Molecular modeling of purinergic receptor P2Y12 and interaction with its antagonists.

Purinergic receptors are a class of cell surface receptors for purines that prefer ATP or ADP over adenosine. The surface receptors for extracellular nucleotides are called P2 receptors. They are activated by both pyrimidine and purine nucleotides. ADP initiates platelet aggregation by 'simultaneous activation of two G protein-coupled receptors, P2Y1 and P2Y12. P2Y12 has been shown to be the target of the thienopyridine drugs, ticlopidine and clopidogrel. Here, the active sites of P2Y12 for ATP as well as ADP are predicted by bioinformatics and molecular modeling. First, the three-dimensional (3D) structure of P2Y12 was constructed by InsightII/Homology module using the corresponding bovine rhodopsin (PDB code: 1HZX) as the template. Then the primary structures were optimized by energy minimization that has been successfully accepted by the Protein Data Bank (PDB code: 1VZ1). Second, a simple scoring matrix was built up based on the analysis of 13 known ATP-binding proteins. And the most probable active sites of P2Y12 were predicted using the scoring matrix, which include three distant areas: "head area" (LGTGPLRTFV, 87-96), "middle area" (VGLITNGLAM, 38-47, and LGAKILSVVI, 139-148), and "bottom area" (RTRGVGKVPR, 222-231). Subsequently the structural model of P2Y12 was docked with ATP/ADP in comparison with P2Y1 (PDB code 1ddd). As a comparison, we docked its antagonists, such as ticlopidine and clopidogrel, to the most probable sites and calculated their intermolecular energy. Our results imply that P2Y12 has the potential to be inhibited by ADP/ATP analogs, and it suggests that P2Y12 acts as a target of new drugs that inhibit platelet aggregation.

Application of FTTP to alpha-helix or beta-strand motifs.

Information concerning protein structure is widely dispersed and cannot easily and rapidly be processed by the biological community. We present a database of tendentious factors of three states of tripeptide units from PDB database, called a bank of tendentious factors of three states of three-peptide units (FTTP). The FTTP database was constructed based on conformational dihedral angle (varphi,psi) library of 20(3) peptide triplets by exhaustively searching through PDB databases. We introduce the FTTP database for the analysis of characteristics common to relative conformational biases of all peptide triplets, especially finding some motifs apt to alpha-helix and beta-strand. Our results show that this will provide a platform for studies of short peptide motifs, folding codons, secondary structure and three-dimensional (3D) structure of proteins. Moreover, FTTP is a unique resource that will allow a comprehensive characterization of peptide triplets and thus improve our understanding of sequence-structure relationship, refined domains, 3D structures, and their associated function. We believe the FTTP database will help biologists in increasing the efficiency of finding useful and relevant information regarding structure-function relationship of proteins. Therefore, this approach will play an important role in protein folding, protein engineering, molecular design, and proteomics.

Conformation biases of amino acids based on tripeptide microenvironment from PDB database.

We have constructed a bank (FTTP) of tendentious factors of three states of three-peptide units from PDB database based on conformational dihedral angle library and demonstrated that amino acid biases toward protein secondary structure are present in natural protein sequences. Our research results reveal that 20 standard amino acids fall into three groups: nine residues inclined to alpha-helix with a common character (e.g. direct side chain aliphatic residues or positive/negative charged residues) arrange in three grades, viz EA, QKRLD, and MN, in turn; seven residues are apt to beta-strand with 2'-branched side chain aliphatic residues or benzyl-included residues, namely PV, IYTC, and F, in three ranks; and four residues SHWG show a double tendency to both alpha and beta. Noticeably, proline has the strongest ability to form extended conformation, especially the Re value up to 9.5298 at position 3 (Table 3). Thus, biases of codons show an evident tendency in protein folding, where GC-rich codons are mainly in charge of forming contracted conformation, especially the codon's first letter plays a dominant role in translating the genomic GC signature into protein sequences and structures. So, biases of amino acids will play an important role in protein folding, folding codons, refining domain, structure prediction, and structural genomics/proteomics.

Interaction of human fibrinogen receptor (GPIIb-IIIa) with decorsin.

AIM: To build up the structure of human fibrinogen receptor GPIIb-IIIa, subsequently combined with its antagonist decorsin, and to investigate the interaction between decorsin and its receptor GPIIb-IIIa at the molecular level. METHODS: A three-dimensional (3D) molecular model of human fibrinogen receptor GPIIb-IIIa was generated by InsightII, a distance geometry-based homologous modeling package. The structure of human fibrinogen receptor GPIIb-IIIa was built by the InsightII/Homology module using the corresponding of integrin alphaVbeta3 (PDB filecode 1JV2) as the template. Then the primary structures were optimized by energy minimization. Subsequently the structural model was docked with its antagonist decorsin (PDB filecode 1dec). RESULTS: A good substrate-receptor interaction model was achieved. The interaction sites with decorsin converge at domain 8 (betaA domain of beta3 subunit) of GPIIb-IIIa. The direct interatomic contacts were made between 16 GPIIb/IIIa residues and 10 decorsin amino-acid residues. These included van der Waals contacts, electrostatic interaction, hydrogen bond, and salt bridge. Residues in contact were concentrated in four dispersed regions of human GPIIb-IIIa: the RGD reaction motif (118-132 of GPIIIa), the span from 210 to 213 of GPIIIa, Thr182 residue and Asp251 residue of GPIIIa; and they were distributed over five segments of decorsin: Asp10 residue, Asn18 and Lys19 residues, Arg28 residue, RGD motif, and Asp35-Pro36-Tyr37 segment. CONCLUSION: This complex model plays an important role in development and research of some new drugs, especially a new guided fusion-type fibrinogen receptor antagonist.