he present invention discloses a composition of hair dye comprising the KRTAP-2 family protein conjugated with a pigment. The present invention discloses the use of lawsone or indigo as natural pigment in the hair dye. The composition also comprises ethanolamine, antimicrobial agent and hair modifying agent. In order to achieve the conjugation of pigment and the protein, lawsone at the concentration of 1-20 mgml-1 is dissolved in acetonitrile solution, indigo at a concentration of 1-5 mgml-1 is dissolved in Tris-HCl buffer. KRTAP-2 protein at a concentration of 1-5 mgml-1 is dissolved in Tris-HCl buffer. The invention discloses the method of conjugation of KRTAP-2 family protein with lawsone or indigo and the method of spraying the hair dye composition to human hair. The hair dye composition is associated with low risk of carcinogenicity, mutagenicity and allergy and increases the penetration of pigment to hair shaft.