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The effect of long-range interactions on the secondary structure formation of proteins

Department of Biological Sciences/Computer Science, Markey Center for Structural Biology, The Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907, USA

(RECEIVED March 25, 2005; FINAL REVISION April 19, 2005; ACCEPTED April 19, 2005)

The influence of long-range residue interactions on defining secondary structure in a protein has long been discussed and is often cited as the current limitation to accurate secondary structure prediction. There are several experimental examples where a local sequence alone is not sufficient to determine its secondary structure, but a comprehensive survey on a large data set has not yet been done. Interestingly, some earlier studies denied the negative effect of long-range interactions on secondary structure prediction accuracy. Here, we have introduced the residue contact order (RCO), which directly indicates the separation of contacting residues in terms of the position in the sequence, and examined the relationship between the RCO and the prediction accuracy. A large data set of 2777 nonhomologous proteins was used in our analysis. Unlike previous studies, we do find that prediction accuracy drops as residues have contacts with more distant residues. Moreover, this negative correlation between the RCO and the prediction accuracy was found not only for -strands, but also for -helices. The prediction accuracy of -strands is lower if residues have a high RCO or a low RCO, which corresponds to the situation that a -sheet is formed by -strands from different chains in a protein complex. The reason why the current study draws the opposite conclusion from the previous studies is examined. The implication for protein folding is also discussed.

Keywords: secondary structure prediction; long-range interaction; residue contact order; -strand formation

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051479505.

Reprint requests to: Daisuke Kihara, Department of Biological Sciences/Computer Science, Markey Center for Structural Biology, The Bindley Bioscience Center, Purdue University, Lilly Hall, West Lafayette, IN 47907, USA; e-mail: dkihara{at}purdue.edu; fax: (765) 496-1189.

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