Prediction of protein motions from amino acid sequence and its application to protein-protein interaction

BACKGROUND: Structural flexibility is an important characteristic of proteins because it is often associated with their function. The movement of a polypeptide segment in a protein can be broken down into two types of motions: internal and external ones. The former is deformation of the segment itself, but the latter involves only rotational and translational motions as a rigid body. Normal Model Analysis (NMA) can derive these two motions, but its application remains limited because it necessitates the gathering of complete structural information. RESULTS: In this work, we present a novel method for predicting two kinds of protein motions in ordered structures. The prediction uses only information from the amino acid sequence. We prepared a dataset of the internal and external motions of segments in many proteins by application of NMA. Subsequently, we analyzed the relation between thermal motion assessed from X-ray crystallographic B-factor and internal/external motions calculated by NMA. Results show that attributes of amino acids related to the internal motion have different features from those related to the B-factors, although those related to the external motion are correlated strongly with the B-factors. Next, we developed a method to predict internal and external motions from amino acid sequences based on the Random Forest algorithm. The proposed method uses information associated with adjacent amino acid residues and secondary structures predicted from the amino acid sequence. The proposed method exhibited moderate correlation between predicted internal and external motions with those calculated by NMA. It has the highest prediction accuracy compared to a naïve model and three published predictors. CONCLUSIONS: Finally, we applied the proposed method predicting the internal motion to a set of 20 proteins that undergo large conformational change upon protein-protein interaction. Results show significant overlaps between the predicted high internal motion regions and the observed conformational change regions

New bleeding model of additives in a polypropylene film under atmospheric pressure

Many additives are commercially used to add more favorable qualities to films. The bleeding process by which the additive in a film comes to the surface is considered. A new bleeding model of additives in a polypropylene film under atmospheric pressure was investigated. Solubility and diffusion are found to be important for explaining this bleeding process. The solubilities and diffusion coefficients of higher fatty acid amides such as erucamide (13-cis-docosenamide) and behenamide (docosanamide) were determined between 40 and 70°C and the difference between the solubilities and the diffusion coefficients was discussed. The experimental results are explained more precisely by assuming two transport processes between the crystalline regions and the amorphous ones. © 2007 Wiley Periodicals, Inc

New bleeding model of additives in a polypropylene film under atmospheric pressure II

金沢大学大学院自然科学研究科出光興産㈱　先進技術研究所　解析技術センター 第二解析技術室Many additives are commercially used to add more favorable qualities to films. The bleeding process by which the additive in a film comes to the surface is considered. A new bleeding model of additives in a polypropylene film under atmospheric pressure was investigated. Solubility and diffusion are found to be important for explaining this bleeding process. It was found that the experimental results were explained more precisely by assuming a twostep transport process between the crystalline regions and the amorphous ones. The solubilities and diffusion coefficients of UV-stabilizers such as 2-(2H-benzotriazol-2-yl)-4(l,l,3,3-tetramethylbutyl)phenol and 2-(2H-benzotriazol-2yl)-4-methylphenol were determined at 4O°C. The difference between the saturation solubilities and the diffusion coefficients of UV-stabilizers was discussed by comparing with the results of molecular dynamics (MD) simulation. © 2007 Wiley Periodicals, Inc

Disturbance in the protein landscape of cochlear perilymph in an Alzheimer’s disease mouse model

Fukuda M., Okanishi H., Ino D., et al. (2024) Disturbance in the protein landscape of cochlear perilymph in an Alzheimer’s disease mouse model. PLoS ONE 19, e0303375. https://doi.org/10.1371/journal.pone.0303375.Hearing loss is a pivotal risk factor for dementia. It has recently emerged that a disruption in the intercommunication between the cochlea and brain is a key process in the initiation and progression of this disease. However, whether the cochlear properties can be influenced by pathological signals associated with dementia remains unclear. In this study, using a mouse model of Alzheimer’s disease (AD), we investigated the impacts of the AD-like amyloid β (Aβ) pathology in the brain on the cochlea. Despite little detectable change in the age-related shift of the hearing threshold, we observed quantitative and qualitative alterations in the protein profile in perilymph, an extracellular fluid that fills the path of sound waves in the cochlea. Our findings highlight the potential contribution of Aβ pathology in the brain to the disturbance of cochlear homeostasis

Endometrial Cancer Diagnosed at an Early Stage during Lynch Syndrome Surveillance: A Case Report

Lynch syndrome is an autosomal dominant inherited disorder caused by a germline pathogenic variant in DNA mismatch repair genes, resulting in multi-organ cancer. Annual transvaginal ultrasonography and endometrial biopsy are recommended for endometrial cancer surveillance in patients with Lynch syndrome in several guidelines; however, evidence is limited. Here, we present the case of a 51-year-old woman with endometrial cancer who underwent robot-assisted laparoscopic simple hysterectomy at an early stage detected by Lynch syndrome surveillance. The patient was a 51-year-old gravida zero woman without any medical history or symptoms. Her sister suffered from bladder, breast, rectal, and endometrial cancer and was diagnosed with Lynch syndrome using a hereditary cancer panel test (VistaSeq®). During gynecologic surveillance, the patient’s endometrial cytology was classified as Papanicolaou class III. Therefore, she underwent endometrial curettage with hysteroscopy and was diagnosed with atypical endometrial hyperplasia. Robot-assisted hysterectomy was performed with a final pathological diagnosis of endometrial cancer (endometrioid carcinoma, Grade 1), stage 1A. She has remained disease-free for more than 12 months. Owing to advances in genetic medicine, prophylactic and therapeutic surgeries for hereditary cancers are increasing. To achieve an early diagnosis and treatment of Lynch syndrome-associated cancers, the importance of Lynch syndrome surveillance should be more widely recognized

High- and Low-Energy Photoemission Study of Strongly Correlated Au–Ga–Ce Quasicrystal Approximants: Localized 4f Nature and Disorder Effects

Nozue G., Fujiwara H., Hamamoto S., et al. High- and Low-Energy Photoemission Study of Strongly Correlated Au–Ga–Ce Quasicrystal Approximants: Localized 4f Nature and Disorder Effects. Journal of the Physical Society of Japan 93(7) 074601, 15 July, 2024; https://doi.org/10.7566/JPSJ.93.074703.We have investigated the electronic structures of Ce-based 1/1 quasicrystal approximants Au₅₉.₂Ga₂₅.₇Ce₁₅.₁ and Au₆₀.₃Ga₂₆.₁Ce₁₃.₆ by hard X-ray photoemission (HAXPES) and high-resolution photoemission spectroscopy. The localized Ce 4f electronic states are revealed for both Au–Ga–Ce approximants. Moreover, disorders in the compounds notably affect their electronic states, which has been detected by the core-level HAXPES. Valence-band photoemission spectra show the slight spectral difference depending on the composition ratio, which can be explained by a rigid-band-like shift

Impact of neoadjuvant intensity-modulated radiation therapy on borderline resectable pancreatic cancer with arterial abutment; a prospective, open-label, phase II study in a single institution

BACKGROUND: Borderline resectable pancreatic cancer (BRPC) is a category of pancreatic cancer that is anatomically widely spread, and curative resection is uncommon with upfront surgery. Intensity-modulated radiation therapy (IMRT) is a form of radiation therapy that delivers precise radiation to a tumor while minimizing the dose to surrounding normal tissues. Here, we conducted a phase 2 study to estimate the curability and efficacy of neoadjuvant chemoradiotherapy using IMRT (NACIMRT) for patients with BRPC with arterial abutment (BRPC-A). METHODS: A total of 49 BRPC-A patients were enrolled in this study and were treated at our hospital according to the study protocol between June 2013 and March 2021. The primary endpoint was microscopically margin-negative resection (R0) rates and we subsequently analyzed safety, histological effect of the treatment as well as survivals among patients with NACIMRT. RESULTS: Twenty-nine patients (59.2%) received pancreatectomy after NACIMRT. The R0 rate in resection patients was 93.1% and that in the whole cohort was 55.1%. No mortality was encountered. Local therapeutic effects as assessed by Evans classification showed good therapeutic effect (Grade 1, 3.4%; Grade 2a, 31.0%; Grade 2b, 48.3%; Grade 3, 3.4%; Grade 4, 3.4%). Median disease-free survival was 15.5 months. Median overall survival in the whole cohort was 35.1 months. The only independent prognostic pre-NACIMRT factor identified was serum carbohydrate antigen 19-9 (CA19-9) > 400 U/ml before NACIMRT. CONCLUSIONS: NACIMRT showed preferable outcome without significant operative morbidity for BRPC-A patients. NACIMRT contributes to good local tumor control, but a high initial serum CA19-9 implies poor prognosis even after neoadjuvant treatment. TRIAL REGISTRATION: UMIN-CTR Clinical Trial: https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000011776 Registration number: UMIN000010113. Date of first registration: 01/03/2013

レーズンから分離した天然酵母のパン酵母としての特性

(1)飯塚パンの元種から酵母(飯塚菌、I)を分離同定したところ、一般のパン酵母として知られるサッカロミセス・セレビシアであった。(2)Iと一般の生イースト(オリエンタル酵母、O;三共、S)と生育状況について比較したところ、YM培地では菌体量が同等であったが、レーズン培地では、1>S>Oの順であった。(3)気体発生量については、レーズン培地で1>S>Oの順であり、中種で同等と判断でき、本捏で1>S>Oの順であった。(4)Iの生育の至適pHを判定したところ、一般の酵母のpH5～6とは違い、pH3.9付近であった。(5)飯塚パン製造時のレーズン添加の影響を見たところ、レーズン添加で膨張体積が増加し、Iの気体発生を促すには、レーズン添加が適していた。以上より、飯塚パン製造には、Iが適しており生育の至適はpH3.9であり、レーズンを含むパンの製造において気体発生量が多くなることを示唆した。The yeast (I), which was isolated from a juice of the naturally fermented raisin maintained by Iizuka, was identified to be one of Saccharomyces cerevisiae species. The growth of I, compared with the popular yeasts (Oriental Yeast Co., O; Sankyo Co., S), was the same as O and/or S in the YM broth. However, in the raisin broth, the order of the growth was I>S>O. The orders for the amounts of gas production were as follows; I>S>O in the liquid culture (the raisin broth), I≒S≒O in the middle culture, and I>S>O in the bread making. The optimum pH for the growth of I was around pH3.9, since that of the popular yeast was pH5～6. The further addition of raisin for the raisin-containing bread making affected to be increasing the gas production, accompanied by increasing the loaf volume