Substrate-Induced Conformational Change and Isomerase Activity of Dienelactone Hydrolase and its Site-Specific Mutants

ChemBioChem ◽  
2012 ◽  
Vol 13 (11) ◽  
pp. 1645-1651 ◽  
Author(s):  
Ian Walker ◽  
James E. Hennessy ◽  
David L. Ollis ◽  
Christopher J. Easton
Keyword(s):  
Conformational Change ◽  
Site Specific ◽  
Isomerase Activity ◽  
Dienelactone Hydrolase

On-demand shape transformation of polymer vesicles via site-specific isomerization of hydrazone photoswitches in monodisperse hydrophobic oligomers

2021 ◽  
Author(s):  
Valene Wang ◽  
Jiwon Kim ◽  
Junyoung Kim ◽  
Seul Woo Lee ◽  
Kyoung Taek Kim
Keyword(s):  
Drug Delivery ◽  
Block Copolymers ◽  
Conformational Change ◽  
Self Assembly ◽  
Shape Control ◽  
Shape Transformation ◽  
Site Specific ◽  
On Demand ◽  
Polymer Vesicles

The shape control of nanostructures formed by the solution self-assembly of block copolymers is of significance for drug delivery. In particular, site-specific perturbation resulting in the conformational change of the...

DNA conformational change produced by the site-specific interstrand cross-link of trans-diamminedichloroplatinum(II)

Biochemistry ◽  
1993 ◽  
Vol 32 (43) ◽  
pp. 11676-11681 ◽  
Author(s):  
Viktor Brabec ◽  
Miroslav Sip ◽  
Marc Leng
Keyword(s):  
Conformational Change ◽  
Cross Link ◽  
Site Specific

Application of Site-Specific Spin Labeling for NMR Detecting Inhibitor-Induced Conformational Change of HIV-1 Reverse Transcriptase

ChemMedChem ◽  
2016 ◽  
Vol 11 (4) ◽  
pp. 363-366 ◽  
Author(s):  
Supaporn Seetaha ◽  
Maho Yagi-Utsumi ◽  
Takumi Yamaguchi ◽  
Kentaro Ishii ◽  
Supa Hannongbua ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Conformational Change ◽  
Spin Labeling ◽  
Site Specific ◽  
Hiv 1

scholarly journals Mechanism by Which Exosites Promote the Inhibition of Blood Coagulation Proteases by Heparin-activated Antithrombin

2007 ◽  
Vol 282 (46) ◽  
pp. 33609-33622 ◽  
Author(s):  
Gonzalo Izaguirre ◽  
Richard Swanson ◽  
Srikumar M. Raja ◽  
Alireza R. Rezaie ◽  
Steven T. Olson
Keyword(s):  
Blood Coagulation ◽  
Conformational Change ◽  
Blood Clotting ◽  
Factor Xa ◽  
Kinetic Studies ◽  
Complex Interaction ◽  
Wild Type ◽  
Site Specific ◽  
Equilibrium Binding ◽  
Diffusion Controlled

Heparin activates the serpin, antithrombin, to inhibit its target blood-clotting proteases by generating new protease interaction exosites. To resolve the effects of these exosites on the initial Michaelis docking step and the subsequent acylation and conformational change steps of antithrombin-protease reactions, we compared the reactions of catalytically inactive S195A and active proteases with site-specific fluorophore-labeled antithrombins that allow monitoring of these reaction steps. Heparin bound to N,N′-dimethyl-N-(acetyl)-N′-(7-nitrobenz-3-oxa-1,3-diazol-4-yl)ethylenediamine (NBD)-fluorophore-labeled antithrombins and accelerated the reactions of the labeled inhibitor with thrombin and factor Xa similar to wild type. Equilibrium binding of NBD-labeled antithrombins to S195A proteases showed that exosites generated by conformationally activating antithrombin with a heparin pentasaccharide enhanced the affinity of the serpin for S195A factor Xa minimally 100-fold. Moreover, additional bridging exosites provided by a hexadecasaccharide heparin activator enhanced antithrombin affinity for both S195A factor Xa and thrombin at least 1000-fold. Rapid kinetic studies showed that these exosite-mediated enhancements in Michaelis complex affinity resulted from increases in kon and decreases in koff and caused antithrombin-protease reactions to become diffusion-controlled. Competitive binding and kinetic studies with exosite mutant antithrombins showed that Tyr-253 was a critical mediator of exosite interactions with S195A factor Xa; that Glu-255, Glu-237, and Arg-399 made more modest contributions to these interactions; and that exosite interactions reduced koff for the Michaelis complex interaction. Together these results show that exosites generated by heparin activation of antithrombin function both to promote the formation of an initial antithrombin-protease Michaelis complex and to favor the subsequent acylation of this complex.

Site-specific observation of the conformational change of a protein with 15N-labeled Tyr residues using NMR

2019 ◽  
Vol 574 ◽  
pp. 34-38
Author(s):  
Satomi Inaba ◽  
Ayako Shiota ◽  
Takuya Yoshida ◽  
Masayuki Oda
Keyword(s):  
Conformational Change ◽  
Site Specific

scholarly journals Site-specific intercalation at the triplex-duplex junction induces a conformational change which is detectable by hypersensitivity to diethylpyrocarbonate

1991 ◽  
Vol 19 (15) ◽  
pp. 4219-4224 ◽  
Author(s):  
David A. Collier ◽  
Jean-Louis Mergny ◽  
N.T. Thuong ◽  
Claude Helene
Keyword(s):  
Conformational Change ◽  
Site Specific

Thiol/disulfide exchange is a prerequisite for CXCR4-tropic HIV-1 envelope-mediated T-cell fusion during viral entry

Blood ◽  
2004 ◽  
Vol 103 (5) ◽  
pp. 1586-1594 ◽  
Author(s):  
Ingrid Markovic ◽  
Tzanko S. Stantchev ◽  
Karen H. Fields ◽  
Linda J. Tiffany ◽  
Melanija Tomiç ◽  
...  
Keyword(s):  
Conformational Change ◽  
Conformational Changes ◽  
Viral Entry ◽  
Structural Rearrangement ◽  
Cell Contact ◽  
Activation Energy Barrier ◽  
Disulfide Exchange ◽  
Isomerase Activity ◽  
Protein Disulfide ◽  
Hiv 1

Abstract Attachment of gp120 to CD4 during HIV-1 entry triggers structural rearrangement in gp120 that enables binding to an appropriate coreceptor. Following coreceptor engagement, additional conformational changes occur in the envelope (Env), resulting in fusion of virion and cell membranes. Catalysts with redox-isomerase activity, such as protein disulfide isomerase (PDI), facilitate Env conversion from its inactive to its fusion-competent conformation. We report here that anti-PDI agents effectively block CXCR4 Env-mediated fusion and spread of virus infection. Exogenously added PDI, in turn, can rescue fusion from this blockade. We further find that PDI facilitates thiol/disulfide rearrangement in gp120 during conformational change, whereas inhibition of this redox shuffling prevents gp41 from assuming the fusogenic 6-helix bundle conformation. At the virus-cell contact site, gp120 induces assembly of PDI, CD4, and CXCR4 into a tetramolecular protein complex serving as a portal for viral entry. Our findings support the hypothesis that Env conformational change depends on a well-coordinated action of a tripartite system in which PDI works in concert with the receptor and the coreceptor to effectively lower the activation energy barrier required for Env conformational rearrangement.

Large-cluster and combined fluorescent and gold immunoprobes

1996 ◽  
Vol 54 ◽  
pp. 892-893
Author(s):  
Richard D. Powell ◽  
James F. Hainfeld ◽  
Carol M. R. Halsey ◽  
David L. Spector ◽  
Shelley Kaurin ◽  
...  
Keyword(s):  
Metal Cluster ◽  
Sulfonyl Chloride ◽  
Gel Filtration ◽  
Cross Linking ◽  
Site Specific ◽  
Fab Fragments ◽  
Cluster Label ◽  
Covalently Linked ◽  
Texas Red ◽  
Fold Excess

Two new types of covalently linked, site-specific immunoprobes have been prepared using metal cluster labels, and used to stain components of cells. Combined fluorescein and 1.4 nm “Nanogold” labels were prepared by using the fluorescein-conjugated tris (aryl) phosphine ligand and the amino-substituted ligand in the synthesis of the Nanogold cluster. This cluster label was activated by reaction with a 60-fold excess of (sulfo-Succinimidyl-4-N-maleiniido-cyclohexane-l-carboxylate (sulfo-SMCC) at pH 7.5, separated from excess cross-linking reagent by gel filtration, and mixed in ten-fold excess with Goat Fab’ fragments against mouse IgG (obtained by reduction of F(ab’)2 fragments with 50 mM mercaptoethylamine hydrochloride). Labeled Fab’ fragments were isolated by gel filtration HPLC (Superose-12, Pharmacia). A combined Nanogold and Texas Red label was also prepared, using a Nanogold cluster derivatized with both and its protected analog: the cluster was reacted with an eight-fold excess of Texas Red sulfonyl chloride at pH 9.0, separated from excess Texas Red by gel filtration, then deprotected with HC1 in methanol to yield the amino-substituted label.

The challenge of detecting modifications on proteins

2020 ◽  
Vol 64 (1) ◽  
pp. 135-153 ◽  
Author(s):  
Lauren Elizabeth Smith ◽  
Adelina Rogowska-Wrzesinska
Keyword(s):  
Mass Spectrometry ◽  
Protein Function ◽  
Chemical Properties ◽  
Lysine Acetylation ◽  
Mass Determination ◽  
Post Translational Modifications ◽  
Site Specific ◽  
The Common

Abstract Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.

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