Insight into protein–protein interactions from analytical ultracentrifugation

2010 ◽  
Vol 38 (4) ◽  
pp. 901-907 ◽  
Author(s):  
Stephen E. Harding ◽  
Arthur J. Rowe
Keyword(s):  
Protein Interactions ◽  
Dynamic Range ◽  
Analytical Ultracentrifugation ◽  
Dissociation Constants ◽  
Interaction Strength ◽  
Sedimentation Equilibrium ◽  
Solution Technique ◽  
Protein Protein Interactions ◽  
Self Association ◽  
Made In

Analytical ultracentrifugation is a free solution technique with no supplementary immobilization, columns or membranes required, and can be used to study self-association and hetero-interactions, stoichiometry, reversibility and interaction strength across a very large dynamic range (dissociation constants from 10−12 M to 10−1 M). In the present paper, we review some of the advances that have been made in the two different types of sedimentation experiment – sedimentation equilibrium and sedimentation velocity – for the analysis of protein–protein interactions and indicate how major complications such as thermodynamic and hydrodynamic non-ideality can be dealt with.

Unravelling protein–protein interactions between complement factor H and C-reactive protein using a multidisciplinary strategy

2010 ◽  
Vol 38 (4) ◽  
pp. 894-900 ◽  
Author(s):  
Stephen J. Perkins ◽  
Azubuike I. Okemefuna ◽  
Ruodan Nan
Keyword(s):  
Protein Interactions ◽  
Dissociation Constants ◽  
Factor H ◽  
Complement Factor H ◽  
Complement Factor ◽  
X Rays ◽  
Protein Protein Interactions ◽  
C Reactive Protein ◽  
Reactive Protein ◽  
Self Association

Experimental studies of protein–protein interactions are very much affected by whether the complexes are fully formed (strong, with nanomolar dissociation constants) or partially dissociated (weak, with micromolar dissociation constants). The functions of the complement proteins of innate immunity are governed by the weak interactions between the activated proteins and their regulators. Complement is effective in attacking pathogens, but not the human host, and imbalances in this process can lead to disease conditions. The inherent complexity in analysing complement interactions is augmented by the multivalency of its main regulator, CFH (complement factor H), for its physiological or pathophysiological ligands. The unravelling of such weak protein–protein or protein–ligand interactions requires a multidisciplinary approach. Synchrotron X-ray solution scattering and constrained modelling resulted in the determination of the solution structure of CFH and its self-associative properties, whereas AUC (analytical ultracentrifugation) identified the formation of much larger CFH multimers through the addition of metals such as zinc. The ligands of CFH, such as CRP (C-reactive protein), also undergo self-association. The combination of X-rays and AUC with SPR (surface plasmon resonance) proved to be essential to identify CRP self-association and revealed how CFH interacts with CRP. We show that CRP unexpectedly binds to CFH at two non-contiguous sites and explain its relevance to age-related macular degeneration.

scholarly journals Analytical Ultracentrifugation as a Matrix-Free Probe for the Study of Kinase Related Cellular and Bacterial Membrane Proteins and Glycans

Molecules ◽  
2021 ◽  
Vol 26 (19) ◽  
pp. 6080
Author(s):  
Stephen E. Harding
Keyword(s):  
Membrane Proteins ◽  
Analytical Ultracentrifugation ◽  
Dissociation Constants ◽  
Short Review ◽  
Sedimentation Equilibrium ◽  
Oligomeric State ◽  
Solvent Systems ◽  
Self Association ◽  
Matrix Free ◽  
Aqueous Detergent

Analytical ultracentrifugation is a versatile approach for analysing the molecular mass, molecular integrity (degradation/aggregation), oligomeric state and association/dissociation constants for self-association, and assay of ligand binding of kinase related membrane proteins and glycans. It has the great property of being matrix free—providing separation and analysis of macromolecular species without the need of a separation matrix or membrane or immobilisation onto a surface. This short review—designed for the non-hydrodynamic expert—examines the potential of modern sedimentation velocity and sedimentation equilibrium and the challenges posed for these molecules particularly those which have significant cytoplasmic or extracellular domains in addition to the transmembrane region. These different regions can generate different optimal requirements in terms of choice of the appropriate solvent (aqueous/detergent). We compare how analytical ultracentrifugation has contributed to our understanding of two kinase related cellular or bacterial protein/glycan systems (i) the membrane erythrocyte band 3 protein system—studied in aqueous and detergent based solvent systems—and (ii) what it has contributed so far to our understanding of the enterococcal VanS, the glycan ligand vancomycin and interactions of vancomycin with mucins from the gastrointestinal tract.

scholarly journals A Dimerization Site at SCR-17/18 in Factor H Clarifies a New Mechanism for Complement Regulatory Control

2021 ◽  
Vol 11 ◽  
Author(s):  
Orla M. Dunne ◽  
Xin Gao ◽  
Ruodan Nan ◽  
Jayesh Gor ◽  
Penelope J. Adamson ◽  
...  
Keyword(s):  
Host Cell ◽  
Analytical Ultracentrifugation ◽  
Dissociation Constants ◽  
Alternative Pathway ◽  
Factor H ◽  
Regulatory Control ◽  
Size Exclusion ◽  
Complement Factor ◽  
Dimer Formation ◽  
Self Association

Complement Factor H (CFH), with 20 short complement regulator (SCR) domains, regulates the alternative pathway of complement in part through the interaction of its C-terminal SCR-19 and SCR-20 domains with host cell-bound C3b and anionic oligosaccharides. In solution, CFH forms small amounts of oligomers, with one of its self-association sites being in the SCR-16/20 domains. In order to correlate CFH function with dimer formation and the occurrence of rare disease-associated variants in SCR-16/20, we identified the dimerization site in SCR-16/20. For this, we expressed, in Pichia pastoris, the five domains in SCR-16/20 and six fragments of this with one-three domains (SCR-19/20, SCR-18/20, SCR-17/18, SCR-16/18, SCR-17 and SCR-18). Size-exclusion chromatography suggested that SCR dimer formation occurred in several fragments. Dimer formation was clarified using analytical ultracentrifugation, where quantitative c(s) size distribution analyses showed that SCR-19/20 was monomeric, SCR-18/20 was slightly dimeric, SCR-16/20, SCR-16/18 and SCR-18 showed more dimer formation, and SCR-17 and SCR-17/18 were primarily dimeric with dissociation constants of ~5 µM. The combination of these results located the SCR-16/20 dimerization site at SCR-17 and SCR-18. X-ray solution scattering experiments and molecular modelling fits confirmed the dimer site to be at SCR-17/18, this dimer being a side-by-side association of the two domains. We propose that the self-association of CFH at SCR-17/18 enables higher concentrations of CFH to be achieved when SCR-19/20 are bound to host cell surfaces in order to protect these better during inflammation. Dimer formation at SCR-17/18 clarified the association of genetic variants throughout SCR-16/20 with renal disease.

Molecular interactions between multihaem cytochromes: probing the protein–protein interactions between pentahaem cytochromes of a nitrite reductase complex

2011 ◽  
Vol 39 (1) ◽  
pp. 263-268 ◽  
Author(s):  
Colin Lockwood ◽  
Julea N. Butt ◽  
Thomas A. Clarke ◽  
David J. Richardson
Keyword(s):  
Protein Interactions ◽  
Nitrite Reductase ◽  
Analytical Ultracentrifugation ◽  
Gel Filtration ◽  
Protein Protein Interactions ◽  
Physiological Conditions ◽  
Sulfate Reducing ◽  
Redox Partner ◽  
Electron Reduction ◽  
Reducing Bacteria

The cytochrome c nitrite reductase NrfA is a 53 kDa pentahaem enzyme that crystallizes as a decahaem homodimer. NrfA catalyses the reduction of NO2− to NH4+ through a six electron reduction pathway that is of major physiological significance to the anaerobic metabolism of enteric and sulfate reducing bacteria. NrfA receives electrons from the 21 kDa pentahaem NrfB donor protein. This requires that redox complexes form between the NrfA and NrfB pentahaem cytochromes. The formation of these complexes can be monitored using a range of methodologies for studying protein–protein interactions, including dynamic light scattering, gel filtration, analytical ultracentrifugation and visible spectroscopy. These methods have been used to show that oxidized NrfA exists in dynamic monomer–dimer equilibrium with a Kd (dissociation constant) of 4 μM. Significantly, the monomeric and dimeric forms of NrfA are equally active for either the six electron reduction of NO2− or HSO3−. When mixed together, NrfA and NrfB exist in equilibrium with NrfAB, which is described by a Kd of 50 nM. Thus, since NrfA and NrfB are present in micromolar concentrations in the periplasmic compartment, it is likely that NrfB remains tightly associated with its NrfA redox partner under physiological conditions.

scholarly journals Structural Insights into the Interactions of Candidal Enolase with Human Vitronectin, Fibronectin and Plasminogen

2020 ◽  
Vol 21 (21) ◽  
pp. 7843 ◽  
Author(s):  
Dorota Satala ◽  
Grzegorz Satala ◽  
Justyna Karkowska-Kuleta ◽  
Michal Bukowski ◽  
Anna Kluza ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Dissociation Constants ◽  
Tight Binding ◽  
Protein Protein Interactions ◽  
Glycolysis Pathway ◽  
Human Proteins ◽  
Activity Center ◽  
Moonlighting Functions ◽  
Structural Insights ◽  
Internal Motif

Significant amounts of enolase—a cytosolic enzyme involved in the glycolysis pathway—are exposed on the cell surface of Candida yeast. It has been hypothesized that this exposed enolase form contributes to infection-related phenomena such as fungal adhesion to human tissues, and the activation of fibrinolysis and extracellular matrix degradation. The aim of the present study was to characterize, in structural terms, the protein-protein interactions underlying these moonlighting functions of enolase. The tight binding of human vitronectin, fibronectin and plasminogen by purified C. albicans and C. tropicalis enolases was quantitatively analyzed by surface plasmon resonance measurements, and the dissociation constants of the formed complexes were determined to be in the 10−7–10−8 M range. In contrast, the binding of human proteins by the S.cerevisiae enzyme was much weaker. The chemical cross-linking method was used to map the sites on enolase molecules that come into direct contact with human proteins. An internal motif 235DKAGYKGKVGIAMDVASSEFYKDGK259 in C. albicans enolase was suggested to contribute to the binding of all three human proteins tested. Models for these interactions were developed and revealed the sites on the enolase molecule that bind human proteins, extensively overlap for these ligands, and are well-separated from the catalytic activity center.

Molecular interactions between desmosomal cadherins

2002 ◽  
Vol 362 (2) ◽  
pp. 317-327 ◽  
Author(s):  
Shabih-e-Hassnain SYED ◽  
Brian TRINNAMAN ◽  
Stephen MARTIN ◽  
Sarah MAJOR ◽  
Jon HUTCHINSON ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Analytical Ultracentrifugation ◽  
Expression System ◽  
Quantitative Information ◽  
Cell Junctions ◽  
Protein Protein Interactions ◽  
Desmosomal Cadherins ◽  
Classical Cadherins ◽  
Escherichia Coli Expression

Desmocollins (Dscs) and desmogleins (Dsgs) are cell-adhesion molecules involved in the formation of desmosome cell—cell junctions and share structural similarities to classical cadherins such as E-cadherin. In order to identify and provide quantitative information on the types of protein—protein interactions displayed by the type 2 isoforms and investigate the role of Ca2+ in this process, we have developed an Escherichia coli expression system to generate recombinant proteins containing the first two extracellular domains, namely Dsg2(1-2) and Dsc2(1-2). Analytical ultracentrifugation, chemical cross-linking, CD, fluorescence and BIAcore have been used to provide the first direct evidence of Ca2+ binding to desmosomal cadherins. These studies suggest that Dsc2(1-2) not only exhibits homophilic interactions in solution, but can also form heterophilic interactions with Dsg2(1-2). The latter, on the other hand, shows much weaker homophilic association. Our results further demonstrate that heterophilic interactions are Ca2+-dependent, whereas the Ca2+-dependence of homophilic association is less clear. Our data indicate that the functional properties of Dsc2(1-2) are more similar to those of classical cadherins, consistent with the observation that Dsc shares a higher level of sequence homology with classical cadherins than does Dsg. In addition to corroborating the conclusions of previously reported transfection studies which suggest the formation of lateral heterodimers and homodimers, our results also provide direct quantitative information on the strength of these interactions which are essential for understanding the adhesion mechanism.

Quantitative Imaging of FRET-Based Biosensors for Cell- and Organelle-Specific Analyses in Plants

2016 ◽  
Vol 22 (2) ◽  
pp. 300-310 ◽  
Author(s):  
Swayoma Banerjee ◽  
Luis Rene Garcia ◽  
Wayne K. Versaw
Keyword(s):  
High Precision ◽  
Protein Interactions ◽  
Posttranslational Modifications ◽  
Dynamic Range ◽  
Quantitative Imaging ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
High Dynamic Range ◽  
Imaging Data ◽  
Protein Protein Interactions

AbstractGenetically encoded Förster resonance energy transfer (FRET)-based biosensors have been used to report relative concentrations of ions and small molecules, as well as changes in protein conformation, posttranslational modifications, and protein–protein interactions. Changes in FRET are typically quantified through ratiometric analysis of fluorescence intensities. Here we describe methods to evaluate ratiometric imaging data acquired through confocal microscopy of a FRET-based inorganic phosphate biosensor in different cells and subcellular compartments of Arabidopsis thaliana. Linear regression was applied to donor, acceptor, and FRET-derived acceptor fluorescence intensities obtained from images of multiple plants to estimate FRET ratios and associated location-specific spectral correction factors with high precision. FRET/donor ratios provided a combination of high dynamic range and precision for this biosensor when applied to the cytosol of both root and leaf cells, but lower precision when this ratiometric method was applied to chloroplasts. We attribute this effect to quenching of donor fluorescence because high precision was achieved with FRET/acceptor ratios and thus is the preferred ratiometric method for this organelle. A ligand-insensitive biosensor was also used to distinguish nonspecific changes in FRET ratios. These studies provide a useful guide for conducting quantitative ratiometric studies in live plants that is applicable to any FRET-based biosensor.

scholarly journals Prediction of Protein-Protein Interaction Strength Using Domain Features with Supervised Regression

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Mayumi Kamada ◽  
Yusuke Sakuma ◽  
Morihiro Hayashida ◽  
Tatsuya Akutsu
Keyword(s):  
Protein Interactions ◽  
Interaction Strength ◽  
Feature Space ◽  
Relevance Vector Machine ◽  
Protein Domain ◽  
Support Vector ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Living Organisms ◽  
Domain Information

Proteins in living organisms express various important functions by interacting with other proteins and molecules. Therefore, many efforts have been made to investigate and predict protein-protein interactions (PPIs). Analysis of strengths of PPIs is also important because such strengths are involved in functionality of proteins. In this paper, we propose several feature space mappings from protein pairs using protein domain information to predict strengths of PPIs. Moreover, we perform computational experiments employing two machine learning methods, support vector regression (SVR) and relevance vector machine (RVM), for dataset obtained from biological experiments. The prediction results showed that both SVR and RVM with our proposed features outperformed the best existing method.

scholarly journals Protein-protein interactions of cytochromes P450 3A4 and 3A5 with their intermediate redox partners cytochromes b5

2015 ◽  
Vol 61 (4) ◽  
pp. 468-474
Author(s):  
O.V. Gnedenko ◽  
A.S. Ivanov ◽  
E.O. Yablokov ◽  
S.A. Usanov ◽  
D.V. Mukha ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Dissociation Constants ◽  
Cytochromes P450 ◽  
Cytochrome B5 ◽  
Electrochemical Analysis ◽  
Monooxygenase System ◽  
Protein Protein Interactions ◽  
Reduction Potentials ◽  
Drug Biotransformation ◽  
Redox Partners

Molecular interactions between proteins redox partners (cytochromes Р450 3А4, 3А5 and cytochrome b5) within the monooxygenase system, which is known to be involved in drug biotransformation, were investigated. Human cytochromes Р450 3A4 and 3А5 (CYP3A4 and CYP3A5) form complexes with various cytochromes b5: the microsomal (b5mc) and mitochondrial (b5om) forms of this protein, as well as with 2 “chimeric” proteins, b5(om-mc), b5(mc-om). Kinetic constants and equilibrium dissociation constants were determined by the SPR biosensor. Essential distinction between CYP3A4 and CYP3A5 was only observed upon their interactions with cytochrome b5om. Electroanalytical characteristics of electrodes with immobilized hemoproteins were obtained. The electrochemical analysis of CYP3A4, CYP3A5, b5mc, b5om, b5(om-mc), and b5(mc-om) immobilized on screen printed graphite electrodes modified with membranous matrix revealed that these proteins have very close reduction potentials -0.435  -0.350 V (vs. Ag/AgCl). Cytochrome b5mc was shown to be capable of stimulating the electrocatalytic activity of CYP3A4 in the presence of its substrate testosterone.

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