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Biophys J, January 2000, p. 136-149, Vol. 78, No. 1

Nonlinear Methods in the Analysis of Protein Sequences: A Case Study in Rubredoxins

Alessandro Giuliani,* Romualdo Benigni,* Paolo Sirabella,dagger Joseph P. Zbilut,Dagger and Alfredo Colosimodagger

 *TCE Laboratory, Istituto Superiore di Sanitá, 00161 Roma, Italy;  dagger Department of Biochemical Sciences, University of Roma "La Sapienza," 00185 Roma, Italy; and  Dagger Department of Molecular Biophysics and Physiology, Rush University, Chicago, Illinois 60612 USA

Two computational methods widely used in time series analysis were applied to protein sequences, and their ability to derive structural information not directly accessible through classical sequence comparisons methods was assessed. The primary structures of 19 rubredoxins of both mesophilic and thermophilic bacteria, coded with hydrophobicity values of amino acid residues, were considered as time series and were analyzed by 1) recurrence quantification analysis and 2) spectral analysis of the sequence major eigenfunctions. The results of the two methods agreed to a large extent and generated a classification consistent with known 3D structural characteristics of the studied proteins. This classification separated in a clearcut manner a thermophilic protein from mesophilic proteins. The classification of primary structures given by the two dynamical methods was demonstrated to be basically different from classification stemming from classical sequence homology metrics. Moreover, on a more detailed scale, the method was able to discriminate between thermophilic and mesophilic proteins from a set of chimeric sequences generated from the mixing of a mesophilic (Rubr Clopa) and a thermophilic (Rubr Pyrfu) protein. Overall, our results point to a new way of looking at protein sequence comparisons.

Biophys J, January 2000, p. 136-149, Vol. 78, No. 1
© 2000 by the Biophysical Society   0006-3495/00/01/136/14  $2.00


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