Article
MgATP-induced conformational change of the catalytic subunit of cAMP-dependent protein kinase.
Department of Chemistry, California State University, San Bernardino, CA 92407, USA.
Biophysical Chemistry (impact factor:
2.2).
03/2005;
113(2):193-9.
DOI:10.1016/j.bpc.2004.08.008
pp.193-9
Source: PubMed
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Citations (0)
- Cited In (2)
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Article: Measurement of binding kinetics between PI3-K and phosphorylated IGF-1R using a surface plasmon resonance biosensor
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ABSTRACT: Quantitative measurement of biochemical and biophysical parameters of molecular recognition events in signaling pathways is very important for understanding biological function. Binding of insulin-like growth factor-1 receptor (IGF-1R) with IGF-1 activates receptor tyrosine phosphorylation and triggers several signaling pathways including phosphatidylinositol-3 kinase (PI3-K)/AKT and extracellular signal-regulated protein kinase (ERK)/mitogen-activated protein kinase (MAPK) pathways. We have analyzed the interactions between PI3-K and IGF-1R with or without IGF-1 stimulation. The results demonstrate that p85 subunits of PI3-K bind to IGF-1R with IGF-1 stimulation in intact cells. The binding kinetics between PI3-K and IGF-1R with or without IGF-1 stimulation were obtained using surface plasmon resonance biosensor. The affinity constant of the PI3-K to phosphorylated IGF-1R was (2.27 ± 0.12) × 108 M−1, which was about 20 times higher than that of PI3-K to unphosphorylated IGF-1R. Moreover, the kinetic effects of Mg2+, ATP and two kinase inhibitors, genistein and quercetin, on the binding between PI3-K and phosphorylated IGF-1R were studied. The data showed that Mg2+ increased the binding affinity of PI3-K with IGF-1R about 2-fold, while genistein decreased the affinity constant 2.7-fold. On the other hand, ATP and quercetin had no significant effects on the affinity constant, although both k a and k d values were increased or decreased by ATP or quercetin, respectively. This study implicated that the PI3-K binding sites on IGF-IR may be different from its phosphorylation and catalytic sites.Microchimica Acta 06/2008; 162(1):253-260. · 3.03 Impact Factor -
Article: Conformational transitions upon ligand binding: holo-structure prediction from apo conformations.
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ABSTRACT: Biological function of proteins is frequently associated with the formation of complexes with small-molecule ligands. Experimental structure determination of such complexes at atomic resolution, however, can be time-consuming and costly. Computational methods for structure prediction of protein/ligand complexes, particularly docking, are as yet restricted by their limited consideration of receptor flexibility, rendering them not applicable for predicting protein/ligand complexes if large conformational changes of the receptor upon ligand binding are involved. Accurate receptor models in the ligand-bound state (holo structures), however, are a prerequisite for successful structure-based drug design. Hence, if only an unbound (apo) structure is available distinct from the ligand-bound conformation, structure-based drug design is severely limited. We present a method to predict the structure of protein/ligand complexes based solely on the apo structure, the ligand and the radius of gyration of the holo structure. The method is applied to ten cases in which proteins undergo structural rearrangements of up to 7.1 A backbone RMSD upon ligand binding. In all cases, receptor models within 1.6 A backbone RMSD to the target were predicted and close-to-native ligand binding poses were obtained for 8 of 10 cases in the top-ranked complex models. A protocol is presented that is expected to enable structure modeling of protein/ligand complexes and structure-based drug design for cases where crystal structures of ligand-bound conformations are not available.PLoS Computational Biology 01/2010; 6(1):e1000634. · 5.22 Impact Factor
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Keywords
5,6-carboxyfluorescein succinimidyl ester
biexponential equation incorporating
C subunit necessary
cAMP-dependent protein kinase
CF)C subunit
CF)C subunit conformation equivalent
CF)C x MgATP binary complex
CF)C x MgATP x IP20 ternary complex
CF)C.MgATP binary complex
compact shape
Conformational changes
equivalent reduction
ethylenediaminetetraacetic acid
proper stereochemical alignment
respective roles
rotational correlation times
slow rotational correlation times phi(F)
target proteins
Time-resolved fluorescence anisotropy
TRFA decays