Molecular simulations of biological processes to aid in the understanding of the function of peroxiredoxins and protein tyrosine kinases


SNIC 2016/1-397


SNAC Medium

Principal Investigator:

Kwangho Nam


Umeå universitet

Start Date:


End Date:


Primary Classification:

10407: Teoretisk kemi

Secondary Classification:

10603: Biofysik

Tertiary Classification:

10601: Strukturbiologi




The project focuses on increasing our understanding of the catalytic mechanisms of peroxiredoxins and protein tyrosine kinases. The two protein systems have been extensively studied in my lab during the last several years, during which computational resources provided by SNIC were essential. We will continue the investigation by a combination of the state of the art quantum mechanical (QM) and molecular mechanical (MM) methods and molecular dynamics (MD) simulations. Due to their biological importance, unraveling catalytic mechanism of these two families of enzymes will provide new insights at a fundamental level regarding enzyme catalysis and allostery. 1. Peroxiredoxins (Prxs) are a family of enzymes that directly reduce hydrogen peroxide (H2O2), a highly toxic byproduct of cell metabolism, to water. In the proposed research, we continue to investigate the catalytic mechanism of human peroxiredoxin V (PrxV). Our present focus is on elucidating the mystery of weak binding of H2O2 and the effects of side chain mutations on the activity of the enzyme. Previously, we have determined the complete reaction free energy profile of the enzyme, and found that the substrate H2O2 is bound weakly to the enzyme. In the coming allocation period, we will perform QM/MM and alchemical free energy simulations to further characterize the effects of active site residue mutations on the catalytic reaction, substrate binding, and pKa of the catalytic cysteine residue of the enzyme. The proposed study will yield new insight into the catalytic and substrate recognition mechanisms of this important enzyme. 2. Protein tyrosine kinases (PTKs) are crucial components in cell signaling performing targeted phosphorylation of protein substrates to make impacts on cell function. Our current focuses are on the catalytic and allosteric mechanisms of insulin receptor kinase (IRK) and insulin-like growth factor 1 receptor kinase (IGF1RK). During the previous allocation periods, we have performed extensive MD and QM/MM free energy simulations, and demonstrated that protein dynamics play crucial role in the catalytic and allosteric mechanisms of IRK and IGF1RK. In the coming allocation period, we will continue the study to deepen our understanding of the roles of protein dynamics in kinase catalysis, by combining the string method with the QM/MM simulation method. Thus combined method is expected to enable concurrent simulations of the protein conformational change and enzyme catalysis. In addition, we will perform alchemical free energy simulations, based on the methods developed by my lab, to determine the effects of kinase phosphorylation on the conformational change and catalytic activity of the kinases and their underlying thermodynamics. Last, we will initiate the investigation of the catalytic mechanism of adenylate kinase in collaboration with Prof. Magnus Wolf-Watz (Umeå University, Umeå, Sweden), who is a world-reading NMR expert studying protein dynamics and catalysis. My lab has been actively developing accelerated QM/MM simulation methods, including the multi-scale ab initio QM/MM method and parallel semiempirical QM/MM method. During the coming allocation period, we will continue the development for better scalability of the developed QM/MM methods.