Proteins have important role in physiological processes and they are involved in movement, catalysis, recognition, regulation etc. Moreover, proteins also have several therapeutical and industrial applications. Advances in Molecular Biology have enabled us to manipulate DNA and express a foreign gene in other organism (hetrologous expression). This has made advancement in the process of making changes in proteins at genetic level. Proteins are not always optimized for their properties for various applications and usefulness of a protein may be limited by low stability and /or undesired substrate specificity. Protein Engineering is the process of developing proteins with desired function by manipulating stability and specificity of a protein. There are two main approaches for protein engineering, rational design and directed evolution (irrational design). In case of rational design, knowledge of the structure and function of the protein is taken into consideration and a rational gene mutation is planned (Fig.1). Mostly, this is done by making rationally designed changes in the gene of the protein cloned in expression vector of hetrologous expression. The production of protein molecules is altered by site directed or site-specific mutagenesis of their genes. However, in some cases protein structure is not available and directed evolution method is required. In this method, random changes (mutation) are done in the protein and a mutant form with desired properties is chosen.