The last stages of the photocycle of the photosynthetic pigment all-trans bacteriorhodopsin (bR570), as well as its proton pump mechanism, are markedly pH dependent. We have measured the relative amount of the accumulated O630 intermediate (Phir), as well as its rise and decay rate constants (kr and kd, respectively), over a wide pH range. The experiments were carried out in deionized membrane suspensions to which varying concentrations of metal cations and of large organic cations were added. The observed pH dependencies, s-shaped curves in the case of Phir and bell-shaped curves for kr and kd, are interpreted in terms of the titration of three protein residues denoted as R1, R2, and R3. The R1 titration is responsible for the increase in Phir, kr, and kd upon lowering the pH from pH approximately 9.5 to 7. At low pH Phir exhibits a secondary rise which is attributed to the titration of a low pKa group, R2. After reaching a maximum at pH approximately 7, kr and kd undergo a decrease upon decreasing the pH, which is attributed to the titration of R3. All three titrations exhibit pKa values which decrease upon increasing the salt concentration. As in the case of the Purple (bR570) if Blue (bR605) equilibrium, divalent cations are substantially more effective than monovalent cations in shifting the pKa values. Moreover, bulky organic cations are as effective as small metal cations. It is concluded that analogously to the Purple if Blue equilibrium, the salt binding sites which control the pKa values of R1, R2, and R3 are located on, or close to, the membrane surface. Possible identifications of the three protein residues are considered. Experiments with the E204Q mutant show that the mutation has markedly affected the R2 (Phir) titration, suggesting that R2 should be identified with Glu-204 or with a group whose pKa is affected by Glu-204. The relation between the R1, R2 and R3 titrations and the proton pump mechanism is discussed. It is evident that the pH dependence of Phir is unrelated to the measured pKa of the group (XH) which releases the proton to the extracellular medium during the photocycle. However, since the same residue may exhibit different pKa values at different stages of the photocycle, it cannot be excluded that R2 or R3 may be identified with XH.

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi981901bDOI Listing

Publication Analysis

Top Keywords

pka values
16
protein residues
12
stages photocycle
8
proton pump
8
pump mechanism
8
metal cations
8
organic cations
8
titration three
8
three protein
8
attributed titration
8

Similar Publications

Despite its importance in understanding biology and computer-aided drug discovery, the accurate prediction of protein ionization states remains a formidable challenge. Physics-based approaches struggle to capture the small, competing contributions in the complex protein environment, while machine learning (ML) is hampered by the scarcity of experimental data. Here, we report the development of p ML (KaML) models based on decision trees and graph attention networks (GAT), exploiting physicochemical understanding and a new experiment p database (PKAD-3) enriched with highly shifted p's.

View Article and Find Full Text PDF

Ofloxacin, a commonly prescribed antibiotic, raises serious environmental concerns due to its persistence in aquatic systems. This study offers new insights into the environmental behavior of ofloxacin and its interactions with carbon-based adsorbents with the aim of enhancing our understanding of its removal mechanisms via adsorption processes. Using a comprehensive computational approach, we analyzed the speciation, pK values, and solubility of ofloxacin across various pH conditions, accounting for all four microspecies, including the often-overlooked neutral form.

View Article and Find Full Text PDF

A ratiometric fluorescent nanoprobe (CDs-Rho), synthesized through the simple covalent amide linkage between carbon dots (CDs) and pH-sensitive rhodamine dye (Rho), was designed for the precise sensing and imaging of extremely alkaline environments. The sensing mechanism involves the opposite pH-dependent fluorescence changes in CDs and Rho, respectively, coupled with pH-regulated FRET efficiency from CDs to Rho. The nanoprobe features a wide pH response window from pH 7.

View Article and Find Full Text PDF

Design of pH-responsive and amphiphilic pullulan-based biological macromolecule for gene delivery.

Int J Biol Macromol

January 2025

Institute of Organic Chemistry and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, D-07743 Jena, Germany; Jena Center for Soft Matters (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, D-07743 Jena, Germany. Electronic address:

Nanomedicine, particularly gene delivery, holds immense potential and offers promising therapeutic options. Non-viral systems gained attention due to their binding capacity, stability and scalability. Among these, natural polysaccharides, such as pullulan, are advantageous in terms of sustainability, biocompatibility and potential degradability.

View Article and Find Full Text PDF

The hydrolysis rates of many organic chemicals are accelerated under alkaline conditions by the presence of hydroxide (HO), which is typically assumed to be the predominant species contributing to base-catalyzed hydrolysis in both natural waters and laboratory buffers used in standard protocols. In this study, we demonstrated that weak bases (e.g.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!