@article{mucha_szyk_rekowski_agris_2004, title={Sequence-altered peptide adopts optimum conformation for modification-dependent binding of the yeast tRNA(Phe) anticodon domain}, volume={23}, ISSN={["1573-4943"]}, DOI={10.1023/B:JOPC.0000016256.20648.0f}, abstractNote={Amino acid contributions to protein recognition of naturally modified RNAs are not understood. Circular dichroism spectra and predictive software suggested that peptide tF2 (S1ISPW5GFSGL10 LRWSY15), selected from a phage display library to bind the modified anticodon domain of yeast tRNAPhe (ASL), adopted a beta-sheet structure. Ala residues incorporated at positions Pro4 and Gly6, both predicted to be involved in a turn, did not alter the peptide binding affinity for the ASLPhe, although major changes in the peptide's CD spectra were observed. Substitutions at three positions Pro4, Gly6, and Gly9, the latter not predicted to be in a turn, reduced the peptide's binding affinity to 4% of that of the unsubstituted tF2 and strongly influenced the peptide's secondary structure. The results suggest that peptides with different conformations, but similar affinities, adopt the optimal binding conformation, indicative of a structurally adaptive model of binding in which the modified RNA serves as a scaffold.}, number={1}, journal={PROTEIN JOURNAL}, author={Mucha, P and Szyk, A and Rekowski, P and Agris, PF}, year={2004}, month={Jan}, pages={33–38} }
 @article{mucha_szyk_rekowski_agris_2003, title={Using capillary electrophoresis to study methylation effect on RNA-peptide interaction}, volume={50}, number={3}, journal={Acta Biochimica Polonica}, author={Mucha, P. and Szyk, A. and Rekowski, P. and Agris, P. F.}, year={2003}, pages={857–864} }
 @article{mucha_szyk_rekowski_guenther_agris_2002, title={Interaction of RNA with phage display selected peptides analyzed by capillary electrophoresis mobility shift assay}, volume={8}, ISSN={["1469-9001"]}, DOI={10.1017/S1355838202020319}, abstractNote={A sensitive capillary electrophoresis mobility shift assay (CEMSA) to analyze RNA/peptide interactions has been developed. Capillary electrophoresis (CE) has been adapted for investigating the interaction between variously methylated 17-nt analogs of the yeast tRNAPhe anticodon stem and loop domain (ASL(Phe)) and 15-amino-acid peptides selected from a random phage display library (RPL). A peptide-concentration-dependent formation of RNA/peptide complex was clearly visible during CEMSA. In the presence of peptide, the UV-monitored CE peak for ASLPhe with three of the five naturally occurring modifications (2'-O-methylcytidine (Cm32), 2'-O-methylguanine (Gm34) and 5-methylcytidine (m5C40) shifted from 18.16 to 20.90 min. The mobility shift was observed only for methylated RNA. The negative effects of diffusion, electroosmotic flow and adhesion of molecules to the capillary internal wall were suppressed by using a buffer containing a sieving polymer and a polyacrylamide-coated capillary. Under these conditions, well-shaped peaks and resolution of RNA free and bound to peptide were achieved. Peptide tF2, the most populated ligand in the RPL, specifically bound triply methylated ASLPhe in a methylated nucleoside-dependent manner. CE was found to be an efficient and sensitive method for the qualitative analysis of RNA-peptide interaction and should be generally applicable to the study of RNA-peptide (protein) interactions.}, number={5}, journal={RNA}, author={Mucha, P and Szyk, A and Rekowski, P and Guenther, R and Agris, PF}, year={2002}, month={May}, pages={698–704} }