Purified U2OS PRβ Protein Interaction Assay Kit from Creative Biomart. U2OS PRβ Protein Interaction Assay Kit can be used for research.
Purified U2OS PRα Protein Interaction Assay Kit from Creative Biomart. U2OS PRα Protein Interaction Assay Kit can be used for research.
Detection of Protein-Protein Interactions Using the GST Fusion Protein Pull-down Technique. Bacterially expressed glutathione S-transferase (GST)-fused proteins are used as probes to perform direct measure of protein-protein interactions and for affinity purification. Slideshow 6521621 by...
TY - JOUR. T1 - Biophysical characterization and modeling of human Ecdysoneless (ECD) protein supports a scaffolding function. AU - Mir, Riyaz A.. AU - Lovelace, Jeff. AU - Schafer, Nicholas P.. AU - Simone, Peter D.. AU - Kellezi, Admir. AU - Kolar, Carol. AU - Spagnol, Gaelle. AU - Sorgen, Paul L. AU - Band, Hamid. AU - Band, Vimla. AU - Borgstahl, Gloria E. PY - 2016/1/1. Y1 - 2016/1/1. N2 - The human homolog of Drosophila ecdysoneless protein (ECD) is a p53 binding protein that stabilizes and enhances p53 functions. Homozygous deletion of mouse Ecd is early embryonic lethal and Ecd deletion delays G1-S cell cycle progression. Importantly, ECD directly interacts with the Rb tumor suppressor and competes with the E2F transcription factor for binding to Rb. Further studies demonstrated ECD is overexpressed in breast and pancreatic cancers and its overexpression correlates with poor patient survival. ECD overexpression together with Ras induces cellular transformation through upregulation of ...
The invention provides reagents and methods for multivalent binding and quantitative capture of components in a sample. In one aspect, reagents and methods for diagnostic assay for antigen, ligand, binding agent, or antibody are provided. Compositions of a non-natural or deliberately constructed nucleic acid-like polymeric scaffold are provided, to which multiple antibodies, peptides or other binding agents can be affixed by hybridization of a oligonucleotide: binding agent complex such that the nucleic acid: binding agent construction displays multivalent behavior when interacting with a multivalent analyte. Methods for constructing and using the scaffolds are described. Such compositions may include assembly of mixed specificity binding agents such that the composition displays multivalent binding behavior against a target containing mixed analytes which can be bound by the construct to effect a binding affinity increase such as is observed in avidity reagents against single analytes expressed
Yeast Two Hybrid system uses a reporter gene to detect the interaction of pair of proteins inside the yeast cell nucleus. In the yeast Two Hybrid System, The interaction of target protein to the protein will bring together transcriptional activator, which then switches on the expression of reporter gene.
This article describes a HaloTag® bioluminescent pull-down workflow for validating protein:protein interaction results obtained with NanoBRET™ assays.
Kinases transfer the γ-phosphate of ATP to other biological molecules, serving as chemical messengers that make the tight regulation of cell-signaling pathways possible. For example, non-receptor tyrosine kinases are found in the cytoplasm (not membrane-bound) and transfer the γ-phosphate of ATP to tyrosine residues of other proteins, often turning these proteins on or off in the context of their respective signaling pathway. This notion of on or off can be useful to holistically conceptualize these pathways but is a gross oversimplification; in reality, many of these enzymes are multi-domain proteins that can exist in multiple conformational states, participate in multiple protein-protein interactions, and experience a gradient of variable activity levels depending on these states. The molecular mechanisms that govern the activity of these kinases is extraordinarily complex, and though much has been discovered in recent years, much remains to be understood, especially for the Tec ...
Cellular membranes act as signaling platforms and control solute transport. Membrane receptors, transporters, and enzymes communicate with intracellular processes through protein-protein interactions. Using a split-ubiquitin yeast two-hybrid screen that covers a test-space of 6.4 × 106 pairs, we identified 12,102 membrane/signaling protein interactions from Arabidopsis. Besides confirmation of expected interactions such as heterotrimeric G protein subunit interactions and aquaporin oligomerization, >99% of the interactions were previously unknown. Interactions were confirmed at a rate of 32% in orthogonal in planta split-green flourescent protein interaction assays, which was statistically indistinguishable from the confirmation rate for known interactions collected from literature (38%). Regulatory associations in membrane protein trafficking, turnover, and phosphorylation include regulation of potassium channel activity through abscisic acid signaling, transporter activity by a WNK kinase, ...
Cellular membranes act as signaling platforms and control solute transport. Membrane receptors, transporters, and enzymes communicate with intracellular processes through protein-protein interactions. Using a split-ubiquitin yeast two-hybrid screen that covers a test-space of 6.4 × 10(6) pairs, we identified 12,102 membrane/signaling protein interactions from Arabidopsis. Besides confirmation of expected interactions such as heterotrimeric G protein subunit interactions and aquaporin oligomerization, >99% of the interactions were previously unknown. Interactions were confirmed at a rate of 32% in orthogonal in planta split-green flourescent protein interaction assays, which was statistically indistinguishable from the confirmation rate for known interactions collected from literature (38%). Regulatory associations in membrane protein trafficking, turnover, and phosphorylation include regulation of potassium channel activity through abscisic acid signaling, transporter activity by a WNK kinase, ...
This article discusses the pull-down technique, which is an invaluable tool for scientists interested in studying cellular pathways via protein-protein interactions.
NanoBRET protein interaction assays use NanoLuc luciferase as the energy donor to create sensitive BRET-based protein:protein interaction assays.
Signals can be regulated by many flexible strategies, including blocking protein catalytic activity, reducing product accumulation, or sequestrating proteins from their site of action. Several protein binding domains that regulate the interaction of proteins with each other have been identified. More recently, the binding domains that allow proteins to bind lipids and, therefore, the plasma membrane have gained increased appreciation. Hurley and Misra review the domains that specifically bind lipid moities. Of great importance is understanding the subtle differences in overall domain structures and how these differences relate to binding specificity. For example, within the C2 domain family, some members bind lipids or proteins and do so in the presence or absence of Ca2+. Of course, as the authors point out, specificity is imparted by the residues flanking each domain and by less conserved residues within the domain. The moderately biophysical approach taken by Hurley and Misra provides a fresh ...
gst pulldown - posted in Protein and Proteomics: hi everyone, I have purified my fusion protein and is now conjugated with gst beads. MY question is, how long can i keep these fusion protein beads? Or should i do gst pulldown immediately? Thank you.
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Herring MP et al. 2021. Dynamic associations between anxiety, depression, and tobacco use in older adults: Results from The Irish Longitudinal Study on Ageing. Journal of Psychiatric Research. 2021;139:99-105
How UL44 binds to DNA and the role of DNA binding in processivity function have not been yet elucidated. To begin to understand these mechanism, we characterized the interaction of UL44 with DNA by means of filter-binding assays and electrophoretic mobility shift assays (EMSA). We found that, similar to HSV-1 UL42, UL44 binds directly to DNA with nanomolar affinity in a manner that does not require ATP hydrolysis or accessory proteins. UL44 binds DNA as a dimer in a sequence-non specific manner and displays higher affinity for ds DNA compared to ss DNA. Affinity of UL44 for ds DNA decreases with increasing ionic strength and this effect is mediated by ion release, suggesting that DNA binding entails electrostatic interactions between the negatively charged phosphates on DNA backbone and the positive charge of basic residues on the back face and disordered loops of UL44 ...
Hi, I´m performing GST Pulldown to identify protein-protein interactions between GST-X and prey proteins in a cellular lysate. The results are not so good so far, because I identify a lot of unspecific proteins (cytoskeletal proteins and so on). So I think i´ll have to improve my method. What things would you change ...
Plexera® develops products for detection and quantification of molecular binding interactions such as protein-protein, antibody-antigen, protein-oligonucleotide, and other molecular binding interactions.
An integral component of understanding E3 ligase function is identifying the enzymes cognate substrate(s) and/or binding proteins. Previous binding partners of BCA2 included Rab7, isolated through yeast-II-hybrid screening [17], tetherin, which was found though brute-force GST-pulldowns [18], and ubiquitin and UBC9 from bacteria-II- hybrid screening [7, 16]. Bacteria and yeast screening systems were used in this study to identify additional potential binding partners of BCA2 (Table 1). Of the potential partners found, 14-3-3σ and hHR23a were chosen for further investigation in the context of BCA2 activity and expression. Through binding experiments we confirmed that the BCA2 protein bound both to 14-3-3σ and hHR23a (Figure 1B and 1C). hHR23a and BCA2 were co-expressed in a mammalian system, while 14-3-3σ was expressed in a bacterial system and incubated with recombinant purified BCA2. The expression levels of wild-type BCA2 and the S132, 133A mutant in HEK293T cells were much lower than ...
Understanding protein-protein interactions (PPI) and their specific functions underpins basic molecular research as well as the development of novel drugs. However, many of the conventional analysis methods do not provide important contextual information that reveals how a protein works in its native cellular environment, nor do they suit high-throughput screening campaigns. This eBook highlights several examples of robust, reproducible protein interaction assays,
The yeast three-hybrid (Y3H) approach shows considerable promise for the unbiased identification of novel small molecule-protein interactions. In recent years, it has been successfully used to link a number of bioactive molecules to novel protein binding partners. However despite its potential importance as a protein target identification method, the Y3H technique has not yet been widely adopted, in part due to the challenges associated with the synthesis of the complex chemical inducers of dimerisation (CIDs). The development of a modular approach using potentially
Biochemical processes within a cell or an organism are usually induced by molecular interaction and recognition events. One major aim of drug discovery is to identify bioactive molecular structures that can be used to sufficiently interfere with such molecular interaction processes and thereby positively influence and eventually cure a disease. Antagonists which prohibit the interactions between naturally occurring ligands and their protein receptors could be represented as good drug candidates. Low molecular weight ligands can interact with macromolecular target through covalent and noncovalent interactions. Noncovalent binding is characterized by equilibrium thermodynamics. Important noncovalent interactions are hydrogen bonds, ionic interactions and hydrophobic contacts. Steric and electronic complementarity between protein receptor and low molecular ligand seem to be the most important prerequisite to allow a tightly and selectively association. In almost any drug discovery project based on ...
AMG 232 is a potent, selective and orally available inhibitor of p53-MDM2 interaction, with an IC50 of 0.6 nM. AMG 232 binds to MDM2 with a Kd of 0.045 nM. - Mechanism of Action & Protocol.
There being a myriad of microbes living on every square inch of our skin, researchers at University of California, San Diego Skaggs School of Pharmacy and
Capto Core 700 Resin Binding Efficiency - Dear Expert, I am using Capto Core 700 for sample run (sample temp. max. 10 deg. Celsius). In case of capto core 700 resin what is the minimum and maximum temperature which can effectively used for...
Capto Core 700 Resin Binding Efficiency - Dear Expert, I am using Capto Core 700 for sample run (sample temp. max. 10 deg. Celsius). In case of capto core 700 resin what is the minimum and maximum temperature which can effectively used for...
U okviru ove doktorske disertacije metodama molekulskog modeliranja proučavane su interakcije nukleinskih kiselina s nekoliko skupina organskih spojeva: derivatima bisfenantridina, guanidiniokarbonil-pirol- arilnim konjugatima, cijaninskim spojevima, te translacijskim (benzimidazolnim i diaminopiperidinskim) inhibitorima hepatitis C virusa. Istraženi su procesi njihovog kompleksiranja, interkaliranja, vezanja u utor te elektrostatskog međudjelovanja s polinukleotidima. Prve tri skupine spojeva imaju svojstvo molekulskog prepoznavanja nukleobaza, pa mogu poslužiti za razvoj novih specifičnih obilježivača pri istraživanju nukleinskih kiselina, te kao predložak za razvoj antitumorskih i antivirusnih lijekova sa svojstvom selektivnog blokiranja određenih sljedova DNA ili RNA. Kao polazišne točke za modeliranje korišteni su rezultati spektroskopskih mjerenja (UV-Vis i CD spektri, fluorimetrijske titracije) te difrakcijske i NMR analize. Istraživanja su provedena metodama molekulskog ...
FLUORESZENZMARKIERUNG (BIOLOGIE); INTRAZELLULÄRE WECHSELWIRKUNGEN (CYTOLOGIE); ERYTHROZYTENMEMBRAN (HISTOLOGIE UND CYTOLOGIE); POLARITÄT, HYDROPHILE UND LIPOPHOBE MOLEKÜLE UND INTERAKTIONEN (BIOPHYSIKALISCHE CHEMIE); FLUORESCENCE LABELLING (BIOLOGY); INTRACELLULAR INTERACTIONS (CYTOLOGY); ERYTHROCYTE MEMBRANE (HISTOLOGY AND CYTOLOGY); POLARITY, HYDROPHILIC AND LIPOPHOBIC MOLECULES AND INTERACTIONS (BIOPHYSICAL CHEMISTRY ...
131D: The low-temperature crystal structure of the pure-spermine form of Z-DNA reveals binding of a spermine molecule in the minor groove.
Dynamic covalent chemistry offers an opportunity to develop synthetic protocols that incorporate a degree of error checking through the dynamic and reversible association of the components of a target structure through covalent bonds. The limited number of organic reactions that form covalent bonds and that are also completely reversible under mild conditions hampers the development of this field. In addition, the ability of systems to select and amplify one species over all others in an equilibrating mixture is limited in approaches which consider only the thermodynamics of the system. We have developed a new dynamic exchange reaction and incorporated it within synthetic replicating systems. The coupling of dynamic exchange and replication creates systems capable of selecting and amplifying single molecular species from complex mixtures with selectivities of better than 15:1 ...
Typically, response-repetition effects are obtained in task-switching experiments: In task repetitions, performance is enhanced when the response, too, rep
Prof. Dr. Winfried Römer and his research team at the University of Freiburg have recently found that bacterial protein impairs important cellular processes
MARCKS like protein Proteins available through Novus Biologicals. Browse our MARCKS like protein Protein catalog backed by our Guarantee+.
Finds sub-sequences or patterns in the sequence and highlights the matching regions. The tool works with standard single letter nucleotide or protein codes including ambiguities and can match Prosite patterns in protein sequences. More... ...
Finds sub-sequences or patterns in the sequence and highlights the matching regions. The tool works with standard single letter nucleotide or protein codes including ambiguities and can match Prosite patterns in protein sequences. More... ...
There are comments on PubPeer for publication: Identification of rickettsial immunoreactive proteins using a proximity ligation assay Western blotting and the traditional immunoproteomic approach (2018)
Amino-acids are essential for optimal health, as they form proteins and serve specific functions, such as assisting with food breakdown, aiding muscle growth and promoting tissue repair.
The C type natriuretic peptide receptor (NPRC) also known as NPR3 is a widely expressed single transmembrane-spanning protein. NPRC functions as a homodimer at the cell surface for the metabolic clearance of a broad range of natriuretic peptides from circulation. The intracellular domain of NPRC is coupled to inhibitory G proteins and is involved in mediating signal transduction. In order to further elucidate the role of NPRC in signal transduction a proteomic approach was taken to identify putative protein binding partners for NPRC in different cell-types. An interrogation of the molecular association between NPRC and its identified protein binding partner(s) was carried out in different cell types to identify the specific interacting domains. The physiological role of the association between NPRC and its protein binding partner(s) were investigated in situ. Furthermore NPRC is subject to post translation modifications including glycosylation and phosphorylation. Although evidence suggests NPRC is
Author: Cartieaux, F. et al.; Genre: Journal Article; Published in Print: 2008; Keywords: induced systemic resistance|br/|chromatography-mass spectrometry|br/|salicylic-acid|br/|functional genomics|br/|acquired-resistance|br/|gene-expression|br/|fusarium-wilt|br/|photosynthetic bradyrhizobia|br/|microarray experiments|br/|biocontrol bacteria; Title: Simultaneous interaction of Arabidopsis thaliana with Bradyrhizobium sp strain ORS278 and Pseudomonas syriugae pv. tomato DC3000 leads to complex transcriptome changes
Publikations-Datenbank der Fraunhofer Wissenschaftler und Institute: Aufsätze, Studien, Forschungsberichte, Konferenzbeiträge, Tagungsbände, Patente und Gebrauchsmuster
Protein binding microarrays (PBM) are a high throughput technology used to characterize protein-DNA binding. The arrays measure a proteins affinity toward thousands of double-stranded DNA sequences at once, producing a comprehensive binding specificity catalog. We present a linear model for predicting the binding affinity of a protein toward DNA sequences based on PBM data. Our model represents the measured intensity of an individual probe as a sum of the binding affinity contributions of the probes subsequences. These subsequences characterize a DNA binding motif and can be used to predict the intensity of protein binding against arbitrary DNA sequences. Our method was the best performer in the Dialogue for Reverse Engineering Assessments and Methods 5 (DREAM5) transcription factor/DNA motif recognition challenge. For the DREAM5 bonus challenge, we also developed an approach for the identification of transcription factors based on their PBM binding profiles. Our approach for TF identification ...
PDZ domains direct protein-protein interactions and serve as models for protein design. Here, we optimized a protein design energy function for the Tiam1 and Cask PDZ domains that combines a molecular mechanics energy, Generalized Born solvent, and an empirical unfolded state model. Designed sequences were recognized as PDZ domains by the Superfamily fold recognition tool and had similarity scores comparable to natural PDZ sequences. The optimized model was used to redesign the two PDZ domains, by gradually varying the chemical potential of hydrophobic amino acids; the tendency of each position to lose or gain a hydrophobic character represents a novel hydrophobicity index. We also redesigned four positions in the Tiam1 PDZ domain involved in peptide binding specificity. The calculated affinity differences between designed variants reproduced experimental data and suggest substitutions with altered specificities.
TY - JOUR. T1 - Characterization of the peptide-binding specificity of Mamu-A*11 results in the identification of SIV-derived epitopes and interspecies cross-reactivity. AU - Sette, Alessandro. AU - Sidney, John. AU - Bui, Huynh Hoa. AU - Del Guercio, Marie France. AU - Alexander, Jeff. AU - Loffredo, John. AU - Watkins, David I.. AU - Mothé, Bianca R.. PY - 2005/4/1. Y1 - 2005/4/1. N2 - The SIV-infected Indian rhesus macaque is the most established model of HIV infection, providing insight into pathogenesis and a system for testing novel vaccines. However, only a limited amount of information is available regarding the peptide-binding motifs and epitopes bound by their class I and class II MHC molecules. In this study, we utilized a library of over 1,000 different peptides and a high throughput MHC-peptide binding assay to detail the binding specificity of the rhesus macaque class I molecule Mamu-A*11. These studies defined the fine specificity of primary anchor positions, and dissected the ...
TY - JOUR. T1 - Many-to-one binding by intrinsically disordered protein regions. AU - Alterovitz, Wei Lun. AU - Faraggi, Eshel. AU - Oldfield, Christopher J.. AU - Meng, Jingwei. AU - Xue, Bin. AU - Huang, Fei. AU - Romero, Pedro. AU - Kloczkowski, Andrzej. AU - Uversky, Vladimir N.. AU - Dunker, A. Keith. PY - 2020/1/1. Y1 - 2020/1/1. N2 - Disordered binding regions (DBRs), which are embedded within intrinsically disordered proteins or regions (IDPs or IDRs), enable IDPs or IDRs to mediate multiple protein-protein interactions. DBR-protein complexes were collected from the Protein Data Bank for which two or more DBRs having different amino acid sequences bind to the same (100% sequence identical) globular protein partner, a type of interaction herein called many-to-one binding. Two distinct binding profiles were identified: independent and overlapping. For the overlapping binding profiles, the distinct DBRs interact by means of almost identical binding sites (herein called similar), or the ...
This protein protein interaction antibody pair set comes with two antibodies to detect the protein-protein interaction, one against the CDC20 protein, and the other against the BUB1B protein for use in in situ Proximity Ligation Assay. See Publication Reference below. (DI0076) - Products - Abnova
This protein protein interaction antibody pair set comes with two antibodies to detect the protein-protein interaction, one against the TRAF5 protein, and the other against the TRAF3 protein for use in in situ Proximity Ligation Assay. See Publication Reference below. (DI0413) - Products - Abnova
We report a new method, Interaction-Dependent PRobe Incorporation Mediated by Enzymes, or ID-PRIME, for imaging protein-protein interactions (PPIs) inside living cells. ID-PRIME utilizes a mutant of Escherichia coli lipoic acid ligase, LplA[superscript W37V], which can catalyze the covalent ligation of a coumarin fluorophore onto a peptide recognition sequence called LAP1. The affinity between the ligase and LAP1 is tuned such that, when each is fused to a protein partner of interest, LplA[superscript W37V] labels LAP1 with coumarin only when the protein partners to which they are fused bring them together. Coumarin labeling in the absence of such interaction is low or undetectable. Characterization of ID-PRIME in living mammalian cells shows that multiple protein-protein interactions can be imaged (FRB-FKBP, Fos-Jun, and neuroligin-PSD-95), with as little as 10 min of coumarin treatment. The signal intensity and detection sensitivity are similar to those of the widely used fluorescent protein ...
Protein-protein interactions are critical to most biological processes, and locating protein-protein interfaces on protein structures is an important task in molecular biology. We developed a new experimental strategy called the absence of interference approach to determine surface residues involved in protein-protein interaction of established yeast two-hybrid pairs of interacting proteins. One of the proteins is subjected to high-level randomization by error-prone PCR. The resulting library is selected by yeast two-hybrid system for interacting clones that are isolated and sequenced. The interaction region can be identified by an absence or depletion of mutations. For data analysis and presentation, we developed a Web interface that analyzes the mutational spectrum and displays the mutational frequency on the surface of the structure (or a structural model) of the randomized protein†. Additionally, this interface might be of use for the display of mutational distributions determined by ...
PDZ domains most commonly bind the C-terminus of their protein targets. Typically the C-terminal four residues of the protein target are considered as the binding motif, particularly the C-terminal residue (P0) and third-last residue (P-2) that form the major contacts with the PDZ domains binding groove. We solved crystal structures of seven human PDZ domains, including five of the seven PDLIM family members. The structures of GRASP, PDLIM2, PDLIM5, and PDLIM7 show a binding mode with only the C-terminal P0 residue bound in the binding groove. Importantly, in some cases, the P-2 residue formed interactions outside of the binding groove, providing insight into the influence of residues remote from the binding groove on selectivity. In the GRASP structure, we observed both canonical and noncanonical binding in the two molecules present in the asymmetric unit making a direct comparison of these binding modes possible. In addition, structures of the PDZ domains from PDLIM1 and PDLIM4 also presented here
Protein sequence and surface plasmon resonance analysis of the anti-IGFBP7 sdAb 4.43. (A) Protein sequence of anti-IGFBP7 sdAb 4.43; CDR1, CDR2 and CDR3 are und
Our results show that LCRs are preferentially located towards sequence extremities, and that proteins with LCRs in their sequence extremities have more protein binding partners than proteins with LCRs in their central regions. Furthermore, we have shown the length of LCRs to be positively correlated with the number of binding partners, but only in the sequence extremities. While t-LCRs can extend free from the rest of the protein structure, c-LCRs are likely to be surrounded by protein globular domains, thus limiting their flexibility and accessibility, and therefore the number of different proteins to which they can mediate binding. By contrast, if t-LCRs themselves tend to act as promiscuous interfaces for protein binding, this would explain our observation that proteins with longer t-LCR regions have a tendency towards a higher number of protein binding partners. Examining the list of over-represented GO terms in Table 7, we hypothesise that t-LCRs play major roles in low-specificity ...
The binding modes of a DNA or RNA binding protein refer to the different possible stable binding conformations between the protein and the nucleic acids. There are two main factors that can produce multiple modes of binding:. 1. Many proteins can contain multiple DNA and RNA binding domains with different sequence-binding preferences. When different combinations of these domains bind to different binding sites, we refer to each DNA or RNA interacting combination as a binding mode of the protein.. 2a. Many proteins can oligomerize into homo- and heterodimers and tetramers - whereby the protein-complex now has more DNA and/or RNA binding domains to bind to larger binding sites. In addition, many of these oligomerizing proteins can also bind as monomers to smaller sites. Often, differently sized protein-complexes have different binding properties and are referred to as having different binding modes. Latent specificity is when the binding specificity of a protein changes significantly when bound ...
Over the past two decades, there have been many attempts to isolate and characterize pharmacological inhibitors targeting Ras-dependent signaling pathways. The small GTPase Ras normally transmits signals downstream of diverse inputs and is a critical signaling node for many cellular activities. Aberrant Ras activity leads to the deregulation of numerous cellular processes including proliferation, survival, cell adhesion and migration, that in turn can contribute to cellular transformation, invasion and metastasis [1], and Ras is mutationally activated in ~30% of cancers [2]. Among the downstream effectors of Ras, the most well-characterized is the Ras-Raf-MAPK signaling pathway, in which Ras interaction with the serine/threonine kinase Raf causes a cascade of kinase activation, with Raf activating the mitogen-activated protein kinase kinases (MAPKK, or MEK) and MEK activating the ERK MAPK, which then translocates to the nucleus to phosphorylate and activate transcription factors to carry out the ...
Binding Affinity Prediction of Protein-Ligand complex containing Zinc [ BAPPL-Z ] server computes the binding free energy of a zinc containing metalloprotein-ligand complex using an all atom energy based empirical scoring function
There are many characteristics of a protein-protein interaction that are important. Obviously, it is important to know which proteins are interacting. In many experiments and computational studies, the focus is on interactions between two different proteins. However, you can have one protein interacting with other copies of itself (oligomerization), or three or more different proteins interacting. The stoichiometry of the interaction is also important - that is, how many of each protein involved are present in a given reaction. Some protein interactions are stronger than others, because they bind together more tightly. The strength of binding is known as affinity. Proteins will only bind each other spontaneously if it is energetically favorable. Energy changes during binding are another important aspect of protein interactions. Many of the computational tools that predict interactions are based on the energy of interactions.. In recent years there has been a strong focus on predicting protein ...
Allelic differences in nuclear protein binding at a genome-wide significant risk variant for schizophrenia in ZNF804A [Letter to the editor]. Molecular Psychiatry 16 (8) , pp. 787-789. 10.1038/mp.2011.21 ...
Defective binding and function of 1,25-dihydroxyvitamin D3 receptors in peripheral mononuclear cells of patients with end-organ resistance to 1,25-dihydroxyvita
The global protein binding assay market size was USD 374.06 million in 2020 & is expected to register a CAGR of 10.8%. Increasing focus on new drug discovery and development processes and rapid developments in pharmaceutical and biotechnological industries are primary factors fueling global market revenue growth
A multiauthored, 17-chapter text based on the workshop held at the Harbor General Hospital, Torrance, California, early in 1971 under the sponsorship of the Endocrine Society. Text includes the discussions that followed each lecture.. This form of the workshop papers provides a systematic, logical, detailed introduction to theoretical concepts and practical execution of radioimmunoassays in the various applications.. The typewriter-typography permitted rapid and relatively inexpensive publication for a book of this size but makes for irritating reading.. Recommended for medical-school, research-institute, and large-hospital libraries. ...
The advantages of the induced fit mechanism arise due to the stabilising effect of strong enzyme binding. There are two different mechanisms of substrate binding; uniform binding which has strong substrate binding, and differential binding which has strong transition state binding. The stabilizing effect of uniform binding increases both substrate and transition state binding affinity and differential binding increases only transition state binding affinity. Both are used by enzymes and have been evolutionarily chosen to minimize the ΔG of the reaction. Enzymes which are saturated, ie. have a high affinity substrate binding, require differential binding to reduce the ΔG, whereas largely substrate unbound enzymes may use either differential or uniform binding. These effects have lead to most proteins using the differential binding mechanism to reduce the ΔG, so most proteins have high affinity of the enzyme to the transition state. Differential binding is carried out by the induced fit ...
This entry represents a domain found in a variety of membrane or lipid associated proteins. It is known as the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain, is found in a variety of membrane or lipid associated proteins. Structurally, this domain forms a beta-sandwich composed of two sheets of four strands each [(PUBMED:10469604), (PUBMED:11985859), (PUBMED:11412104)]. The most highly conserved regions coincide with the beta-strands, with most of the highly conserved residues being buried within the protein. An exception to this is a surface lysine or arginine that occurs on the surface of the fifth beta-strand of the eukaryotic domains. In pancreatic lipase, the lysine in this position forms a salt bridge with the procolipase protein. The conservation of a charged surface residue may indicate the location of a conserved ligand-binding site. It is thought that this domain may mediate membrane attachment via other protein binding partners.. ...
This entry represents a domain found in a variety of membrane or lipid associated proteins. It is known as the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain, is found in a variety of membrane or lipid associated proteins. Structurally, this domain forms a beta-sandwich composed of two sheets of four strands each [(PUBMED:10469604), (PUBMED:11985859), (PUBMED:11412104)]. The most highly conserved regions coincide with the beta-strands, with most of the highly conserved residues being buried within the protein. An exception to this is a surface lysine or arginine that occurs on the surface of the fifth beta-strand of the eukaryotic domains. In pancreatic lipase, the lysine in this position forms a salt bridge with the procolipase protein. The conservation of a charged surface residue may indicate the location of a conserved ligand-binding site. It is thought that this domain may mediate membrane attachment via other protein binding partners.. ...
DNA constructs and protein interaction assays. All constructs were generated by subcloning PCR amplification products into appropriate vectors, and each construct was verified by automated DNA sequencing. cDNA fragments encoding the C terminus of the D1 (residues 365-446), D2 (residues 428-443), D3 (residues 385-400), D4 (residues 370-387), and D5 (residues 360-477) receptors were ligated into the yeast GAL4 DNA-binding domain expression vector pAS2-1 (Clontech, Palo Alto, CA). For the D2 receptor screen, the D2-pAS2-1 bait plasmid and the human brain cDNA library in the GAL4 activation domain vector pACT2 (Clontech) were simultaneously cotransformed into the yeast strain MaV103 as previously described (Lin et al., 2001). Positive clones were identified by growth on Leu−/Trp−/His−/Ura−selection plates. Protein interaction was assayed for by β-galactosidase activity via the nitrocellulose filter lift method (Lin et al., 2001).. To identify the sites of interaction between D2 or D3 ...
The Src homology 2 (SH2) domain is a protein interaction domain (PID) contained within SRC and other intracellular signal-transducing proteins, many of which drive tumorigenesis, which mediates protein-protein interactions via the docking of SH2 domain-containing proteins to phosphotyrosine (pY) residues on other proteins. Membrane lipids have recently been shown to regulate protein-protein interactions mediated by a different PID and to bind to several SH2 domains. To elucidate the role of lipids in SH2 domain-mediated protein-protein interactions and signal transduction, Park, Sheng, Silkov, Jung, and colleagues performed surface plasmon resonance analysis to systematically characterize the binding affinities of 76 of the 121 known SH2 domains for plasma membrane (PM)-mimetic vesicles which recapitulate the lipid profile of cytofacial PM. Sixty-eight out of the 76 SH2 domains analyzed exhibited moderately high to high levels of affinity for PM-mimetic vesicles. Twelve of 18 SH2 domains ...
The regulation of protein function through oligomerization is a common theme in biological systems. In this work, I have focused on the effects of the oligomeric states of the human Rad52 protein on activities related to DNA binding. HsRad52, a member of the RAD52 epistasis group, is thought to play an important and as yet undefined role in homologous recombination. HsRad52 preferentially binds to ssDNA over dsDNA and stimulates HsRad51-mediated strand exchange (Benson et al., 1998). In either the presence or absence of DNA, HsRad52 has been observed to form both 10 nm ring-like structures as well as higher order oligomers consisting of multiple 10 nm rings (Van Dyck et al., 1998; Van Dyck et al., 1999). Earlier protein-protein interaction studies mapped the domain responsible for HsRad52 self-association in the N-terminus (residues 85-159) (Shen et al., 1996). Data presented here identifies a novel self-association domain in the C-terminus of HsRad52 that is responsible for the formation of higher
Mass spectrometry (MS) was used to characterise the binding of the 58 kDa protein OppA to 11 peptides with diverse properties. Peptides with two, three and five amino acid residues were added to OppA, and the mass spectra showed that the highest-affinity complexes are formed between OppA and tripeptide ligands. Lower-affinity complexes were observed for OppA and dipeptide ligands, and no complex formation was detected with pentapeptides or a tripeptide in which the N-terminal amino group was acetylated. Tripeptides containing a single d amino acid residue were found not to bind to native OppA. Evidence from the peak width and the, charge in the spectra of the complexes suggests that the bound peptides are encapsulated by the protein in a solvent-filled cavity in the gas phase of the mass spectrometer. Analysis of the proportions of peptide-bound and free proteins under low-energy MS conditions shows a good correlation with solution-phase K(d) measurements where available. Increasing the internal energy
Integrins undergo large‐scale conformational changes (Springer & Dustin, 2012). In the bent‐closed (BC) conformation, the integrin ectodomain folds at knees in the α‐ and β‐subunits so that the head and upper legs associate with the lower legs (Fig 1A). In two extended states, the extended‐closed (EC) and extended‐open (EO) conformations, extension of the α‐ and β‐knees raises the headpiece above the lower legs on cell surfaces (Fig 1A). In transition from EC to EO, that is, headpiece opening, the ligand‐binding metal ion‐dependent adhesion site (MIDAS) in the β‐subunit βI domain rearranges. This reshaping of the ligand‐binding site is linked by α‐helix pistoning within the βI domain to swing of the hybrid domain away from the integrin α‐subunit (Fig 1A). Although the affinities of these states have not yet been measured, previous studies have correlated integrin adhesiveness and high affinity for ligand with the EO conformation (Takagi et al, 2002, 2003; ...
TY - JOUR. T1 - Non-covalent complexes of HIV gp120 with CD4 and/or mAbs enhance activation of gp120-specific T clones and provide intermolecular help for anti-CD4 antibody production. AU - Manca, F.. AU - Seravalli, E.. AU - Valle, M. T.. AU - Fenoglio, D.. AU - Kunkl, A.. AU - Li Pira, G.. AU - Zolla-Pazner, S.. AU - Celada, F.. PY - 1993. Y1 - 1993. N2 - The dangerous liaison between CD4 and gp120 that offers the first entry opportunity to HIV may also provoke perturbations of the immune control of the host with far-reaching immunopathological consequences. We wondered whether a mechanism of intermolecular help (T help across the gap of a non-covalent bond, in contrast to the intramolecular help of carrier to hapten) could break self-tolerance and be the cause of the frequent anti-CD4 autoantibodies found in AIDS patients. To determine whether this hypothesis deserves further testing, we designed a series of in vitro and in vivo experiments of increasing complexity, focused on the ...
We present a technological advancement for the estimation of the affinities of Protein-Protein Interactions (PPIs) in living cells. A novel set of vectors is introduced that enables a quantitative yeast two-hybrid system based on fluorescent fusion proteins. The vectors allow simultaneous quantification of the reaction partners (Bait and Prey) and the reporter at the single-cell level by flow cytometry. We validate the applicability of this system on a small but diverse set of PPIs (eleven protein families from six organisms) with different affinities; the dissociation constants range from 117 pM to 17 µM. After only two hours of reaction, expression of the reporter can be detected even for the weakest PPI. Through a simple gating analysis, it is possible to select only cells with identical expression levels of the reaction partners. As a result of this standardization of expression levels, the mean reporter levels directly reflect the affinities of the studied PPIs. With a set of PPIs with known
The covalent interaction of 2-methoxystypandrone (2-MS) with DTT. (a) The Michael addition reaction of α,β-unsaturated carbonyl of 2-MS with DTT; (b) TLC phot
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