Conserved Conformational Dynamics Control PTP1B Enzymatic Activity

Abstract

The long-accepted paradigm of biochemistry is that enzyme function depends on the three-dimensional (3D) structure. However, this paradigm is changing. Namely, the emerging view is that protein function also depends on intrinsic protein dynamics. Further, while sequence conservation is well-correlated with conservation of structure, it is unknown if sequence also conserves protein dynamics. To understand the role of dynamics, and its potential conservation, on enzyme function we studied Protein Tyrosine Phosphatase 1B (PTP1B), one of the most well-studied PTPs, as a model system. First, to establish a comprehensive understanding of PTP1B dynamics, we performed a full 13C methyl relaxation study of Ile, Leu and Val (ILV) residues of PTP1B. In combination with earlier published 15N experiments, these data provided a detailed understanding of PTP1B protein motions on different timescales allowing their influence on PTP1B function to be defined. Second, by applying co-evolutionary coupling analysis, we identified an evolutionarily conserved domain that controls PTP1B turnover. Through a combination of biochemical and biophysical techniques, our study shows that the increase in activity of PTP1B is solely achieved through a change in the underlying dynamics. These data demonstrate that within the sequence is conserved the information not only for structure but also dynamics which work together to optimize protein function. Further, our study shows that ED analysis provides valuable insights to improve the catalytic efficiency of enzymes far distant from the catalytic center as well as that it has the power to identify novel regulatory elements (therapeutic binding pockets) that can be leveraged for the control of enzymes.