Surface-Based Studies of Heparin/Heparan Sulfate-Protein Interactions: Considerations for Surface Immobilisation of HS/Heparin Saccharides and Monitoring Their Interactions with Binding Proteins

Heparan sulfate is ubiquitously expressed on the cell surface and in the extracellular matrix of all animal cells. These negatively-charged carbohydrate chains play essential roles in many important cellular functions by interacting with various heparan sulfate binding proteins (HSBP). This review discusses methods for targeting these complex biomolecules, as strategies for treating human disease.

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PlncRNADB: A Repository of Plant lncRNAs and lncRNA-RBP Protein Interactions

Current Bioinformatics ◽

10.2174/1574893614666190131161002 ◽

2019 ◽

Vol 14 (7) ◽

pp. 621-627 ◽

Cited By ~ 3

Author(s):

Youhuang Bai ◽

Xiaozhuan Dai ◽

Tiantian Ye ◽

Peijing Zhang ◽

Xu Yan ◽

...

Keyword(s):

Protein Interactions ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Populus Trichocarpa ◽

Noncoding Rnas ◽

Reference Database ◽

Protein Coding ◽

Arabidopsis Lyrata ◽

User Friendly

Background: Long noncoding RNAs (lncRNAs) are endogenous noncoding RNAs, arbitrarily longer than 200 nucleotides, that play critical roles in diverse biological processes. LncRNAs exist in different genomes ranging from animals to plants. Objective: PlncRNADB is a searchable database of lncRNA sequences and annotation in plants. Methods: We built a pipeline for lncRNA prediction in plants, providing a convenient utility for users to quickly distinguish potential noncoding RNAs from protein-coding transcripts. Results: More than five thousand lncRNAs are collected from four plant species (Arabidopsis thaliana, Arabidopsis lyrata, Populus trichocarpa and Zea mays) in PlncRNADB. Moreover, our database provides the relationship between lncRNAs and various RNA-binding proteins (RBPs), which can be displayed through a user-friendly web interface. Conclusion: PlncRNADB can serve as a reference database to investigate the lncRNAs and their interaction with RNA-binding proteins in plants. The PlncRNADB is freely available at http://bis.zju.edu.cn/PlncRNADB/.

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Identification and characterization of heparan sulfate-binding proteins from human lung carcinoma cells.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(17)45428-7 ◽

1990 ◽

Vol 265 (32) ◽

pp. 19697-19703

Author(s):

M E Bilozur ◽

C Biswas

Keyword(s):

Heparan Sulfate ◽

Lung Carcinoma ◽

Binding Proteins ◽

Human Lung ◽

Carcinoma Cells ◽

Lung Carcinoma Cells ◽

Human Lung Carcinoma ◽

Identification And Characterization

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Identification of a C/EBP-Rel complex in avian lymphoid cells

Molecular and Cellular Biology ◽

10.1128/mcb.14.10.6635-6646.1994 ◽

1994 ◽

Vol 14 (10) ◽

pp. 6635-6646

Author(s):

J A Diehl ◽

M Hannink

Keyword(s):

Gene Expression ◽

Affinity Chromatography ◽

Protein Interactions ◽

Binding Proteins ◽

Regulation Of Gene Expression ◽

Lymphoid Cells ◽

Cytokine Gene Expression ◽

Protein Protein Interactions ◽

Dna Complex ◽

Dna Affinity Chromatography

Protein-protein interactions between the CCAAT box enhancer-binding proteins (C/EBP) and the Rel family of transcription factors have been implicated in the regulation of cytokine gene expression. We have used sequence-specific DNA affinity chromatography to purify a complex from avian T cells that binds to a consensus C/EBP motif. Our results provide evidence that Rel-related proteins are components of the C/EBP-DNA complex as a result of protein-protein interactions with the C/EBP proteins. A polyclonal antiserum raised against the Rel homology domain of v-Rel and antisera raised against two human RelA-derived peptides specifically induced a supershift of the C/EBP-DNA complex in mobility shift assays using the affinity-purified C/EBP. In addition, several kappa B-binding proteins copurified with the avian C/EBP complex through two rounds of sequence-specific DNA affinity chromatography. The kappa B-binding proteins are distinct from the C/EBP proteins that directly contact DNA containing the C/EBP binding site. The identification of a protein complex that binds specifically to a consensus C/EBP site and contains both C/EBP and Rel family members suggests a novel mechanism for regulation of gene expression by Rel family proteins.

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Maneuvers on PCNA Rings during DNA Replication and Repair

Genes ◽

10.3390/genes9080416 ◽

2018 ◽

Vol 9 (8) ◽

pp. 416 ◽

Cited By ~ 23

Author(s):

Dea Slade

Keyword(s):

Dna Replication ◽

Protein Interactions ◽

Proliferating Cell Nuclear Antigen ◽

Binding Proteins ◽

Nuclear Antigen ◽

Vast Number ◽

Post Translational Modifications ◽

Dna Replication And Repair ◽

Replicative Polymerases ◽

Proliferating Cell

DNA replication and repair are essential cellular processes that ensure genome duplication and safeguard the genome from deleterious mutations. Both processes utilize an abundance of enzymatic functions that need to be tightly regulated to ensure dynamic exchange of DNA replication and repair factors. Proliferating cell nuclear antigen (PCNA) is the major coordinator of faithful and processive replication and DNA repair at replication forks. Post-translational modifications of PCNA, ubiquitination and acetylation in particular, regulate the dynamics of PCNA-protein interactions. Proliferating cell nuclear antigen (PCNA) monoubiquitination elicits ‘polymerase switching’, whereby stalled replicative polymerase is replaced with a specialized polymerase, while PCNA acetylation may reduce the processivity of replicative polymerases to promote homologous recombination-dependent repair. While regulatory functions of PCNA ubiquitination and acetylation have been well established, the regulation of PCNA-binding proteins remains underexplored. Considering the vast number of PCNA-binding proteins, many of which have similar PCNA binding affinities, the question arises as to the regulation of the strength and sequence of their binding to PCNA. Here I provide an overview of post-translational modifications on both PCNA and PCNA-interacting proteins and discuss their relevance for the regulation of the dynamic processes of DNA replication and repair.

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The 3-O-sulfation of heparan sulfate modulates protein binding and lyase degradation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2012935118 ◽

2021 ◽

Vol 118 (3) ◽

pp. e2012935118

Author(s):

Pradeep Chopra ◽

Apoorva Joshi ◽

Jiandong Wu ◽

Weigang Lu ◽

Tejabhiram Yadavalli ◽

...

Keyword(s):

Heparan Sulfate ◽

Binding Proteins ◽

Factor Xa ◽

Tissue Expression ◽

Cell Entry ◽

Synthetic Approach ◽

Array Technology ◽

Wide Range ◽

Simplex Virus

Humans express seven heparan sulfate (HS) 3-O-sulfotransferases that differ in substrate specificity and tissue expression. Although genetic studies have indicated that 3-O-sulfated HS modulates many biological processes, ligand requirements for proteins engaging with HS modified by 3-O-sulfate (3-OS) have been difficult to determine. In particular, the context in which the 3-OS group needs to be presented for binding is largely unknown. We describe herein a modular synthetic approach that can provide structurally diverse HS oligosaccharides with and without 3-OS. The methodology was employed to prepare 27 hexasaccharides that were printed as a glycan microarray to examine ligand requirements of a wide range of HS-binding proteins. The binding selectivity of antithrombin-III (AT-III) compared well with anti-Factor Xa activity supporting robustness of the array technology. Many of the other examined HS-binding proteins required an IdoA2S-GlcNS3S6S sequon for binding but exhibited variable dependence for the 2-OS and 6-OS moieties, and a GlcA or IdoA2S residue neighboring the central GlcNS3S. The HS oligosaccharides were also examined as inhibitors of cell entry by herpes simplex virus type 1, which, surprisingly, showed a lack of dependence of 3-OS, indicating that, instead of glycoprotein D (gD), they competitively bind to gB and gC. The compounds were also used to examine substrate specificities of heparin lyases, which are enzymes used for depolymerization of HS/heparin for sequence determination and production of therapeutic heparins. It was found that cleavage by lyase II is influenced by 3-OS, while digestion by lyase I is only affected by 2-OS. Lyase III exhibited sensitivity to both 3-OS and 2-OS.

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A crosslinked and ribosylated actin trimer does not interact productively with myosin

Biochemistry and Cell Biology ◽

10.1139/bcb-2018-0082 ◽

2019 ◽

Vol 97 (2) ◽

pp. 140-147 ◽

Cited By ~ 1

Author(s):

Navneet Sidhu ◽

John F. Dawson

Keyword(s):

Binding Site ◽

Protein Interactions ◽

Binding Proteins ◽

Binding Protein ◽

Dnase I ◽

Protein Protein Interactions ◽

Adp Ribosylation ◽

Myosin Binding ◽

Pointed End

A purified F-actin-derived actin trimer that interacts with end-binding proteins did not activate or bind the side-binding protein myosin under rigor conditions. Remodeling of the actin trimer by the binding of gelsolin did not rescue myosin binding, nor did the use of different means of inhibiting the polymerization of the trimer. Our results demonstrate that ADP-ribosylation on all actin subunits of an F-actin-derived trimer inhibits myosin binding and that the binding of DNase-I to the pointed end subunits of a crosslinked trimer also remodels the myosin binding site. Taken together, this work highlights the need for a careful balance between modification of actin subunits and maintaining protein–protein interactions to produce a physiologically relevant short F-actin complex.

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N1-Propargylguanosine Modified mRNA Cap Analogs: Synthesis, Reactivity, and Applications to the Study of Cap-Binding Proteins

Molecules ◽

10.3390/molecules24101899 ◽

2019 ◽

Vol 24 (10) ◽

pp. 1899

Author(s):

Michal Kopcial ◽

Blazej A. Wojtczak ◽

Renata Kasprzyk ◽

Joanna Kowalska ◽

Jacek Jemielity

Keyword(s):

Protein Interactions ◽

Binding Proteins ◽

Molecular Probes ◽

Translation Initiation Factor ◽

Initiation Factor ◽

Binding Assays ◽

Fluorescent Properties ◽

Eukaryotic Translation ◽

Eukaryotic Translation Initiation ◽

Fluorescent Tags

The mRNA 5′ cap consists of N7-methylguanosine bound by a 5′,5′-triphosphate bridge to the first nucleotide of the transcript. The cap interacts with various specific proteins and participates in all key mRNA-related processes, which may be of therapeutic relevance. There is a growing demand for new biophysical and biochemical methods to study cap–protein interactions and identify the factors which inhibit them. The development of such methods can be aided by the use of properly designed fluorescent molecular probes. Herein, we synthesized a new class of m7Gp3G cap derivatives modified with an alkyne handle at the N1-position of guanosine and, using alkyne-azide cycloaddition, we functionalized them with fluorescent tags to obtain potential probes. The cap derivatives and probes were evaluated in the context of two cap-binding proteins, eukaryotic translation initiation factor (eIF4E) and decapping scavenger (DcpS). Biochemical and biophysical studies revealed that N1-propargyl moiety did not significantly disturb cap–protein interaction. The fluorescent properties of the probes turned out to be in line with microscale thermophoresis (MST)-based binding assays.

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Identification of Src, Fyn, and Lyn SH3-binding proteins: implications for a function of SH3 domains.

Molecular and Cellular Biology ◽

10.1128/mcb.14.7.4509 ◽

1994 ◽

Vol 14 (7) ◽

pp. 4509-4521 ◽

Cited By ~ 166

Author(s):

Z Weng ◽

S M Thomas ◽

R J Rickles ◽

J A Taylor ◽

A W Brauer ◽

...

Keyword(s):

Protein Interactions ◽

Tyrosine Kinases ◽

Protein Tyrosine Kinase ◽

Binding Proteins ◽

Direct Interaction ◽

Sh3 Domain ◽

Peptide Ligand ◽

Sh3 Domains ◽

Protein Tyrosine ◽

Peptide Motifs

Src homology 3 (SH3) domains mediate protein-protein interactions necessary for the coupling of cellular proteins involved in intracellular signal transduction. We previously established solution-binding conditions that allow affinity isolation of Src SH3-binding proteins from cellular extracts (Z. Weng, J. A. Taylor, C. E. Turner, J. S. Brugge, and C. Seidel-Dugan, J. Biol. Chem. 268:14956-14963, 1993). In this report, we identified three of these proteins: Shc, a signaling protein that couples membrane tyrosine kinases with Ras; p62, a protein which can bind to p21rasGAP; and heterogeneous nuclear ribonucleoprotein K, a pre-mRNA-binding protein. All of these proteins contain proline-rich peptide motifs that could serve as SH3 domain ligands, and the binding of these proteins to the Src SH3 domain was inhibited with a proline-rich Src SH3 peptide ligand. These three proteins, as well as most of the other Src SH3 ligands, also bound to the SH3 domains of the closely related protein tyrosine kinases Fyn and Lyn. However, Src- and Lyn-specific SH3-binding proteins were also detected, suggesting subtle differences in the binding specificity of the SH3 domains from these related proteins. Several Src SH3-binding proteins were phosphorylated in Src-transformed cells. The phosphorylation of these proteins was not detected in cells transformed by a mutant variant of Src lacking the SH3 domain, while there was little change in tyrosine phosphorylation of other Src-induced phosphoproteins. In addition, the coprecipitation of v-Src with two tyrosyl-phosphorylated proteins with M(r)s of 62,000 and 130,000 was inhibited by incubation with a Src SH3 peptide ligand, suggesting that the binding of these substrate proteins is dependent on interactions with the SH3 domain. These results strongly suggest a role for the Src SH3 domain in the recruitment of substrates to this protein tyrosine kinase, either through direct interaction with the SH3 domain or indirectly through interactions with proteins that bind to the SH3 domain.

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