Biomedical subjects

H Komooka

Publications and source records attributed to H Komooka.

4 recordsLinked to original sources

PubMed1997

A computer modeling study of the interaction between tissue factor pathway inhibitor and blood coagulation factor Xa.

Activation of blood coagulation factor X to factor Xa (FXa) is inhibited by tissue factor pathway inhibitor (TFPI). The second Kunitz-type inhibitory domain (K2) of TFPI binds a catalytic domain of FXa, whereas the first domain (K1) does not. We analyzed computer models of complexes of FXa with K1 or K2, which were made using a crystal structure of FXa. Favorable hydrophobic interaction was observed in the complex of FXa with K2. Furthermore, we constructed a tertiary structure of FXa using CHIMERA to assess the accuracy of a homology modeling method. The isolated model structure of FXa agreed well with the crystal structure, but analyses of complexes of this structure with K1 or K2 revealed that the models of complexes could not provide clear evidence of greater binding ability to K2 because of the positional difference of a few side chains interacting with the inhibitor.

Amino Acid Sequence↗

PubMed1994

Factor IX Bm Kiryu: a Val-313-to-Asp substitution in the catalytic domain results in loss of function due to a conformational change of the surface loop: evidence obtained by chimaeric modelling.

Factor IX Kiryu is a naturally occurring mutant of factor IX that has 2.5% coagulant activity, even though normal plasma levels of factor IX antigen are detected. Factor IX Kiryu was purified from a patient's plasma by immunoaffinity chromatography with a calcium-dependent anti-factor IX monoclonal antibody column. It was cleaved normally by factor XIa in the presence of Ca2+, yielding a two-chain factor IXa. However, the resulting factor IXa showed only 1.5% of the normal factor IXa in terms of factor X activation in the presence of factor VIII, phospholipids, and Ca2+, and had 20% of the normal esterase activity for Z-Arg-p-nitrobenzyl ester. Therefore factor IXa Kiryu showed the defect of the catalytic triad or primary substrate binding site as well as defective interaction with factors VIII/X. Single-strand conformational polymorphism analysis and DNA sequencing of the amplified DNA revealed a missense point mutation, a T-to-A substitution at nucleotide number 31,059 of the factor IX Kiryu gene. This mutation resulted in the amino acid substitution of Val-313 by Asp in the catalytic domain. Restriction enzyme analysis of the amplified DNA showed that the mutation was inherited from the patient's mother. The chimaeric method was employed to construct a model of the serine protease domain of factor IXa, and the resultant model suggested that the Val-313 to Asp substitution altered the conformation of the substrate-binding site. These data combined with our previous findings on a Gly-311-to-Glu mutant of factor IX suggest that the loop conformation from Gly-311 to ARg-318 is important for the expression of coagulant activity.

Amino Acid Sequence↗

PubMed1994

Three-dimensional model of the human PAF receptor.

The amino acid sequence analysis of the human platelet-activating factor (PAF) receptor showed that residues thought to be important structurally and functionally were well conserved. This suggested similarities of the three-dimensional structure (3D structure) between the human PAF receptor and other receptors that couple to guanine nucleotide binding (G) proteins. Thus, a three-dimensional model of this receptor was constructed using the 3D structure of bacteriorhodopsin as the reference protein, by means of the BIOCES[E] computer-modeling system. This model has seven alpha-helical transmembrane segments which form a central core and an S-S bond between the second and third extracellular loops. The distance of the S-S bond is about 2 A, which is thought to be reasonable. In the transmembrane domain, the side chains of Asp-63, Asn-285 and Asp-289 became oriented toward the central core and form a negatively charged site. This receptor model suggests that the positively charged choline moiety of PAF is attracted to this negatively charged site by electrostatic forces and that PAF may induce conformational changes in the receptor, leading to G-protein activation.

Amino Acid Sequence↗

PubMed1993

Protein modelling using a chimera reference protein derived from exons.

Bovine pancreatic beta-trypsin (PDB ID-code: 1TPO) which is registered in the Brookhaven Protein Data Bank (PDB) consists of four exons. The results of homology searches for each exon in the PDB showed that homologous proteins were tonin (PDB ID-code: 1TON), rat mast cell protease (PDB ID-code: 3RP2__A), kallikrein A (PDB ID-code: 2PKA__B) and kallikrein A (2PKA__B) respectively. Thus, for the three-dimensional structure prediction of 1TPO, a chimera protein was constructed from the three proteins mentioned above and the 3-D structure prediction was performed using this chimera reference protein. The modelled structure of 1TPO was energetically optimized by molecular mechanics and molecular dynamics simulation and was compared with its X-ray crystal structure registered in the PDB. The root mean square deviations (r.m.s.d.) of main chain atoms and the neighbouring active site (5 A sphere from His57, Asp102 and Ser195) between the modelled structure and the X-ray structure were 1.66 and 0.94 A respectively. Porcine pancreatic elastase (PDB ID-code: 3EST) which is registered in the PDB was used as the reference protein and the modelled structure from 3EST was also compared with the X-ray data. The r.m.s.d. of main chain atoms and that of the active site were 2.14 and 1.18 A respectively. These results clearly support the propriety of this method using the chimera reference protein.

Algorithms↗