Systematic Analysis of Post-Translational Modifications for Increased Longevity of Biotherapeutic Proteins

Protein-based therapeutics (PPTs) are drugs used to treat a variety of different conditions in the human body by alleviating enzymatic deficiencies, augmenting other proteins and drugs, modulating signal pathways, and more. However, many PPTs struggle from a short half-life due to degradation caused by irreversible protein aggregation in the bloodstream. Currently, the most researched strategies for improving the efficiency and longevity of PPTs are post-translational modifications (PTMs). The goal of our research was to determine which type of PTM increases longevity the most for each of three commonly-used therapeutic proteins by comparing the docking scores (DS) and binding free energies (BFE) from protein aggregation and reception simulations. DS and BFE values were used to create a quantitative index that outputs a relative number from −1 to 1 to show reduced performance, no change, or increased performance. Results showed that methylation was the most beneficial for insulin (p < 0.1) and human growth hormone (p < 0.0001), and both phosphorylation and methylation were somewhat optimal for erythropoietin (p < 0.1 and p < 0.0001, respectively). Acetylation consistently provided the worst benefits with the most negative indices, while methylation had the most positive indices throughout. However, PTM efficacy varied between PPTs, supporting previous studies regarding how each PTM can confer different benefits based on the unique structures of recipient proteins.

Post-translational modifications of prostaglandin-endoperoxide synthase 2 in colorectal cancer:An update

The biosynthesis of prostanoids is involved in both physiological and pathological processes. The expression of prostaglandin-endoperoxide synthase 2(PTGS2; also known as COX-2) has been traditionally associated to the onset of several pathologies, from inflammation to cardiovascular, gastrointestinal and oncologic events. For this reason, the search of selective PTGS2 inhibitors has been a focus for therapeutic interventions. In addition to the classic non-steroidal anti-inflammatory drugs, selective and specific PTGS2 inhibitors, termed coxibs, have been generated and widely used. PTGS2 activity is less restrictive in terms of substrate specificity than the homeostatic counterpart PTGS1, and it accounts for the elevated prostanoid synthesis that accompanies several pathologies. The main regulation of PTGS2 occurs at the transcription level. In addition to this, the stability of the mRNA is finely regulated through the interaction with several cytoplasmic elements, ranging from specificmicroR NAs to proteins that control mR NA degradation. Moreover, the protein has been recognized to be the substrate for several post-translational modifications that affect both the enzyme activity and the targeting for degradation via proteasomal and non-proteasomal mechanisms. Among these modifications, phosphorylation, glycosylation and covalent modifications by reactive lipidic intermediates and by free radicals associated to the proinflammatory condition appear to be the main changes. Identification of these post-translational modifications is relevant to better understand the role of PTGS2 in several pathologies and to establish a correct analysis of the potential function of this protein in diseases progress. Finally, these modifications can be used as biomarkers to establish correlations with other parameters, including the immunomodulation dependent on molecular pathological epidemiology determinants, which may provide a better frame for potential therapeutic interventions.

Aberrant post-translational protein modifications in the pathogenesis of alcohol-induced liver injury

It is likely that the majority of proteins will undergo post-translational modification, be it enzymatic or non-enzymatic. These modified protein(s) regulate activity, localization and interaction with other cellular molecules thereby maintaining cellular hemostasis. Alcohol exposure significantly alters several of these post-translational modifications leading to impairments of many essential physiological processes. Here, we present new insights into novel modifications following ethanol exposure and their role in the initiation and progression of liver injury. This critical review condenses the proceedings of a symposium at the European Society for the Biomedical Research on Alcoholism Meeting held September 12-15, 2015, in Valencia, Spain.

Protein post-translational modifications after spinal cord injury

Deficits in intrinsic neuronal capacities in the spinal cord,a lack of growth support,and suppression of axonal outgrowth by inhibitory molecules mean that spinal cord injury almost always has devastating consequences.As such,one of the primary targets for the treatment of spinal cord injury is to develop strategies to antagonize extrinsic or intrinsic axonal growth-inhibitory factors or enhance the factors that support axonal growth.Among these factors,a series of individual protein level disorders have been identified during the generation of axons following spinal cord injury.Moreover,an increasing number of studies have indicated that post-translational modifications of these proteins have important implications for axonal growth.Some researchers have discovered a variety of post-translational modifications after spinal cord injury,such as tyrosination,acetylation,and phosphorylation.In this review,we reviewed the post-translational modifications for axonal growth,functional recovery,and neuropathic pain after spinal cord injury,a better understanding of which may elucidate the dynamic change of spinal cord injury-related molecules and facilitate the development of a new therapeutic strategy for spinal cord injury.

Post-translational modifications of hepatitis C viral proteins and their biological significance

Replication of hepatitis C virus(HCV)depends on the interaction of viral proteins with various host cellular proteins and signalling pathways.Similar to cellular proteins,post-translational modifications(PTMs)of HCV proteins are essential for proper protein function and regulation,thus,directly affecting viral life cycle and the generation of infectious virus particles.Cleavage of the HCV polyprotein by cellular and viral proteases into more than 10 proteins represents an early protein modification step after translation of the HCV positivestranded RNA genome.The key modifications include the regulated intramembranous proteolytic cleavage of core protein,disulfide bond formation of core,glycosylation of HCV envelope proteins E1 and E2,methylation of nonstructural protein 3(NS3),biotinylation of NS4A,ubiquitination of NS5B and phosphorylation of core and NS5B.Other modifications like ubiquitination of core and palmitoylation of core and NS4B proteins have been reported as well.For some modifications such as phosphorylation of NS3 and NS5A and acetylation of NS3,we have limited understanding of their effects on HCV replication and pathogenesis while the impact of other modifications is far from clear.In this review,we summarize the available information on PTMs of HCV proteins and discuss their relevance to HCV replication and pathogenesis.

Human T-lymphotropic virus proteins and post-translational modification pathways

Cell life from the cell cycle to the signaling transduction and response to stimuli is finely tuned by protein post-translational modifications(PTMs).PTMs alter the conformation,the stability,the localization,and hence the pattern of interactions of the targeted protein.Cell pathways involve the activation of enzymes,like kinases,ligases and transferases,that,once activated,act on many proteins simultaneously,altering the state of the cell and triggering the processes they are involved in.Viruses enter a balanced system and hijack the cell,exploiting the potential of PTMs either to activate viral encoded proteins or to alter cellular pathways,with the ultimate consequence to perpetuate through their replication.Human T-lymphotropic virus type 1(HTLV-1)is known to be highly oncogenic and associates with adult T-cell leukemia/lymphoma,HTLV-1-associated myelopathy/tropical spastic paraparesis and other inflammatory pathological conditions.HTLV-1 protein activity is controlled by PTMs and,in turn,viral activity is associated with the modulation of cellular pathways based on PTMs.More knowledge is acquired about the PTMs involved in the activation of its proteins,like Tax,Rex,p12,p13,p30,HTLV-I basic leucine zipper factorand Gag.However,more has to be understood at the biochemical level in order to counteract the associated fatal outcomes.This review will focus on known PTMs that directly modify HTLV-1 components and on enzymes whose activity is modulated by viral proteins.

Complex interactomes and post-translational modifications of the regulatory proteins HABP4 and SERBP1 suggest pleiotropic cellular functions

The 57 kDa antigen recognized by the Ki-1 antibody,is also known as intracellular hyaluronic acid binding protein 4 and shares 40.7%identity and 67.4%similarity with serpin mRNA binding protein 1,which is also named CGI-55,or plasminogen activator inhibitor type-1-RNA binding protein-1,indicating that they might be paralog proteins,possibly with similar or redundant functions in human cells.Through the identification of their protein interactomes,both regulatory proteins have been functionally implicated in transcriptional regulation,mRNA metabolism,specifically RNA splicing,the regulation of mRNA stability,especially,in the context of the progesterone hormone response,and the DNA damage response.Both proteins also show a complex pattern of post-translational modifications,involving Ser/Thr phosphorylation,mainly through protein kinase C,arginine methylation and SUMOylation,suggesting that their functions and locations are highly regulated.Furthermore,they show a highly dynamic cellular localization pattern with localizations in both the cytoplasm and nucleus as well as punctuated localizations in both granular cytoplasmic protein bodies,upon stress,and nuclear splicing speckles.Several reports in the literature show altered expressions of both regulatory proteins in a series of cancers as well as mutations in their genes that may contribute to tumorigenesis.This review highlights important aspects of the structure,interactome,post-translational modifications,sub-cellular localization and function of both regulatory proteins and further discusses their possible functions and their potential as tumor markers in different cancer settings.

Computer-Assisted analysis of subcellular localization signals and post-translational modifications of human prion proteins

In the present work, computational analyses were applied to study the subcellular localiza-tion and posttranslational modifications of hu-man prion proteins (PrPs). The tentative location of prion protein was determined to be in the nu-cleolus inside the nucleus by the following bio-informatics tools: Hum-PLoc, Euk-PLoc and Nuc-PLoc. Based on our results signal peptides with average of 22 base pairs in N-terminal were identified in human PrPs. This theoretical study demonstrates that PrP is post-translationally modified by: 1) attachment of two N-linked complex carbohydrate moieties (N181 and N197), 2) attachmet of glycosylphosphatidylinositol (GPI) at serine 230 and 3) formation of two di-sulfide bonds between “6–22” and “179–214” cysteines. Furthermore, ten protein kinase phosphorylation sites were predicted in human PrP. The above-noted phosphorylation was car-ried out by PKC and CK2. By using bioinfor-matics tools, we have shown that computation-ally human PrPs locate particularly into the nu-cleolus.

Microfluidic Immunoprecipitation for Post-Translational Modified Protein Purification

In this paper, we report an antibody functionalized microimmunopreci- pitation （IX IP） method used for enrich lowabundant post-translational modified （PT~ proteins. The device is fabricated by inert, nontoxic and disposable polydimethylsiloxane （PDMS） using a silane-based chemical modification protocol, which yield antibody- terminated PDMS surfaces. In this study, the IX IP device is specifically designed for the purification of carbonylated protein, a representative example here to illustrate the potential applications for any other PTMs, which could be immuno-tagged by specific antibodies. The test model in vitro oxidized bovine serum albumin （BSA） was first derivitized by dinitrophenylhydrazide （DNPH） and then captured by the anti-DNP immobilized on this Ix lP device. The surface functional group mapping was systematically analyzed and validated by fluorescence microscopy. Quantitative study of DNP-derivatized carbonylated protein capture recovery and elution efficiency of the device was also studied. We also envision that this proteome enrichment Ix IP device can be assembled with other lab-on-a-chip components, such as microelectrophoresis or micro-chromatographic devices for follow-up protein analysis. This selective enrichment of modified proteins greatly facilitates the study of low abundant protein biomarkers discovery.

详解RStudio中使用lm函数及summary函数建模与模型检验的输出结果

使用RStudio,通过各种随机函数生成样本数据,再使用stats包的lm函数及summary函数建立线性回归模型,并对其输出结果的各项细则详细解读,叙述所用的理论与公式,并尝试用各种方法重新编程,从而对这个函数的建模原理得到更好的把握,能有助于更好地使用此函数建立合适的模型,并灵活地利用RStudio编程实现各种建模需要的输出结果。

Summary of the Best Evidence for Tube Feeding Intolerance in Critically Ill Children

Objective:To summarize the evidence of tube feeding intolerance in critically ill children,aiming to provide evidence-based information for clinical nursing staff.Methods:Evidence search was done in Chinese and English databases to guide network and professional associations at home and abroad.The search time limit was from January 2014 to January 2024,nearly 10 years of relevant literature,mainly including guidelines,consensus,expert advice,best practice,evidence summary,system evaluation,and meta-analysis.Literature quality evaluation and evidence extraction were independently performed by two researchers.Results:This paper included 13 articles,including three guidelines,three systematic evaluations,three expert opinions,and four expert consensus.Twenty-six pieces of evidence were summarized from 10 aspects of feeding intolerance definition,team building,nutritional assessment,nutritional preparation,feeding protocol,feeding route,feeding management,pipeline management,gastric residual volume,and drug application.Conclusion:This paper summarized the evidence of tube feeding intolerance in critically ill children,which can provide evidence-based information for clinical practice.The abdominal signs should be closely observed when evaluating feeding intolerance,focusing on the prevention and reduction of feeding interruption.

英文概要(summary)的写作

读懂原材料是写好概要的关键。拟就合适题目及简要提纲也是不可或缺的。据此成文再详加润色。根据内容需要适当引用例子、数据及引语等 。

探究高职英语泛读课中撰写Summary对培养学生阅读意识的作用

在分析英语泛读课的教学目标及高职英语学生的英语阅读现状的基础上,培养学生正确的泛读意识是高职英语泛读教师的首要工作。通过实践分析学生撰写阅读材料概要(Summary)对阅读意识培养的重要性以及阐述学生掌握撰写文章概要的具体做法。

Summary of Report on Cardiovascular Diseases in China,2012

The prevalence of cardiovascular diseases （CVDs） is associated with the socioeconomic prosperity, lifestyle changes, accelerated process of ageing and urbanization. The prevalence of CVDs is continuously increasing in China and will remain an upward trend in the next 10 years. CVDs are the leading cause of death for Chinese in both urban area and rural area. Nowadays, 41.09% of deaths in rural area and 42.52% of deaths in urban area are caused by CVDs in China. The burden of CVDs remains heavy and has become an important public health problem. Effective strategies should be enforced urgently for the prevention of CVDs under the supervision of the government. In 2012, the Ministry of Health of China and 14 governmental departments jointly issued the Work Plan for Chronic Disease Prevention and Control in China （2012-2015）, a guideline for the prevention of chronic diseases, especially CVDs in China.

一种基于Summary的改进型BLASTN算法

BLASTN是生物信息学实验中常用的局部相似性搜索软件。为此,提出了一种以BloomFilter为基础的算法,用于对BLASTN中的SeedFinding进行改进,以提高BLASTN的整体效率。该算法对原数据库文件制作Summary,在搜索过程中通过查询Summary以回避大量无效的匹配工作,并对算法的各方面进行分析,给出测试结果。

Characteristics of Chinese male patients with breast cancer:summary of the published papers

Objective:The extremely low incidence of male breast cancer (MBC) leads to lack of prospective randomized phase III studies worldwide. Especially in China,all studies on Chinese patients with MBC were based on small sample size and single institute experience. The aim of this study was to provide overall view of characteristics of Chinese patients with MBC by means of summarizing all related papers published in Chinese journals. Methods: An online search was made in CBM,VIP,CNKI,and CBA databases to find all published articles of interest on Chinese patients with MBC. And eight subjects including the proportion of MBC in all breast cancer,age,tumor location,clinical stages,pathological subtypes,treatment modalities,ER/PR expression,and 5-year survival rate were selected to calculate the proportion and their 95% interval confidence. Results: There were 122 papers with 2584 patients enrolled. The basic features of Chinese patients with MBC included:(1) MBC only with a proportion of 1.06% of all the breast cancer; (2) The mean age at diagnosis was 57.6 years old; (3) Tumor mainly located in the areolar region (74.83%) with obvious nipple and/or skin involvement; (4) Nearly 62.62% patients were in early stage before accepting treatment; (5) Infiltrating ductal carcinoma accounted for 79.05% of all pathological subtypes; (6) ER/PR expression rate was 65.86%; (7) Radical resection was up to 86.06% in all surgical modalities; (8) The 5-year survival rate was 57.33%. Conclusion: The results showed in this study were an overall view of Chinese patients with MBC whose characteristics were similar to that reported in the West. Though this study provided a little bit stronger confidence than a single study collected in this paper,studies with more powerful evidence are urgently demanding in China.

Executive Summary中译探微

Executive summary是英文文件中使用频率很高的一个术语,而它的中文译法却多达十几种。本文对此进行了资料收集、分析和对比,并在深入研究和思考的基础上提出了新的译法,旨在促其术语规范化。

Panel discussion on Disp cher Training Simulator-A summary

On the“International Conference on Power SystemTechnology,1991”,a panel discussion on Dis-patcher Training Simulator(DTS)was held.Since DTS is a very in-teresting topic both in China and abroad,not only many audienceswere attracted by this panel discussion,they also raised many inter-esting questions and discussed with the panelists.Highlights of thefour papers presented by panelists as well as their related discus-sions are summarized below.