Dynamics of endoglucanase catalytic domains: implications towards thermostability

Authors: YENNAMALLI, RAGOTHAMAN - Iowa State University; WOLT, JEFFREY - Iowa State University; Sen, Taner

Submitted to: Journal of Biomolecular Structure and Dynamics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/8/2011
Publication Date: 11/2/2011
Citation: Yennamalli, R.M., Wolt, J.D., Sen, T.Z. 2011. Dynamics of endoglucanase catalytic domains: implications towards thermostability. Journal of Biomolecular Structure and Dynamics. 29(3):424-596.

Interpretive Summary: Thermostable proteins, specifically industrially important enzymes, are frequently studied in protein engineering studies. Understanding the thermostability helps in engineering to enhance protein activity thereby leading to a cost effective process. For biofuel production, enzymes currently used in biomass to bioethanol conversion are derived from microorganisms. Some of the limitations of the current technology are low yield and high cost of production of pre-processing enzymes, like endoglucanases. A more efficiently designed thermophilic endoglucanase to be inserted in maize will be very promising. However, thermophilic endoglucanases are poorly understood since previous studies to derive rules of thermophilicity focused on a large number of protein families, but not on particular folds of the same enzyme. In this study, we study the relationship and thermostability. We observed specific differences in the dynamic behavior between the thermophilic and mesophilic proteins, which suggest that cooperative dynamics play a dominant role in thermostability. These findings will help scientists to design more efficient enzymes for bioethanol production from maize, which will benefit the U.S. economy.

Technical Abstract: The function of proteins is controlled by their dynamics inherently determined by their structure. Exploring the protein structure-dynamics relationship is important to develop an understanding of protein function that allows tapping the potential of economically important proteins, such as endoglucanases. Endoglucanases play a crucial role in the production of biofuels to break down plant cellulose, which requires sustained activity and thermostability at high processing temperatures. Although tertiary structures of many endoglucanase proteins are available, the relationship between thermostability and protein dynamics in endoglucanases is not explored fully. In this study, we have generated elastic network models for thermophilic and mesophilic endoglucanases with the (a/B)8 fold in unbound and bound states with saccharides. The comparative analyses of the models shed light on the relation between protein dynamics and thermostability and substrate binding. We observed specific differences in the dynamic behavior of catalytic residues: while both the nucleophile and the acid/base donor residues show positively correlated motions in the thermophile, their dynamics is uncoupled in the mesophile. The kinetically hot residues that are usually found in the functionally important locations were observed to be located at the substrate binding sides for both the thermophilic and the mesophilic proteins, indicating that they are dynamically critical during hydrolysis. We also observed that the thermophilic protein contained larger dynamic domains compared to its mesophilic counterpart in some slow normal modes, which suggests that cooperative dynamics play a dominant role in thermostability.