John Kendrew and myoglobin: Protein structure determination in the 1950s

The essay reviews John Kendrew's pioneering work on the structure of myoglobin for which he shared the Nobel Prize for Chemistry in 1962. It reconstructs the status of protein X‐ray crystallography at the time Kendrew entered the field in 1945, after distinctive service in operational research during the war. It reflects on the choice of sperm whale myoglobin as research material. In particular, it highlights Kendrew's early use of digital electronic computers for crystallographic computations and the marshaling of other tools and approaches that made it possible to solve the structure at increasing resolution. The essay further discusses the role of models in structure resolution and their broader reception. It ends by briefly reviewing Kendrew's other contributions in the formation and institutionalization of molecular biology.     

Phosphatidylinositol‐4 kinase III beta and oxysterol‐binding protein accumulate unesterified cholesterol on poliovirus‐induced membrane structure

Studies on anti‐picornavirus compounds have revealed an essential role of a novel cellular pathway via host phosphatidylinositol‐4 kinase III beta (PI4KB) and oxysterol‐binding protein (OSBP) family I in poliovirus (PV) replication. However, the molecular role for this pathway in PV replication has yet to be determined. Here, viral and host proteins modulating production of phosphatidylinositol 4‐phosphate (PI4P) and accumulation of unesterified cholesterol (UC) in cells were analyzed and the role of the PI4KB/OSBP pathway in PV replication characterized. Virus protein 2BC was identified as a novel interactant of PI4KB. PI4KB and VCP/p97 bind to a partially overlapped region of 2BC with different sensitivity to a 2C inhibitor. Production of PI4P and accumulation of UC were enhanced by virus protein 2BC, but suppressed by virus proteins 3A and 3AB. In PV‐infected cells, a PI4KB inhibitor suppressed production of PI4P, and both a PI4KB inhibitor and an OSBP ligand suppressed accumulation of UC on virus‐induced membrane structure. Inhibition of PI4KB activity caused dissociation of OSBP from virus‐induced membrane structure in PV‐infected cells. Synthesis of viral nascent RNA in PV‐infected cells was not affected in the presence of PI4KB inhibitor and OSBP ligand; however, transient pre‐treatment of PV‐infected cells with these inhibitors suppressed viral RNA synthesis. These results suggest that virus proteins modulate PI4KB activity and provide PI4P for recruitment of OSBP to accumulate UC on virus‐induced membrane structure for formation of a virus replication complex.     

Sequence and structure space of RNA-binding peptides

Studies of RNA-binding peptides, and recent combinatorial library experiments in particular, have demonstrated that diverse peptide sequences and structures can be used to recognize specific RNA sites. The identification of large numbers of sequences capable of binding to a particular site has provided extensive phylogenetic information used to deduce basic principles of recognition. The high frequency at which RNA-binding peptides are found in large sequence libraries suggests plausible routes to evolve sequence-specific binders, facilitating the design of new binding molecules and perhaps reflecting characteristics of natural evolution.     

Modulation of immunogenicity of poly(sarcosine) displayed on various nanoparticle surfaces due to different physical properties

Poly(sarcosine) displayed on polymeric micelle is reported to trigger a T cell‐independent type2 reaction with B1a cells in the mice to produce IgM and IgG3 antibodies. In addition to polymeric micelle, three kinds of vesicles displaying poly(sarcosine) on surface were prepared here to evaluate the amounts and avidities of IgM and IgG3, which were produced in mice, to correlate them with physical properties of the molecular assemblies. The largest amount of IgM was produced after twice administrations of a polymeric micelle of 35 nm diameter ( G1 ). On the other hand, the production amount of IgG3 became the largest after twice administrations of G3 (vesicle of 229 nm diameter) or G4 (vesicle of 85 nm diameter). The augmented avidity of IgG3 after the twice administrations compared with that at the single administration was the highest with G3 . These differences in immune responses are discussed in terms of surface density of poly(sarcosine) chains, nanoparticle size, hydrophobic component of poly(L‐lactic acid) or (Leu‐ or Val‐Aib)_n, and membrane elasticity of the nanoparticles. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.     

茵陈五苓散联合利拉鲁肽对肥胖型2型糖尿病患者糖脂代谢、胰岛素敏感性和氧化应激的影响

摘要 目的：探讨茵陈五苓散联合利拉鲁肽对肥胖型2型糖尿病（T2DM）患者糖脂代谢、胰岛素敏感性和氧化应激的影响。方法：选取2021年12月~2022年12月期间广州中医药大学附属佛山中医院收治的160例痰湿内蕴型肥胖T2DM患者。根据随机数字表法将患者分为对照组（利拉鲁肽治疗,80例）和研究组（茵陈五苓散联合利拉鲁肽治疗,80例）。对比两组疗效、糖脂代谢指标、肥胖相关指标、胰岛素敏感性、氧化应激和不良反应发生情况。结果：与对照组相比,研究组的临床总有效率更高（P<0.05）。研究组治疗后体质量指数（BMI）、空腹血糖（FBG）、腰臀比（WHR）、餐后2 h血糖（2hPG）、丙二醛（MDA）、糖化血红蛋白（HbAlc）、稳态模型胰岛素抵抗指数（HOMA-IR）、总胆固醇（TC）、黄嘌呤氧化酶（XO）、甘油三酯（TG）、低密度脂蛋白胆固醇（LDL-C）较对照组低（P<0.05）。治疗后研究组稳态模型胰岛β细胞功能指数（HOMA-β）、高密度脂蛋白胆固醇（HDL-C）、超氧化物歧化酶（SOD）高于对照组（P<0.05）。两组不良反应发生率组间对比未见差异（P>0.05）。结论：茵陈五苓散联合利拉鲁肽治疗肥胖型T2DM患者疗效确切,可调节糖脂代谢水平,降低胰岛素敏感性,减轻氧化应激,且具有一定安全性,值得临床借鉴应用。     

血清微小RNA-141-3p、微小RNA-150-5p与鼻咽癌患者临床病理特征和放疗敏感性的关系研究

摘要 目的：探讨血清微小核糖核酸（miRNA）-141-3p、miR-150-5p与鼻咽癌（NPC）患者临床病理特征和放疗敏感性的关系。方法：收集2019年1月～2022年7月在我院接受放疗的92例NPC患者为NPC组,根据放疗疗效分为抵抗组和敏感组,另选取同期80名在我院体检的健康志愿者为对照组。比较对照组、NPC组血清miR-141-3p、miR-150-5p表达。分析NPC患者血清miR-141-3p、miR-150-5p表达与临床病理特征的关系。利用单因素和多因素Logistic回归分析NPC患者放疗抵抗的影响因素。结果：与对照组比较,NPC组血清miR-141-3p表达升高,miR-150-5p表达降低（P＜0.05）。NPC患者血清miR-141-3p、miR-150-5p表达在不同分化程度、TNM分期和淋巴结转移中比较有差异（P＜0.05）。92例NPC患者放疗抵抗发生率为22.83%（21/92）。单因素分析显示,抵抗组TNM分期Ⅲ～Ⅳa期和miR-141-3p ≥ 2.60比例高于敏感组,miR-150-5p ≥ 0.80比例低于敏感组（P＜0.05）。多因素Logistic回归分析显示,miR-141-3p ≥ 2.60为NPC患者放疗抵抗的独立危险因素,miR-150-5p ≥ 0.80为独立保护因素（P＜0.05）。结论：NPC患者血清miR-141-3p高表达,miR-150-5p低表达,与分化程度、TNM分期、淋巴结转移和放疗敏感性有关,有望成为NPC患者放疗抵抗的评价指标。     

Notch3 expression in capillary pericytes predicts worse graft outcome in human renal grafts with antibody‐mediated rejection

Microvasculature consisting of endothelial cells and pericytes is the main site of injury during antibody‐mediated rejection (ABMR) of renal grafts. Little is known about the mechanisms of activation of pericytes in this pathology. We have found recently that activation of Notch3, a mediator of vascular smooth muscle cell proliferation and dedifferentiation, promotes renal inflammation and fibrosis and aggravates progression of renal disease. Therefore, we studied the pericyte expression of Notch3 in 49 non‐selected renal graft biopsies (32 for clinical cause, 17 for graft surveillance). We analysed its relationship with patients’ clinical and morphological data, and compared with the expression of partial endothelial mesenchymal transition (pEndMT) markers, known to reflect endothelial activation during ABMR. Notch3 was de novo expressed in pericytes of grafts with ABMR, and was significantly correlated with the microcirculation inflammation scores of peritubular capillaritis and glomerulitis and with the expression of pEndMT markers. Notch3 expression was also associated with graft dysfunction and proteinuria at the time of biopsy and in the long term. Multivariate analysis confirmed pericyte expression of Notch3 as an independent risk factor predicting graft loss. These data suggest that Notch3 is activated in the pericytes of renal grafts with ABMR and is associated with poor graft outcome.     

High sequence coverage by in-capillary proteolysis of native proteins and simultaneous analysis of the resulting peptides by nanoelectrospray ionization-mass spectrometry and tandem mass spectrometry

Losses of proteolytic peptides during extraction and/or purification procedures succeeding in-gel or in-solution digests of proteins frequently occur in the course of protein identification investigations. In order to overcome this disadvantage, the method of in-capillary digest was developed: native proteins were incubated in the presence of endoproteases in the electrospray capillary and the resulting peptides were analyzed by nanoelectrospray-mass spectrometry during the ongoing proteolysis. In-capillary digest of apomyglobin by use of trypsin in a molar ratio of 25:1 yielded complete degradation already after 15 min. The sequence coverage based on formation of molecular ions was 100% and peptide ions could be fragmented by collision-induced dissociation and sequenced. When myoglobin was incubated in the electrospray capillary with trypsin in a molar ratio of 500:1, a clear shift from molecular ions and miscleaved peptide ions to the expected final tryptic peptide ions was observed over a 2 h period. The peptide spectra obtained from tryptic in-capillary proteolysis of bovine serum albumin and apotransferrin, respectively, gave rise to sequence coverages of more than 40% for both proteins. The data obtained from the peptide maps as well as from collision-induced dissociation (CID) of selected peptides were more than sufficient for protein identification by database searches. An elephant milk protein preparation was used to demonstrate the application of in-capillary proteolysis on protein mixtures. Tryptic digest, simultaneous analysis of the proteolytic peptides by use of CID, and subsequent sequencing allowed the identification of lactoferrin, alphas1-casein, beta-casein, delta-casein, and kappa-casein by homology search.