Binding free energy calculation and structural analysis for antigen-antibody complex

金沢大学大学院自然科学研究科計算科学金沢大学理学部Recently, much attention has been directed to calculational prediction for binding free energy and structural analysis for biomolecule complex in solvate state. We investigated Influenza Hemagglutinin (wild type HA), mutated HA and its neutralize antibody Fab fragment complex in explicit solvent water molecules by molecular dynamics simulation(MD). B-factor and binding free energy of loop structures in the complex structure are calculated. The calculation result supports the experimental result in a qualitative tendency. MD calculation also shows that hydrogen bond distance differs between wild type HA and mutated HA, which contributes to the difference of binding free energy and structural stability. These result suggests that pattern of making hydrogen bonds in crystal structure are almost kept even in solvate state. © 2006 American Institute of Physics

A method of classification and recognition of blue copper protein

金沢大学大学院自然科学研究科計算科学金沢大学理学部Some proteins in blue copper proteins have similar properties. In some cases it is not easy to distinguish the proteins each other. The study to recognize and classify in blue copper proteins has important roles to recognize the difference of similar properties, for examples, structures and residue sequences in blue copper proteins. There are many methods being developed to predict protein structure from many approachs, which one still not satisfactory yet. Therefore it is a challenge for scientists to develop or improve their methods. One of promising method is artificial neural networks (ANN). ANN is learning machine methods consisted of input, hidden and output layer. ANN is tested to recognize secondary structure in blue copper protein. It is found that ANN can distinguish for 7-type of secondary structure and recognize 72% secondary structure in blue copper protein. © 2006 American Institute of Physics

Molecular dynamics study of hydration water behavior in blue copper protein

金沢大学大学院自然科学研究科計算科学金沢大学理学部We carry out the molecular dynamics(MD) simulation of type 1 blue copper protein azurin in room and some lower temperatures to investigate the behavior of hydration water molecules in the protein surface. In this study, we find the anomalous behavior of the water molecules, which depend on the system temperatures. These water molecules have hydrogen bond to the protein surface residues. We specify the residues type, being classified as the hydration donor and the hydration acceptor of water molecules. We analyze the residue type, and the bond length and bond strength between solvent water molecules in each temperature. Moreover, we estimate the B-factor of these residues which indicates the fluctuation of hydration residues in each temperature. B-factor values depend on the system temperatue althought the number of hydration residue do not depend on the temperature. © 2006 American Institute of Physics

Treatment of Renal Cell Carcinoma with 2-Stage Total en bloc

Metastatic renal cell carcinoma of the bone occurs at a high rate, and the prognosis is poor. In general, total en bloc spondylectomy is considered when there is only one vertebral metastasis and the primary disease is treated. However, palliative surgery is selected when the primary disease is not being treated or metastasis occurs to an important organ. We encountered a patient in whom lung and vertebra metastases were already present at the time of the first examination at our department and the prognosis was considered poor. However, molecular targeted therapy was markedly effective and enabled 2-stage total en bloc spondylectomy. As of one year after total en bloc spondylectomy, the condition has improved to cane gait, and surgery for lung metastasis is planned. Molecular target drugs might markedly change the current therapeutic strategy for renal cell carcinoma

A Case of Delayed Myelopathy Caused by Atlantoaxial Subluxation without Fracture

We report a case of delayed myelopathy caused by atlantoaxial subluxation without fracture. The patient was a 38-year-old male who became aware of weakness in extremities. The patient had a history of hitting his head severely while diving into a swimming pool at the age of 14 years old. At that time, cervical spine plain X-ray images showed no fracture, and the cervical pain disappeared after use of a collar for several weeks. At his first visit to our department, X-ray images showed an unstable atlantoaxial joint. After surgery, weakness of the extremities gradually improved. At 6 months after surgery, bone union was completed and the symptoms disappeared. This case shows that atlantoaxial ligament injuries are difficult to diagnose and may easily be missed. A high level of suspicion is important in such cases, since neurological compromise or deterioration may occur many years after the injury