A theoretical analysis of the use of zonal gel filtration in the detection and purification of protein-ligand complexes.
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ABSTRACT:
SUBMITTER: Nimmo IA
PROVIDER: S-EPMC1184186 | biostudies-other | 1978 Feb
REPOSITORIES: biostudies-other
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Project description:If a solution of macromolecule of concentration c and volume a, initially saturated with a ligand of dissociation constant K, is gel filtered through a volume v of solution initially free of ligand, the saturation y with which it emerges is given by the equation y-lny-1=Kv/ca.
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Project description:A new affinity chromatography method was developed by modifying a zonal elution method. The new method targets transient protein-protein interactions, such as those encountered during direct ligand transfer between the ligand transporter and its cognate receptor. A ligand-loaded transport protein is immobilized on the solid support, and a plug containing a putative receptor is flowed through the column. Elution profiles of proteins not interacting with the immobilized transporter can be approximated with a simple Gaussian curve, while the elution profiles of cognate receptors show significant delay and exhibit complex shape. Ligand transfer from the immobilized transporter molecules to the receptors is verified by both UV absorbance measurements and mass spectrometry. The sensitivity of the method is demonstrated using retinoic acid (RA) transfer from various isoforms of cellular RA binding proteins (CRABPs) and RA receptor ? (RAR?). Although these interactions have been hypothesized long ago to proceed via direct mechanism (i.e., via transient docking of the receptor and the transporter), the existing biophysical techniques failed to detect the presence of the transporter-receptor complexes. However, the modified zonal elution method provides unequivocal evidence of direct interaction between RAR? and one of the CRABP isoforms (CRABP II) during the ligand transfer to the receptor.
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Project description:BACKGROUND: Recent advances in molecular biology have led to the accumulation of large amounts of data on protein-protein interaction networks in different species. An important challenge for the analysis of these data is to extract functional modules such as protein complexes and biological processes from networks which are characterised by the present of a significant number of false positives. Various computational techniques have been applied in recent years. However, most of them treat protein interaction as binary. Co-complex relations derived from affinity purification/mass spectrometry (AP-MS) experiments have been largely ignored. METHODS: This paper presents a new algorithm for detecting protein complexes from AP-MS data. The algorithm intends to detect groups of prey proteins that are significantly co-associated with the same set of bait proteins. We first construct AP-MS data as a bipartite network, where one set of nodes consists of bait proteins and the other set is composed of prey proteins. We then calculate pair-wise similarities of bait proteins based on the number of their commonly shared neighbours. A hierarchical clustering algorithm is employed to cluster bait proteins based on the similarities and thus a set of 'seed' clusters is obtained. Starting from these 'seed' clusters, an expansion process is developed to identify prey proteins which are significantly associated with the same set of bait proteins. Then, a set of complete protein complexes is derived. In application to two real AP-MS datasets, we validate biological significance of predicted protein complexes by using curated protein complexes and well-characterized cellular component annotation from Gene Ontology (GO). Several statistical metrics have been applied for evaluation. RESULTS: Experimental results show that, the proposed algorithm achieves significant improvement in detecting protein complexes from AP-MS data. In comparison to the well-known MCL algorithm, our algorithm improves the accuracy rate by about 20% in detecting protein complexes in both networks and increases the F-Measure value by about 50% in Krogan_2006 network. Greater precision and better accuracy have been achieved and the identified complexes are demonstrated to match well with existing curated protein complexes. CONCLUSIONS: Our study highlights the significance of taking co-complex relations into account when extracting protein complexes from AP-MS data. The algorithm proposed in this paper can be easily extended to the analysis of other biological networks which can be conveniently represented by bipartite graphs such as drug-target networks.
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Project description:This article illustrates the use of gel permeation chromatography (GPC, organic-phase size exclusion chromatography) to separate nanocrystals from weakly-bound small molecules, including solvent, on the basis of size. A variety of colloidal inorganic nanocrystals of different size, shape, composition, and surface termination are shown to yield purified samples with greatly reduced impurity concentrations. Additionally, the method is shown to be useful in achieving a change of solvent without requiring precipitation of the nanocrystals. By taking advantage of the different rates at which small molecules and nanoparticles travel through the column, we show that it is furthermore possible to use the GPC column as a multi-functional flow reactor that can accomplish in sequence the steps of initial purification, ligand exchange with controlled reactant concentration and interaction time, and subsequent cleanup without requiring a change of phase. This example of process intensification via GPC is shown to yield nearly complete displacement of the initial surface ligand population upon reaction with small molecule and macromolecular reactants to form ligand-exchanged nanocrystal products.
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Project description:1. Sepharose 6B gel-filtration analysis of soluble adenylate cyclase from bovine corpus luteum is described. Both zonal and frontal techniques of analysis were used. 2. Under conditions of zonal analysis recoveries of activity were low. It was concluded that dissociation of two or more components of the adenylate cyclase complex was occurring on the column and that the maintenance of the complex was essential for the high-activity state of the catalytic unit. Two peaks of adenylate cyclase activity, of approximate mol. wts. 45,000 and 160,000 were detected. 3. The theory of frontal analysis (or steady-state gel filtration), applied to the study of the interacting components of the adenylate cyclase complex is discussed, and activity profiles are predicted. Activity profiles obtained experimentally be frontal analysis compared well with the theoretically predicted profile and provide evidence that dissociation of a high-activity complex, with concomitant loss of activity, does occur. Recoveries of activity under conditions of frontal analysis were higher than with zonal analysis. 4. The effects of concentration and removal of detergent on the activity of the soluble enzyme are discussed.
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Project description:Equilibrium-dialysis experiments showed that Tris or citrate in the solution prevented copper from occupying completely the specific metal-binding sites on human transferrin. Differential measurements of sedimentation velocity under conditions where two atoms of copper per molecule of protein were bound showed an increase in s(0) (20,w), relative to that of the apoprotein, practically the same as that produced by two atoms of iron. Gel-filtration experiments made under the same conditions to investigate the effect of copper binding on the Stokes radius of the protein showed merely that it lost most of the metal as it passed down the column.
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Project description:Mapping Atheroprotective Functions and Related Proteins/Lipoproteins in Size Fractionated Human Plasma
2017-02-23 | PXD005520 | Pride