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Inorganic Chemistry Sep 2023Nitrogenase is a fascinating enzyme in biology that reduces dinitrogen from air to ammonia through stepwise reduction and protonation. Despite it being studied in detail...
Nitrogenase is a fascinating enzyme in biology that reduces dinitrogen from air to ammonia through stepwise reduction and protonation. Despite it being studied in detail by experimental and computational groups, there are still many unknown factors in the catalytic cycle of nitrogenase, especially related to the addition of protons and electrons and their order. A recent biomimetic study characterized a potential dinitrogen-bridged diiron cluster as a synthetic model of nitrogenase. Using strong acid and reductants, the dinitrogen was converted into ammonia molecules, but details of the mechanism remains unknown. In particular, it was unclear from the experimental studies whether the proton and electron transfer steps are sequential or alternating. Moreover, the work failed to establish what the function of the diiron core is and whether it split into mononuclear iron fragments during the reaction. To understand the structure and reactivity of the biomimetic dinitrogen-bridged diiron complex [(PFeH)(μ-N)] with triphenylphosphine ligands, we performed a density functional theory study. Our computational methods were validated against experimental crystal structure coordinates, Mössbauer parameters, and vibrational frequencies and show excellent agreement. Subsequently, we investigated the alternating and consecutive addition of electrons and protons to the system. The calculations identify a number of possible reaction channels, namely, same-site protonation, alternating protonation, and complex dissociation into mononuclear iron centers. The calculations show that the overall mechanism is not a pure sequential set of electron and proton transfers but a mixture of alternating and consecutive steps. In particular, the first reaction steps will start with double proton transfer followed by an electron transfer, while thereafter, there is another proton transfer and a second electron transfer to give a complex whereby ammonia can split off with a low energetic barrier. The second channel starts with alternating protonation of the two nitrogen atoms, whereafter the initial double proton transfer, electrons and protons are added sequentially to form a hydrazine-bound complex. The latter split off ammonia spontaneously after further protonation. The various reaction channels are analyzed with valence bond and orbital diagrams. We anticipate the nitrogenase enzyme to operate with mixed alternating and consecutive protonation and electron transfer steps.
Topics: Ammonia; Protons; Iron; Nitrogen; Nitrogenase
PubMed: 37650683
DOI: 10.1021/acs.inorgchem.3c02089 -
The Journal of Physical Chemistry. B Apr 2022Proteins are polyelectrolytes with acidic and basic amino acids Asp, Glu, Arg, Lys, and His, making up ≈25% of the residues. The protonation state of residues,...
Proteins are polyelectrolytes with acidic and basic amino acids Asp, Glu, Arg, Lys, and His, making up ≈25% of the residues. The protonation state of residues, cofactors, and ligands defines a "protonation microstate". In an ensemble of proteins some residues will be ionized and others neutral, leading to a mixture of protonation microstates rather than in a single one as is often assumed. The microstate distribution changes with pH. The protein environment also modifies residue proton affinity so microstate distributions change in different reaction intermediates or as ligands are bound. Particular protonation microstates may be required for function, while others exist simply because there are many states with similar energy. Here, the protonation microstates generated in Monte Carlo sampling in MCCE are characterized in HEW lysozyme as a function of pH and bacterial photosynthetic reaction centers (RCs) in different reaction intermediates. The lowest energy and highest probability microstates are compared. The Δ, Δ, and Δ between the four protonation states of Glu35 and Asp52 in lysozyme are shown to be calculated with reasonable precision. At pH 7 the lysozyme charge ranges from 6 to 10, with 24 accepted protonation microstates, while RCs have ≈50,000. A weighted Pearson correlation analysis shows coupling between residue protonation states in RCs and how they change when the quinone in the Q site is reduced. Protonation microstates can be used to define input MD parameters and provide insight into the motion of protons coupled to reactions.
Topics: Electron Transport; Hydrogen-Ion Concentration; Ligands; Monte Carlo Method; Muramidase; Photosynthetic Reaction Center Complex Proteins; Protons; Rhodobacter sphaeroides
PubMed: 35344367
DOI: 10.1021/acs.jpcb.2c00139 -
Journal of Clinical Oncology : Official... Sep 2014Proton beam therapy, the most common form of heavy-particle radiation therapy, is not a new invention, but it has gained considerable public attention because of the... (Review)
Review
Proton beam therapy, the most common form of heavy-particle radiation therapy, is not a new invention, but it has gained considerable public attention because of the high cost of installing and operating the rapidly increasing number of treatment centers. This article reviews the physical properties of proton beam therapy and focuses on the up-to-date clinical evidence comparing proton beam therapy with the more standard and widely available radiation therapy treatment alternatives. In a cost-conscious era of health care, the hypothetical benefits of proton beam therapy will have to be supported by demonstrable clinical gains. Proton beam therapy represents, through its scale and its cost, a battleground for the policy debate around managing expensive technology in modern medicine.
Topics: Dose-Response Relationship, Radiation; Humans; Neoplasms; Proton Therapy; Protons; Radiotherapy Dosage; Randomized Controlled Trials as Topic
PubMed: 25113772
DOI: 10.1200/JCO.2014.55.1945 -
Biomolecules Nov 2022The transmembrane transport of weak acid and base metabolites depends on the local pH conditions that affect the protonation status of the substrates and the... (Review)
Review
The transmembrane transport of weak acid and base metabolites depends on the local pH conditions that affect the protonation status of the substrates and the availability of co-substrates, typically protons. Different protein designs ensure the attraction of substrates and co-substrates to the transporter entry sites. These include electrostatic surface charges on the transport proteins and complexation with seemingly transport-unrelated proteins that provide substrate and/or proton antenna, or enzymatically generate substrates in place. Such protein assemblies affect transport rates and directionality. The lipid membrane surface also collects and transfers protons. The complexity in the various systems enables adjustability and regulation in a given physiological or pathophysiological situation. This review describes experimentally shown principles in the attraction and facilitation of weak acid and base transport substrates, including monocarboxylates, ammonium, bicarbonate, and arsenite, plus protons as a co-substrate.
Topics: Protons; Biological Transport; Membrane Transport Proteins; Hydrogen-Ion Concentration
PubMed: 36551222
DOI: 10.3390/biom12121794 -
Annual Review of Biophysics 2013Posttranslational modification is an evolutionarily conserved mechanism for regulating protein activity, binding affinity, and stability. Compared with established... (Review)
Review
Posttranslational modification is an evolutionarily conserved mechanism for regulating protein activity, binding affinity, and stability. Compared with established posttranslational modifications such as phosphorylation or ubiquitination, posttranslational modification by protons within physiological pH ranges is a less recognized mechanism for regulating protein function. By changing the charge of amino acid side chains, posttranslational modification by protons can drive dynamic changes in protein conformation and function. Addition and removal of a proton is rapid and reversible and, in contrast to most other posttranslational modifications, does not require an enzyme. Signaling specificity is achieved by only a minority of sites in proteins titrating within the physiological pH range. Here, we examine the structural mechanisms and functional consequences of proton posttranslational modification of pH-sensing proteins regulating different cellular processes.
Topics: Animals; Disease; Eukaryotic Cells; Humans; Hydrogen-Ion Concentration; Prokaryotic Cells; Protein Conformation; Protein Processing, Post-Translational; Protons
PubMed: 23451893
DOI: 10.1146/annurev-biophys-050511-102349 -
Nature Communications Sep 2022Spinster (Spns) lipid transporters are critical for transporting sphingosine-1-phosphate (S1P) across cellular membranes. In humans, Spns2 functions as the main S1P...
Spinster (Spns) lipid transporters are critical for transporting sphingosine-1-phosphate (S1P) across cellular membranes. In humans, Spns2 functions as the main S1P transporter in endothelial cells, making it a potential drug target for modulating S1P signaling. Here, we employed an integrated approach in lipid membranes to identify unknown conformational states of a bacterial Spns from Hyphomonas neptunium (HnSpns) and to define its proton- and substrate-coupled conformational dynamics. Our systematic study reveals conserved residues critical for protonation steps and their regulation, and how sequential protonation of these proton switches coordinates the conformational transitions in the context of a noncanonical ligand-dependent alternating access. A conserved periplasmic salt bridge (Asp60:Arg289) keeps the transporter in a closed conformation, while proton-dependent conformational dynamics are significantly enhanced on the periplasmic side, providing a pathway for ligand exchange.
Topics: Anion Transport Proteins; Endothelial Cells; Humans; Ligands; Lysophospholipids; Protons; Signal Transduction; Sphingosine
PubMed: 36055994
DOI: 10.1038/s41467-022-32759-2 -
PloS One 2018The transfer of protons through proton translocating channels is a complex process, for which direct samplings of different protonation states and side chain...
The transfer of protons through proton translocating channels is a complex process, for which direct samplings of different protonation states and side chain conformations in a transition network calculation provide an efficient, bias-free description. In principle, a new transition network calculation is required for every unsampled change in the system of interest, e.g. an unsampled protonation state change, which is associated with significant computational costs. Transition networks void of or including an unsampled change are termed unperturbed or perturbed, respectively. Here, we present a prediction method, which is based on an extensive coarse-graining of the underlying transition networks to speed up the calculations. It uses the minimum spanning tree and a corresponding sensitivity analysis of an unperturbed transition network as initial guess and refinement parameter for the determination of an unknown, perturbed transition network. Thereby, the minimum spanning tree defines a sub-network connecting all nodes without cycles and minimal edge weight sum, while the sensitivity analysis analyzes the stability of the minimum spanning tree towards individual edge weight reductions. Using the prediction method, we are able to reduce the calculation costs in a model system by up to 80%, while important network properties are maintained in most predictions.
Topics: Computer Simulation; Forecasting; Ion Transport; Models, Biological; Protons; Transition Elements; Water
PubMed: 30540792
DOI: 10.1371/journal.pone.0207718 -
Protein Science : a Publication of the... Apr 2021Acid-base reactions that are exceedingly unfavorable under standard conditions can be catalytically important at enzyme active sites. For example, in triose phosphate... (Review)
Review
Acid-base reactions that are exceedingly unfavorable under standard conditions can be catalytically important at enzyme active sites. For example, in triose phosphate isomerase, a glutamate side chain (nominal pK ≈ 4 in solution) can in fact deprotonate a CH group that is vicinal to a carbonyl (pK ≈ 18 in solution). This is true because of three distinct interactions: (a) ground state pK shifts due to environment polarity and electrostatics; (b) dramatic increases in effective molarity due to optimization of proximity and orientation; and (c) transition state pK shifts due to binding interactions and the formation of strong low barrier hydrogen bonds. In this report, we review the literature showing that the sum of these three effects supplies more than enough free energy to push forward proton transfer reactions that under standard conditions are exceedingly nonspontaneous and slow.
Topics: Hydrogen Bonding; Models, Molecular; Protons; Static Electricity
PubMed: 33554401
DOI: 10.1002/pro.4037 -
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 -
Organic Letters Jan 2023A novel class of stable monoareno-pentalenes is introduced that have an olefinic proton on each five-membered ring of the pentalene subunit. Their synthesis was...
A novel class of stable monoareno-pentalenes is introduced that have an olefinic proton on each five-membered ring of the pentalene subunit. Their synthesis was accomplished via a regioselective carbopalladation cascade reaction between -arylacetyleno -dibromoolefins and TIPS-acetylene. These molecules could be experimental probes of magnetic (anti)aromaticity effects.
Topics: Protons; Molecular Structure; Alkenes; Acetylene
PubMed: 36576234
DOI: 10.1021/acs.orglett.2c03752