Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data

Protein Data Bank Japan (PDBj), a founding member of the worldwide Protein Data Bank (wwPDB) has accepted, processed and distributed experimentally determined biological macromolecular structures for 20 years. During that time, we have continuously made major improvements to our query search interface of PDBj Mine 2, the BMRBj web interface, and EM Navigator for PDB/BMRB/EMDB entries. PDBj also serves PDB‐related secondary database data, original web‐based modeling services such as Homology modeling of complex structure (HOMCOS), visualization services and utility tools, which we have continuously enhanced and expanded throughout the years. In addition, we have recently developed several unique archives, BSM‐Arc for computational structure models, and XRDa for raw X‐ray diffraction images, both of which promote open science in the structural biology community. During the COVID‐19 pandemic, PDBj has also started to provide feature pages for COVID‐19 related entries across all available archives at PDBj from raw experimental data and PDB structural data to computationally predicted models, while also providing COVID‐19 outreach content for high school students and teachers.

Protein Data Bank: the single global archive for 3D macromolecular structure data

The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.

A novel loss-of-function mutation of GATA3 (p.R299Q) in a Japanese family with Hypoparathyroidism, Deafness, and Renal Dysplasia (HDR) syndrome

BACKGROUND

Hypoparathyroidism, deafness, and renal dysplasia (HDR) syndrome is a rare autosomal dominant disorder caused by mutations in the zinc finger transcription factor gene, GATA3. GATA3 has 2 zinc finger domains, which play an important role in the increase in target gene transcription activity.

CASE PRESENTATION

A 50-year-old woman and her 27-year-old daughter were followed up because of hypoparathyroidism. They had bilateral sensorineural deafness. Abdominal computed tomography scanning revealed renal dysplasia in the mother, but no renal anomaly in the daughter. Direct sequencing of GATA3 gene revealed a novel heterozygous missense mutation at codon 299 (p.R299Q) in exon 4. This mutation is located at the junction between the 2 zinc fingers. The structure prediction showed that it caused a conformation change in this junction area, affecting the spatial position of the zinc fingers. Additionally, a more marked conformation change was observed in the N-terminal zinc finger region compared to that in the C-terminal region. Functional analysis of this mutant protein using an in vitro luciferase reporter assay system confirmed that the mutation abolished the enhancing effects of wild-type GATA3 on the promoter activity of the consensus GATA responsive element and that of human PTH gene.

CONCLUSION

We identified a novel R299Q mutation in GATA3 in a Japanese family with HDR syndrome. We confirmed that R299Q is a loss-of-function mutation, due to the extensive conformational change in the zinc fingers of GATA3.

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.

[Consideration of surgical treatment for recurrence after the resection of hepatic metastases from colorectal cancer]

We considered treatment for recurrence following the resection of hepatic metastases from colorectal cancer. The subjects of this study were 15 of 29 patients who had undergone WHF arterial infusion following resection of hepatic metastases from colorectal cancer, in whom there was a recurrence. Of these 15 cases, 6 involved recurrence in a single organ (residual liver, 4; lung, 1; local area, 1), 7 involved two organs (residual liver and lung, 2; residual liver and local area, 2; residual liver and bone, 1; spleen and intra-abdominal lymph node, 1; intra-abdominal lymph node and peritoneum, 1) and 2 involved three organs (lung, bone and abdominal wall, 1; lung, peritoneum and distal lymph node, 1). Reresection was performed in all cases in which recurrence occurred in a single organ. For those cases in which recurrence occurred in two or more organs, reresection and infusion were performed in the 4 cases of recurrence in the residual liver and reresection was performed in the case of recurrence in the spleen and intra-abdominal lymph node (No. 16), the case of local recurrence and the case involving the abdominal wall. The 5-year survival rate of the 29 cases who underwent initial hepatic resection was 61.9%. Five years following resection, the recurrence rate in the residual liver was 38.3%. The survival rates following treatment for recurrence were 76.9, 51.3 and 25.6% for 1, 3 and 5 years, respectively. Of the 8 deaths which have occurred to date, only one was directly related to an increase in hepatic metastases. Following resection of hepatic metastases from colorectal cancer, WHF provides a high rate of prevention as well as a high survival rate. Furthermore, with regard to recurrence following WHF treatment, if the recurrence is in only one organ, there is the possibility of achieving effective treatment by reresection (WHF = 5-FU 1,000 mg/m2 5 hrs qw).

Telemedical support using real-time ultrasonography and endoscopy images

We developed a telecommunications apparatus (TMS-6101, NIHON KOHDEN WELLNESS CORPORATION, Tokyo, Japan) and evaluated its clinical utility as a telemedical support system. It is capable of transmitting on a real-time basis such vital signs as blood pressure, arterial O2 saturation and ECG recordings, which are measured at bedside using the Life-Mate monitor (NIHON KOHDEN WELLNESS Co.). It is also capable of transmitting moving video-camera pictures in real time. In this study we assessed its application for telemedical supports with particular emphasis on ultrasonography and endoscopy images since reports of such applications are lacking. Employing this system, several kinds of technically demanding endoscopic procedures were supported successfully under the supervision of at least one off-site specialist physician. The system proved to be a very useful medical resource, since it facilitated high quality medical care and specialist consultation at any location without those specialists traveling to the scene.

Evaluation of coronary blood flow reserve by 13N-NH3 positron emission computed tomography (PET) with dipyridamole in the treatment of hypertension with the ACE inhibitor (Cilazapril)

PURPOSE

The purpose of this study was to evaluate the effect of treatment with an angiotensin-converting enzyme (ACE) inhibitor (Cilazapril) for early hypertensive patients in terms of coronary blood flow reserve evaluated by 13NH3-positron emission tomography (PET).

METHODS

Before and after 12 weeks of ACE inhibitor treatment, 13NH3-PET with dipyridamole provocation test was performed, and definite myocardial perfusion and coronary flow reserve (CFR) were calculated.

RESULTS

Compared to our normal subjects previously reported (2.61+/-0.74), average coronary flow reserve was decreased (1.70+/-0.64 in hypertensive patients), and improved after treatment (1.77+/-0.52), but not significantly. Of 12 patients, five (42%) showed improved coronary flow reserve from 1.34 to 1.99 without a significant change in the resting flow. Only one patient (8%) showed deterioration after the ACE inhibitor treatment. The coronary vascular resistance (CVR) after ACE inhibitor treatment of the patients with CFR < 2.0 decreased significantly compared with those with CFR> or = 2.0 (p < 0.03).

CONCLUSIONS

These results indicate that hypertensive patients at the early stage show decreased coronary flow reserve despite having normal resting flow. Treatment with an ACE inhibitor (Cilazapril) for 12 weeks improved coronary flow reserve in 42% of our patients. The CVR of the patients with CFR < 2.0 showed improvement compared to those with CFR> or = 2.0. This result indicates that an ACE inhibitor (e.g., Cilazapril) should be one of the choices for improving CFR if hypertensive patients in early stage show signs of ischemia or diastolic dysfunction, which may be one of the sequels of reserve restriction.

[Typical normal cases and normal cases with abnormal image pattern in every myocardial SPECT radiopharmaceutical]

Working group of cardiac nuclear medicine was made as a Japanese part of society of international cardiac nuclear medicine under the cooperation between Japanese society of nuclear medicine and Japanese society of cardiology. We investigated typical normal cases and normal cases with abnormal image pattern in every myocardial SPECT radiopharmaceutical as one of the research activity of working group. From 11 faculties, 16 T1 cases, 14 BMIPP cases, 8 MIBG cases, 8 MIBI cases and 14 tetrofosmin cases were submitted as typical normal cases, and 12 T1 cases, 5 BMIPP cases, 12 MIBG cases, 10 MIBI cases and 5 tetrofosmin cases were submitted as normal cases with abnormal image pattern. We summarized the condition of SPECT data acquisition of each faculties. And we added the discussion from literature about how to discriminate normal cases with abnormal image pattern from abnormal cases. In MIBG, patterns of typical normal cases and normal cases with abnormal image pattern were slightly different from other 4 pharmaceuticals. In other 4 pharmaceuticals, diaphragmatic attenuation, breast attenuation, apical thinning and others were presented as normal cases with abnormal image pattern.

[Expression and function of cardiovascular local renin-angiotensin system]

Cardiovascular renin-angiotensin system plays an important roll in physiological and pathological status. Its autocrine and paracrine functions are to regulate vascular tone, cardiac contractility and to regulate cardiac and vascular growth. It is well known that systemic hypertension induces cardiac hypertrophy, and it can be prevented by antihypertensive drugs. But its mechanism is still unclear. In our study all antihypertensive drugs could prevent left ventricular hypertrophy of genetic hypertension model SHR. Left ventricular Angiotensinogen m-RNA expression of SHR was 2 fold higher than WKY's. All antihypertensive drugs could also prevent left ventricular angiotensinogen m-RNA expression. It is suggested that mechanism of left ventricular hypertrophy which is induced by systemic hypertension is related with cardiac angiotensinogen m-RNA expression. And it can be modulated by any kind of antihypertensive drug treatments.

[Changes in plasma superoxide dismutase like activity during general anesthesia and surgery in man]

Superoxide radicals are highly reactive products that are known to induce various pathological changes in man. Superoxide dismutase is an enzyme that scavanges superoxide radicals. We measured plasma superoxide dismutase (SOD) like activity according to electron spin resonance using DMPO as a trap. The subjects of the study were 48 surgical patients who underwent various elective surgery. They ranged from 10 to 74 years in age. Anesthetic agents employed were enflurane in 50% O2 + 50% N2O, modified NLA with pentazocine, original NLA and fentanyl + ketamine (FK). In NLA group, 70% N2O and 30% O2 were given and 70% air and 30% O2 were administered to the patients of FK group. The mean plasma SOD like activity before the anesthetic induction in surgical patients of all groups was 5.70 +/- 0.41 U.ml-1. There is no significant difference compared with the value of normal persons. A marked reduction in plasma SOD like activity was obtained during surgery in any type of anesthesia in this study. Neither anesthetic agents used in this study nor the extent of surgery contributed to the degree of SOD like activity reduction. Surgical duration over two hours was the most contributing factor to reduce the SOD like activity. There was no correlation between plasma SOD like activity and age or serum total protein.

Use of complex ray theory in the design of a laser diode module

Use of complex ray theory in the design of optical devices with a thick lens is presented. As a thick lens consists of convex and concave interfaces, the transmission characteristics of an optical beam through a curved dielectric interface is investigated using complex ray theory and the mode expansion method. As an example, this procedure is applied to the design of a laser diode module with a spherical lens.