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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

[The structural organization of binding determinants in insulin-like growth factor-I (IGF-I) molecule]

A P Kolychev

    Zhurnal Evoliutsionnoi Biokhimii I Fiziologii
    |March 20, 2010
    PubMed

    Insulin-like growth factor I (IGF-I) is a peptide related to insulin and IGF-II. These three related peptides produce similar biological effects, but each of them has its irreplaceable physiological significance in the organism. Multisided functional role of IGF-I in the organisms is due to its unique binding properties. Specifically, but with different degree of affinity, it is able to interact with three receptors (IGF-l-receptor, insulin receptor, and IGF-2-receptor) and six binding proteins (IGFBP 1-6). To interact with each of the above objects, the 1GF-I molecule contains individual structural determinants--binding domains (BD) providing strict specificity of interaction with them. Responsible for the IGF-I biological effects and binding with IGF-l-receptor is alpha-domain, for binding with insulin receptor--beta-, IGF-2--gamma-, while with all BP--delta-BD, respectively. Results of experimental study of binding domains are not a always can be estimated unanimously. The proposed by the author system of criteria for evaluation of changes in affinity of the IGF-I analogies proposed by the author allows unraveling the structural organization of each of the domains and tracing dependence on it of the peptide affinity to the particular object. This work considers composition, organization, and principle of formation of affinity of there binding IGF-I domains (alpha-, gamma-, and delta-BD). The alpha-domain includes three tyrosines from three different molecule sites (B-24, C-3 1, and A-60) disposed spatially in the direct vicinity on its one surface. The delta-domain also is considered as the domain participating in the high-affinity interaction; by composition and location in molecule it principally differs from alpha-BD, with the structural organization that so far has not been decoded. Analyzed in detail is the key significance of the N-terminal site of the B-chain--the linear site of the domain--for binding of IGF-I with BP, functional heterogeneity of its constituent residues, and the characteristic principle of formation of affinity to BP. Analysis indicates a probability of the second site of delta-BD, quite possibly not the only one, and a high sensitivity of the domain to configuration of the IGF-I molecule surface. Structural organization and peculiarities of affinity formation in the gamma-domain argammae studied the best in three related peptides; it consists of two linearly exposed sites of A-chain. Composition of the site S-1 A (Phe8, Arg9, Serl 0) provides a possibility of binding the ligand with IGF-I-receptor, while the level ofaf-finity to it depends on the composition of S-2. The S-2 composition A (Arg14, Arg15) determines the low affinity of IGF-I to the IGF-2-receptor. The clear functioning of IGF-I and elimination of mixture of functions at the level of the binding activity depend on the spatial autonomy of different nature BD, difference in structural organization of each of the domains, and a peculiarity of principles affinity in each formation case. The spatial coordination of several BD sites is the condition for transmission of the "structural sig-nal" by regulatory peptide. The performed analysis provides the direct notion of dependence of the binding ability of the IGF-I molecule that has BD of different nature on their structural peculiarities and allows using the revealed regularities at searching for BD in the newly discovered insulin-like peptides.

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