale Energy and Pseudo Amino Acid Composition. Amino Acids 33, 69–74 (2007)
Chou, K.C.: Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins: Structure, Function, and Genetics 43, 246–255 (2001)
Vapnik, V.: Statistical Learning Theory. Wiley, New York (1998)
Hsu, C., Lin, C.J.: A comparison of methods for multi-class support vector machines. IEEE Transactions on Neural Networks 13, 415–425 (2002)
Chou, K.C., Zhang, C.T.: Review: Prediction of protein structural classes. Crit Rev Biochem Mol. Biol. 30, 275–349 (1995)
Zhou, G.P., Assa-Munt, N.: Some insights into protein structural class prediction. Protein: structure, function, and genetics 44, 57–59 (2001)
Glase, F., Steinberg, D.M., Vakser, I.A., Ben-Tal, N.: Residue frequencies and pairing preferences at protein–protein interfaces. Protein: structure, function, and genetics 43, 89–102 (2001)
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Zhang, SW., Chen, W., Zhao, CH., Cheng, YM., Pan, Q. (2007). Predicting Protein Quaternary Structure with Multi-scale Energy of Amino Acid Factor Solution Scores and Their Combination. In: Zhang, D. (eds) Medical Biometrics. ICMB 2008. Lecture Notes in Computer Science, vol 4901. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77413-6_9
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DOI: https://doi.org/10.1007/978-3-540-77413-6_9
Publisher Name: Springer, Berlin, Heidelberg
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