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Biochimica Et Biophysica Acta.... Jun 2022Membrane transporters and receptors often rely on conserved hydrogen bonds to assemble transient paths for ion transfer or long-distance conformational couplings. For...
Membrane transporters and receptors often rely on conserved hydrogen bonds to assemble transient paths for ion transfer or long-distance conformational couplings. For transporters and receptors that use proton binding and proton transfer for function, inter-helical hydrogen bonds of titratable protein sidechains that could change protonation are of central interest to formulate hypotheses about reaction mechanisms. Knowledge of hydrogen bonds common at sites of potential interest for proton binding could thus inform and guide studies on functional mechanisms of protonation-coupled membrane proteins. Here we apply graph-theory approaches to identify hydrogen-bond motifs of carboxylate and histidine sidechains in a large data set of static membrane protein structures. We find that carboxylate-hydroxyl hydrogen bonds are present in numerous structures of the dataset, and can be part of more extended H-bond clusters that could be relevant to conformational coupling. Carboxylate-carboxyamide and imidazole-imidazole hydrogen bonds are represented in comparably fewer protein structures of the dataset. Atomistic simulations on two membrane transporters in lipid membranes suggest that many of the hydrogen bond motifs present in static protein structures tend to be robust, and can be part of larger hydrogen-bond clusters that recruit additional hydrogen bonds.
Topics: Hydrogen Bonding; Imidazoles; Membrane Proteins; Membrane Transport Proteins; Protons
PubMed: 35217000
DOI: 10.1016/j.bbamem.2022.183896 -
Biophysical Journal Aug 2021Through molecular dynamics (MD) and free energy simulations in electric fields, we examine the factors influencing conductance of bacterial voltage-gated sodium channel...
Through molecular dynamics (MD) and free energy simulations in electric fields, we examine the factors influencing conductance of bacterial voltage-gated sodium channel NaMs. The channel utilizes four glutamic acid residues in the selectivity filter (SF). Previously, we have shown, through constant pH and free energy calculations of pKa values, that fully deprotonated, singly protonated, and doubly protonated states are all feasible at physiological pH, depending on how many ions are bound in the SF. With 173 MD simulations of 450 or 500 ns and additional free energy simulations, we determine that the conductance is highest for the deprotonated state and decreases with each additional proton bound. We also determine that the pKa value of the four glutamic residues for the transition between deprotonated and singly protonated states is close to the physiological pH and that there is a small voltage dependence. The pKa value and conductance trends are in agreement with experimental work on bacterial Na channels, which show a decrease in maximal conductance with lowering of pH, with pKa in the physiological range. We examine binding sites for Na in the SF, compare with previous work, and note a dependence on starting structures. We find that narrowing of the gate backbone to values lower than the crystal structure's backbone radius reduces the conductance, whereas increasing the gate radius further does not affect the conductance. Simulations with some amount of negatively charged lipids as opposed to purely neutral lipids increases the conductance, as do simulations at higher voltages.
Topics: Bacteria; Bacterial Proteins; Binding Sites; Molecular Dynamics Simulation; Protons; Voltage-Gated Sodium Channels
PubMed: 34214541
DOI: 10.1016/j.bpj.2021.06.013 -
Accounts of Chemical Research Apr 2017Protons are vastly abundant in a wide range of exciting macromolecules and thus can be a powerful probe to investigate the structure and dynamics at atomic resolution... (Review)
Review
Protons are vastly abundant in a wide range of exciting macromolecules and thus can be a powerful probe to investigate the structure and dynamics at atomic resolution using solid-state NMR (ssNMR) spectroscopy. Unfortunately, the high signal sensitivity, afforded by the high natural-abundance and high gyromagnetic ratio of protons, is greatly compromised by severe line broadening due to the very strong H-H dipolar couplings. As a result, protons are rarely used, in spite of the desperate need for enhancing the sensitivity of ssNMR to study a variety of systems that are not amenable for high resolution investigation using other techniques including X-ray crystallography, cryo-electron microscopy, and solution NMR spectroscopy. Thanks to the remarkable improvement in proton spectral resolution afforded by the significant advances in magic-angle-spinning (MAS) probe technology, H ssNMR spectroscopy has recently attracted considerable attention in the structural and dynamics studies of various molecular systems. However, it still remains a challenge to obtain narrow H spectral lines, especially from proteins, without resorting to deuteration. In this Account, we review recent proton-based ssNMR strategies that have been developed in our laboratory to further improve proton spectral resolution without resorting to chemical deuteration for the purposes of gaining atomistic-level insights into molecular structures of various crystalline solid systems, using small molecules and peptides as illustrative examples. The proton spectral resolution enhancement afforded by the ultrafast MAS frequencies up to 120 kHz is initially discussed, followed by a description of an ensemble of multidimensional NMR pulse sequences, all based on proton detection, that have been developed to obtain in-depth information from dipolar couplings and chemical shift anisotropy (CSA). Simple single channel multidimensional proton NMR experiments could be performed to probe the proximity of protons for structure determination using H-H dipolar couplings and to evaluate the changes in chemical environments as well as the relative orientation to the external magnetic field using proton CSA. Due to the boost in signal sensitivity enabled by proton detection under ultrafast MAS, by virtue of high proton natural abundance and gyromagnetic ratio, proton-detected multidimensional experiments involving low-γ nuclei can now be accomplished within a reasonable time, while the higher dimension also offers additional resolution enhancement. In addition, the application of proton-based ssNMR spectroscopy under ultrafast MAS in various challenging and crystalline systems is also presented. Finally, we briefly discuss the limitations and challenges pertaining to proton-based ssNMR spectroscopy under ultrafast MAS conditions, such as the presence of high-order dipolar couplings, friction-induced sample heating, and limited sample volume. Although there are still a number of challenges that must be circumvented by further developments in radio frequency pulse sequences, MAS probe technology and approaches to prepare NMR-friendly samples, proton-based ssNMR has already gained much popularity in various research domains, especially in proteins where uniform or site-selective deuteration can be relatively easily achieved. In addition, implementation of the recently developed fast data acquisition approaches would also enable further developments in the design and applications of proton-based ultrafast MAS multidimensional ssNMR techniques.
Topics: Nuclear Magnetic Resonance, Biomolecular; Peptides; Proteins; Protons; Small Molecule Libraries
PubMed: 28353338
DOI: 10.1021/acs.accounts.7b00082 -
Current Biology : CB Sep 2000Proton transfer into and out of proteins is important, both for many enzyme reaction mechanisms and proton pumping across membranes. Recent work on several proteins has... (Review)
Review
Proton transfer into and out of proteins is important, both for many enzyme reaction mechanisms and proton pumping across membranes. Recent work on several proteins has revealed stringent requirements for amino-acid side chains and subtle reorganisation of hydrogen-bond networks involving bound water molecules.
Topics: Hydrogen-Ion Concentration; Kinetics; Proteins; Protons
PubMed: 10996087
DOI: 10.1016/s0960-9822(00)00662-x -
Current Opinion in Structural Biology Dec 2022Many important protein functions are carried out through proton-coupled conformational dynamics. Thus, the ability to accurately model protonation states dynamically has... (Review)
Review
Many important protein functions are carried out through proton-coupled conformational dynamics. Thus, the ability to accurately model protonation states dynamically has wide-ranging implications. Over the past two decades, two main types of constant pH methods (discrete and continuous) have been developed to enable proton-coupled molecular dynamics (MD) simulations. In this short review, we discuss the current status of the development and highlight recent applications that have advanced our understanding of protein structure-function relationships. We conclude the review by outlining the remaining challenges in the method development and projecting important areas for future applications.
Topics: Molecular Dynamics Simulation; Protons; Hydrogen-Ion Concentration; Proteins; Molecular Conformation
PubMed: 36410222
DOI: 10.1016/j.sbi.2022.102498 -
BioTechniques Feb 2011Fluorescent probes for monitoring mitochondrial membrane potential are frequently used for assessing mitochondrial function, particularly in the context of cell fate... (Review)
Review
Fluorescent probes for monitoring mitochondrial membrane potential are frequently used for assessing mitochondrial function, particularly in the context of cell fate determination in biological and biomedical research. However, valid interpretation of results obtained with such probes requires careful consideration of numerous controls, as well as possible effects of non-protonic charges on dye behavior. In this context, we provide an overview of some of the important technical considerations, controls, and parallel complementary assays that can be employed to help ensure appropriate interpretation of results, thus providing a practical usage guide for monitoring mitochondrial membrane potentials with cationic probes. In total, this review will help illustrate both the strengths and potential pitfalls of common mitochondrial membrane potential dyes, and highlight best-usage approaches for their efficacious application in life sciences research.
Topics: Animals; Fluorescent Dyes; Humans; Membrane Potential, Mitochondrial; Mitochondria; Protons
PubMed: 21486251
DOI: 10.2144/000113610 -
Molecules (Basel, Switzerland) Sep 2022Malondialdehyde (MDA) engages in a triel bond (TrB) with TrX (Tr = B and Al; X = H, F, Cl, and Br) in three modes, in which the hydroxyl O, carbonyl O, and central...
Malondialdehyde (MDA) engages in a triel bond (TrB) with TrX (Tr = B and Al; X = H, F, Cl, and Br) in three modes, in which the hydroxyl O, carbonyl O, and central carbon atoms of MDA act as the electron donors, respectively. A H···X secondary interaction coexists with the TrB in the former two types of complexes. The carbonyl O forms a stronger TrB than the hydroxyl O, and both of them are better electron donors than the central carbon atom. The TrB formed by the hydroxyl O enhances the intramolecular H-bond in MDA and thus promotes proton transfer in MDA-BX (X = Cl and Br) and MDA-AlX (X = halogen), while a weakening H-bond and the inhibition of proton transfer are caused by the TrB formed by the carbonyl O. The TrB formed by the central carbon atom imposes little influence on the H-bond. The BH substitution on the central C-H bond can also realise the proton transfer in the triel-bonded complexes between the hydroxyl O and TrH (Tr = B and Al).
Topics: Carbon; Halogens; Malondialdehyde; Models, Chemical; Protons
PubMed: 36144822
DOI: 10.3390/molecules27186091 -
Advanced Science (Weinheim,... Jun 2022Despite the clinical potential, photodynamic therapy (PDT) relying on singlet oxygen ( O ) generation is severely limited by tumor hypoxia and endosomal entrapment....
Despite the clinical potential, photodynamic therapy (PDT) relying on singlet oxygen ( O ) generation is severely limited by tumor hypoxia and endosomal entrapment. Herein, a proton-driven transformable O -nanotrap (ANBDP NPs) with endosomal escape capability is presented to improve hypoxic tumor PDT. In the acidic endosomal environment, the protonated O -nanotrap ruptures endosomal membranes via a "proton-sponge" like effect and undergoes a drastic morphology-and-size change from nanocubes (≈94.1 nm in length) to nanospheres (≈12.3 nm in diameter). Simultaneously, anthracenyl boron dipyrromethene-derived photosensitizer (ANBDP) in nanospheres transforms to its protonated form (ANBDPH) and switches off its charge-transfer state to achieve amplified O photogeneration capability. Upon 730 nm photoirradiation, ANBDPH prominently produces O and traps generated- O in the anthracene group to form endoperoxide (ANOBDPH). Benefitting from the hypoxia-tolerant O -release property of ANOBDPH in the dark, the O -nanotrap brings about sustained therapeutic effect without further continuous irradiation, thereby achieving remarkable antitumor performance.
Topics: Humans; Hypoxia; Photochemotherapy; Photosensitizing Agents; Protons; Tumor Hypoxia
PubMed: 35435332
DOI: 10.1002/advs.202200128 -
Journal of the American Chemical Society Aug 2023The degree to which redox-driven proton pumps regulate net charge during electron transfer (ΔZ) remains undetermined due to difficulties in measuring the net charge of...
The degree to which redox-driven proton pumps regulate net charge during electron transfer (ΔZ) remains undetermined due to difficulties in measuring the net charge of solvated proteins. Values of ΔZ can reflect reorganization energies or redox potentials associated with ET and can be used to distinguish ET from proton(s)-coupled electron transfer (PCET). Here, we synthesized protein "charge ladders" of a Rieske [2Fe-2S] subunit from (truncRp) and made 120 electrostatic measurements of ΔZ across pH. Across pH 5-10, truncRp is suspected of transitioning from ET to PCET, and then to two proton-coupled ET (2PCET). Upon reduction, we found that truncRp became more negative at pH 6.0 by one unit (ΔZ = -1.01 ± 0.14), consistent with single ET; was isoelectric at pH 8.8 (ΔZ = -0.01 ± 0.45), consistent with PCET; and became more positive at pH 10.6 (ΔZ = +1.37 ± 0.60), consistent with 2PCET. These ΔZ values are attributed to protonation of H154 and H134. Across pH, redox potentials of Rp (measured previously) correlated with protonation energies of H154 and H134 and ΔZ for truncRp, supporting a discrete proton pumping mechanism for Rieske proteins at the Fe-coordinating histidines.
Topics: Protons; Electrons; Electron Transport; Oxidation-Reduction; Proteins
PubMed: 37486967
DOI: 10.1021/jacs.3c03006 -
The Journal of Physical Chemistry. B Jul 2020When the electrostatic environment surrounding binding partners changes between unbound and bound states, the net uptake or release of a proton is possible by either...
When the electrostatic environment surrounding binding partners changes between unbound and bound states, the net uptake or release of a proton is possible by either binding partner. This process is pH-dependent in that the free energy required to uptake or release the proton varies with pH. This pH-dependence is typically not considered in conventional free energy methods where the use of fixed protonation states is the norm. In the present paper, we apply a simple two-step approach to calculate the pH-dependent binding free energy of a model cucubit[7]uril host/guest system. By use of λ-dynamics with an enhanced sampling protocol, adaptive landscape flattening, p shifts and reference binding free energies upon complexation were determined. This information enables the construction of pH-dependent binding profiles that accurately capture the p shifts and reproduce binding free energies at the different pH conditions that were observed experimentally. Our calculations illustrate a general framework for computing pH-dependent binding free energies but also point to some issues in modeling the molecular charge distributions within this series of molecules with CGenFF. However, by introducing some minor charge modifications to the CGenFF force field, we saw significant improvement in accuracy of the calculated p shifts.
Topics: Hydrogen-Ion Concentration; Physical Phenomena; Protons; Static Electricity; Thermodynamics
PubMed: 32628482
DOI: 10.1021/acs.jpcb.0c03671