Network Of Conformational Transitions Revealed By Molecular Dynamics Simulations Of Human Carbonic Anhydrase ?

Carbonic Anhydrase(CAs,EC 4.2.1.1),as one of the metal enzymes containing Zn2+,can catalyze the rapid interconversion of carbon oxide(CO2)and water to bicarbonate(HCO3-)and protons(H+),which plays a fundamental role in the physiology and pathology of the human body.Among the carbonic anhydrase,the CAII shows the highest efficiency to catalyze the interconversion of carbon dioxide and water and attracts the most research.The function of carbonic anhydrase has close relationship with its conformation and conformational change.Thus,it is of much significance to study the conformational change of CAII in the biosystem to deepen people's understanding of the biological processes associated with carbonic anhydrase and the causes of disease formation.In this paper,based on the molecular dynamics(MD)simulation as well as the clustering analysis,we study the conformational change of HCA II in aqueous solution to reveal the relation between its conformational change and function as well as its molecular level mechanism.The research results can be summarized as follows:First,we used the MD simulation to reveal the dynamics of HCA II in aqueous solution and the trajectories have been obtained.By analyzing the trajectories,we choose the distance of certain amino acid to characterize the movement of loops in HCA ?.Then,we used the Wordom software to do the clustering analysis of the loops in HCA II and the results show that:multiple conformations can be adopted by loop1 and loop2,and the conformations can be continuously converted.Loopl has three conformation states:closed(clusters 2),semi-open(clusters 1,3,and 4)as well as open conformations(cluster 5).For loop2,its conformations are open(clusters 1,3,4,and 5)or even super-open(cluster2).Lastly,in our simulations,about one half of the conformations are accessible to CO2,while another one half not.The longest continuous periods of CO2 accessible and CO2 inaccessible conformations are all about 20%of total simulation time.Therefore,for the HCA ?,the lasting time of CO2 accessible conformations is long enough for its entry,but the lasting time of CO2 accessible conformations is also not short,CO2 must "select" a right time to enter HCA ? and bind.In other words,the conformational changes of HCA? upon CO2 binding favor the conformational selection(CS)model as the conformation of the loop 1 is variable,and its open conformations can exist prior to CO2 binding:when the loop 1 is semi-open or open,CO2 enters and binds to HCA ?;when loop 1 is closed,such entry is forbidden.The situation for larger ligands are similar,but the lasting time of their accessible conformations is shorter.However,in this process,there are still some minor induced fit(IF)elements:once CO2 enters the binding pocket,loop 1 will close and compress the pocket so that CO2 is buried into the active site,then the side chains of His-119,Leu-198,Thr-199 and Trp-209 are attracted by CO2,rotate towards and bind to CO2.These results revise our previous view of its functional mechanism of conformational change upon ligands binding and offering valuable structural insights into the workings of HCA ?.