Method Developed for Quick Analysis of Conformational Changes in Proteins

Proteins
MurD 1 involves in the synthesis of the peptidoglycan layer, which is crucial for the growth of bacteria, by using energy from ATP in order to add D-Glu to a UMA substrate. Accompanying the progress of that enzyme reaction, the conformation, and in particular, the arrangement of domain 3 (pink) relative to domains 1 and 2 (light blue), undergoes a drastic change from an open state to a closed state. We have succeeded in analyzing the conformational changes in detail by the use of a paramagnetic lanthanide ions 2 (Ln3+, red balls) fixed on the protein to observe the changes in PCS, which is one of the paramagnetic effects. In the NMR 3 spectrum that is shown as an example in the box at the bottom of the figure, there is a big difference between the PCS before ligand binding (the shift of the position of the green-gray signals) and the PCS after ligand binding (the shift of the position of the red-blue signals). By using such PCS changes it is possible to precisely observe conformational changes. 

We have monitored the conformation of MurD, an enzyme related to the synthesis of the bacterial cell wall, and succeeded in observing its conformational changes in detail.

・MurD has received attention as a new stepping-stone to antibacterial agents.

・This success is expected to lead to the development of new drugs.

Outline
Proteins, which perform many important functions in the body, fulfill their functions by changing their shapes (conformations) flexibly. It is known that MurD, an enzyme related to the synthesis of the bacterial cell wall, undergoes significant conformational changes to fulfill its function, but the details have not been understood. We have succeeded in monitoring the conformation of MurD by using the technique of nuclear magnetic resonance (NMR), and in making detailed observations of how the binding to a low-molecular substrate triggers the conformational changes of MurD during the enzymatic reaction. MurD has received attention as a new stepping-stone to antibacterial agents, so the results obtained by this research are expected to lead to the development of new drugs.

This research was performed under a grant-in-aid from the Creation of Innovation Centers for Advanced Interdisciplinary Research Areas Program of the Ministry of Education, Culture, Sports, Science and Technology.

Terms
1 MurD: A enzyme involved in the synthesis of the peptidoglycan layer that forms the bacterial cell wall. It is an enzyme unique to bacteria, so it has received attention as a stepping-stone to anti-bacterial agents.

2 Paramagnetic lanthanide ion: Among the elements of the lanthanide series that constitute the rare-earth elements, those that show paramagnetism in their ionic forms. By observing paramagnetic effects from the NMR signals of proteins, one can capture long-range structural information of the protein from the lanthanide ion.

3 Nuclear magnetic resonance (NMR): A method to observe nuclear spins in a protein in a strong magnetic field, to investigate structure, dynamics, and interaction of proteins, at atomic resolution.

InquiriesCoordinating Office, Future Drug Discovery and Medical Care Innovation Project, Hokkaido University