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Journal of the American Chemical Society Dec 2007The protonation states of buried histidine residues in human deoxyhemoglobin were unambiguously identified by using a neutron crystallographic technique. Unexpectedly,...
The protonation states of buried histidine residues in human deoxyhemoglobin were unambiguously identified by using a neutron crystallographic technique. Unexpectedly, the neutron structure reveals that both the alpha- and beta-distal histidines (Hisalpha58 and Hisbeta63) adopt a positively charged, fully (doubly) protonated form, suggesting their contribution to the Bohr effect. In addition, the neutron data provide an accurate picture of the alpha1beta1 hydrogen-bonding network and allow us to observe unambiguously the nature of the intradimeric interactions at an atomic level.
Topics: Hemoglobins; Histidine; Humans; Models, Molecular; Neutron Diffraction; Protein Structure, Tertiary; Protons
PubMed: 17990881
DOI: 10.1021/ja0749441 -
Journal of Biological Inorganic... Jun 2016The [NiFe] hydrogenases catalyse the reversible conversion of H2 to protons and electrons. The active site consists of a Fe ion with one carbon monoxide, two cyanide,...
The [NiFe] hydrogenases catalyse the reversible conversion of H2 to protons and electrons. The active site consists of a Fe ion with one carbon monoxide, two cyanide, and two cysteine (Cys) ligands. The latter two bridge to a Ni ion, which has two additional terminal Cys ligands. It has been suggested that one of the Cys residues is protonated during the reaction mechanism. We have used combined quantum mechanical and molecular mechanics (QM/MM) geometry optimisations, large QM calculations with 817 atoms, and QM/MM free energy simulations, using the TPSS and B3LYP methods with basis sets extrapolated to the quadruple zeta level to determine which of the four Cys residues is more favourable to protonate for four putative states in the reaction mechanism, Ni-SIa, Ni-R, Ni-C, and Ni-L. The calculations show that for all states, the terminal Cys-546 residue is most easily protonated by 14-51 kJ/mol, owing to a more favourable hydrogen-bond pattern around this residue in the protein.
Topics: Cysteine; Desulfovibrio vulgaris; Hydrogen Bonding; Hydrogenase; Protons; Quantum Theory
PubMed: 26940957
DOI: 10.1007/s00775-016-1348-9 -
The Journal of Physical Chemistry. B Jun 2009The protonation sites and conformations of protonated glycine and its peptides (Gly(1-5)) have been investigated using infrared multiple photon dossociation (IRMPD)...
The protonation sites and conformations of protonated glycine and its peptides (Gly(1-5)) have been investigated using infrared multiple photon dossociation (IRMPD) spectroscopy in combination with theoretical calculations. For small peptides, protonation is generally presumed to occur at the amine nitrogen of the N-terminus or a nitrogen of a basic side chain. However, for triglycine, the experimental and calculated results indicate that one of the main species is an isomer in which the proton is bound to an amide oxygen. The amide II vibrational mode is found to be very sensitive to the protonation site. When the protonation site is at the amine nitrogen, the amide II mode appears around 1540 cm(-1) for diglycine, tetraglycine, pentaglycine, and one of the main isomers of triglycine (GGGH02). When the proton is bound to an amide oxygen, the amide II mode is blue-shifted to 1590 cm(-1), as seen in GGGH01. IR spectra have been obtained to provide direct evidence that an amide oxygen may serve as the protonation site in a peptide. An analogous result is found for the tripeptide of alanine. In the progression from glycine to pentaglycine, the corresponding conformations of the most stable isomers vary from linear to cyclic structures. Both glycine and diglycine are linear structures, while the most stable isomers of the tetra- and pentapeptides are both cyclic structures. For triglycine, the linear and cyclic isomers are found to coexist. The carbonyl stretches also directly reflect the conformational changes. For the linear isomers of the di- and tripeptides of glycine, two well-separated bands are observed. The amide I modes appear slightly above 1700 cm(-1), but as a result of the fact that the C horizontal lineO bond in the carboxylic acid moiety is stronger than those of the amide carbonyls, the corresponding band appears near 1800 cm(-1). However, for the cyclic isomers of the tri-, tetra-, and pentapeptides, the carbonyl oxygen in the carboxylic acid group acts as a proton acceptor to form a very strong intramolecular hydrogen bond with the protonated amine terminus. This results in a weakening of the C horizontal lineO bond, such that the amide I modes are nearly identical in frequency to the carbonyl stretch of the carboxylic acid group.
Topics: Amino Acid Sequence; Glycine; Models, Molecular; Oligopeptides; Photons; Protein Conformation; Protons; Spectrophotometry, Infrared; Spectrum Analysis
PubMed: 19485314
DOI: 10.1021/jp811468q -
Journal of the American Society For... Feb 2011The site of protonation in a molecule can greatly affect the fragments observed in product ion MS/MS spectra. In electrospray positive ionization mass spectra,...
The site of protonation in a molecule can greatly affect the fragments observed in product ion MS/MS spectra. In electrospray positive ionization mass spectra, protonation usually occurs predominantly on the most basic site on the molecule to produce the thermodynamically favored protonated species. However, the literature is unclear whether liquid phase or gas phase thermodynamics has the greater influence. This paper describes the protonation and fragmentation behavior of crizotinib and two of its impurities. Crizotinib has two possible protonation sites, a pyridine nitrogen and a secondary amine, piperidine nitrogen; the former is the favored site in the gas phase and the latter the more favored site in the liquid phase. The impurities contain alkyl substitution on the piperidine nitrogen, producing tertiary amine species. Literature precedence suggests that in the liquid phase, the piperidine nitrogen is still the most basic site but, in the gas phase, the pyridine nitrogen and the piperidine nitrogen have very similar basicities. Fragmentation data for the three molecules suggest that the secondary and tertiary amines protonate preferentially and almost exclusively on different sites. We propose that the secondary amine protonates on the piperidine nitrogen (influenced by solution thermodynamics) and the two tertiary amine structures protonate on the pyridine nitrogen because of steric hindrance at the most basic site of the molecule, allowing kinetic control of the protonation process.
Topics: Crizotinib; Drug Contamination; Molecular Conformation; Nitrogen; Piperidines; Protons; Pyrazoles; Pyridines; Spectrometry, Mass, Electrospray Ionization; Tandem Mass Spectrometry
PubMed: 21472595
DOI: 10.1007/s13361-010-0037-0 -
The Journal of Physical Chemistry. B Apr 2007The photoactive yellow protein (PYP) acts as a light sensor to its bacterial host: it responds to light by changing shape. After excitation by blue light, PYP undergoes...
The photoactive yellow protein (PYP) acts as a light sensor to its bacterial host: it responds to light by changing shape. After excitation by blue light, PYP undergoes several transformations, to partially unfold into its signaling state. One of the crucial steps in this photocycle is the protonation of p-coumaric acid after excitation and isomerization of this chromophore. Experimentalists still debate on the nature of the proton donor and on whether it donates the hydrogen directly or indirectly. To obtain better knowledge of the mechanism, we studied this proton transfer using Car-Parrinello molecular dynamics, classical molecular dynamics, and computer simulations combining these two methods (quantum mechanics/molecular mechanics, QMMM). The simulations reproduce the chromophore structure and hydrogen-bond network of the protein measured by X-ray crystallography and NMR. When the chromophore is protonated, it leaves the assumed proton donor, glutamic acid 46, with a negative charge in a hydrophobic environment. We show that the stabilization of this charge is a very important factor in the mechanism of protonation. Protonation frequently occurs in simplified ab initio simulations of the chromophore binding pocket in vacuum, where amino acids can easily hydrogen bond to Glu46. When the complete protein environment is incorporated in a QMMM simulation on the complete protein, no proton transfer is observed within 14 ps. The hydrogen-bond rearrangements in this time span are not sufficient to stabilize the new protonation state. Force field molecular dynamics simulations on a much longer time scale have shown which internal rearrangements of the protein are needed. Combining these simulations with more QMMM calculations enabled us to check the stability of protonation states and clarify the initial requirements for the proton transfer in PYP.
Topics: Bacterial Proteins; Computer Simulation; Hydrogen Bonding; Light; Models, Chemical; Molecular Structure; Photoreceptors, Microbial; Protons; Quantum Theory; Thermodynamics
PubMed: 17388542
DOI: 10.1021/jp067158b -
Journal of Mass Spectrometry : JMS Oct 1996Mild gas-phase acids C4H9+ and NH4+ protonate pyrrole at C-2 and C-3 but not at the nitrogen atom, as determined by deuterium labeling and neutralization-reionization...
Mild gas-phase acids C4H9+ and NH4+ protonate pyrrole at C-2 and C-3 but not at the nitrogen atom, as determined by deuterium labeling and neutralization-reionization mass spectrometry. Proton affinities in pyrrole are calculated by MP2/6-311G(2d,p) as 866, 845 and 786 kJ mol-1 for protonation at C-2, C-3 and N, respectively. Vertical neutralization of protonated pyrrole generates bound radicals that in part dissociate by loss of hydrogen atoms. Unimolecular loss of hydrogen atom from C-2- and C-3-protonated pyrrole cations is preceded by proton migration in the ring. Protonation of gaseous imidazole is predicted to occur exclusively at the N-3 imine nitrogen to yield a stable aromatic cation. Proton affinities in imidazole are calculated as 941, 804, 791, 791 and 724 for the N-3, C-4, C-2, C-5 and N-1 positions, respectively. Radicals derived from protonated imidazole are only weakly bound. Vertical neutralization of N-3-protonated imidazole is accompanied by large Franck-Condon effects which deposit on average 183 kJ mol-1 vibrational energy in the radicals formed. The radicals dissociate unimolecularly by loss of hydrogen atom, which involves both direct N-H bond cleavage and isomerization to the more stable C-2 H-isomer. Potential energy barriers to isomerizations and dissociations in protonated pyrrole and imidazole isomers and their radicals were investigated by ab initio calculations.
Topics: Imidazoles; Isomerism; Mass Spectrometry; Protons; Pyrazoles
PubMed: 8916426
DOI: 10.1002/(SICI)1096-9888(199610)31:10<1173::AID-JMS412>3.0.CO;2-D -
Journal of Chemical Theory and... Dec 2018We have performed a systematic computational study of the relative energies of possible protonation states of the FeMo cluster in nitrogenase in the E-E states, i.e.,...
We have performed a systematic computational study of the relative energies of possible protonation states of the FeMo cluster in nitrogenase in the E-E states, i.e., the resting state and states with 1-4 electrons and protons added but before N binds. We use the combined quantum mechanics and molecular mechanics (QM/MM) approach, including the complete solvated heterotetrameric enzyme in the calculations. The QM system consisted of 112 atoms, i.e., the full FeMo cluster, as well all groups forming hydrogen bonds to it within 3.5 Å. It was treated with either the TPSS-D3 or B3LYP-D3 methods with the def2-SV(P) or def2-TZVPD basis sets. For each redox state, we calculated relative energies of at least 50 different possible positions for the proton, added to the most stable protonation state of the level with one electron less. We show quite conclusively that the resting E state is not protonated using quantum refinement and by comparing geometries to the crystal structure. The E state is protonated on S2B, in agreement with most previous computational studies. However, for the E-E states, the two QM methods give diverging results, with relative energies that differ by over 300 kJ/mol for the most stable E states. TPSS favors hydride ions binding to the Fe ions. The first bridges Fe2 and Fe6, whereas the next two bind terminally to either Fe4, Fe5, or Fe6 with nearly equal energies. On the other hand, B3LYP disfavors hydride ions and instead suggests that 1-3 protons bind to the central carbide ion.
Topics: Hydrogen Bonding; Molecular Dynamics Simulation; Nitrogenase; Oxidation-Reduction; Protein Conformation; Protons; Quantum Theory
PubMed: 30354152
DOI: 10.1021/acs.jctc.8b00778 -
Dalton Transactions (Cambridge, England... Mar 2015Density functional calculations indicate that protonation of a μ3-S atom in cubanoid clusters [Fe4S4X4](2-) leads to a large extension of one Fe-S(H) bond such that the...
Density functional calculations indicate that protonation of a μ3-S atom in cubanoid clusters [Fe4S4X4](2-) leads to a large extension of one Fe-S(H) bond such that the SH ligand is doubly-bridging, μ-SH. Triply-bridging SH in these clusters is unstable, relative to μ-SH. The theory for the geometric and electronic structures of the protonated [Fe4S4X4](2-) clusters (X = Cl, SEt, SMe, SPh, OMe, OPh) is presented in this paper. The principal results are (1) the unique Fe atom in [Fe4S3(SH)X4](-) is three-coordinate, with planar or approximately planar stereochemistry, (2) approximately equi-energetic endo and exo isomers occur for pyramidal μ-SH, (3) the structural changes caused by protonation reverse without barrier on deprotonation, (4) the most stable electronic states have S = 0 and oppositely signed spin densities on the Fe atoms bearing the μ-SH bridge, (5) interconversions between endo and exo isomers, and between ground and excited states, occur through concerted lengthenings and shortenings of Fe-S(H) interactions, on relatively flat energy surfaces, (6) protonation of an X ligand does not change the characteristics of protonation of μ3-S. Experimental tests of this theory are suggested, and applications discussed.
Topics: Electrons; Iron Compounds; Isomerism; Models, Molecular; Protons; Sulfur; Sulfur Compounds
PubMed: 25664573
DOI: 10.1039/c4dt03681f -
The Journal of Physical Chemistry. A Sep 2005Protonated fluorobenzene ions (C6H6F+) are produced by chemical ionization of C6H5F in the cell of a FT-ICR mass spectrometer using either CH5+ or C2H5+. The resulting...
Protonated fluorobenzene ions (C6H6F+) are produced by chemical ionization of C6H5F in the cell of a FT-ICR mass spectrometer using either CH5+ or C2H5+. The resulting protonation sites are probed by IR multiphoton dissociation (IRMPD) spectroscopy in the 600-1700 cm-1 fingerprint range employing the free electron laser at CLIO (Centre Laser Infrarouge Orsay). Comparison with quantum chemical calculations reveals that the IRMPD spectra are consistent with protonation in para and/or ortho position, which are the thermodynamically favored protonation sites. The lack of observation of protonation at the F substituent, when CH5+ is used as protonating agent, is attributed to the low-pressure conditions in the ICR cell where the ions are produced. Comparison of the C6H6F+ spectrum with IR spectra of C6H5F and C6H7+ reveals the effects of both protonation and H F substitution on the structural properties of these fundamental aromatic molecules.
Topics: Fluorobenzenes; Protons; Spectrophotometry, Infrared
PubMed: 16834169
DOI: 10.1021/jp052907v -
Physical Chemistry Chemical Physics :... Jan 2009Density functional theory methods have been used to investigate the effects of adding one to four protons to a one-plane guanine quartet (G4) and a two-plane guanine...
Density functional theory methods have been used to investigate the effects of adding one to four protons to a one-plane guanine quartet (G4) and a two-plane guanine quartet stack (2G4). The singly protonated G4 complex prefers protonation at the Watson-Crick face of the O6 moiety. However, all multi-protonated G4 complexes favour protonation at the Hoogsteen face of the O6 centres. The proton affinities have also been calculated for the addition of one, two, three and four protons to the central oxygens of G4 and have been compared with those of monomeric guanine and other biochemically appropriate bases. These results suggest that a G4 might reasonably readily accept two protons. For the singly to quadruply protonated 2G4's, the added protons prefer to distribute over both planes with maximally two per plane. Furthermore, unlike the (G4-nH+) n>or= 2 complexes, protonation at the Watson-Crick faces of the O6 moieties is found to be preferred for all protonation states. In addition, (2G4-nH+) n=1-4 complexes were also obtained in which inter-plane hydrogen bonds were formed, effectively enabling the protons to 'sit between' planes.
Topics: G-Quadruplexes; Models, Molecular; Molecular Conformation; Protons; Quantum Theory
PubMed: 19088983
DOI: 10.1039/b811717a