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Journal of Biomolecular NMR Dec 2023H-detected solid-state NMR spectroscopy has been becoming increasingly popular for the characterization of protein structure, dynamics, and function. Recently, we showed...
H-detected solid-state NMR spectroscopy has been becoming increasingly popular for the characterization of protein structure, dynamics, and function. Recently, we showed that higher-dimensionality solid-state NMR spectroscopy can aid resonance assignments in large micro-crystalline protein targets to combat ambiguity (Klein et al., Proc. Natl. Acad. Sci. U.S.A. 2022). However, assignments represent both, a time-limiting factor and one of the major practical disadvantages within solid-state NMR studies compared to other structural-biology techniques from a very general perspective. Here, we show that 5D solid-state NMR spectroscopy is not only justified for high-molecular-weight targets but will also be a realistic and practicable method to streamline resonance assignment in small to medium-sized protein targets, which such methodology might not have been expected to be of advantage for. Using a combination of non-uniform sampling and the signal separating algorithm for spectral reconstruction on a deuterated and proton back-exchanged micro-crystalline protein at fast magic-angle spinning, direct amide-to-amide correlations in five dimensions are obtained with competitive sensitivity compatible with common hardware and measurement time commitments. The self-sufficient backbone walks enable efficient assignment with very high confidence and can be combined with higher-dimensionality sidechain-to-backbone correlations from protonated preparations into minimal sets of experiments to be acquired for simultaneous backbone and sidechain assignment. The strategies present themselves as potent alternatives for efficient assignment compared to the traditional assignment approaches in 3D, avoiding user misassignments derived from ambiguity or loss of overview and facilitating automation. This will ease future access to NMR-based characterization for the typical solid-state NMR targets at fast MAS.
Topics: Nuclear Magnetic Resonance, Biomolecular; Proteins; Magnetic Resonance Spectroscopy; Amides; Automation; Protons
PubMed: 37943392
DOI: 10.1007/s10858-023-00424-5 -
Journal of Chemical Information and... May 2014Benzylpenicillin, a member of the β-lactam antibiotic class, has been widely used to combat bacterial infections since 1947. The general mechanism is well-known: a...
Benzylpenicillin, a member of the β-lactam antibiotic class, has been widely used to combat bacterial infections since 1947. The general mechanism is well-known: a serine protease enzyme (i.e., DD-peptidase) forms a long lasting intermediate with the lactam ring of the antibiotic known as acylation, effectively preventing biosynthesis of the bacterial cell wall. Despite this overall mechanistic understanding, many details of binding and catalysis are unclear. Specifically, there is ongoing debate about active site protonation states and the role of general acids/bases in the reaction. Herein, a unique combination of MD simulations, QM/MM minimizations, and QM/MM orbital analyses is combined with systematic variation of active site residue protonation states. Critical interactions that maximize the stability of the bound inhibitor are examined and used as metrics. This approach was validated by examining cefoxitin interactions in the CTX-M β-lactamase from E. coli and compared to an ultra high-resolution (0.88 Å) crystal structure. Upon confirming the approach used, an investigation of the preacylated Streptomyces R61 active site with bound benzylpenicillin was performed, varying the protonation states of His298 and Lys65. We concluded that protonated His298 and deprotonated Lys65 are most likely to exist in the R61 active site.
Topics: Molecular Dynamics Simulation; Penicillin-Binding Proteins; Protein Conformation; Protein Stability; Protons; Quantum Theory; Static Electricity
PubMed: 24697903
DOI: 10.1021/ci5000517 -
Journal of Radiation Research Jun 2023
Topics: Protons; Japan; Heavy Ion Radiotherapy; Proton Therapy
PubMed: 37210628
DOI: 10.1093/jrr/rrad034 -
ChemistryOpen Jan 2022Bio-inorganic complexes inspired by hydrogenase enzymes are designed to catalyze the hydrogen evolution reaction (HER). A series of new diiron hydrogenase mimic...
Bio-inorganic complexes inspired by hydrogenase enzymes are designed to catalyze the hydrogen evolution reaction (HER). A series of new diiron hydrogenase mimic complexes with one or two terminal tris(4-methoxyphenyl)phosphine and different μ-bridging dithiolate ligands and show catalytic activity towards electrochemical proton reduction in the presence of weak and strong acids. A series of propane- and benzene-dithiolato-bridged complexes was synthesized, crystallized, and characterized by various spectroscopic techniques and quantum chemical calculations. Their electrochemical properties as well as the detailed reaction mechanisms of the HER are elucidated by density functional theory (DFT) methods. The nature of the μ-bridging dithiolate is critically controlling the reaction and performance of the HER of the complexes. In contrast, terminal phosphine ligands have no significant effects on redox activities and mechanism. Mono- or di-substituted propane-dithiolate complexes afford a sequential reduction (electrochemical; E) and protonation (chemical; C) mechanism (ECEC), while the μ-benzene dithiolate complexes follow a different reaction mechanism and are more efficient HER catalysts.
Topics: Catalysis; Hydrogen; Hydrogenase; Ligands; Protons
PubMed: 34981908
DOI: 10.1002/open.202100238 -
International Journal of Molecular... Apr 2022The process of protonation of [2,6-BHOCCH] was investigated both theoretically and experimentally. The most suitable conditions for protonation of the derivative...
The process of protonation of [2,6-BHOCCH] was investigated both theoretically and experimentally. The most suitable conditions for protonation of the derivative [2,6-BHOCCH] were found. The process of protonation was carried out in the presence of an excess of trifluoromethanesulfonic acid CFSOH at room temperature in dichloromethane solution. The structure of the resulting complex [2,6-BHOCCH*H] was established using NMR data and the results of DFT calculations. An additional proton atom H was found to be localized on one of the facets that was opposite the boron atom in a substituted position, and which bonded mainly with one apical boron atom. The main descriptors of the B-H bond were established theoretically using QTAIM and NBO approaches. In addition, the mechanism of [2,6-BHOCCH] protonation was investigated.
Topics: Boron; Magnetic Resonance Spectroscopy; Models, Molecular; Protons
PubMed: 35457007
DOI: 10.3390/ijms23084190 -
Biophysical Journal Aug 2017Proton transfer in cytochrome c oxidase from the cellular inside to the binuclear redox center (BNC) can occur through two distinct pathways, the D- and K-channels. For...
Proton transfer in cytochrome c oxidase from the cellular inside to the binuclear redox center (BNC) can occur through two distinct pathways, the D- and K-channels. For the protein to function as both a redox enzyme and a proton pump, proton transfer into the protein toward the BNC or toward a proton loading site (and ultimately through the membrane) must be highly regulated. The P → F transition is the first step in a catalytic cycle that requires proton transfer from the bulk at the N-side to the BNC. Molecular dynamics simulations of the P → F intermediate of this transition, with 16 different combinations of protonation states of key residues in the D- and K-channel, show the impact of the K-channel on the D-channel to be protonation-state dependent. Strength as well as means of communication, correlations in positions, or communication along the hydrogen-bonded network depends on the protonation state of the K-channel residue K362. The conformational and hydrogen-bond dynamics of the D-channel residue N139 is regulated by an interplay of protonation in the D-channel and K362. N139 thus assumes a gating function by which proton passage through the D-channel toward E286 is likely facilitated for states with protonated K362 and unprotonated E286. In contrast, proton passage through the D-channel is hindered by N139's preference for a closed conformation in situations with protonated E286.
Topics: Electron Transport Complex IV; Hydrogen Bonding; Molecular Dynamics Simulation; Oxidation-Reduction; Protein Conformation; Protons
PubMed: 28834718
DOI: 10.1016/j.bpj.2017.07.005 -
Angewandte Chemie (International Ed. in... Jul 2022Photoacids show a strong increase in acidity in the first electronic excited state, enabling real-time studies of proton transfer in acid-base reactions, proton...
Photoacids show a strong increase in acidity in the first electronic excited state, enabling real-time studies of proton transfer in acid-base reactions, proton transport in energy storage devices and biomolecular sensor protein systems. Several explanations have been proposed for what determines photoacidity, ranging from variations in solvation free energy to changes in electronic structure occurring along the four stages of the Förster cycle. Here we use picosecond nitrogen K-edge spectroscopy to monitor the electronic structure changes of the proton donating group in a protonated aromatic amine photoacid in solution upon photoexcitation and subsequent proton transfer dynamics. Probing core-to-valence transitions locally at the amine functional group and with orbital specificity, we clearly reveal pronounced electronic structure, dipole moment and energetic changes on the conjugate photobase side. This result paves the way for a detailed electronic structural characterization of the photoacidity phenomenon.
Topics: Acids; Amines; Electronics; Protons; Spectrum Analysis
PubMed: 35325500
DOI: 10.1002/anie.202200709 -
Physica Medica : PM : An International... May 2014Suitable instrumentation for laser-accelerated proton (ion) beams is critical for development of integrated, laser-driven ion accelerator systems. Instrumentation aimed... (Review)
Review
Suitable instrumentation for laser-accelerated proton (ion) beams is critical for development of integrated, laser-driven ion accelerator systems. Instrumentation aimed at beam diagnostics and control must be applied to the driving laser pulse, the laser-plasma that forms at the target and the emergent proton (ion) bunch in a correlated way to develop these novel accelerators. This report is a brief overview of established diagnostic techniques and new developments based on material presented at the first workshop on 'Instrumentation for Diagnostics and Control of Laser-accelerated Proton (Ion) Beams' in Abingdon, UK. It includes radiochromic film (RCF), image plates (IP), micro-channel plates (MCP), Thomson spectrometers, prompt inline scintillators, time and space-resolved interferometry (TASRI) and nuclear activation schemes. Repetition-rated instrumentation requirements for target metrology are also addressed.
Topics: Lasers; Particle Accelerators; Protons; Spectrum Analysis
PubMed: 24100298
DOI: 10.1016/j.ejmp.2013.09.002 -
Acta Crystallographica. Section D,... Feb 2017There are more H atoms than any other type of atom in an X-ray crystal structure of a protein-ligand complex, but as H atoms only have one electron they diffract X-rays...
There are more H atoms than any other type of atom in an X-ray crystal structure of a protein-ligand complex, but as H atoms only have one electron they diffract X-rays weakly and are `hard to see'. The positions of many H atoms can be inferred by our chemical knowledge, and such H atoms can be added with confidence in `riding positions'. For some chemical groups, however, there is more ambiguity over the possible hydrogen placements, for example hydroxyls and groups that can exist in multiple protonation states or tautomeric forms. This ambiguity is far from rare, since about 25% of drugs have more than one tautomeric form. This paper focuses on the most common, `prototropic', tautomers, which are isomers that readily interconvert by the exchange of an H atom accompanied by the switch of a single and an adjacent double bond. Hydrogen-exchange rates and different protonation states of compounds (e.g. buffers) are also briefly discussed. The difference in heavy (non-H) atom positions between two tautomers can be small, and careful refinement of all possible tautomers may single out the likely bound ligand tautomer. Experimental methods to determine H-atom positions, such as neutron crystallography, are often technically challenging. Therefore, chemical knowledge and computational approaches are frequently used in conjugation with experimental data to deduce the bound tautomer state. Proton movement is a key feature of many enzymatic reactions, so understanding the orchestration of hydrogen/proton motion is of critical importance to biological chemistry. For example, structural studies have suggested that, just as a chemist may use heat, some enzymes use directional movement to protonate specific O atoms on phosphates to catalyse phosphotransferase reactions. To inhibit `wriggly' enzymes that use movement to effect catalysis, it may be advantageous to have inhibitors that can maintain favourable contacts by adopting different tautomers as the enzyme `wriggles'.
Topics: Crystallization; Crystallography, X-Ray; DNA; DNA Topoisomerases, Type II; Hydrogen; Isomerism; Ligands; Models, Molecular; Protein Conformation; Proteins; Protons; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Small Molecule Libraries
PubMed: 28177309
DOI: 10.1107/S2059798316020283 -
The Journal of Physical Chemistry. B Jul 2022Identifying the p values of aspartic acid (Asp) and glutamic acid (Glu) in active sites is essential for understanding enzyme reaction mechanisms. In this study, we...
Identifying the p values of aspartic acid (Asp) and glutamic acid (Glu) in active sites is essential for understanding enzyme reaction mechanisms. In this study, we investigated the correlation between the C═O stretching vibrational frequency (ν) of protonated carboxylic acids and the p values using density functional theory calculations. In unsaturated carboxylic acids (e.g., benzoic acid analogues), ν decreases as the p increases (the negative correlation), whereas in saturated carboxylic acids (e.g., acetic acid analogues, Asp, and Glu), ν increases as the p increases (the positive correlation) as long as the structure of the H-bond network around the acid is identical. The negative/positive correlation between ν and p can be rationalized by the presence or absence of the C═C double bond. The p shift was estimated from the ν shift of Asp and Glu in proteins on the basis of the negative correlation derived from benzoic acids. The previous estimations should be revisited by using the positive correlation derived in this study, as demonstrated by quantum mechanical/molecular mechanical calculations of ν and electrostatic calculations of p on a key Asp85 in the proton-transfer pathway of bacteriorhodopsin.
Topics: Aspartic Acid; Bacteriorhodopsins; Carboxylic Acids; Glutamic Acid; Proteins; Protons
PubMed: 35763701
DOI: 10.1021/acs.jpcb.2c02193