Selection of a native fold by peptide recognition. Insight into TRX folding mechanism.

SANTOS, J; SICA, M; ERMACORA, M R; DELFINO, J M

Montevideo, Uruguay

Congreso; International Conference on Biological Physics and the 5th Southern Cone Biophysics Congress,; 2007

Selection of a native fold by peptide recognition. Insight into TRX folding mechanism   Javier Santos a,b,c, Mauricio P. Sica a,b, Mario R. Ermácora a,b, José María Delfino b,c   a Departamento de Ciencia y Tecnología. Universidad Nacional de Quilmes. Roque Sáenz Peña 180, Bernal, Buenos Aires. Argentina b Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) c Departamento de Química Biológica. IQUIFIB. UBA, Facultad de Farmacia y Bioquímica Junín 956 - CP (C1113AAD). Ciudad de Buenos Aires. Argentina e-mail: jsantos@qb.ffyb.uba.ar     Selective interactions among protein building blocks are vital in biological processes, such as protein folding or molecular recognition. Interaction between C-terminal (helix-5) and fragment TRX1-93 of E. coli thioredoxin (TRX) embodies an interesting model to study in a fine detail a molecular recognition event involving reciprocal structure selection where both partners gain order. We have previously, shown that packing of helix-5 against the remaining of the protein plays a key role in stabilizing the native fold of TRX. This fact points the potential role played by the so-called L row: four L residues clustered along one side of helix-5. Pairs of leucine side chains spaced by (i, i+4) are known to stabilize alanine-based peptide helices. This situation represents the most frequently observed class of pairwise side chain interaction in protein helices and requires that the c1 rotamers of residues i and i+4 be trans and gauche+, respectively. Here, we study the tendency of TRX94-108: LSKGQLKEFLDANLAY that includes helix-5 where three out of four L residues are positioned at (i, i+4) to form a stable structure in solution. We analyzed the conformation of this peptide by circular dichroism spectroscopy (CD). Independently molecular dynamics simulations were carried out to produce a realistic atomic description of low energy structures and their structural changes. Apparently, TRX94-108 is unstructured in solution as determined by CD. Nevertheless, its tendency to form helical structure was confirmed by addition of TFE, an organic solvent that stabilizes a-helical structure in peptides in regions showing an intrinsic helical propensity in aqueous solution. Indeed, TRX94-108 shows half maximal ellipticity (at 220 nm) in 20% of TFE. Correspondingly, molecular dynamics simulations and bioinformatics analysis suggest that some residues in this peptide are prone to develop helical structure in solution. In this context, we ask here whether a particular set of group interactions could encompass a key role in the acquisition of secondary and native‑tertiary structure. We then proceeded to analyze the significance of contacts involving L93, L103 and L107 of TRX to stabilize TRX structure by replacing A by L. Consistently, L99 and L103 emerge from the analysis with enhanced importance.   secretaryicbp2007@congresoselis.com.uy