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Electrostatic screening and backbone preferences of amino acid residues in urea-denatured ubiquitin

National Institute of Chemistry, SI 1115 Ljubljana, Slovenia

(RECEIVED August 11, 2006; FINAL REVISION October 16, 2006; ACCEPTED November 12, 2006)

Local structures in denatured proteins may be important in guiding a polypeptide chain during the folding and misfolding processes. Existence of local structures in chemically denatured proteins is a highly controversial issue. NMR parameters [coupling constants ³ J(H,H^N) and chemical shifts] of chemically denatured proteins in general deviate little from their values in small peptides. These peptides were presumed to be completely unstructured; therefore, it was considered that chemically denatured proteins are random coils. But recent experimental studies show that small peptides adopt relatively stable structures in aqueous solutions. Small deviations of the NMR parameters from their values in small peptides may thus actually indicate the existence of local structures in chemically denatured proteins. Using NMR data and theoretical predictions we show here that fluctuating -strands exist in urea-denatured ubiquitin (8 M urea at pH 2). Residues in such -strands populate more frequently the left side of the broad region of – space. Urea-denatured ubiquitin contains no detectable -sheet secondary structures; nevertheless, the fluctuating -strands in urea-denatured ubiquitin coincide to the -strands in the native state. Formation of -strands is in accord with the electrostatic screening model of unfolded proteins. The free energy of a residue in an unfolded protein is in this model determined by the local backbone electrostatics and its screening by backbone solvation. These energy terms introduce strong electrostatic coupling between neighboring residues, which causes cooperative formation of -strands in denatured proteins. We propose that fluctuating -strands in denatured proteins may serve as initiation sites to form fibrils.

Keywords: forces and stability; protein structure/folding; computational analysis of protein structure; protein structure prediction; chemically denatured proteins; NMR spectroscopy; prions

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