scholarly journals Beyond antibodies ? lessons from bacterial ?immunity?

2006 ◽  
Vol 27 (2) ◽  
pp. 80
Author(s):  
Stewart D Nuttall ◽  
Suzy M Juraja ◽  
Jennifer A Carmichael
Keyword(s):  
Binding Proteins ◽  
Specific Binding ◽  
Immune Surveillance ◽  
Specific Protein ◽  
Protein Scaffolds ◽  
Immune Systems ◽  
Alternative Protein ◽  
Human Proteins ◽  
Specific Binding Molecules ◽  
Highly Evolved

Isolation and production of highly specific protein-based binding molecules are crucial to the ever expanding diagnostics, therapeutics and protein array fields. Traditionally, such reagents have been sourced from vertebrate immune systems, where antibodies have evolved over millennia into highly effective molecules of immune surveillance capable of targeting a huge range of targets in response to infection and disease. Now, a growing number of alternative protein scaffolds are being investigated as specific binding molecules incorporating a diverse and powerful range of binding and recognition interfaces. These are being sourced from human proteins, from alternative immune molecules present in evolutionarily old vertebrates, and from highly evolved binding proteins in prokaryotic systems.

scholarly journals Toxin Neutralization Using Alternative Binding Proteins

Toxins ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 53 ◽  
Author(s):  
Timothy Jenkins ◽  
Thomas Fryer ◽  
Rasmus Dehli ◽  
Jonas Jürgensen ◽  
Albert Fuglsang-Madsen ◽  
...  
Keyword(s):  
Binding Protein ◽  
Low Cost ◽  
Protein Scaffolds ◽  
Comprehensive Overview ◽  
Alternative Protein ◽  
Human Proteins ◽  
Cost Of Production ◽  
High Level ◽  
Antibody Derivatives ◽  
Derivatives Of

Animal toxins present a major threat to human health worldwide, predominantly through snakebite envenomings, which are responsible for over 100,000 deaths each year. To date, the only available treatment against snakebite envenoming is plasma-derived antivenom. However, despite being key to limiting morbidity and mortality among snakebite victims, current antivenoms suffer from several drawbacks, such as immunogenicity and high cost of production. Consequently, avenues for improving envenoming therapy, such as the discovery of toxin-sequestering monoclonal antibodies against medically important target toxins through phage display selection, are being explored. However, alternative binding protein scaffolds that exhibit certain advantages compared to the well-known immunoglobulin G scaffold, including high stability under harsh conditions and low cost of production, may pose as possible low-cost alternatives to antibody-based therapeutics. There is now a plethora of alternative binding protein scaffolds, ranging from antibody derivatives (e.g., nanobodies), through rationally designed derivatives of other human proteins (e.g., DARPins), to derivatives of non-human proteins (e.g., affibodies), all exhibiting different biochemical and pharmacokinetic profiles. Undeniably, the high level of engineerability and potentially low cost of production, associated with many alternative protein scaffolds, present an exciting possibility for the future of snakebite therapeutics and merit thorough investigation. In this review, a comprehensive overview of the different types of binding protein scaffolds is provided together with a discussion on their relevance as potential modalities for use as next-generation antivenoms.

Insulin-like growth factors and their binding proteins in pleural fluid

1997 ◽  
pp. 467-473 ◽  
Author(s):  
Y Le Bouc ◽  
A Bellocq ◽  
C Philippe ◽  
L Perin ◽  
M Garabedian ◽  
...  
Keyword(s):  
Growth Factors ◽  
Pleural Fluid ◽  
Binding Proteins ◽  
Specific Binding ◽  
Gel Filtration ◽  
Specific Protein ◽  
Hydroxyvitamin D ◽  
Igf I ◽  
Acid Gel ◽  
Insulin Like Growth Factors

We investigated the expression and potential regulatory role of insulin-like growth factors (IGFs) and their specific binding proteins (BPs) in tuberculous and nontuberculous pleuritis. By using a radioimmunoassay after acid gel filtration chromatography, we found that mean concentrations of IGF-I were 211.9 +/- 20.2 microg/l and 203.2 +/- 31.1 microg/l in pleural fluid of 14 patients with tuberculous pleuritis and 9 patients with malignant pleuritis respectively. These values were near those in serum of the same patients (221.3 +/- 19.5 microg/l and 204.6 +/- 21.0 microg/l respectively). By using a specific protein-binding assay, we found that mean concentrations of IGF-II were 345.3 +/- 61.0 microg/l and 167.6 +/- 22.7 microg/l in tuberculous and malignant pleural effusions respectively. These values were significantly lower than those in serum of the same patients (628.3 +/- 79.0 microg/l, P<0.025 and 532.0 +/- 85.9 microg/l, P<0.025 respectively). Because bioavailability and bioactivity of IGFs may be regulated by their binding to IGFBPs, we studied IGFBP patterns in the pleural fluid of 6 patients with tuberculous pleuritis. As assessed by Western ligand blotting the levels of IGFBP-1 and IGFBP-2 were increased whereas those of IGFBP-3 were decreased in pleural fluid in comparison with serum. The decrease in IGFPB-3 levels reflected increased proteolysis, as assessed by Western immunoblotting. In spite of this presence of IGFBPs, IGFs could be responsible for the local biosynthesis of 1.25-dihydroxyvitamin D (1,25-(OH)2D) since pleural fluid levels of both IGF-I and IGF-II significantly correlated with those of 1,25-(OH)2D. These results indicate that IGFs are detectable in pleural fluid and may contribute to control the activity of 25-hydroxyvitamin D-1alpha hydroxylase in tuberculous pleuritis.

Recent advances in the scaffold engineering of protein binders

2020 ◽  
Vol 21 ◽  
Author(s):  
Mohammad Karimi Baba Ahmadi ◽  
Seyed Abolgasem Mohammadi ◽  
Manoochehr Makvandi ◽  
Morteza Mamouei ◽  
Mohammad Rahmati ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Binding Proteins ◽  
Science Studies ◽  
Specific Binding ◽  
Protein Scaffolds ◽  
High Solubility ◽  
Single Domain Antibody ◽  
Human Antibodies ◽  
Domain Antibody ◽  
Protein Binders

: In recent years, extensive attention has been given to the generation of new classes of ligand-specific binding proteins to supplement monoclonal antibodies. A combination of protein engineering and display technologies has bee used to manipule non-human antibodies for humanization and stabilization purposes or even the generation of new binding proteins. Engineered protein scaffolds can now be directed against therapeutic targets to treat cancer and immunological disorders. Although very few of these scaffolds have successfully passed clinical trials, their remarkable properties such as robust folding, high solubility, and small size motivates their employment as tool for biology and applied science studies. Here, we have focused on the generation new non-Ig binding proteins and single domain antibody manipulation, with a glimpse of their applications.

THE THYROXINE-BINDING PROPERTIES OF SERUM PROTEINS. A COMPETITIVE BINDING TECHNIQUE EMPLOYING SEPHADEX G-25

1975 ◽  
Vol 65 (3) ◽  
pp. 319-332 ◽  
Author(s):  
R. L. SUTHERLAND ◽  
M. W. SIMPSON-MORGAN
Keyword(s):  
Binding Proteins ◽  
Serum Proteins ◽  
Binding Capacity ◽  
Specific Binding ◽  
Competitive Binding ◽  
Association Constants ◽  
Binding Properties ◽  
Rat Serum ◽  
Human Proteins ◽  
Dilute Blood

SUMMARY A competitive binding technique is described for the estimation of the thyroxine (T4)-binding properties of serum proteins in dilute blood serum and lymph. When used in conjunction with an assay for total T4 the following parameters can be estimated: the number of functionally different T4 binding proteins, their individual association constants and binding capacities for T4, the amount of T4 which is bound to each binding species, and the concentration of unbound (free) T4. Both human and sheep serum have three functionally different T4-binding proteins. The association constants for the three human proteins were 9·5 × 109, 1·6 × 108 and 3·1 × 105 1/mol for T4-binding globulin (TBG), T4-binding prealbumin (TBPA) and serum albumin, respectively. The corresponding sheep proteins, TBG, TBP-2 and albumin, had association constants of 8·9 × 109, 1·4 × 108 and 3·5 × 1051/mol. Human TBG had a mean binding capacity of 21·3 μg/100 ml and that of ovine TBG was 12·8 μg/100 ml. The other specific binding proteins (TBPA in man and TBP-2 in sheep) had mean binding capacities of 307 and 359 μg/100 ml respectively. Two functionally different T4-binding proteins were identified in rat serum.

Second messenger-specific protein kinases in a salt-absorbing intestinal epithelium

1990 ◽  
Vol 258 (5) ◽  
pp. C879-C888 ◽  
Author(s):  
C. Toskulkao ◽  
N. T. Nash ◽  
K. Leach ◽  
M. C. Rao
Keyword(s):  
Protein Kinase ◽  
Ion Transport ◽  
Protein Phosphorylation ◽  
Molecular Mass ◽  
Rat Brain ◽  
Protein Kinases ◽  
Binding Proteins ◽  
Specific Binding ◽  
Specific Protein ◽  
Transport Processes

Calcium, adenosine 3',5'-cyclic monophosphate (cAMP), and guanosine 3',5'-cyclic monophosphate (cGMP) can regulate the same or different ion transport processes within an epithelium, presumably via independent protein phosphorylation mechanisms. Because there have been few detailed studies characterizing these processes in epithelia, we examined the distribution of Ca-, cAMP-, and cGMP-specific protein kinases and substrates in vitro in a homogenous salt-absorbing epithelium, the winter flounder intestine. In this tissue cGMP and Ca inhibit Na-K-2Cl cotransport, cAMP increases anion permeability, and phorbol esters do not affect ion transport. The Ca-specific kinases are calmodulin (CaM) dependent. The tissue possesses type III Ca-CaM protein kinase and its specific substrate elongation factor 2 and type II but not type I Ca-CaM kinase. Addition of phosphatidylserine (PS) and Ca to crude or DEAE-cellulose-purified cytosol neither increased the phosphorylation of exogenous histone H1 substrate nor that of any endogenous substrates. Although these suggest the absence of Ca-phospholipid-dependent kinase (PKC), the cytosol has a 78-kDa protein recognizable by a highly specific polyclonal sheep antibody to rat brain PKC. Both the particulate and cytosolic fractions possess cAMP-specific binding proteins and cAMP-specific phosphoprotein substrates. The particulate fraction cAMP-binding proteins are of molecular mass 50 kDa (pI 5.2) and 48 kDa with multiple isoforms (pI 5.6-6.2); these proteins generate different peptide maps. The cytosol chiefly contains a 50-kDa (pI 5.2) cAMP binding protein that is similar to the particulate 50-kDa protein on peptide mapping. The flounder cAMP binding proteins have the same pI but lower molecular mass and different peptide profiles than the rat brain RII (54/52 kDa) and RI (50 kDa) cAMP regulatory proteins. The cGMP-specific protein kinase was less prominent, very low levels of cGMP-specific binding proteins being detected either by equilibrium binding or by photoaffinity labeling. A prominent kinase substrate in homogenates is a 50-kDa protein, the phosphorylation of which is increased by Ca and cGMP but decreased by cAMP. When intact tissue was prelabeled with 32Pi and then exposed to cGMP, the phosphorylation of a number of substrates including that of a 50-kDa protein was increased. In summary, the flounder intestine possesses the necessary protein phosphorylation mechanisms to account for the regulation of its ion transport processes by second messengers.

Quantitative characterization of conformational-specific protein–DNA binding using a dual-spectral interferometric imaging biosensor

Nanoscale ◽  
2016 ◽  
Vol 8 (10) ◽  
pp. 5587-5598 ◽  
Author(s):  
Xirui Zhang ◽  
George G. Daaboul ◽  
Philipp S. Spuhler ◽  
Peter Dröge ◽  
M. Selim Ünlü
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Specific Binding ◽  
Specific Protein ◽  
Dna Binding Proteins ◽  
Interferometric Imaging ◽  
Quantitative Characterization ◽  
Binding Mechanisms

DNA-binding proteins play crucial roles in the maintenance and functions of the genome and yet, their specific binding mechanisms are not fully understood.

scholarly journals Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA

2018 ◽  
Author(s):  
Ei-Wen Yang ◽  
Jae Hoon Bahn ◽  
Esther Yun-Hua Hsiao ◽  
Boon Xin Tan ◽  
Yiwei Sun ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Specific Binding ◽  
Specific Protein ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Allele Specific ◽  
Rna Interaction

AbstractAllele-specific protein-RNA binding is an essential aspect that may reveal functional genetic variants influencing RNA processing and gene expression phenotypes. Recently, genome-wide detection of in vivo binding sites of RNA binding proteins (RBPs) is greatly facilitated by the enhanced UV crosslinking and immunoprecipitation (eCLIP) protocol. Hundreds of eCLIP-Seq data sets were generated from HepG2 and K562 cells during the ENCODE3 phase. These data afford a valuable opportunity to examine allele-specific binding (ASB) of RBPs. To this end, we developed a new computational algorithm, called BEAPR (Binding Estimation of Allele-specific Protein-RNA interaction). In identifying statistically significant ASB sites, BEAPR takes into account UV cross-linking induced sequence propensity and technical variations between replicated experiments. Using simulated data and actual eCLIP-Seq data, we show that BEAPR largely outperforms often-used methods Chi-Squared test and Fisher’s Exact test. Importantly, BEAPR overcomes the inherent over-dispersion problem of the other methods. Complemented by experimental validations, we demonstrate that ASB events are significantly associated with genetic regulation of splicing and mRNA abundance, supporting the usage of this method to pinpoint functional genetic variants in post-transcriptional gene regulation. Many variants with ASB patterns of RBPs were found as genetic variants with cancer or other disease relevance. About 38% of ASB variants were in linkage disequilibrium with single nucleotide polymorphisms from genome-wide association studies. Overall, our results suggest that BEAPR is an effective method to reveal ASB patterns in eCLIP and can inform functional interpretation of disease-related genetic variants.

scholarly journals Effect of specific binding of human albumin, fibrinogen, and immunoglobulin G on surface characteristics of bacterial strains as revealed by partition experiments in polymer phase systems

1980 ◽  
Vol 29 (3) ◽  
pp. 879-885
Author(s):  
H Miörner ◽  
E Myhre ◽  
L Björck ◽  
G Kronvall
Keyword(s):  
Protein Binding ◽  
Surface Properties ◽  
Immunoglobulin G ◽  
Specific Binding ◽  
Polymer Concentration ◽  
Specific Protein ◽  
Bacterial Cells ◽  
Bacterial Strains ◽  
Human Proteins ◽  
Phase Systems

Four strains of gram-positive cocci with different combinations of positive binding of human proteins were investigated with respect to changes in physicochemical surface properties after specific protein binding. Staphylococcus aureus Cowan I, two group A beta-hemolytic streptococci, and one group G streptococcal strain were studied; they represented three different combinations of reactivity for human serum albumin, human immunoglobulin G, and fibrinogen. Using single-tube partition of bacterial cells in a dextran-polyethylene glycol system of constant polymer concentration but varying ionic compositions, it was possible to detect changes in the partition of bacteria after specific protein binding. There was a correlation between the binding of radiolabled human proteins to the bacterial strains and the effect of human proteins on the partition of the bacteria in the phase systems. Thus, the specific binding of proteins to the bacteria changes their physicochemical surface properties. These types of bacteria-protein interactions may play an important role in modulating host-parasite relationships.

Human Fibronectin Extra-Domain B (EDB)-Specific Aptide (APTEDB) Radiolabelling with Technetium-99m as a Potent Targeted Tumour-Imaging Agent

2018 ◽  
Vol 18 (2) ◽  
pp. 277-285 ◽  
Author(s):  
Mohsen Mohammadgholi ◽  
Nourollah Sadeghzadeh ◽  
Mostafa Erfani ◽  
Saeid Abediankenari ◽  
Seyed Mohammad Abedi ◽  
...  
Keyword(s):  
Radioligand Binding ◽  
Specific Binding ◽  
Specific Protein ◽  
Tumour Imaging ◽  
Specific Binding Ratio ◽  
Tumour Uptake ◽  
Technetium 99M ◽  
In Vivo Experiments ◽  
Human Fibronectin

Background: Human fibronectin extra-domain B (EDB) is particularly expressed during angiogenesis progression. It is, thus, a promising marker of tumour growth. Aptides are a novel class of peptides with high-affinity binding to specific protein targets. APTEDB is an antagonist-like ligand that especially interacts with human fibronectin EDB. Objective: This study was the first attempt in which the hydrazinonicotinamide (HYNIC)-conjugated APTEDB was labelled with technetium-99m (99mTc) as an appropriate radiotracer and tricine/EDDA exchange labeling. Methods: Radiochemical purity, normal saline, and serum stability were evaluated by HPLC and radio-isotope TLC scanner. Other examinations, such as protein-binding calculation, dissociation radioligand binding assay, and partition coefficient constant determination, were also carried out. The cellular-specific binding of 99mTc- HYNIC-conjugated APTEDB was assessed in two EDB-positive (U87MG) and EDB-negative (U373MG) cell lines. Bio-distribution was investigated in normal mice as well as in U87MG and U373MG tumour-bearing mice. Eventually, the radiolabelled APTEDB was used for tumour imaging using planar SPECT. Results: Radiolabelling was achieved with high purity (up to 97%) and accompanied by high solution (over 90% after overnight) and serum (80% after 2 hours) stability. The obtained cellular-specific binding ratio was greater than nine-fold. In-vivo experiments showed rapid blood clearance with mainly renal excretion and tumour uptake specificity (0.48±0.03% ID/g after 1h). The results of the imaging also confirmed considerable tumour uptake for EDB-positive cell line compared with the EDB-negative one. Conclusion: Aptides are considered to be a potent candidate for biopharmaceutical applications. They can be modified with imaging or therapeutic agents. This report shows the capability of 99mTc-HYNIC-APTEDB for human EDB-expressing tumours detection.

Genetic regulation of nitrogen metabolism in the fungi

1997 ◽  
Vol 61 (1) ◽  
pp. 17-32
Author(s):  
G A Marzluf
Keyword(s):  
Nitrogen Metabolism ◽  
Protein Interactions ◽  
Fungal Pathogens ◽  
Metabolic Regulation ◽  
Specific Binding ◽  
Genetic Regulation ◽  
Nitrogen Sources ◽  
Specific Protein ◽  
Genes Encoding ◽  
Gata Family

In the fungi, nitrogen metabolism is controlled by a complex genetic regulatory circuit which ensures the preferential use of primary nitrogen sources and also confers the ability to use many different secondary nitrogen sources when appropriate. Most structural genes encoding nitrogen catabolic enzymes are subject to nitrogen catabolite repression, mediated by positive-acting transcription factors of the GATA family of proteins. However, certain GATA family members, such as the yeast DAL80 factor, act negatively to repress gene expression. Selective expression of the genes which encode enzymes for the metabolism of secondary nitrogen sources is often achieved by induction, mediated by pathway-specific factors, many of which have a GAL4-like C6/Zn2 DNA binding domain. Regulation within the nitrogen circuit also involves specific protein-protein interactions, as exemplified by the specific binding of the negative-acting NMR protein with the positive-acting NIT2 protein of Neurospora crassa. Nitrogen metabolic regulation appears to play a significant role in the pathogenicity of certain animal and plant fungal pathogens.

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