α-Fetoprotein (AFP) is a major serum protein typi- cal for the embryonic period of the development of all mammals (and possibly all vertebrates). AFP is also the best known tumor marker highly specific for primary liver cancer and teratoma [1-4]. Being discovered almost half a century ago, it is still an attractive object for intensive studies. Human and some animal AFPs (including those of mouse, rat, rabbit, guinea pig, etc.) have been isolated, purified, and characterized (see for review [5-7]). The primary structure of AFP has been reported for nine mammalian species (Swiss-Prot, TrEMBL databases). However, the biological role of AFP during embryonal development and in the adult organism (under normal conditions and during carcinogenesis) still remains unclear. Modern databases (SwissProt, TrEMBL, PIR, etc.) and computer programs (BLAST, FASTA, ClustalW, etc.) provide the necessary tools for comparison of primary structures of proteins and peptides required for identifica- tion of similar sequences and functionally important sites. It is suggested that proteins exhibiting similar (identical) functions are characterized by the presence in their pri- mary structures of sites with similar amino acid sequences underlying these functions. Usually these are short seg- ments of the polypeptide chain containing up to 10-15 residues. Using analysis of structural–functional interre- lationships, it is possible to predict putative protein func- tions by searching for amino acid sequences similar to those in known physiologically active proteins. At the beginning of the 1990s, Mizejewski proposed the hypothesis of the “modular cassette” [8, 9]. According to this hypothesis, the AFP molecule contains a set of structurally and functionally different elements in short amino acid sequences tightly packed in the polypeptide chain. Signal sites similar to heterodimeriza- tion motifs of nuclear receptors for steroid and thyroid hormones were proposed as such structural elements rec- ognized in human AFP. Based on data of high affinity of mouse and rat AFPs to estrogens [10-13], primary struc- tures of AFP and estrogen receptor α (ERα) have been compared. This revealed that the C-end of a DNA bind- ing domain of ERα contains a binding site for heat shock proteins (HSP), which is located near the estradiol-bind- ing site. Human AFP contains a peptide segment of 34 residues similar to functionally important sites of HSP-70 [14]. Later this segment was synthesized chemically using the solid phase chemistry and defined as P149. Biological testing revealed that it inhibits estrogen-dependent cell ISSN 0006-2979, Biochemistry (Moscow), 2006, Vol. 71, No. 2, pp. 120-132. © Pleiades Publishing, Inc., 2006. Original Russian Text © A. A. Terentiev, N. T. Moldogazieva, 2006, published in Biokhimiya, 2006, Vol. 71, No. 2, pp. 157-172. REVIEW 120 * To whom correspondence should be addressed. Structural and Functional Mapping of α-Fetoprotein A. A. Terentiev* and N. T. Moldogazieva Russian State Medical University, ul. Ostrovityanova 1, 117997 Moscow, Russia; fax: (7-495) 434-0588; E-mail: aaterent@mtu-net.ru Received November 11, 2004 Revision received July 18, 2005 Abstract—α-Fetoprotein (AFP) is a major mammalian oncofetal protein, which is also present in small quantities in adults. It is a member of the albuminoid gene superfamily, which consists of AFP, serum albumin, vitamin D binding protein, and α-albumin (afamin). Although physicochemical and immunological properties of AFP have been well-studied, its biologi- cal role in embryo- and carcinogenesis and in adult organisms as well as mechanisms underlying its functioning remain unclear. During the recent decades, the biological role of AFP has been evaluated by identification of its functionally impor- tant sites. Comparison of primary structure of AFP and some physiologically active proteins revealed similarity of some polypeptide regions. This has been used for prediction of AFP functions (i.e., its multifunctionality). Localization of func- tionally important sites followed by determination of their amino acid composition and type of biological activity has pro- vided valuable information for structural–functional mapping of AFP. Some peptide fragments of AFP have been synthe- sized and tested for biological activity. This review summarizes data on structural–functional interrelationships. We also describe functionally important AFP sites found by various groups during the last decade of structural–functional mapping of AFP with experimentally confirmed and putative biologically active sites. DOI: 10.1134/S0006297906020027 Key words: AFP, α-fetoprotein, peptide fragments, structural–functional mapping, multifunctionality