scholarly journals Molecular mechanism of ATP versus GTP selectivity of adenylate kinase

2018 ◽  
Vol 115 (12) ◽  
pp. 3012-3017 ◽  
Author(s):  
Per Rogne ◽  
Marie Rosselin ◽  
Christin Grundström ◽  
Christian Hedberg ◽  
Uwe H. Sauer ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Adenylate Kinase ◽  
Function Analysis ◽  
Substrate Selectivity ◽  
Cellular Functions ◽  
X Ray ◽  
Precise Control ◽  
X Ray Crystallography ◽  
The Family ◽  
Atp Analogs

Enzymatic substrate selectivity is critical for the precise control of metabolic pathways. In cases where chemically related substrates are present inside cells, robust mechanisms of substrate selectivity are required. Here, we report the mechanism utilized for catalytic ATP versus GTP selectivity during adenylate kinase (Adk) -mediated phosphorylation of AMP. Using NMR spectroscopy we found that while Adk adopts a catalytically competent and closed structural state in complex with ATP, the enzyme is arrested in a catalytically inhibited and open state in complex with GTP. X-ray crystallography experiments revealed that the interaction interfaces supporting ATP and GTP recognition, in part, are mediated by coinciding residues. The mechanism provides an atomic view on how the cellular GTP pool is protected from Adk turnover, which is important because GTP has many specialized cellular functions. In further support of this mechanism, a structure–function analysis enabled by synthesis of ATP analogs suggests that a hydrogen bond between the adenine moiety and the backbone of the enzyme is vital for ATP selectivity. The importance of the hydrogen bond for substrate selectivity is likely general given the conservation of its location and orientation across the family of eukaryotic protein kinases.

Configurational and conformational studies on condensation products of biogenic amines with 2,5-anhydro-D-mannose

1985 ◽  
Vol 63 (11) ◽  
pp. 2915-2921 ◽  
Author(s):  
Ian M. Piper ◽  
David B. MacLean ◽  
Romolo Faggiani ◽  
Colin J. L. Lock ◽  
Walter A. Szarek
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Hydrogen Bond ◽  
Direct Methods ◽  
Conformational Studies ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Twist Conformation ◽  
Cell Dimensions ◽  
Internal Hydrogen Bond

The products of a Pictet–Spengler condensation of tryptamine and of histamine with 2,5-anhydro-D-mannose have been studied by X-ray crystallography to establish their absolute configuration. 1(S)-(α-D-Arabinofuranosyl)-1,2,3,4-tetrahydro-β-carboline (1), C16H20N20O4, is monoclinic, P21 (No. 4), with cell dimensions a = 13.091(4), b = 5.365(1), c = 11.323(3) Å, β = 115.78(2)°, and Z = 2. 4-(α-D-Arabinofuranosyl)imidazo[4,5-c]-4,5,6,7-tetrahydropyridine (3), C11H17N3O4, is orthorhombic, P212121 (No. 19), with cell dimensions a = 8.118(2), b = 13.715(4), c = 10.963(3) Å, and Z = 4. The structures were determined by direct methods and refined to R1 = 0.0514, R2 = 0.0642 for 3210 reflections in the case of 1, and to R1 = 0.0312, R2 = 0.0335 for 1569 reflections in the case of 3. Bond lengths and angles within both molecules are normal and agree well with those observed in related structures. In 3 the base and sugar adopt a syn arrangement, which is maintained by an internal hydrogen bond between O(2′) and N(3). The sugar adopts a normal 2T3 twist conformation. The sugar has the opposite anti arrangement in the β-carboline 1 and the conformation of the sugar is unusual; it is close to an envelope conformation with O(4′) being the atom out of the plane. This conformation is caused by a strong intermolecular hydrogen bond from O(5′) in a symmetry-related molecule to O(4′). Both compounds are held together in the crystal by extensive hydrogen-bonding networks. The conformations of the compounds in solution have been investigated by 1H nmr spectroscopy, and the results obtained were compared with those obtained by X-ray crystallography for 1 and 3.

The crystal structure of ethyl-Z-3-amino-2-benzoyl-2-butenoate and measurement of the barrier to E,Z-isomerization

1980 ◽  
Vol 58 (17) ◽  
pp. 1821-1828 ◽  
Author(s):  
Gary D. Fallon ◽  
Bryan M. Gatehouse ◽  
Allan Pring ◽  
Ian D. Rae ◽  
Josephine A. Weigold
Keyword(s):  
Crystal Structure ◽  
Nuclear Magnetic Resonance ◽  
Hydrogen Bond ◽  
Free Energy ◽  
Magnetic Resonance ◽  
Energy Of Activation ◽  
X Ray ◽  
X Ray Crystallography ◽  
Free Energy Of Activation ◽  
Nuclear Magnetic

Ethyl-3-amino-2-benzoyl-2-butenoate crystallizes from pentane as either the E (mp 82–84 °C) or the Z-isomer (mp 95.5–96.5 °C). The E isomer is less stable, and changes spontaneously into the Z, which bas been identified by X-ray crystallography. The structure is characterised by an N–H/ester CO hydrogen bond and a very long C2—C3 bond (1.39 Å). Nuclear magnetic resonance methods have been used to measure the rate of [Formula: see text] isomerization at several temperatures, leading to the estimate that the free energy of activation at 268 K is 56 ± 8 kJ.

scholarly journals Structural and functional properties of a magnesium transporter of the SLC11/NRAMP family

eLife ◽  
2022 ◽  
Vol 11 ◽  
Author(s):  
Karthik Ramanadane ◽  
Monique S Straub ◽  
Raimund Dutzler ◽  
Cristina Manatschal
Keyword(s):  
Hydration Shell ◽  
Transition Metal Ions ◽  
Ion Binding ◽  
X Ray ◽  
X Ray Crystallography ◽  
Protein Architecture ◽  
Large Pool ◽  
Structural And Functional Properties ◽  
The Family ◽  
Magnesium Transporter

Members of the ubiquitous SLC11/NRAMP family catalyze the uptake of divalent transition metal ions into cells. They have evolved to efficiently select these trace elements from a large pool of Ca2+ and Mg2+, which are both orders of magnitude more abundant, and to concentrate them in the cytoplasm aided by the cotransport of H+ serving as energy source. In the present study, we have characterized a member of a distant clade of the family found in prokaryotes, termed NRMTs, that were proposed to function as transporters of Mg2+. The protein transports Mg2+ and Mn2+ but not Ca2+ by a mechanism that is not coupled to H+. Structures determined by cryo-EM and X-ray crystallography revealed a generally similar protein architecture compared to classical NRAMPs, with a restructured ion binding site whose increased volume provides suitable interactions with ions that likely have retained much of their hydration shell.

scholarly journals Reactions and interactions between peri-groups in 1-dimethylamino-naphthalene salts: an example of a “through space” amide

2016 ◽  
Vol 88 (4) ◽  
pp. 317-331
Author(s):  
Amélie Wannebroucq ◽  
Andrew P. Jarmyn ◽  
Mateusz B. Pitak ◽  
Simon J. Coles ◽  
John D. Wallis
Keyword(s):  
Hydrogen Bond ◽  
Methyl Ester ◽  
Carbonyl Group ◽  
Dimethylamino Group ◽  
X Ray ◽  
X Ray Crystallography ◽  
Electron Donation ◽  
Protonated Cation

Abstract8-Dimethylaminonaphthalene-1-carbaldehyde reacts readily at 0°C with benzoyl or pivaloyl chloride by O-acylation and formation of a N–C bond (1.566(2)–1.568(3) Å) between the peri-substituents to give a salt. The reaction is promoted by electron donation from the dimethylamino group to the carbonyl group, akin to the properties of an amide. In contrast, the corresponding methyl ester and N,N-diisopropylamide react with acid in ether by protonation of the dimethylamino group and formation of a hydrogen bond to the carbonyl group, while under similar conditions the N,N-dimethylamide undergoes ready hydrolysis to the acid. The structures of products are determined by X-ray crystallography, and from the latter hydrolysis crystals containing zwitterionic 1-dimethylammonium-naphthalene-8-carboxylate and the corresponding O-protonated cation along with dimethylammonium and triflate ions were obtained.

A Solid-State NMR Approach to Structure Determination of Membrane-Associated Peptides and Proteins

1997 ◽  
Author(s):  
S.J. Opella ◽  
L.E. Chirlian
Keyword(s):  
Nmr Spectroscopy ◽  
Membrane Proteins ◽  
Structural Biology ◽  
Experimental Studies ◽  
Globular Proteins ◽  
Biological Properties ◽  
Cellular Functions ◽  
X Ray ◽  
X Ray Crystallography ◽  
Form And Function

Structural biology relies on detailed descriptions of the three-dimensional structures of peptides, proteins, and other biopolymers to explain the form and function of biological systems ranging in complexity from individual molecules to entire organisms. NMR spectroscopy and X-ray crystallography, in combination with several types of calculations, provide the required structural information. In recent years, the structures of several hundred proteins have been determined by one or both of these experimental methods. However, since the protein molecules must either reorient rapidly in samples for multidimensional solution NMR spectroscopy or form high quality single crystals in samples for X-ray crystallography, nearly all of the structures determined up to now have been of the soluble, globular proteins that are found in the cytoplasm and periplasmof cells and fortuitously have these favorable properties. Since only a minority of biological properties are expressed by globular proteins, and proteins, in general, have evolved in order to express specific functions rather than act as samples for experimental studies, there are other classes of proteins whose structures are currently unknown but are of keen interest in structural biology. More than half of all proteins appear to be associated with membranes, and many cellular functions are expressed by proteins in other types of supramolecular complexes with nucleic acids, carbohydrates, or other proteins. The interest in the structures of membrane proteins, structural proteins, and proteins in complexes provides many opportunities for the further development and application of NMR spectroscopy. Our understanding of polypeptides associated with lipids in membranes, in particular, is primitive, especially compared to that for globular proteins. This is largely a consequence of the experimental difficulties encountered in their study by conventional NMR and X-ray approaches. Fortunately, the principal features of two major classes of membrane proteins have been identified from studies of several tractable examples. Bacteriorhodopsin (Henderson et al., 1990), the subunits of the photosynthetic reaction center (Deisenhofer et al., 1985), and filamentous bacteriophage coat proteins (Shon et al., 1991; McDonnell et al., 1993) have all been shown to have long transmembrane hydrophobic helices, shorter amphipathic bridging helices in the plane of the bilayers, both structured and mobile loops connecting the helices, and mobile N- and C-terminal regions.

scholarly journals 1-[N-Methyl-N-(Phenyl)amino]-3- (4-Methylphenyl)Thiourea

Molbank ◽  
10.3390/m1052 ◽  
2019 ◽  
Vol 2019 (1) ◽  
pp. M1052 ◽  
Author(s):  
Chien Yeo ◽  
Edward Tiekink
Keyword(s):  
Hydrogen Bond ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Elemental Analysis ◽  
Title Compound ◽  
Molecular Conformation ◽  
Phenyl Hydrazine ◽  
X Ray ◽  
X Ray Crystallography

The title compound, 1-[N-methyl-N-(phenyl)amino]-3-(4-methylphenyl)thiourea (1), was synthesized by the reaction of 1-methyl-1-phenyl hydrazine and 4-tolyl isothiocyanate, and was characterized by spectroscopy (1H and 13C{1H} NMR, IR, and UV), elemental analysis as well as by single crystal X-ray crystallography. In the solid state, the molecule exists as the thioamide tautomer and features an anti-disposition of the thioamide–N–H atoms; an intramolecular N–H⋯N hydrogen bond is noted. The molecular conformation resembles that of the letter L. In the molecular packing, thioamide-N1–H⋯S1(thione) hydrogen bonds lead to centrosymmetric eight-membered {⋯HNCS}2 synthons. The dimers are assembled into a supramolecular layer in the bc-plane by phenyl- and methyl-C–H⋯π(phenyl) interactions.

scholarly journals Charting Hydrogen Bond Anisotropy

2019 ◽  
Author(s):  
Diogo Santos-Martins ◽  
Stefano Forli
Keyword(s):  
Hydrogen Bond ◽  
Chemical Biology ◽  
Solid Phase ◽  
Electronic Configuration ◽  
Interaction Energies ◽  
X Ray ◽  
X Ray Crystallography ◽  
Chemical Groups ◽  
High Degree ◽  
Context Free

<div>Hydrogen bond (HB) is an essential interaction in countless phenomena, and regulates the chemistry of life. HBs are characterized by two main features, strength and directionality, with a high degree of heterogeneity across different chemical groups. These characteristics are dependent on the electronic configuration of the atoms involved in the interaction, which, in turn, is influenced strongly by the molecular environment where they are found. Studies based on the analysis of HB in solid phase, such as X-ray crystallography, suffer from significant biases due to the packing forces. These will tend to better describe strong HBs at the expenses of weak ones, which are either distorted or under represented. Using quantum mechanics (QM), we calculated interaction energies for about a hundred acceptor and donors, in a rigorously defined set of geometries. We performed about 180,000 independent QM calculations, covering all relevant angular components, and mapping strength and directionality in a context free from external biases, with both single-site and cooperative HBs. We show that by quantifying directionality, there is not correlation with strength, and therefore these two components need to be addressed separately. Results demonstrate that there are very strong HB acceptors (e.g.,DMSO) with nearly isotropic interactions, and weak ones (e.g.,thioacetone) with a sharp directional profile. Similarly, groups can have comparable directional propensity, but be very distant in the strength spectrum (e.g., thioacetone and pyridine). These findings have implications for biophysics and molecular recognition, providing new insight for chemical biology, protein engineering, and drug design. The results require rethinking the way directionality is described, with implications for the thermodynamics of HB.</div>

scholarly journals Expanding the Family of Tetrahalide Iron Complexes: Synthesis, Structure and Biological Applications.

2020 ◽  
Author(s):  
Nusrat Abedin ◽  
Abdullah Hamed A Alshehri ◽  
Ali M A Almughrbi ◽  
Olivia Moore ◽  
Sheikh Alyza ◽  
...  
Keyword(s):  
Antimicrobial Properties ◽  
Biological Properties ◽  
Biological Applications ◽  
X Ray ◽  
Mononuclear Iron ◽  
X Ray Crystallography ◽  
Gram Positive Bacteria ◽  
Axial Ligands ◽  
The Family ◽  
Resistant Strains

A neutral octahedral mononuclear iron(II) tetrabromide complex, [Fe(Hampy)<sub>2</sub>Br<sub>4</sub>], that consists of equatorial bromide and protonated aminopyrazinium axial ligands is successfully synthesised through redox chemistry and analysed using X-ray crystallography. The iron(II) oxidation state is balanced by the protonated pyrazinium nitrogen just outside the coordination sphere. The biological properties of this and two other related complexes are investigated using both Gram-negative and Gram-positive bacteria as well as methicillin resistant strains. They all exhibit some antimicrobial properties albeit at moderate to poor concentrations. However, the tetrahalide complexes analysed exhibit excellent anti biofilm properties well below cytotoxic levels.

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