Submitted to: Plant Physiology and Biochemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/16/2004
Publication Date: 12/15/2004
Citation: Saenz-Rivera, J., Sarath, G., Arredondo-Peter, R. 2004. Modeling the tertiary structure of a maize (zea mays ssp. mays) non-symbiotic hemoglobin. Plant Physiology and Biochemistry. 42:891-892. Interpretive Summary: Plants contain three classes of hemoglobins (Hbs), the symbiotic, truncated and non-symbiotic Hbs. The functions of the symbiotic Hbs are known, but the functions of the truncated and non-symbiotic Hbs are not. The non-symbiotic Hbs are ubiquitous and thought be involved in plant responses to the environment, most notably during stress and or during changes in cell metabolism. It is anticipated that non-symbiotic Hbs will interact with other proteins to elicit their effects in plant cells. One approach towards understanding these protein-protein interactions is to predict the three-dimensional (tertiary structure) models of Hbs using computational methods. In this study we have modeled the tertiary structure of a maize (Zea mays ssp. mays) non-symbiotic hemoglobin (Hbm) using the known tertiary structure of rice Hb1 as a template. We first tested our method by predicting a tertiary structure of soybean leghemoglobin a (Lba) using the known structure of rice Hb1 as a template. The tertiary structure of soybean Lba predicted by our method and the solved (known) structures of native soybean Lba were similar, indicating that the computer methods used in this work could be useful for predicting the tertiary structures of other plant Hbs. Our predicted tertiary structure of Hbm indicated that it was very similar to the known structure of rice Hb1 and could be thus expected to share similar properties. Interestingly our model of the Hbm protein showed the existence of a pocket-like region (the N/C cavity) where interactions with organic molecules or proteins could be possible. These structural features of the Hbm molecule may regulate its activity and function in the maize plant.
Technical Abstract: The tertiary structure of a maize (Zea mays ssp. mays) non-symbiotic hemoglobin (Hbm) was modeled using computer tools and the known tertiary structure of rice Hb1 as a template. This method was tested by predicting the tertiary structure of soybean leghemoglobin a (Lba) from rice Hb1 template. The tertiary structures of predicted and native Lba are similar, indicating that the computer methods used in this work are useful tools for predicting tertiary structures of plant Hbs. Predicted tertiary structure of Hbm has a long pre-helix A and large CD-loop. The positions of the distal and proximal His are identical in Hbm and rice Hb1, which suggests that heme-Fe is hexacoordinate in Hbm and that the kinetic properties of Hbm and rice Hb1 are identical, i.e. that Hbm has a high O2-affinity. Thermostability analysis showed that Hbm CD-loop is unstable and may provide mobility to helix E, resulting in the possibility of positioning the distal His closer to the heme-Fe for hexacoordination and ligand stabilization. Analysis of the C-terminal half of Hbm showed the existence of a pocket-like region (the N/C cavity) where interactions with organic molecules or proteins could be possible. Lys K94 protrudes into the N/C cavity, suggesting that K94 may sense the binding of molecules to the N/C cavity. Thus, it is likely that the instability of the CD-loop and the possibility of binding molecules to the N/C cavity are essential for positioning amino acids in the heme pocket and in regulating Hbm activity and function.