Peptide Sequence Influence on the Confrontational Dynamics of the Intrinsically Disordered AT-Hook 3 Peptide

Alexander Bolufer, Alyssa Garabedian, and Francisco Fernandez-Lima

Florida International University

Title: Peptide Sequence Influence on the Conformational Dynamics of the Intrinsically Disordered ATHP 3 Peptide

Alexander Bolufer¹; Alyssa Garabedian¹; Francisco Fernandez-lima^1,2

¹ Department of Chemistry and Biochemistry, Florida International University, Miami, USA

² Biomolecular Science Institute, Florida International University, Miami, USA

Many DNA binding proteins are intrinsically disordered and cannot be studied using tradition crystallography and NMR techniques. Our group, over the last decade has developed several structural biology tools based on mass spectrometry for the characterization of the biomolecular structure, dynamics, folding pathways and binding kinetics. In the present work, we studied the conformational changes of the AT-hook peptide 3 (ATHP 3) binding motifs of the intrinsically disordered, architectural transcription factor High Mobility Group A2 protein. Trapped Ion Mobility Spectrometry coupled to Mass Spectrometry (TIMS-MS) was used to study the conformational space and to measure the collisional cross sections as a function of the charge state and single point mutation of the ATHP 3. Candidate structures were proposed to all kinetically trapped intermediates observed using molecular dynamics (MD). For the first time, conformational motifs were described and the main intramolecular interactions that stabilized the intermediate structures are described for ATHP 3.