Molecular probes for cellular imaging of post-translational proteoforms

And Function ◽

Insight Into ◽

In Cells

Specific post-translational modification (PTM) states of a protein affect its property and function; understanding their dynamics in cells would provide deep insight into diverse signaling pathways and biological processes. However,...

The Diverse Contributions of Fucose Linkages in Cancer

Cancers ◽

10.3390/cancers11091241 ◽

2019 ◽

Vol 11 (9) ◽

pp. 1241 ◽

Cited By ~ 9

Author(s):

Tyler S. Keeley ◽

Shengyu Yang ◽

Eric Lau

Keyword(s):

Cell Surface ◽

Signaling Pathways ◽

Cancer Biology ◽

Surface Proteins ◽

Biological Processes ◽

Therapeutic Approaches ◽

Cell Surface Proteins ◽

Clinical Diagnostic

Fucosylation is a post-translational modification of glycans, proteins, and lipids that is responsible for many biological processes. Fucose conjugation via α(1,2), α(1,3), α(1,4), α(1,6), and O’- linkages to glycans, and variations in fucosylation linkages, has important implications for cancer biology. This review focuses on the roles that fucosylation plays in cancer, specifically through modulation of cell surface proteins and signaling pathways. How L-fucose and serum fucosylation patterns might be used for future clinical diagnostic, prognostic, and therapeutic approaches will be discussed.

Impact of protein glycosylation on lipoprotein metabolism and atherosclerosis

Cardiovascular Research ◽

10.1093/cvr/cvaa252 ◽

2020 ◽

Author(s):

Angela Pirillo ◽

Monika Svecla ◽

Alberico Luigi Catapano ◽

Adriaan G Holleboom ◽

Giuseppe Danilo Norata

Keyword(s):

Genetic Diseases ◽

Clinical Manifestations ◽

Lipoprotein Metabolism ◽

Protein Glycosylation ◽

Biological Processes ◽

Lipoprotein Receptors ◽

Additional Information ◽

Rare Genetic Diseases ◽

And Function

Abstract Protein glycosylation is a post-translational modification consisting in the enzymatic attachment of carbohydrate chains to specific residues of the protein sequence. Several types of glycosylation have been described, with N-glycosylation and O-glycosylation being the most common types impacting on crucial biological processes, such as protein synthesis, trafficking, localization, and function. Genetic defects in genes involved in protein glycosylation may result in altered production and activity of several proteins, with a broad range of clinical manifestations, including dyslipidaemia and atherosclerosis. A large number of apolipoproteins, lipoprotein receptors, and other proteins involved in lipoprotein metabolism are glycosylated, and alterations in their glycosylation profile are associated with changes in their expression and/or function. Rare genetic diseases and population genetics have provided additional information linking protein glycosylation to the regulation of lipoprotein metabolism.

Identification of the Protein Glycation Sites in Human Myoglobin as Rapidly Induced by d-Ribose

Molecules ◽

10.3390/molecules26195829 ◽

2021 ◽

Vol 26 (19) ◽

pp. 5829

Author(s):

Jing-Jing Liu ◽

Yong You ◽

Shu-Qin Gao ◽

Shuai Tang ◽

Lei Chen ◽

...

Keyword(s):

Mass Spectrometry ◽

High Performance ◽

Protein Glycation ◽

Valuable Insight ◽

Liquid Chromatography Mass Spectrometry ◽

Lysine Residues ◽

Human Myoglobin ◽

And Function ◽

Protein glycation is an important protein post-translational modification and is one of the main pathogenesis of diabetic angiopathy. Other than glycated hemoglobin, the protein glycation of other globins such as myoglobin (Mb) is less studied. The protein glycation of human Mb with ribose has not been reported, and the glycation sites in the Mb remain unknown. This article reports that d-ribose undergoes rapid protein glycation of human myoglobin (HMb) at lysine residues (K34, K87, K56, and K147) on the protein surface, as identified by ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) and electrospray ionization tandem mass spectrometry (ESI-MS/MS). Moreover, glycation by d-ribose at these sites slightly decreased the rate of the met heme (FeIII) in reaction with H2O2 to form a ferryl heme (FeIV=O). This study provides valuable insight into the protein glycation by d-ribose and provides a foundation for studying the structure and function of glycated heme proteins.

Structure and function of neural networks in the retina

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100102213 ◽

1988 ◽

Vol 46 ◽

pp. 26-27

Author(s):

Peter Sterling

Keyword(s):

Ganglion Cells ◽

Three Dimensional ◽

Structure And Function ◽

Synaptic Connections ◽

Visual Axis ◽

One Dimensional ◽

Cat Retina ◽

Ultrathin Sections ◽

And Function ◽

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

Thousands of human sequences provide deep insight into single genomes

Nature ◽

10.1038/d41586-020-01485-4 ◽

2020 ◽

Vol 581 (7809) ◽

pp. 385-386

Author(s):

Deanna M. Church

Keyword(s):

Deep Insight ◽

An Insight into Oligopeptide Transporter 3 (OPT3) family proteins

Protein and Peptide Letters ◽

10.2174/0929866527666200625202028 ◽

2020 ◽

Vol 27 ◽

Author(s):

Fırat Kurt

Keyword(s):

Stress Responses ◽

Chelating Agent ◽

Biological Processes ◽

Biotic And Abiotic Stress ◽

Oligopeptide Transporter ◽

Binding Residues ◽

Fe Homeostasis ◽

Proteins Interactions ◽

Insight Into ◽

Selection Of

: Oligopeptide transporter 3 (OPT3) proteins are one of the subsets of OPT clade, yet little is known about these transporters. Therefore, homolog OPT3 proteins in several plant species were investigated and characterized using bioinformatical tools. Motif and co-expression analyses showed that OPT3 proteins may be involved in both biotic and abiotic stress responses as well as growth and developmental processes. AtOPT3 usually seemed to take part in Fe homeostasis whereas ZmOPT3 putatively interacted with proteins involved in various biological processes from plant defense system to stress responses. Glutathione (GSH), as a putative alternative chelating agent, was used in the AtOPT3 and ZmOPT3 docking analyses to identify their putative binding residues. The information given in this study will contribute to the understanding of OPT3 proteins’ interactions in various pathways and to the selection of potential ligands for OPT3s.

Review of Progress in Predicting Protein Methylation Sites

Current Organic Chemistry ◽

10.2174/1385272823666190723141347 ◽

2019 ◽

Vol 23 (15) ◽

pp. 1663-1670 ◽

Cited By ~ 1

Author(s):

Chunyan Ao ◽

Shunshan Jin ◽

Yuan Lin ◽

Quan Zou

Keyword(s):

Gene Expression ◽

Signal Transduction ◽

Transcriptional Activity ◽

Regulation Of Gene Expression ◽

Protein Methylation ◽

Biological Processes ◽

Regulatory Enzymes ◽

Lysine Residues ◽

Arginine Residues

Protein methylation is an important and reversible post-translational modification that regulates many biological processes in cells. It occurs mainly on lysine and arginine residues and involves many important biological processes, including transcriptional activity, signal transduction, and the regulation of gene expression. Protein methylation and its regulatory enzymes are related to a variety of human diseases, so improved identification of methylation sites is useful for designing drugs for a variety of related diseases. In this review, we systematically summarize and analyze the tools used for the prediction of protein methylation sites on arginine and lysine residues over the last decade.

Computational Approaches to Predict the Non-canonical DNAs

Current Bioinformatics ◽

10.2174/1574893614666190126143438 ◽

2019 ◽

Vol 14 (6) ◽

pp. 470-479 ◽

Cited By ~ 3

Author(s):

Nazia Parveen ◽

Amen Shamim ◽

Seunghee Cho ◽

Kyeong Kyu Kim

Keyword(s):

Computational Methods ◽

Genetic Instability ◽

Computational Prediction ◽

Structure And Function ◽

Sequence Motifs ◽

Computational Approaches ◽

Functional Roles ◽

And Function ◽

Genetic Events ◽

Background: Although most nucleotides in the genome form canonical double-stranded B-DNA, many repeated sequences transiently present as non-canonical conformations (non-B DNA) such as triplexes, quadruplexes, Z-DNA, cruciforms, and slipped/hairpins. Those noncanonical DNAs (ncDNAs) are not only associated with many genetic events such as replication, transcription, and recombination, but are also related to the genetic instability that results in the predisposition to disease. Due to the crucial roles of ncDNAs in cellular and genetic functions, various computational methods have been implemented to predict sequence motifs that generate ncDNA. Objective: Here, we review strategies for the identification of ncDNA motifs across the whole genome, which is necessary for further understanding and investigation of the structure and function of ncDNAs. Conclusion: There is a great demand for computational prediction of non-canonical DNAs that play key functional roles in gene expression and genome biology. In this study, we review the currently available computational methods for predicting the non-canonical DNAs in the genome. Current studies not only provide an insight into the computational methods for predicting the secondary structures of DNA but also increase our understanding of the roles of non-canonical DNA in the genome.

Mobile-Friendly Dashboards to Display Associations Between Cited-by and Similar Journals on Mobile Health Research: A Bibliometric Study (Preprint)

10.2196/preprints.11771 ◽

2018 ◽

Author(s):

Tsair-Wei Chien ◽

Hsien-Yi Wang ◽

Yang Shao ◽

Willy Chou

Keyword(s):

Social Network ◽

Mobile Health ◽

Health Research ◽

Similarity Criteria ◽

Network Density ◽

Deep Insight ◽

Density Indices ◽

The Subject ◽

The Given ◽

BACKGROUND Researchers often spend a great deal of time and effort retrieving related journals for their studies and submissions. Authors often designate one article and then retrieve other articles that are related to the given one using PubMed’s service for finding cited-by or similar articles. However, to date, none present the association between cited-by and similar journals related to a given journal. Authors need one effective and efficient way to find related journals on the topic of mobile health research. OBJECTIVE This study aims (1) to show the related journals for a given journal by both cited-by and similarity criteria; (2) to present the association between cited-by and similarity journals related to a given journal; (3) to inspect the patterns of network density indices among clusters classified by social network analysis (SNA); (4) to investigate the feature of Kendall's coefficient(W) of concordance. METHODS We obtained 676 abstracts since 2013 from Medline based on the keywords of ("JMIR mHealth and uHealth"[Journal]) on June 30, 2018, and plotted the clusters of related journals on Google Maps by using MS Excel modules. The features of network density indices were examined. The Kendall coefficient (W) was used to assess the concordance of clusters across indices. RESULTS This study found that (1) the journals related to JMIR mHealth and uHealth are easily presented on dashboards; (2) a mild association(=0.14) exists between cited-by and similar journals related to JMIR mHealth and uHealth; (3) the median Impact Factor were 3.37 and 2.183 based on the representatives of top ten clusters grouped by the cited-by and similar journals, respectively; (4) all Kendall’s coefficients(i.e., 0.82, 0.89, 0.92, and 0.75) for the four sets of density centrality have a statistically significant concordance (p < 0.05). CONCLUSIONS SNA provides deep insight into the relationships of related journals to a given journal. The results of this research can provide readers with a knowledge and concept diagram to use with future submissions to a given journal in the subject category of Mobile Health Research. CLINICALTRIAL Not available

The Multifaceted Roles of USP15 in Signal Transduction

International Journal of Molecular Sciences ◽

10.3390/ijms22094728 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4728

Author(s):

Tanuza Das ◽

Eun Joo Song ◽

Eunice EunKyeong Kim

Keyword(s):

Signal Transduction ◽

Signaling Pathways ◽

Cellular Networks ◽

Clinical Applications ◽

Regulatory Mechanisms ◽

Signaling Networks ◽

Comprehensive Overview ◽

E3 Ligases ◽

Disease Markers

Ubiquitination and deubiquitination are protein post-translational modification processes that have been recognized as crucial mediators of many complex cellular networks, including maintaining ubiquitin homeostasis, controlling protein stability, and regulating several signaling pathways. Therefore, some of the enzymes involved in ubiquitination and deubiquitination, particularly E3 ligases and deubiquitinases, have attracted attention for drug discovery. Here, we review recent findings on USP15, one of the deubiquitinases, which regulates diverse signaling pathways by deubiquitinating vital target proteins. Even though several basic previous studies have uncovered the versatile roles of USP15 in different signaling networks, those have not yet been systematically and specifically reviewed, which can provide important information about possible disease markers and clinical applications. This review will provide a comprehensive overview of our current understanding of the regulatory mechanisms of USP15 on different signaling pathways for which dynamic reverse ubiquitination is a key regulator.