Use of in silico (computer) methods to predict and analyze the tertiary structure of plant hemoglobins

Abstract

Amino acid sequences for more than 60 plant hemoglobins (Hbs) are deposited in databases, but the tertiary structure of only 4 plant Hbs have been reported; thus, the gap between the reported sequences and structures of plant Hbs is large. Elucidating the structure of plant Hbs is essential to fully understanding the function of these proteins in plant cells. Determining the actual protein structure by experimental methods (i.e., by X-ray crystallography) requires considerable protein material and is expensive; thus, this type of work is limited to few laboratories around the world. In silico (computer) methods to predict the tertiary structure of proteins from amino acid sequences have been implemented and are helping reduce the sequence-structure gap. Thus, in silico methods are useful tools for predicting the tertiary structure of several plant Hbs from amino acid sequences deposited in databases. In this chapter, we describe a method for predicting and analyzing the structure of a rice Hb2 from the template structure of native rice Hb1. This method is based on a comparative modeling method that uses programs from the SWISS-MODEL server.