Binding of the fluorescent substrate analog 2',3'-O-(2,4,6-trinitrophenylcyclohexadienylidene)adenosine 5'-triphosphate to the gastric hydrogen ion-potassium-ATPase: evidence for cofactor-induced conformational changes in the enzyme

Biochemistry ◽  
1990 ◽  
Vol 29 (13) ◽  
pp. 3179-3186 ◽  
Author(s):  
Larry D. Faller
Keyword(s):  
Conformational Changes ◽  
Hydrogen Ion ◽  
Fluorescent Substrate ◽  
Substrate Analog ◽  
Potassium Atpase

Location of the carbohydrates present in the hydrogen ion-potassium ATPase vesicles isolated from hog gastric mucosa

Biochemistry ◽  
1990 ◽  
Vol 29 (3) ◽  
pp. 701-706 ◽  
Author(s):  
Kathleen Hall ◽  
Gonzalo Perez ◽  
Debra Anderson ◽  
Cecilia Gutierrez ◽  
Keith Munson ◽  
...  
Keyword(s):  
Gastric Mucosa ◽  
Hydrogen Ion ◽  
Potassium Atpase

scholarly journals ACTION OF TRITON X-100 ON CHLOROPLAST MEMBRANES

1967 ◽  
Vol 33 (2) ◽  
pp. 395-410 ◽  
Author(s):  
David W. Deamer ◽  
Antony Crofts
Keyword(s):  
Ion Transport ◽  
Conformational Changes ◽  
Active Material ◽  
Active Species ◽  
Hydrogen Ion ◽  
Electron Microscopic ◽  
Chloroplast Membranes ◽  
Ionic Equilibrium ◽  
Hydrogen Ion Transport ◽  
Triton X

Addition of Triton X-100 to chloroplast suspensions to a final concentration of 100–200 µM causes an approximate tripling of chloroplast volume and complete inhibition of light-induced conformational changes, light-dependent hydrogen ion transport, and photophosphorylation. Electron microscopic studies show that chloroplasts treated in this manner manifest extensive swelling in the form of vesicles within their inner membrane structure. Triton was adsorbed to chloroplast membranes in a manner suggesting a partition between the membrane phase and the suspending medium, rather than a strong, irreversible binding. This adsorption results in the production of pores through which ions may freely pass, and it is suggested that the inhibition of conformational changes, hydrogen ion transport, and photophosphorylation by Triton is due to an inability of treated chloroplast membranes to maintain a light-dependent pH gradient. The observed swelling is due to water influx in response to a fixed, osmotically active species within the chloroplasts, after ionic equilibrium has occurred. This is supported by the fact that chloroplasts will shrink upon Triton addition if a nonpenetrating, osmotically active material such as dextran or polyvinylpyrrolidone is present externally in sufficient concentration (>0.1 mM) to offset the osmotic activity of the internal species.

scholarly journals Energetics and kinetics of substrate analog-coupled staphylococcal nuclease folding revealed by a statistical mechanical approach

2020 ◽  
Vol 117 (33) ◽  
pp. 19953-19962
Author(s):  
Takuya Mizukami ◽  
Shunta Furuzawa ◽  
Satoru G. Itoh ◽  
Saho Segawa ◽  
Teikichi Ikura ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Intrinsically Disordered Proteins ◽  
Flux Ratio ◽  
Staphylococcal Nuclease ◽  
Binding Energies ◽  
Disordered Proteins ◽  
Flux Analysis ◽  
Intrinsically Disordered ◽  
Substrate Analog ◽  
Statistical Mechanical

Protein conformational changes associated with ligand binding, especially those involving intrinsically disordered proteins, are mediated by tightly coupled intra- and intermolecular events. Such reactions are often discussed in terms of two limiting kinetic mechanisms, conformational selection (CS), where folding precedes binding, and induced fit (IF), where binding precedes folding. It has been shown that coupled folding/binding reactions can proceed along both CS and IF pathways with the flux ratio depending on conditions such as ligand concentration. However, the structural and energetic basis of such complex reactions remains poorly understood. Therefore, we used experimental, theoretical, and computational approaches to explore structural and energetic aspects of the coupled-folding/binding reaction of staphylococcal nuclease in the presence of the substrate analog adenosine-3′,5′-diphosphate. Optically monitored equilibrium and kinetic data, combined with a statistical mechanical model, gave deeper insight into the relative importance of specific and Coulombic protein–ligand interactions in governing the reaction mechanism. We also investigated structural aspects of the reaction at the residue level using NMR and all-atom replica-permutation molecular dynamics simulations. Both approaches yielded clear evidence for accumulation of a transient protein–ligand encounter complex early in the reaction under IF-dominant conditions. Quantitative analysis of the equilibrium/kinetic folding revealed that the ligand-dependent CS-to-IF shift resulted from stabilization of the compact transition state primarily by weakly ligand-dependent Coulombic interactions with smaller contributions from specific binding energies. At a more macroscopic level, the CS-to-IF shift was represented as a displacement of the reaction “route” on the free energy surface, which was consistent with a flux analysis.

Evidence for the presence of a carbohydrate moiety in fluorescein isothiocyanate labeled fragments of rat gastric hydrogen ion-potassium ATPase

Biochemistry ◽  
1989 ◽  
Vol 28 (8) ◽  
pp. 3183-3187 ◽  
Author(s):  
Mindy M. Tai ◽  
Wha Bin Im ◽  
John P. Davis ◽  
David P. Blakeman ◽  
Heidi A. Zurcher-Neely ◽  
...  
Keyword(s):  
Fluorescein Isothiocyanate ◽  
Carbohydrate Moiety ◽  
Hydrogen Ion ◽  
Potassium Atpase

Role of Met-542 as a guide for the conformational changes of Phe-601 that occur during the reaction of β-galactosidase (Escherichia coli)

2010 ◽  
Vol 88 (5) ◽  
pp. 861-869 ◽  
Author(s):  
Megan L. Dugdale ◽  
Dayna L. Dymianiw ◽  
Bhawanjot K. Minhas ◽  
Igor D’Angelo ◽  
Reuben E. Huber
Keyword(s):  
Energy Level ◽  
Transition State ◽  
Conformational Changes ◽  
Open Loop ◽  
Side Chain ◽  
Transition State Analog ◽  
Substrate Analogs ◽  
Transition State Analogs ◽  
Substrate Analog

The Met-542 residue of β-galactosidase is important for the enzyme’s activity because it acts as a guide for the movement of the benzyl side chain of Phe-601 between two stable positions. This movement occurs in concert with an important conformational change (open vs. closed) of an active site loop (residues 794–803). Phe-601 and Arg-599, which interact with each other via the π electrons of Phe-601 and the guanidium cation of Arg-599, move out of their normal positions and become disordered when Met-542 is replaced by an Ala residue because of the loss of the guide. Since the backbone carbonyl of Phe-601 is a ligand for Na+, the Na+ also moves out of its normal position and becomes disordered; the Na+ binds about 120 times more poorly. In turn, two other Na+ ligands, Asn-604 and Asp-201, become disordered. A substrate analog (IPTG) restored Arg-599, Phe-601, and Na+ to their normal open-loop positions, whereas a transition state analog (d-galactonolactone) restored them to their normal closed-loop positions. These compounds also restored order to Phe-601, Asn-604, Asp-201, and Na+. Binding energy was, however, necessary to restore structure and order. The Ks values of oNPG and pNPG and the competitive Ki values of substrate analogs were 90–250 times higher than with native enzyme, whereas the competitive Ki values of transition state analogs were ~3.5–10 times higher. Because of this, the E•S energy level is raised more than the E•transition state energy level and less activation energy is needed for galactosylation. The galactosylation rates (k2) of M542A–β-galactosidase therefore increase. However, the rate of degalactosylation (k3) decreased because the E•transition state complex is less stable.

scholarly journals Fluorescent substrate analog for monitoring chain elongation by undecaprenyl pyrophosphate synthase in real time

2011 ◽  
Vol 417 (1) ◽  
pp. 136-141 ◽  
Author(s):  
Kuo-Hsun Teng ◽  
Annie P.-C. Chen ◽  
Chih-Jung Kuo ◽  
Yu-Chin Li ◽  
Hon-Ge Liu ◽  
...  
Keyword(s):  
Real Time ◽  
Chain Elongation ◽  
Fluorescent Substrate ◽  
Substrate Analog

scholarly journals Catalysis-associated Conformational Changes Revealed by Human CD38 Complexed with a Non-hydrolyzable Substrate Analog

2007 ◽  
Vol 282 (34) ◽  
pp. 24825-24832 ◽  
Author(s):  
Qun Liu ◽  
Irina A. Kriksunov ◽  
Christelle Moreau ◽  
Richard Graeff ◽  
Barry V. L. Potter ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Substrate Analog
Sign in / Sign up

Export Citation Format

Share Document