Significance of Knotted Structures for Function of Proteins and Nucleic Acids - September 17-21, 2014

Significance of Knotted Structures for Function of Proteins and Nucleic Acids

Poster Session II

56 – POS Board 28 Full Characterization of the Native State Dynamics of the Pierced Lasso Bundle Leptin 1 Ellinor Haglund , 2 Brian Fuglestad, 3 Jeffrey K. Noel, 3 José N. Onuchic & 4 Patricia A. Jennings 1 Center for Theoretical Biological Physics (CTBP) and department of physics, University of California at San Diego (UCSD), La Jolla, CA USA. 2 Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA. 3 Center for Theoretical Biological Physics at Rice and UCSD (CTBP) and department of Physics, Rice University, Houston, TX USA. 4 Departments of Chemistry and Biochemistry, University of California at San Diego (UCSD), La Jolla, CA USA Recently, we discovered a new structural complexity in the pleiotropic hormone leptin, where the C-terminal disulphide bridge creates a covalent-loop through which part of the polypeptide chain is threaded (as seen in knotted proteins, Figure bellow). We explored whether other proteins contain a similar intriguing knot-like structure as in leptin and discovered 11 structural homologous proteins in the PDB forming a new class of knot-like proteins. We call this new helical family class the Pierced Lasso Bundle (PLB). Structure based models showed that the dynamics of the native state are altered through oxidation, where the dynamics of the threaded state is more malleable then the unthreaded state, suggesting a mode of controlling receptor interaction and biological activity. To further investigate the malleable behavior of the PLBs we used relaxation/dispersion NMR experiments together with MD structure based models and explicit solvent simulations to fully understand the NSD of leptin. The results show increased dynamics in the covalent-loop controlling the threaded topology as well as in one of the receptor interphases engaging the second receptor to form the active quaternary receptor-ligand complex. Finally, complete comprehension of the native state of leptin and its complex topology can significantly influence ab initio predictions of newly identified protein targets as well as guide therapeutic research and drug design.

Figure. A cartoon representation of leptin. The front and top view of the protein in a cartoon representation, where the two cysteines are highlighted in yellow. Helix A through D are part of the four helix bundle while helix 4’ is outside the bundle in loop 4. Under oxidizing conditions the cysteines forms a disulphide bridge creating a 50 residue long covalent-loop/lasso (blue). Examining the structure lead to the discovery of a threaded topology where helix C and half of helix B are threaded through the lasso creating a Pierced Lasso Bundle topology. The right panel shows a schematic figure of the top view colored in the same manner as the cartoon representation.

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