Heme-regulated eukaryotic initiation factor 2␣ (eIF2␣) kinase (HRI) functions in response to the heme iron concentration. At the appropriate heme iron concentrations under normal conditions, HRI function is suppressed by binding of the heme iron. Conversely, upon heme iron shortage, HRI autophosphorylates and subsequently phosphorylates the substrate, eIF2␣, leading to the termination of protein synthesis. The molecular mechanism of heme sensing by HRI, including identification of the specific binding site, remains to be established. In the present study we demonstrate that His-119/His-120 and Cys-409 are the axial ligands for the Fe(III)-protoporphyrin IX complex (hemin) in HRI, based on spectral data on site-directed mutant proteins. Cys-409 is part of the heme-regulatory CysPro motif in the kinase domain. A P410A full-length mutant protein displayed loss of heme iron affinity. Surprisingly, inhibitory effects of the heme iron on catalysis and changes in the heme dissociation rate constants in full-length His-119/His-120 and Cys-409 mutant proteins were marginally different to wild type. In contrast, heme-induced inhibition of Cys-409 mutants of the isolated kinase domain and N-terminal-truncated proteins was substantially weaker than that of the full-length enzyme. A pulldown assay disclosed heme-dependent interactions between the N-terminal and kinase domains. Accordingly, we propose that heme regulation is induced by interactions between heme and the catalytic domain in conjunction with global tertiary structural changes at the N-terminal domain that accompany heme coordination and not merely by coordination of the heme iron with amino acids on the protein surface.Eukaryotic cells decrease their overall rates of protein synthesis for survival in response to a variety of stress conditions, such as shortage of amino acids, UV light illumination, virus infection, and accumulation of denatured proteins. Much of the decrease in protein synthesis is caused by phosphorylation of eukaryotic initiation factor 2␣ (eIF2␣) 4 at Ser-51 by eIF2␣ kinases that respond specifically to stress (1-4). Heme-regulated eIF2␣ kinase or heme-regulated inhibitor (HRI) is a member of the eIF2␣ kinase family that controls globin synthesis in response to the heme concentration in reticulocytes (5-8). HRI is inactive at normal heme concentrations. Under conditions of heme deficiency, the enzyme is activated by autophosphorylation and subsequently phosphorylates eIF2␣ at Ser-51. In addition to globin, HRI controls the synthesis of tryptophan 2,3-dioxygenase and cytochrome P450 2B in liver upon acute porphyria (9, 10). Thus, HRI is possibly one of the most important existing heme sensor protein families for eukaryote survival in response to cell emergency states.Heme-responsive/sensing proteins, also known as "heme sensor proteins" are a current focus of investigation. In these proteins heme association (or dissociation) per se regulates various important physiological functions, such as transcription, proteolysis, and kinase activity (11...

Molecular recognition plays a central role in many biological processes. For enzymatic reactions and slow protein-protein recognition events, turn-over rates and on-rates in the millisecond-to-second time scale have been connected to internal protein dynamics detected with atomic resolution by NMR spectroscopy, and in particular conformational sampling could be established as a mechanism for enzyme-substrate and protein-protein recognition. [1][2][3][4][5] Recent theoretical studies indicate that faster rates of conformational interconversion in the microsecond time scale might limit on-rates for protein-protein recognition. [6,7] However experimental proofs were lacking so far, mainly because such rates could not be determined accurately enough and kinetic experiments in the microsecond time range are difficult to perform.Nevertheless, for proteins and TAR-RNA, [8][9][10] recent studies based on residual dipolar couplings (RDCs) and other NMR spectroscopy techniques [11,12] have detected substantial internal dynamics in a time window from the rotational correlation time t c (one-digit nanoseconds) to approximately 50 ms, [8,[13][14][15] called the supra-t c window in the following. However, the exact rates of internal dynamics within this four orders of magnitude wide time window could not be determined.Supra-t c dynamics in ubiquitin [9] and TAR-RNA [16] could be connected to the conformational sampling required for molecular recognition. While the amplitudes of motions have been indirectly detected by RDCs and characterized in great detail, it has so far been impossible to directly observe these motions and to determine the exact rate of these supra-t c motions. In contrast, conformational sampling in enzymes occurs on a time scale that is 100 to 1000 times slower than supra-t c dynamics and therefore NMR relaxation dispersion (RD) techniques have been able to establish the functional link to enzyme kinetics with atomic resolution at physiological conditions.[1, 2, 5] However, for technical reasons, RD is not sensitive to motion faster than approximately 50 ms (RD window) and therefore does not access motion in the supra-t c window at room temperature.Here we determine the rate of interconversion between conformers of free ubiquitin by a combination of NMR RD experiments in super-cooled solution and dielectric relaxation spectroscopy (DR). Furthermore, we corroborate the motional amplitudes in the RDC-derived ensembles quantitatively with the observed amplitudes of RD and DR. The methods utilized herein can be used to directly study protein dynamics in a time range that was previously inaccessible.Significant motional amplitude in the supra-t c window has been observed using RDC measurements, and was connected to the conformational sampling for a protein in the ground

The effect of fluorine substitution on the aromaticity of polycyclic hydrocarbons (PAH) is investigated. Magnetically induced current densities, current pathways, and current strengths, which can be used to assess molecular aromaticity, are calculated using the gauge-including magnetically induced current method (GIMIC). The degree of aromaticity of the individual rings is compared to those obtained using calculated nucleus-independent chemical shifts at the ring centers (NICS(0) and NICS(0)(zz)). Calculations of explicitly integrated current strengths for selected bonds show that the aromatic character of the investigated polycyclic hydrocarbons is weakened upon fluorination. In contrast, the NICS(0) values for the fluorinated benzenes increase noteworthy upon fluorination, predicting a strong strengthening of the aromatic character of the arene rings. The integrated current strengths also yield explicit current pathways for the studied molecules. The current pathways of the investigated linear polyacenes, pyrene, anthanthrene, coronene, ovalene, and phenanthro-ovalene are not significantly affected by fluorination. NISC(0) and NICS(0)(zz) calculations provide contradictory degrees of aromaticity of the fused individual ring. Obtained NICS values do not correlate with the current strengths circling around the individual rings.

The aromatic pathways and the degree of aromaticity of expanded porphyrins have been determined by explicit calculations of the routes and strengths of the magnetically induced currents using the gauge-including magnetically induced current (GIMIC) approach. Density functional theory calculations show that the doubly twisted hexaphyrins fulfilling Hückel's (4n + 2) pi-electron rule for aromaticity and those obeying the 4n pi-electron rule for antiaromaticity are aromatic and antiaromatic, respectively. The investigated [26]hexaphyrin (2) and (3) and [30]hexaphyrin (5) isomers are aromatic, and [28]hexaphyrin (4) is antiaromatic. The formally antiaromatic [24]hexaphyrin (1) does not sustain any strong ring current and must be considered nonaromatic. A detailed analysis of the current pathways of the hexaphyrins is presented. It was found that the current pathways of the investigated aromatic hexaphyrins are not always dominated by the flow along the inner route through the non-hydrogenated C-N-C moieties, as previously proposed. The current flow is often split into two branches at the pyrrole rings, but sometimes it takes the outer route via the C=C bond of the pyrrole. The current pathway of the weak paratropic ring current of [24]hexaphyrin is dominated by the outer C=C route. The calculations show that the routes of the current transport cannot be assessed merely by inspection or from nucleus independent chemical shifts; explicit calculations of the current pathways are compulsory. The current-density studies also show that the pyrrole rings do not sustain any strong ring currents of their own.

The electronic absorption and emission spectra of the [n]cycloparaphenylenes with n = 6,7,...,11 ([n]CP) have been studied at the time-dependent density functional theory level. The calculations show that the optical gap increases with increasing size of the ring due to reduced ring strain in the larger carbon nanohoops, whereas the energy of the first bright state follows the opposite trend for the studied [n]CPs. For the excited-state structures, the C-C bonds between the phenylene groups have a significant double-bond character giving rise to a continuous electron delocalisation pathway around the ring. The torsion angles between the phenylene moieties are much smaller for the excited state than for the ground state suggesting that the excited state has a stronger electron delocalisation around the carbon nanohoop than for the ground state. The double bond character of the phenylene C-C bonds declines and the phenylene torsion angle increases with increasing ring size. The aromatic stabilisation of the excited state due to the continuous electron delocalisation pathway is probably the main reason for the large Stokes shift. The excited state of the larger [n]CPs are less aromatic than the smaller ones explaining why the Stokes shift decreases with increasing size of the ring. For large [n]CPs, the excitation-energy spectrum forms bands making localisation of the excitons feasible. Localisation of the excitons probably leads to the observed ring-size independence of the electronic excitation spectra for large [n]CPs.

Protonated forms of the tetrazine ligand L2 (3,6-bis(morpholin-4-ylethyl)-1,2,4,5-tetrazine) interact with iodide in aqueous solution forming relatively stable complexes (ΔG° = -11.6(4) kJ mol for HL2 + I = (HL2)I and ΔG° = -13.4(2) kJ mol for HL2 + I = [(HL2)I]). When solutions of [(HL2)I] are left in contact with air, crystals of the oxidation product (HL2)(I)I·4HO are formed. Unfortunately, the low solubility of I complexes prevents the determination of their stability constants. The crystal structures of HL2I·HO (1), HL2(I)·2HO (2) and (HL2)(I)I·4HO (3) were determined by means of X-ray diffraction analyses. In all crystal structures, it was found that the interaction between I and I with HL2 is dominated by anion interactions with the π electron density of the receptor. Only in the case of 1, the iodide anions involved in close anion-π interactions with the ligand tetrazine ring form an additional H-bond with the protonated morpholine nitrogen of an adjacent ligand molecule. Conversely, in crystals of 2 and 3 there are alternate segregated planes which contain only protonated ligands hydrogen-bonded to cocrystallized water molecules or I and I forming infinite two-dimensional networks established through short interhalogen contacts, making these crystalline products good candidates to behave as solid conductors. In the solid complexes, the triiodide anion displays both end-on and side-on interaction modes with the tetrazine ring, in agreement with density functional theory calculations indicating a preference for the alignment of the I molecular axis with the molecular axis of the ligand. Further information about geometries and structures of triiodide anions in 2 and 3 was acquired by the analysis of their Raman spectra.

Ligands L1 and L2, consisting of a tetrazine ring decorated with two morpholine pendants of different lengths, show peculiar anion-binding behaviors. In several cases, even the neutral ligands, in addition to their protonated HL(+) and H2L(2+) (L = L1 and L2) forms, bind anions such as F(-), NO3(-), PF6(-), ClO4(-), and SO4(2-) to form stable complexes in water. The crystal structures of H2L1(PF6)2·2H2O, H2L1(ClO4)2·2H2O, H2L2(NO3)2, H2L2(PF6)2·H2O, and H2L2(ClO4)2·H2O show that anion-π interactions are pivotal for the formation of these complexes, although other weak forces may contribute to their stability. Complex stability constants were determined by means of potentiometric titration in aqueous solution at 298.1 K, while dissection of the free-energy change of association (ΔG°) into its enthalpic (ΔH°) and entropic (TΔS°) components was accomplished by means of isothermal titration calorimetry measurements. Stability constants are poorly regulated by anion-ligand charge-charge attraction. Thermodynamic data show that the formation of complexes with neutral ligands, which are principally stabilized by anion-π interactions, is enthalpically favorable (-ΔG°, 11.1-17.5 kJ/mol; ΔH°, -2.3 to -0.5 kJ/mol; TΔS°, 9.0-17.0 kJ/mol), while for charged ligands, enthalpy changes are mostly unfavorable. Complexation reactions are invariably promoted by large and favorable entropic contributions. The importance of desolvation phenomena manifested by such thermodynamic data was confirmed by the hydrodynamic results obtained by means of diffusion NMR spectroscopy. In the case of L2, complexation equilibria were also studied in a 80:20 (v/v) water/ethanol mixture. In this mixed solvent of lower dielectric constant than water, the stability of anion complexes decreases, relative to water. Solvation effects, mostly involving the ligand, are thought to be responsible for this peculiar behavior.

We report calculations of the gauge-independent magnetically induced current densities in [n]cycloparaphenylenes ([n]CP), n = 6-11. In addition to the neutral [n]CPs, the dianion of [6]CP and the current densities of the corresponding metal complexes Li 2 [6]CP and Mg[6]CP are also investigated. By the ring current criterion, the [6]CP with 4n π electrons has a slight antiaromatic character, while [7]CP has (4n þ 2) π electrons and is weakly aromatic with a ring current susceptibility strength that is about 25% of the ring current of benzene. The larger neutral [n]CPs, n = 8-11, do not sustain any net ring current around the nanohoop and are essentially nonaromatic. The weak paramagnetic ring current susceptibility of [6]CP flows along a 4n π pathway on either edge of the phenylene rings. For the dianions, the ring current susceptibility strengths are 24-35 nA/T diatropic and thus the addition of two electrons induces an electron delocalization and an aromatic character of the nanohoops. The dilithium complex of [6]CP with (4n þ 2) π electrons is aromatic with a net ring current strength of 28 nA/T or 2.4 times the ring current strength of benzene, involving all 62 π electrons in the current pathway. The 1 H NMR chemical shieldings and the nucleus-independent chemical shifts correlate with the strengths of the magnetically induced currents. The aromatic [n]cycloparaphenylenes have a quinoid structure, whereas the weakly aromatic or nonaromatic ones are benzoidic.