scholarly journals Oxygen activation in neuronal NO synthase: resolving the consecutive mono-oxygenation steps

2012 ◽  
Vol 443 (2) ◽  
pp. 505-514 ◽  
Author(s):  
Davide Papale ◽  
Chiara Bruckmann ◽  
Ben Gazur ◽  
Caroline S. Miles ◽  
Christopher G. Mowat ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Direct Reaction ◽  
Chemical Mechanisms ◽  
Signalling Molecule ◽  
Proton Source ◽  
In The Wild ◽  
Additional Hydrogen Bond ◽  
Oxide Synthase ◽  
Haem Iron ◽  
Additional Hydrogen

The vital signalling molecule NO is produced by mammalian NOS (nitric oxide synthase) enzymes in two steps. L-arginine is converted into NOHA (Nω-hydroxy-L-arginine), which is converted into NO and citrulline. Both steps are thought to proceed via similar mechanisms in which the cofactor BH4 (tetrahydrobiopterin) activates dioxygen at the haem site by electron transfer. The subsequent events are poorly understood due to the lack of stable intermediates. By analogy with cytochrome P450, a haem-iron oxo species may be formed, or direct reaction between a haem-peroxy intermediate and substrate may occur. The two steps may also occur via different mechanisms. In the present paper we analyse the two reaction steps using the G586S mutant of nNOS (neuronal NOS), which introduces an additional hydrogen bond in the active site and provides an additional proton source. In the mutant enzyme, BH4 activates dioxygen as in the wild-type enzyme, but an interesting intermediate haem species is then observed. This may be a stabilized form of the active oxygenating species. The mutant is able to perform step 2 (reaction with NOHA), but not step 1 (with L-arginine) indicating that the extra hydrogen bond enables it to discriminate between the two mono-oxygenation steps. This implies that the two steps follow different chemical mechanisms.

scholarly journals Crystal structure of 2,2-dichloro-1-(piperidin-1-yl)butane-1,3-dione

2015 ◽  
Vol 71 (1) ◽  
pp. o19-o19 ◽  
Author(s):  
Markus Schwierz ◽  
Helmar Görls ◽  
Wolfgang Imhof
Keyword(s):  
Hydrogen Bond ◽  
Three Dimensional ◽  
Chair Conformation ◽  
Piperidine Ring ◽  
Carbonyl Groups ◽  
Infinite Layer ◽  
Compound C ◽  
Methylene Groups ◽  
Additional Hydrogen Bond ◽  
Additional Hydrogen

In the title compound, C9H13Cl2NO2, the piperidine ring shows a chair conformation and the O—C—C—O torsion angle between the carbonyl groups is 183.6 (4)°. In the crystal, molecules are linked into an infinite layer along theabplane by a bifurcated C—H...O hydrogen bond between the carbonyl O atom adjacent to the methyl group and one of the methylene groups next to nitrogen and an additional hydrogen bond of the C—H...Cl type. These layers are connected into a three-dimensional supramolecular arrangement by O...Cl contacts [2.8979 (12) and 3.1300 (12) Å].

scholarly journals Increased neutralization of SARS-CoV-2 Delta variant by nanobody (Nb22) and the structural basis

2021 ◽  
Author(s):  
Xilin Wu ◽  
Yaxing Wang ◽  
Lin Cheng ◽  
Linjing Zhu ◽  
Sen Ma ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Therapeutic Agent ◽  
Spike Protein ◽  
Structural Basis ◽  
Receptor Binding Domain ◽  
Ic50 Value ◽  
Additional Hydrogen Bond ◽  
Crystal Structural ◽  
Alpha Variant ◽  
Additional Hydrogen

Delta variant, also known as B.1.617.2, has become a predominant circulating variant in many countries since it first emerged in India in December 2020. Delta variant is less sensitive to serum neutralization from COVID-19 convalescent individuals or vaccine recipients, relative to Alpha strains. It was also resistant to neutralization by some anti-receptor binding domain (RBD) and anti-N-terminal domain (NTD) antibodies in clinics. Previously, we reported the discovery of nanobodies isolated from an alpaca immunized with spike protein, exhibiting ultrahigh potency against SARS-CoV-2 and its mutated variants, where a novel inhalable bispecific Nb15 protected SARS-CoV-2 infection in hACE2 mice. Here, we found that Nb22-Fc, among our previously reported nanobodies, exhibited 8.4-fold increased neutralization potency against Delta variant with an IC50 value of 0.41 ng/ml (5.13 pM) relative to Alpha variant. Furthermore, our crystal structural analysis reveals that the binding of Nb22 on SARS-CoV-2 RBD effectively blocks the binding of RBD to ACE2 during virus infection. Furthermore, the L452R mutation in RBD of Delta variant forms an additional hydrogen bond with the hydroxy group of T30 of Nb22, leading to the increased neutralization potency of Nb22 against Delta variant. Thus, Nb22 is a potential therapeutic agent against SARS-CoV-2, especially the highly contagious Delta variant.

scholarly journals (E)-4-Methoxy-N′-(2,3,4-trimethoxybenzylidene)benzohydrazide monohydrate

IUCrData ◽  
2016 ◽  
Vol 1 (9) ◽  
Author(s):  
S. Veeramanikandan ◽  
H. Benita Sherine ◽  
B. Gunasekaran ◽  
G. Chakkaravarthi
Keyword(s):  
Hydrogen Bond ◽  
Three Dimensional ◽  
Water Molecules ◽  
Aromatic Rings ◽  
Compound C ◽  
Dimensional Network ◽  
Additional Hydrogen Bond ◽  
Methoxy Substituent ◽  
Imine Bond ◽  
Additional Hydrogen

The asymmetric unit of the title compound, C18H20N2O5·H2O, consists of a benzohydrazide molecule which exists in anEconformation with respect to the C=N imine bond and a water molecule. The dihedral angle between the aromatic rings is 41.67 (9)°. The methoxy substituent of the 4-methoxyphenyl group is twisted at an angle of 6.8 (3)° out of the plane of the attached benzene ring. In the 2,4,5-trimethoxyphenyl unit, thepara-methoxy group is coplanar with the ring [C—C—O—C = −1.5 (3)°], whereas theortho- andmeta-methoxy groups are twisted out of the plane of the ring [C—C—O—C = 75.4 (2) and −67.1 (2)°, respectively]. Two molecules are connected by two water moleculesviaO—H...O hydrogen bonds, generating anR22(8) ring motif. One of the water H atoms forms an additional hydrogen bond to an N atom. The water molecules act as an acceptor for an N—H...O hydrogen bond. As a result, a three-dimensional network is formed.

scholarly journals Down-regulation of NF-κB signalling by polyphenolic compounds prevents endotoxin-induced liver injury in a rat model

2011 ◽  
Vol 18 (1) ◽  
pp. 70-79 ◽  
Author(s):  
Sushma Bharrhan ◽  
Kanwaljit Chopra ◽  
Sunil K Arora ◽  
Jaideep S Toor ◽  
Praveen Rishi
Keyword(s):  
Liver Injury ◽  
Therapeutic Agent ◽  
Polyphenolic Compounds ◽  
Oxygen Species ◽  
Enhanced Production ◽  
Signalling Molecule ◽  
Tnf Α ◽  
Oxide Synthase ◽  
Inducible Nitric Oxide ◽  
Pharmacological Basis

Activation of NF-κB has been reported to play a key role in causing endotoxin-induced hepatic damage through enhanced production of reactive oxygen species and pro-inflammatory mediators. In this context, the potential of polyphenolic phytochemicals in preventing endotoxin-induced liver damage remains unclear. Here, we demonstrate that catechin and quercetin have the potential to down-regulate the initial signalling molecule NF-κB which may further inhibit the downstream cascade including TNF-α and NO. These results were confirmed using N-nitro-L-arginine methyl ester (L-NAME), the inhibitor of inducible nitric oxide synthase (iNOS) along with the biochemical and histological alterations occurring in the presence and absence of supplementation with both the polyphenols. However, catechin was found to be more effective than quercetin against endotoxin-induced liver injury. These findings suggest that these polyphenols may form a pharmacological basis for designing a therapeutic agent against endotoxin-mediated oxidative damage.

Hydrogen-bond patterns in 1,4-dihydro-2,3-quinoxalinediones: ligands for the glycine modulatory site on the NMDA receptor

1996 ◽  
Vol 52 (3) ◽  
pp. 487-499 ◽  
Author(s):  
M. Kubicki ◽  
T. W. Kindopp ◽  
M. V. Capparelli ◽  
P. W. Codding
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Binding Site ◽  
Three Dimensional ◽  
Hydrogen Bonding Pattern ◽  
Wide Range ◽  
Show Evidence ◽  
Additional Hydrogen Bond ◽  
Hydrogen Bond Patterns ◽  
Solvent Molecules

The crystal structures of five 1,4-dihydro-2,3-quinoxalinediones, antagonists of the NMDA modulatory glycine binding site on the excitary amino acid (EAA) receptor complex, have been determined: (I) 6,7-dinitro-1,4-dihydro-2,3-quinoxalinedione (DNQX); (II) 5,7-dinitro-1,4-dihydro-2,3-quinoxalinedione (MNQX); (III) 6-nitro-1,4-dihydro-2,3-quinoxalinedione hydrate; (IV) 6,7-dichloro-1,4-dihydro-2,3-quinoxalinedione; (V) 5,7-dichloro-1,4-dihydro-2,3-quinoxalinedione dimethylformamide. The crystal structure of the most active compound (II) contains a unique intramolecular N—H...O(NO2) hydrogen bond, which may be important for activity, as semiempirical calculations show that this bond is stable over a wide range of dihedral angles between the planes of the molecule and of the nitro group. In the other compounds the intermolecular hydrogen bonds connect molecules into three-dimensional networks. In compounds (I), (III) and (IV) head-to-tail: π-stacking is found between molecules connected by a center of symmetry. The geometries of the hydrogen-bonded —NH—C=O fragments show evidence of π-cooperativity or resonance-assisted hydrogen bonding. Graph-set analysis of the hydrogen-bond patterns of quinoxalinedione derivatives shows a tendency to form two types of hydrogen-bonding motifs: a centrosymmetric dimeric ring and an infinite chain. Even though this pattern may be modified by the presence of additional hydrogen-bond acceptors and/or donors, as well as by solvent molecules, general similarities have been found. Comparison of all quinoxalinedione structures suggests that the hydrogen-bonding pattern necessary for the biological activity at the glycine binding site contains one donor and two acceptors.

scholarly journals Effects of mutating Asn-52 to isoleucine on the haem-linked properties of cytochrome c

1994 ◽  
Vol 302 (1) ◽  
pp. 95-101 ◽  
Author(s):  
A Schejter ◽  
T I Koshy ◽  
T L Luntz ◽  
R Sanishvili ◽  
I Vig ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Site Directed Mutagenesis ◽  
Wild Type ◽  
General Increase ◽  
Reduction Potentials ◽  
Cytochromes C ◽  
In The Wild ◽  
Order Of Magnitude ◽  
The Stability ◽  
Haem Iron

Asn-52 of rat cytochrome c and baker's yeast iso-1-cytochrome c was changed to isoleucine by site-directed mutagenesis and the mutated proteins expressed in and purified from cultures of transformed yeast. This mutation affected the affinity of the haem iron for the Met-80 sulphur in the ferric state and the reduction potential of the molecule. The yeast protein, in which the sulphur-iron bond is distinctly weaker than in vertebrate cytochromes c, became very similar to the latter: the pKa of the alkaline ionization rose from 8.3 to 9.4 and that of the acidic ionization decreased from 3.4 to 2.8. The rates of binding and dissociation of cyanide became markedly lower, and the affinity was lowered by half an order of magnitude. In the ferrous state the dissociation of cyanide from the variant yeast cytochrome c was three times slower than in the wild-type. The same mutation had analogous but less pronounced effects on rat cytochrome c: it did not alter the alkaline ionization pKa nor its affinity for cyanide, but it lowered its acidic ionization pKa from 2.8 to 2.2. These results indicate that the mutation of Asn-52 to isoleucine increases the stability of the cytochrome c closed-haem crevice as observed earlier for the mutation of Tyr-67 to phenylalanine [Luntz, Schejter, Garber and Margoliash (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 3524-3528], because of either its effects on the hydrogen-bonding of an interior water molecule or a general increase in the hydrophobicity of the protein in the domain occupied by the mutated residues. The reduction potentials were affected in different ways; the Eo of rat cytochrome c rose by 14 mV whereas that of the yeast iso-1 cychrome c was 30 mV lower as a result of the change of Asn-52 to isoleucine.

scholarly journals Crystal Structures of the Ferrous Dioxygen Complex of Wild-type Cytochrome P450eryF and Its Mutants, A245S and A245T

2005 ◽  
Vol 280 (23) ◽  
pp. 22102-22107 ◽  
Author(s):  
Shingo Nagano ◽  
Jill R. Cupp-Vickery ◽  
Thomas L. Poulos
Keyword(s):  
Hydrogen Bond ◽  
Water Molecule ◽  
Crystal Structures ◽  
Proton Donor ◽  
Initial Structure ◽  
Hydrogen Bond Network ◽  
Wild Type ◽  
In The Wild ◽  
Site Water ◽  
Bond Network

Cytochrome P450eryF (CYP107A) from Saccaropolyspora ertherea catalyzes the hydroxylation of 6-deoxyerythronolide B, one of the early steps in the biosynthesis of erythromycin. P450eryF has an alanine rather than the conserved threonine that participates in the activation of dioxygen (O2) in most other P450s. The initial structure of P450eryF (Cupp-Vickery, J. R., Han, O., Hutchinson, C. R., and Poulos, T. L. (1996) Nat. Struct. Biol. 3, 632–637) suggests that the substrate 5-OH replaces the missing threonine OH group and holds a key active site water molecule in position to donate protons to the iron-linked dioxygen, a critical step for the monooxygenase reaction. To probe the proton delivery system in P450eryF, we have solved crystal structures of ferrous wild-type and mutant (Fe2+) dioxygen-bound complexes. The catalytic water molecule that was postulated to provide protons to dioxygen is absent, although the substrate 5-OH group donates a hydrogen bond to the iron-linked dioxygen. The hydrogen bond network observed in the wild-type ferrous dioxygen complex, water 63-Glu360-Ser246-water 53-Ala241 carbonyl in the I-helix cleft, is proposed as the proton transfer pathway. Consistent with this view, the hydrogen bond network in the O2·A245S and O2 ·A245T mutants, which have decreased or no enzyme activity, was perturbed or disrupted, respectively. The mutant Thr245 side chain also perturbs the hydrogen bond between the substrate 5-OH and dioxygen ligand. Contrary to the previously proposed mechanism, these results support the direct involvement of the substrate in O2 activation but raise questions on the role water plays as a direct proton donor to the iron-linked dioxygen.

scholarly journals Crystal water as the molecular glue for obtaining different co-crystal ratios: the case of gallic acid tris-caffeine hexahydrate

2018 ◽  
Vol 74 (4) ◽  
pp. 559-562
Author(s):  
L. Vella-Zarb ◽  
U. Baisch
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Gallic Acid ◽  
Carbonyl Oxygen ◽  
Crystalline Solid ◽  
Water Molecules ◽  
Crystal Water ◽  
Classical Hydrogen Bond ◽  
Additional Hydrogen

The crystal structure of the hexahydrate co-crystal of gallic acid and caffeine, C7H6O5·3C8H10N4O2·6H2O or GAL3CAF·6H2O, is a remarkable example of the importance of hydrate water acting as structural glue to facilitate the crystallization of two components of different stoichiometries and thus to compensate an imbalance of hydrogen-bond donors and acceptors. The water molecules provide the additional hydrogen bonds required to form a crystalline solid. Whereas the majority of hydrogen bonds forming the intermolecular network between gallic acid and caffeine are formed by crystal water, only one direct classical hydrogen bond between two molecules is formed between the carboxylic oxygen of gallic acid and the carbonyl oxygen of caffeine with d(D...A) = 2.672 (2) Å. All other hydrogen bonds either involve crystal water or utilize protonated carbon atoms as donors.

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