Lipid accumulation and protein modifications of Bruch’s membrane in age-related macular degeneration

Age-related macular degeneration(AMD)is a progressive retinal disease,which is the leading cause of blindness in western countries.There is an urgency to establish new therapeutic strategies that could prevent or delay the progression of AMD more efficiently.Until now,the pathogenesis of AMD has remained unclear,limiting the development of the novel therapy.Bruch’s membrane(BM)goes through remarkable changes in AMD,playing a significant role during the disease course.The main aim of this review is to present the crucial processes that occur at the level of BM,with special consideration of the lipid accumulation and protein modifications.Besides,some therapies targeted at these molecules and the construction of BM in tissue engineering of retinal pigment epithelium(RPE)cells transplantation were listed.Hopefully,this review may provide a reference for researchers engaged in pathogenesis or management on AMD.

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.

Electron transfer in protein modifications:from detection to imaging

Signal pathways participate in vital biological processes and regulate complex life activities through protein modifications.Protein modifications in signal pathways are accompanied by electron transfer.The study of electronic behavior helps to explore the physical and chemical processes in signal pathways,receiving extensive attention.There are some excellent reviews that have summarized methods for signal pathway detection,while few discussions are from an electron transfer perspective.This review describes the relationship between signal pathways and electron transfer in protein modification.Subsequently,we summarize the electron transfer-based detection methods,such as electrochemical,photoelectrochemical and electrochemiluminescence methods.Additionally,the applications of signal pathway detection in mechanism study and imaging are also reviewed.Finally,a comprehensive discussion of the summary and outlooks in this field is presented,aiming to provide valuable guidance for the molecular mechanism of life processes and the development of new analytical techniques.

2007 International Symposium on Protein Modification and Degradation in Beijing(SPMDB2007)

Presidents of Symposium Depei Liu,President of Chinese Academy of Medical Sciences Zhu Chen,Vice President of Chinese Academy ofSciences.

Chemical Modification of Food Proteins

Acylation has been shown to be an effective toolfor improving surface functional properties of plant proteins.Soy bean protein has been extensively modified throughchemical and enzvmatic treatments.Their effectiveness lies intheir high nutritional value and low cost,which promotetheir use as ingredients for the formulation of food products.This paper reports a complete review of chemical modificationof various proteins from plant and animal sources,The nutri-tive and toxicological aspects through in vitro and in vivotests are also described.

Structure and allergenicity of a-lactalbumin:effects of ultrasonic prior to glycation and subsequent phosphorylation

Bovineα-lactalbumin(BLA)induced severe cow's milk allergy.In this study,a novel strategy combining ultrasonication,performed before glycation,and phosphorylation was proposed to reduce BLA allergenicity.Result showed that IgE-and IgG-binding capacities and the release rates of histamine and interleukin-6 from RBL-2 H3 were reduced.Moreover,intrinsic fluorescence intensity and surface hydrophobicity were decreased,whereas glycated sites(R10,N44,K79,K108,N102 and K114)and phosphorylated sites(Y36 and S112)of BLA were increased.Minimum allergenicity was detected during BLA treatment after ultrasonic prior to glycation and subsequent phosphorylation because of considerable increase in glycated and phosphorylated sites.Therefore,the decrease in allergenicity of BLA,the effect correlated well with the shielding effect of glycated sites combined with phosphorylated sites and the conformational changes.This study provides important theoretical foundations for improving and using the ultrasonic technology combined with protein modification in allergenic protein processing.

Evaluation of laboratory and environmental exposure systems for protein modification upon gas pollutants and environmental factors

Chemical modifications of proteins induced by ambient ozone(O_(3))and nitrogen oxides(NOx)are of public health concerns due to their potential to trigger respiratory diseases.The laboratory and environmental exposure systems have been widely used to investigate their relevant mechanism in the atmosphere.Using bovine serum albumin(BSA)as a model protein,we evaluated the two systems and aimed to reduce the uncertainties of both the reactants and products in the corresponding kinetic study.In the laboratory simulation system,the generated gaseous pollutants showed negligible losses.Ten layers of BSA were coated on the flow tube with protein extraction recovery of 87.4%.For environmental exposure experiment,quartz fiber filter was selected as the upper filter with low gaseous O_(3)(8.0%)and NO_(2)(1.7%)losses,and cellulose acetate filter was appropriate for the lower filter with protein extraction efficiency of 95.2%.The protein degradation process was observed without the exposure to atmospheric oxidants and contributed to the loss of protein monomer mass fractions,while environmental factors(e.g.,molecular oxygen and ultraviolet)may cause greater protein monomer losses.Based on the evaluation,the study exemplarily applied the two systems to protein modification and both showed that O_(3) promotes the protein oligomerization and nitration,while increased temperature can accelerate the oligomerization and increased relative humidity can inhibit the nitration in the environmental exposure samples.The developed laboratory and environmental systems are suitable for studying protein modifications formed under different atmospheric conditions.A combination of the two will further reveal the actual mechanism of protein modifications.

磷酸化肽段质量数的分布特征

基于双向电泳和液相色谱的蛋白质鉴定是蛋白质组最常用的技术,质谱谱图的好坏对鉴定的成功率起决定性作用.其中,某些不确定的修饰和非蛋白污染物是影响谱图质量的难以忽略的因素.……

Analysis of the Arabidopsis Floral Proteome:Detection of over 2000 Proteins and Evidence for Posttranslational Modifications

The proteome of the Arabidopsis flower has not been extensively studied previously. Here, we report a proteomic analysis of the wild type Arabidopsis flower. Using both two-dimensional electrophoresis/mass spectrometry （2-DGEIMS） and multi-dimensional protein identification technology （MudPIT） approaches, we identified 2 446 proteins. Although a single experiment or analysis uncovered only a subset of the proteins we identified, a combination of multiple experiments and analyses facilitated the detection of a greater number of proteins. When proteins are grouped according to RNA expression levels revealed by microarray experiments, we found that proteins encoded by genes with relatively high levels of expression were detected with greater frequencies. On the other hand, at the level of the individual gene/protein, there was not a good correlation between protein spot intensity and microarray values. We also obtained strong evidence for post-translational modification from 2-DGE and MudPIT data. We detected proteins that are annotated to function in protein synthesis, folding, modification, and degradation, as well as the presence of regulatory proteins such as transcription factors and protein kinases. Finally, sequence and evolutionary analysis of genes for active methyl group metabolisms suggests that these genes are highly conserved. Our results allow the formulation of hypotheses regarding post-translational regulation of proteins in the flower, providing new understanding about Arabidopsis flower development and physiology.

PLMD：An updated data resource of protein lysine modifications

Post-translational modifications（PTMs） occurring at protein lysine residues,or protein lysine modifications（PLMs）,play critical roles in regulating biological processes.Due to the explosive expansion of the amount of PLM substrates and the discovery of novel PLM types,here we greatly updated our previous studies,and presented a much more integrative resource of protein lysine modification database（PLMD）.In PLMD,we totally collected and integrated 284,780 modification events in 53,501 proteins across 176 eukaryotes and prokaryotes for up to 20 types of PLMs,including ubiquitination, acetylation, sumoylation, methylation ,succinylation,malonylation,glutarylation,giycation,formylation,hydroxylation,butyrylation,propionylation,crotonylation,pupylation,neddylation,2-hydroxyisobutyrylation,phosphoglycerylation,carboxylation,lipoylation and biotinylation.Using the data set,a motif-based analysis was performed for each PLM type,and the results demonstrated that different PLM types preferentially recognize distinct sequence motifs for the modifications.Moreover,various PLMs synergistically orchestrate specific cellular biological processes by mutual crosstalks with each other,and we totally found 65,297 PLM events involved in 90 types of PLM co-occurrences on the same lysine residues.Finally,various options were provided for accessing the data,while original references and other annotations were also present for each PLM substrate.Taken together,we anticipated the PLMD database can serve as a useful resource for further researches of PLMs.PLMD 3.0 was implemented in PHP ＋ MySQL and freely available at http：//plmd.biocuckoo.org.

Proteomics of protein post-translational modifications implicated in neurodegeneration

Mass spectrometry(MS)-based proteomics has developed into a battery of approaches that is exceedingly adept at identifying with high mass accuracy and precision any of the following:oxidative damage to proteins(redox proteomics),phosphorylation(phosphoproteomics),ubiquitination(diglycine remnant proteomics),protein fragmentation(degradomics),and other posttranslational modifications(PTMs).Many studies have linked these PTMs to pathogenic mechanisms of neurodegeneration.To date,identifying PTMs on specific pathology-associated proteins has proven to be a valuable step in the evaluation of functional alteration of proteins and also elucidates biochemical and structural explanations for possible pathophysiological mechanisms of neurodegenerative diseases.This review provides an overview of methods applicable to the identification and quantification of PTMs on proteins and enumerates historic,recent,and potential future research endeavours in the field of proteomics furthering the understanding of PTM roles in the pathogenesis of neurodegeneration.

Aging and uremia:Is there cellular and molecular crossover?

Many observers have noted that the morphological changes that occur in chronic kidney disease(CKD) patients resemble those seen in the geriatric population, with strikingly similar morbidity and mortality profiles and rates of frailty in the two groups, and shared characteristics at a pathophysiological level especially in respect to the changes seen in their vascular andimmune systems. However, whilst much has been documented about the shared physical characteristics of aging and uremia, the molecular and cellular similarities between the two have received less attention. In order to bridge this perceived gap we have reviewed published research concerning the common molecular processes seen in aging subjects and CKD patients, with specific attention to altered proteostasis, mitochondrial dysfunction, post-translational protein modification, and senescence and telomere attrition. We have also sought to illustrate how the cell death and survival pathways apoptosis, necroptosis and autophagy are closely interrelated, and how an understanding of these overlapping pathways is helpful in order to appreciate the shared molecular basis behind the pathophysiology of aging and uremia. This analysis revealed many common molecular characteristics and showed similar patterns of cellular dysfunction. We conclude that the accelerated aging seen in patients with CKD is underpinned at the molecular level, and that a greater understanding of these molecular processes might eventually lead to new much needed therapeutic strategies of benefit to patients with renal disease.

Protein post-translational modification by lysine succinylation:Biochemistry,biological implications,and therapeutic opportunities

Lysine succinylation(Ksuc)is a novel protein post-translational modification(PTM)wherein a succinyl group modifies a lysine residue.Ksuc leads to significant chemical and struc-tural changes to the modified protein.Recent studies have shown that Ksuc might play an important role in organism physiology and some pathophysiological processes,such as tumor-igenesis and metabolic diseases.To provide an understanding of the molecular mechanism and functions of Ksuc in different organisms,we reviewed the current literature about Ksuc,mainly summarizing the research advances in eukaryotes and prokaryotes based on both traditional study methods and site prediction tools.We also discussed inhibitors or activators associated with Ksuc that may contribute to proteomic studies and could be useful in future clinical prac-tice.A deeper understanding of Ksuc may shed new light on life science at the protein level and could lead to novel therapeutic strategies for various diseases.

Common therapeutic target for both cancer and obesity

Obesity and cancer are two interrelated conditions of high epidemiological need, with studies showing that obesity is responsible for nearly 25% of the relative contribution to cancer incidence. Given the connection between these conditions, a drug that can operate on both obesity and cancer is highly desirable. Such a drug is accomplishablethrough the development of potent anti-angiogenesis agents due to the shared underlying role of angiogenesis in the development of both diseases. Prior research has demonstrated a key role of type-2 methionine aminopeptidase(Met AP2) for angiogenesis, which has led to the development of numerous of novel inhibitors. Several irreversible Met AP2 inhibitors have entered clinical trials without great success. Though this lack of success could be attributed to off-target adverse effects, the underlying causes remain unclear. More promising reversible inhibitors have been recently developed with excellent pre-clinical results. However, due to insufficient knowledge of the biological functions of N-terminal protein processing, it is hard to predict whether these novel inhibitors would successfully pass clinical trials and thereby benefit cancer and obesity patients. Significantly more efforts are needed to advance our understanding of the regulation of methionine aminopeptidases and the processes by which they govern the function of proteins.

Multi-omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces

Streptomycetes possess numerous gene clusters and the potential to produce a large amount of natural products.Histone deacetylase(HDAC)inhibitors play an important role in the regulation of histone modifications in fungi,but their roles in prokaryotes remain poorly understood.Here,we investigated the global effects of the HDAC inhibitor,sodium butyrate(SB),on marine-derived Streptomyces olivaceus FXJ 8.021,particularly focusing on the activation of secondary metabolite biosynthesis.The antiSMASH analysis revealed 33 secondary metabolite biosynthetic gene clusters(BGCs)in strain FXJ 8.021,among which the silent lobophorin BGC was activated by SB.Transcriptomic data showed that the expression of genes involved in lobophorin biosynthesis(ge00097–ge00139)and CoA-ester formation(e.g.,ge02824),as well as the glycolysis/gluconeogenesis pathway(e.g.,ge01661),was significantly up-regulated in the presence of SB.Intracellular CoA-ester analysis confirmed that SB triggered the biosynthesis of CoA-ester,thereby increasing the precursor supply for lobophorin biosynthesis.Further acetylomic analysis revealed that the acetylation levels on 218 sites of 190 proteins were up-regulated and those on 411 sites of 310 proteins were down-regulated.These acetylated proteins were particularly enriched in transcriptional and translational machinery components(e.g.,elongation factor GE04399),and their correlations with the proteins involved in lobophorin biosynthesis were established by protein–protein interaction network analysis,suggesting that SB might function via a complex hierarchical.

Insertion of unnatural metal ligand in the heme pocket of nitrophorin through protein semi-synthesis:Toward biomimicking binuclear active sites

Herein,we report a semi-synthetic strategy affording a nitrophorin 2(NP2)variant with a N,N'-bis(2-pyridylmethyl)amine(Dpa)ligand as sidechain selectively installed at position 27,which was assembled from a synthetic peptide thioester bearing the Dpa ligand and an expressed protein segment via native chemical ligation.The semi-synthetic NP2 was able to accept the natural heme b cofactor and the Dpa ligand was able to bind Cu(Ⅱ)/Fe(Ⅲ)ions,leading to heteronuclear active site.

Antibody-Like Phosphorylation Sites in Focus of Statistically Based Bilingual Approach

In accordance with previous reports, the sequences related to phosporylated protein segments occur in conserved variable domains of immunoglobulins including first of all certain N-terminally located segments. Consequently, we look here for the sequences 1) composing human and mouse proteins different from antigen receptors, 2) identical with or highly similar to nucleotide sequence representatives of conserved variable immunoglobulin segments and 3) identical with or closely related to phosphorylation sites. More precisely, we searched for the corresponding actual pairs of DNA and protein sequence segments using five-step bilingual approach employing among others a) different types of BLAST searches, b) two in-principle-different machine-learning methods predicting phosphorylated sites and c) two large databases recording existing phosphorylation sites. The approach identified seven existing phosphorylation sites and thirty-seven related human and mouse segments achieving limits for several predictions or phylogenic parameters. Mostly serines phosporylated with ataxia-telangiectasia-related kinase (involved in regulation of DNA-double-strand-break repair) were indicated or predicted in this study. Hypermutation motifs, located in effective positions of the selected sequence segments, occurred significantly less frequently in transcribed than non-transcribed DNA strands suggesting thus the incidence of mutation events. In addition, marked differences between the numbers and proportions of human and mouse cancer-related sequence items were found in different steps of selection process. The possible role of hypermutation changes within the selected segments and the observed structural relationships are discussed here with respect to DNA damage, carcinogenesis, cancer vaccination, ageing and evolution. Taken together, our data represent additional and sometimes perhaps complementary information to the existing databases of empirically proven phosphorylation sites or pathogenically important spots.

Modificaomics:deciphering the functions of biomolecule modifications

The spatiotemporal expression of genes is sophisticatedly controlled through three main layers: transcriptional, translational and post-translational. Now increasing chemical modifications are discovered on genomic DNA, RNA and proteins. These modifications are recognized as additional layer of regulatory mechanisms in controlling gene expression that defines cell status. So far,more than 150 chemical modifications are identified in nucleic acids,and more than 400 discrete types of modifications are identified in proteins. How these modifications are interpreted are fundamental questions to our understanding of living organisms. The omics sciences of systems biology, including genomics, transcriptomics, proteomics, and metabolomics, have been in existence for decades. Due to the large numbers of modifications occurring in DNA, RNA and proteins with regulatory roles, we propose the modificaomics from the words of modification and omics. Modificaomics mainly refers to the comprehensive study of the modifications on DNA, RNA and proteins. In this review, we conceive modificaomics by introducing the discovered modifications in DNA, RNA and proteins as well as summarizing their biological functions. We hope the proposed modificaomics can provide a whole picture of modifications of these biopolymers and simulate the study of the functions of the modifications on DNA, RNA and proteins.

A New Pyridoxal Derivative for Transamination of N-Terminus of Proteins

A new pyridoxal-5-phosphate （PLP） derivative FHMDP was developed for the transamination of different pep- tides with three most hindered amino acid residues （Leu, Ile, Val） as their N-terminus. Compared to the previously reported reactions of PLP derivatives, the N-terminus transamination could be accomplished efficiently with the new compound.

Multifunctional Polymer-Protein Conjugates Generated by Multicomponent Reactions

Recently,multifunctional polymers for protein conjugation have been facilely synthesized through the multicomponent reactions(MCRs).In this mini-review,current progress in the generation of multifuncti onal polymers with protei n-reactive groups via MCRs is summarized.These mult functional polymers react with model therapeutic proteins,forming multifunctional polymer-protein conjugates,which are prototypes of sophisticated theranostic agents and antibacterial vaccine candidates.In comparison with the traditional multi-step synthesis,the preparation of multifunctional polymers for protein conjugation through MCRs is straightforward and convenient.Due to these properties,MCRs have the potential to become a new general strategy to achieve polymer-protein conjugates for biological and medical applications.