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Mac1 mediates copper (Cu)-dependent expression of genes involved in high-affinity uptake of copper ions in Saccharomyces cerevisiae. Mac1 is a transcriptional activator in Cu-deficient cells, but is inhibited in Cureplete cells. Mac1 resides within the nucleus in both Cu-deficient and Cu-loaded cells. Cu inhibition of Mac1 appears to result from binding of eight copper ions within a C-terminal segment consisting of two Cys-rich motifs. In addition, two zinc ions are bound within the N-terminal DNA-binding domain. Only 4–5 mol. eq. Cu are bound to a mutant Mac1 (His279Gln substitution) that is impervious to Cu inhibition. The CuMac1 complex is luminescent, indicative of copper bound in the Cu(I) state. Cu binding induces a molecular switch resulting in an intramolecular interaction in Mac1 between the N-terminal DNA-binding domain and the C-terminal activation domain. This allosteric interaction is Cu dependent and is not observed when Mac1 contained the mutant His279Gln substitution. Fusion of the minimal DNA-binding domain of Mac1 (residues 1–159) to the minimal Cu-binding activation domain (residues 252–341) yields a functional Cu-regulated transcriptional activator. These results suggest that Cu repression of Mac1 arises from a Cu-induced intramolecular interaction that inhibits both DNA binding and transactivation activities. [ABSTRACT FROM AUTHOR]

• New pentacoordinated semicarbazone copper complex was reported. • Factors that lead to the formation of a pentacoordinated complex instead of the expected hexacoordinated complex were analyzed. • Absence of the Cu-O bond in the pentacoordinated complex leads to redistribution of the energies in the remaining Cu-ligand bonds. • The metal-ligand energies change as a function of the length of each Cu-ligand bond. • Supramolecular similarity index ID was calculated and an isostructural behavior was observed. The structural characterization of a new pentacoordinated semicarbazone copper complex, [Cu(N,N',O -HSCPy)(N,N' -HSCPy)][ClO 4 ] 2 (1) is reported. The structure of 1 was compared to the hexacoordinated complex, [Cu(N,N',O -HSCPy) 2 ][ClO 4 ] 2 ⋅H 2 O (2), which was already published, to shed some light on the formation of both forms. Energetic data of Cu-ligand bonds showed that the absence of a Cu-O bond in cation 1 does not significantly change the total stabilization energy in the pentacoordinate cation relative to the hexacoordinate cation (less than 4%). This is because the Cu-ligand bonds have their energies redistributed into the five existing bonds of 1. Additionally, we extended the study revisiting analogous HSCPy complexes with other coordinated metals (M), with general formula [M(N,N',O -HSCPy) 2 ][X] 2 ⋅solvent, where M = Ni (3), Co (4), Zn (5), Fe (6), and Mn (7); X = ClO 4 , and solvent = H 2 O (3-6) or EtOH (7); and complex [Cu(N,N',O -HSCPy) 2 ][ClO 4 ][I 3 ] (8) was included in this series. In general, all additional complexes showed similar behavior to that of the Cu-hexacoordinated complex (2). In this sense, was possible to observe that the energies of the bonds M-O and M-N have strong linear correlation in the three groups: M-O3′//M-O3, M-N1′//M-N1, and M-N2′//M-N2, for complexes 2-7 (r = 0.9766; N = 18). Also, a strong correlation between stabilization energy data of metal-ligand and their respective bond lengths (r =0.9393; N = 47) was observed in all studied complexes (1 - 8). The supramolecular geometric similarity index ID was calculated comparing 2 with 1, 3-8. It was observed a high geometric similarity between 2 and 3-6 (ID < 0.95), indicating an isostructural behavior. The comparison between 2 and complexes 1,8 indicated values in the intermediate region (ID = 0.75) and close to a border region with an intermediate-to-high region of similarity (ID = 0.83), respectively. The similarity comparison between 2 and 7 had a value of 0.77, in the intermediate region of similarity, showing that the change of a water molecule for an ethanol molecule considerably affected the crystal packing. Image, graphical abstract [ABSTRACT FROM AUTHOR]

The synthesis of a novel telluroxane cluster, [(R 2 TeO)(μ -TeO 2)(OTeR 2)][TeO(OH) 2 ] (R=C 6 H 5 NNC 6 H 4) is achieved by the oxidation of bis[2-(phenylazo)-phenyl- C,N ́] telluride with NaIO 4. The X-ray crystallographic diffraction studies in corroboration with Density Functional Theory calculation reveal that the cluster is stabilized by intramolecular Te···N and intra- and intermolecular O∙∙∙Te secondary bonding interactions. [Display omitted] The oxidation reaction of diorganotelluride R 2 Te, 1 (where R = C 6 H 5 NNC 6 H 4) with NaIO 4 resulted in the isolation of a telluroxane cluster, namely [(R 2 TeO)(μ -TeO 2)(OTeR 2)][TeO(OH) 2 ], 2. The formation of 2 was confirmed by multinuclear (1H, 13C and 125Te) NMR and FT-IR spectroscopy, and elemental analysis. The structure of compound 2 was further corroborated by X-ray crystallographic studies. It is observed that telluroxane cluster 2 was stabilized by intramolecular Te···N and intra- and intermolecular O∙∙∙Te secondary bonding interactions. The detailed electronic structural properties of the cluster were thoroughly investigated by Density Functional Theory (DFT) calculations. In particular, the hybridization of the Te atoms were calculated by Natural Bonding Orbital (NBO) analysis. The natural charges accumulated on the Te and the O atoms in compound 2 were calculated by Natural Population Analysis (NPA). In addition, the HOMO-LUMO energy gap in 2 was calculated. [ABSTRACT FROM AUTHOR]

• Geometrical parameters and electronic properties of gardona and its related compounds were discussed. • Spectroscopic properties have been examined by FT-IR, FT-Raman, UV–visible, NMR techniques and DFT methods. • Interamolecular interactions were analysed using NBO analysis. • Finger print plots were identified by using Hirshfeld surface analysis. • Molecular docking analysis explained bioactivity of the compound. The aim of this study is to provide deeper knowledge of structural activity, spectroscopic analysis, chemical reactivity and insecticidal activity of gardona and its related compounds by combining experimental and computational methods. The natures of the hydrogen bonds were characterized by NBO analysis. Hirshfeld surfaces display all of the intermolecular interactions within the molecule. The 1H and 13C NMR spectra were recorded. The evaluated HOMO and LUMO energies indicate the chemical stability of the molecules. The molecular docking was made on the compounds to study the hydrogen bond interaction and the minimum binding energy. Insecticidal activities of extracts were determined against larvae of Corcyra cephalonica. Image, graphical abstract [ABSTRACT FROM AUTHOR]

Oxido bridges commonly form between iron(III) ions, but their bond angles and symmetry vary with the circumstances. A large number of oxido-bridged dinuclear iron(III) complexes have been structurally characterized. Some of them belong to the C2 point group, possessing bent Fe–O–Fe bonds, while some others belong to the Ci symmetry, possessing the linear Fe–O–Fe bonds. The question in this study is what determines the structures and symmetry of oxido-bridged dinuclear iron(III) complexes. In order to gain further insights, three oxido-bridged dinuclear iron(III) complexes were newly prepared with 2,2′-bipyridine (bpy) and 1,10-phenanthroline (phen) ligands: [Fe2OCl2(bpy)4][PF6]2 (1), [Fe2O(NO3)2(bpy)4][PF6]2·0.6MeCN·0.2(2-PrOH) (2), and [Fe2OCl2(phen)4][PF6]2·MeCN·0.5H2O (3). The crystal structures of 1, 2, and 3 were determined by the single-crystal X-ray diffraction method, and all of them were found to have the bent Fe–O–Fe bonds. Judging from the crystal structure, some intramolecular interligand hydrogen bonds were found to play an important role in fixing the structures. Additional density functional theory (DFT) calculations were conducted, also for a related oxido-bridged dinuclear iron(III) complex with a linear Fe–O–Fe bond. We conclude that the Fe–O–Fe bridge tends to bend like a water molecule, but is often stretched by interligand steric repulsion, and that the structures are mainly controlled by the intramolecular interligand interactions. [ABSTRACT FROM AUTHOR]

This article is probably the first such comprehensive review of theoretical methods for estimating the energy of intramolecular hydrogen bonds or other interactions that are frequently the subject of scientific research. Rather than on a plethora of numerical data, the main focus is on discussing the theoretical rationale of each method. Additionally, attention is paid to the fact that it is very often possible to use several variants of a particular method. Both of the methods themselves and their variants often give wide ranges of the obtained estimates. Attention is drawn to the fact that the applicability of a particular method may be significantly limited by various factors that disturb the reliability of the estimation, such as considerable structural changes or new important interactions in the reference system. [ABSTRACT FROM AUTHOR]

• The bonding properties are similar but not identical in isoelectronic species of nearly planar superatoms. • The change of covalent contribution is related to the decrease of 5f energy level in the actinide embedded planar superatoms. • The bonding is affected by the uncertainty electronic configuration of the intramolecular interaction. The electronic structure of isoelectronic superatoms formed by actinides embedded gold ring, An@Au 6 ([Ac@Au 6 − and Th@Au 6 , [Pa@Au 6 +), have been analyzed to investigate the intramolecular interaction using density functional theory. The bonding properties are similar but not identical. The probability densities of 1P and 1D superatomic molecular orbitals are similar, and compared with 6d orbitals, 5f orbitals show localization behaviors, and the change in their contribution of the covalent bonding relate to the decrease in 5f energy levels. Moreover, additional evidence for the bonding being affected by the uncertainty of electronic configuration could be gathered. [ABSTRACT FROM AUTHOR]

Src homology 3 (SH3) domains are small protein modules involved in the regulation of important cellular pathways such as proliferation and migration, which canonically prefer to recognize and interact with proline-rich peptide ligands with class I or class II motif. Previously, we identified two self-binding peptides (SBPs) in human c -Src tyrosine kinase, of which the first SBP (fSBP) segment ( 248 SK P QT Q G L AK 257 ) fulfills intramolecular interaction with the kinase SH3 domain to regulate the kinase function. The segment (and its equivalents in other c -Src family members) does not contain canonical class II motif (PxxQxL versus PxxPx+), but can bind to SH3 domain in a routine class II mode. Existing theories such as non-polyproline-II binding conformation, unusual peptide-binding pocket and extensive use of contacts cannot explain this atypical recognition phenomenon. Here, we performed a systematic investigation of SH3-fSBP binding in different conditions, including the segment in full-length kinase or in isolated state, the kinase in different forms and the fSBP residue mutations, by using microsecond molecular dynamics simulations, conformational clustering analyses and binding energetics calculations. We purposed a new mechanism that the protein context is primarily responsible for the atypical intramolecular SH3-fSBP recognition in c -Src kinase, which can promote the tight packing of segment against domain surface, support the segment polyproline-II (PPII) conformation in unbound state, and avoid unfavorable segment interactions with SH3 charged region by forming a C-terminal t -turn. In addition, the only proline residue Pro250 of fSBP segment is also required for the segment recognition by SH3 domain in c -Src kinase context; lack of Pro250 residue the segment exhibits considerable disorder and cannot maintain in PPII helical conformation, thus largely impairing the domain-segment binding capability. Further binding analysis confirms that the isolated fSBP peptide cannot bind effectively to SH3 domain out of kinase context, whereas its mutant version, i.e. fSBP(Q253P/L255R) peptide, which possesses the canonical class II motif, exhibits an increased affinity to the domain.Communicated by Ramaswamy H. Sarma.

Heme-regulatory motifs (HRMs) are present in many proteins that are involved in diverse biological functions. The C-terminal tail region of human heme oxygenase-2 (HO2) contains two HRMs whose cysteine residues form a disulfide bond; when reduced, these cysteines are available to bind Fe 3+ -heme. Heme binding to the HRMs occurs independently of the HO2 catalytic active site in the core of the protein, where heme binds with high affinity and is degraded to biliverdin. Here, we describe the reversible, protein-mediated transfer of heme between the HRMs and the HO2 core. Using hydrogen-deuterium exchange (HDX)-MS to monitor the dynamics of HO2 with and without Fe 3+ -heme bound to the HRMs and to the core, we detected conformational changes in the catalytic core only in one state of the catalytic cycle-when Fe 3+ -heme is bound to the HRMs and the core is in the apo state. These conformational changes were consistent with transfer of heme between binding sites. Indeed, we observed that HRM-bound Fe 3+ -heme is transferred to the apo-core either upon independent expression of the core and of a construct spanning the HRM-containing tail or after a single turnover of heme at the core. Moreover, we observed transfer of heme from the core to the HRMs and equilibration of heme between the core and HRMs. We therefore propose an Fe 3+ -heme transfer model in which HRM-bound heme is readily transferred to the catalytic site for degradation to facilitate turnover but can also equilibrate between the sites to maintain heme homeostasis., (© 2020 Fleischhacker et al.)

The first representatives of a new class of organogermanium compounds, the acylamides of C-germylcarboxylic acids, N-acetyl-N-methyl-3-(trichlorogermyl)propionamide and N-3-(trichlorogermyl)propionylurethane, were synthesized. An X-ray structural study of ClGeCHCHC(O)NMeC(O)Me revealed a greater Ge...O intramolecular distance than that reported earlier for 3-(trichlorogermyl)propionamides. The Ge atom configuration is somewhat distorted towards a trigonal bipyramid. [ABSTRACT FROM AUTHOR]

Five novel hydrazones derived from substituted isatins were synthesized as potential anion sensors. Using UV-VIS, FTIR, NMR and fluorescence spectroscopy, these compounds' tautomeric equilibrium and Z-E photoisomerization were studied in DMF and CHCl3, depending on the hydrazone concentrations, the presence of basic anions and light stimulation. Anion recognition aspects (PF6−, HSO4−, Br−, Cl−, NO3−, F− and CH3COO−) and these receptors' detection limits were also studied. We also tested the light-stimulated ON-OFF functionality of these compounds in the presence or absence of these anions. [ABSTRACT FROM AUTHOR]

Intramolecular interaction is a common mechanism that regulates protein activities. Conventionally, such interactions are investigated by classical in vitro biochemical assays. Here, we describe a protocol for studying the intramolecular interaction of cell motility and engulfment 1 (ELMO1) in mammalian cells by using proximity ligation assay (PLA). PLA is a specific and sensitive method that allows the observation of interacting proteins by target-specific antibody detection coupled to rolling circle amplification. ELMO1 is the regulatory subunit of ELMO1-dedicator of cytokinesis 180 (DOCK180) bipartite Rac1 guanine nucleotide exchange factor (GEF) which adopts a closed autoinhibitory conformation via an intramolecular interaction of its N-terminal ELMO inhibitory domain (EID) and C-terminal ELMO autoregulatory domain (EAD). In the assay, PLA signals are detected in cells transfected with ELMO1 1-315 and ELMO1 315-727 fragments. Moreover, overexpression of FE65, a neuronal adaptor which has been shown to disrupt ELMO1 intramolecular interaction, reduces the PLA signals of the two ELMO1 fragments significantly. Together, our results demonstrate that PLA can be employed for studying protein intramolecular interaction., Competing Interests: Competing interestsThe authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2019 The Authors; exclusive licensee Bio-protocol LLC.)

Ebola virus (EBOV) VP40 is a major driving force of nascent virion production and a negative regulator of genome replication/transcription. Here, we showed that the YIGL sequence at the C-terminus of EBOV VP40 is important for virus-like particle (VLP) production and the regulation of genome replication/transcription. Accordingly, a mutation in the YIGL sequence caused defects in VLP production and genome replication/transcription. The residues I293 and L295 in the YIGL sequence were particularly critical for VLP production. Furthermore, an in silico analysis indicated that the amino acids surrounding the YIGL sequence contribute to intramolecular interactions within VP40. Among those surrounding residues, F209 was shown to be critical for VLP production. These results suggested that the VP40 YIGL sequence regulates two different viral replication steps, VLP production and genome replication/transcription, and the nearby residue F209 influences VLP production.

The NS4A protein of dengue virus (DENV) has a cytosolic N terminus and four transmembrane domains. NS4A participates in RNA replication and the host antiviral response. However, the roles of amino acid residues within the N-terminus of NS4A during the life cycle of DENV are not clear. Here we explore the function of DENV NS4A by introducing a series of alanine substitutions into the N-terminus of NS4A in the context of a DENV infectious clone or subgenomic replicon. Nine of 17 NS4A mutants displayed a lethal phenotype due to the impairment of RNA replication. M2 and M14 displayed a more than 10 000-fold reduction in viral yields and moderate defects in viral replication by a replicon assay. Sequencing analyses of pseudorevertant viruses derived from M2 and M14 viruses revealed one consensus reversion mutation, A21V, within NS4A. The A21V mutation apparently rescued viral RNA replication in the M2 and M14 mutants although not to wild-type (WT) levels but resulted in 100- and 1000-fold lower titres than that of the WT, respectively. M2 Rev1 (M2+A21V) and M14 Rev1 (M14+A21V) mutants displayed phenotypes of smaller plaque size and WT-like assembly/secretion by a transpackaging assay. A defect in the virus-induced cytopathic effect (CPE) was observed in HEK-293 cells infected with either M2 Rev1 or M14 Rev1 mutant virus by MitoCapture staining, cell proliferation and lactate dehydrogenase release assays. In conclusion, the results revealed the essential roles of the N-terminal NS4A in both RNA replication and virus-induced CPE. Intramolecular interactions in the N-terminus of NS4A were implicated.

Ubiquitination, the covalent attachment of ubiquitin to proteins, by E3 ligases of the HECT (homologous to E6AP C terminus) family is critical in controlling diverse physiological pathways. Stringent control of HECT E3 ligase activity and substrate specificity is essential for cellular health, whereas deregulation of HECT E3s plays a prominent role in disease. The cell employs a wide variety of regulatory mechanisms to control HECT E3 activity and substrate specificity. Here, we summarize the current understanding of these regulatory mechanisms that control HECT E3 function. Substrate specificity is generally determined by interactions of adaptor proteins with domains in the N-terminal extensions of HECT E3 ligases. These N-terminal domains have also been found to interact with the HECT domain, resulting in the formation of inhibitory conformations. In addition, catalytic activity of the HECT domain is commonly regulated at the level of E2 recruitment and through HECT E3 oligomerization. The previously mentioned regulatory mechanisms can be controlled through protein-protein interactions, post-translational modifications, the binding of calcium ions, and more. Functional activity is determined not only by substrate recruitment and catalytic activity, but also by the type of ubiquitin polymers catalyzed to the substrate. While this is often determined by the specific HECT member, recent studies demonstrate that HECT E3s can be modulated to alter the type of ubiquitin polymers they catalyze. Insight into these diverse regulatory mechanisms that control HECT E3 activity may open up new avenues for therapeutic strategies aimed at inhibition or enhancement of HECT E3 function in disease-related pathways.

Genetic defects in SHANK genes are associated with autism. Deletions and truncating mutations suggest haploinsufficiency for Shank3 as a major cause of disease which may be analyzed in appropriate Shank deficient mouse models. Here we will focus on the functional analysis of missense mutations found in SHANK genes. The relevance of most of these mutations for Shank function, and their role in autism pathogenesis is unclear. This is partly due to the fact that mutations spare the most well studied functional domains of Shank3, such as the PDZ and SAM domains, or the short proline-rich motifs which are required for interactions with postsynaptic partners Homer, Cortactin, dynamin, IRSp53 and Abi-1. One set of mutations affects the N-terminal part, including the highly conserved SPN domain and ankyrin repeats. Functional analysis from several groups has indicated that these mutations (e.g., R12C; L68P; R300C, and Q321R) interfere with the critical role of Shank3 for synapse formation. More recently the structural analysis of the SPN-ARR module has begun to shed light on the molecular consequences of mutations in the SPN of Shank3. The SPN was identified as a Ras association domain, with high affinities for GTP-bound, active forms of Ras and Rap. The two autism related mutations in this part of the protein, R12C and L68P, both abolish Ras binding. Further work is directed at identifying the consequences of Ras binding to Shank proteins at postsynaptic sites.

Rab GTPases are key regulators of membrane trafficking, and many are activated by guanine nucleotide exchange factors bearing a d ifferentially e xpressed in n ormal and n eoplastic cells (DENN) domain. By activating the small GTPase Rab12, DENN domain-containing protein 3 (DENND3) functions in autophagy. Here, we identified a structural domain (which we name PHenn) containing a pleckstrin homology subdomain that binds actin and is required for DENND3 function in autophagy. We found that a hydrophobic patch on an extended β-turn of the PHenn domain mediates an intramolecular interaction with the DENN domain of DENND3. We also show that DENND3 binds actin through a surface of positively charged residues on the PHenn domain. Substitutions that blocked either DENN or actin binding compromised the role of DENND3 in autophagy. These results provide new mechanistic insight into the structural determinants regulating DENND3 in autophagy and lay the foundation for future investigations of the DENN protein family., (© 2018 by The American Society for Biochemistry and Molecular Biology, Inc.)

Transient receptor potential (TRP) channels are regulated by diverse stimuli comprising thermal, chemical, and mechanical modalities. They are also commonly regulated by phosphatidylinositol-4,5-bisphosphate (PIP2), with underlying mechanisms largely unknown. We here revealed an intramolecular interaction of the TRPP3 N and C termini (N-C) that is functionally essential. The interaction was mediated by aromatic Trp81 in pre-S1 domain and cationic Lys568 in TRP-like domain. Structure-function analyses revealed similar N-C interaction in TRPP2 as well as TRPM8/-V1/-C4 via highly conserved tryptophan and lysine/arginine residues. PIP2 bound to cationic residues in TRPP3, including K568, thereby disrupting the N-C interaction and negatively regulating TRPP3. PIP2 had similar negative effects on TRPP2. Interestingly, we found that PIP2 facilitates the N-C interaction in TRPM8/-V1, resulting in channel potentiation. The intramolecular N-C interaction might represent a shared mechanism underlying the gating and PIP2 regulation of TRP channels., (Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.)

Mrc1 and its vertebrate homologue Claspin serve as a mediator for replication stress checkpoint signaling, receiving the signal from Mec1/Rad3/ATR sensor kinase and transmitting it to the effector Rad53/Cds1/Chk1 kinase. They are likely to be a part of the replisome and facilitate the S-phase progression by promoting replication fork progression. Recent reports on Mrc1/Claspin indicate their new role in regulating the replication initiation through interaction with Cdc7, a key conserved serine-threonine kinase that triggers firing at each replication origin. Mrc1/Claspin has a specific domain that specifically interacts with Cdc7, and this domain is involved also in intramolecular interaction with its N-terminal segment. Mechanisms for novel regulation of origin firing and its timing through recruitment of Cdc7 to Mrc1/Claspin will be discussed.

The Ca 2+ and Ca 2+ /calmodulin-dependent protein kinase (CCaMK) is an important effector protein of Ca 2+ /calmodulin-mediated signaling, and in legumes, it is a critical regulator of plant-rhizobia and mycorrhizal symbioses. CCaMK contains a kinase domain, a calmodulin-binding/autoinhibitory domain and a visinin-like domain. Previous studies revealed the presence of 2 phosphorylation sites, S343 and S344, in the calmodulin-binding domain. Mutations at these sites affected the kinase activity and downstream rhizobium and mycorrhizal symbioses, which highlighted the importance of these residues in regulating protein activity. This addendum further clarifies the regulation of CCaMK by identifying an intramolecular interaction between residue(s) in the kinase domain and phosphorylation sites S343 and S344. This interaction turns off the substrate phosphorylation capacity of CCaMK.

The Rab family of small GTPases functions in multiple aspects of cellular membrane trafficking. Proteins bearing a d ifferentially e xpressed in n ormal and n eoplastic cells (DENN) domain have emerged as the largest family of Rab-activating guanine nucleotide exchange factors (GEFs). Rab12 functions in the initiation of starvation-induced autophagy, and our previous work revealed that its activator, DENN domain-containing protein 3 (DENND3), is phosphorylated and activated upon starvation. However, how the GEF activity of DENND3 toward Rab12 is regulated at the molecular level is still not understood. Here, we combine size-exclusion chromatography, Förster resonance energy transfer, pulldown, and in vitro GEF assays to demonstrate that regulation of GEF activity is achieved through an intramolecular interaction that is controlled by a key residue in DENND3, tyrosine 940. Our study sheds light on the regulation of Rab12 activation and lays the groundwork for characterizing the regulation of other DENN domain-containing proteins., (© 2017 by The American Society for Biochemistry and Molecular Biology, Inc.)

We report the full assignment of 1 H and 13 C NMR signals belonging to α-glucosyl rhoifolin (Rhf-G), a novel transglycosylated compound synthesized from a flavone glycoside, rhoifolin, as well as its chemical structure. Furthermore, we report the complete NMR signal assignment for another transglycosylated compound, α-glucosyl rutin (Rutin-G), as the signals corresponding to its sugar moieties had not been identified. Electrospray ionization-mass spectrometry along with multiple NMR methods revealed that Rhf-G possesses three sugar moieties in its chemical structure. The additional glucose was bound directly via a transglycosylation to rhoifolin at position 3a of the sugar moiety. Interestingly, intramolecular hydrogen bonds in the basic Rhf-G and Rutin-G skeletons were confirmed by HMBC experiments. These findings will be helpful for comprehensive NMR studies on transglycosylated compounds in food, cosmetic, and pharmaceutical fields., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Organofluorine is a weak hydrogen-bond (HB) acceptor. Bernet et al. have demonstrated its capability to perturb OH···O intramolecular hydrogen bonds (IMHBs), using conformationally rigid carbohydrate scaffolds including levoglucosan derivatives. These investigations are supplemented here by experimental and theoretical studies involving six new levoglucosan derivatives, and complement the findings of Bernet et al. However, it is shown that conformational analysis is instrumental in interpreting the experimental data, due to the occurrence of non-intramolecular hydrogen-bonded populations which, although minor, cannot be neglected and appears surprisingly significant. The DFT conformational analysis, together with the computation of NMR parameters (coupling constants and chemical shifts) and wavefunction analyses (AIM, NBO), provides a full picture. Thus, for all compounds, the most stabilized structures show the OH groups in a conformation allowing IMHB with O5 and O6, when possible. Furthermore, the combined approach points out the occurrence of various IMHBs and the effect of the chemical modulations on their features. Thus, two-center or three-center IMHB interactions are observed in these compounds, depending on the presence or absence of additional HB acceptors, such as methoxy or fluorine.

Mrc1 is a conserved checkpoint mediator protein that transduces the replication stress signal to the downstream effector kinase. The loss of mrc1 checkpoint activity results in the aberrant activation of late/dormant origins in the presence of hydroxyurea. Mrc1 was also suggested to regulate orders of early origin firing in a checkpoint-independent manner, but its mechanism was unknown. Here we identify HBS (Hsk1 bypass segment) on Mrc1. An Δ HBS mutant does not activate late/dormant origin firing in the presence of hydroxyurea but causes the precocious and enhanced activation of weak early-firing origins during normal S-phase progression and bypasses the requirement for Hsk1 for growth. This may be caused by the disruption of intramolecular binding between HBS and NTHBS (N-terminal target of HBS). Hsk1 binds to Mrc1 through HBS and phosphorylates a segment adjacent to NTHBS, disrupting the intramolecular interaction. We propose that Mrc1 exerts a "brake" on initiation (through intramolecular interactions) and that this brake can be released (upon the loss of intramolecular interactions) by either the Hsk1-mediated phosphorylation of Mrc1 or the deletion of HBS (or a phosphomimic mutation of putative Hsk1 target serine/threonine), which can bypass the function of Hsk1 for growth. The brake mechanism may explain the checkpoint-independent regulation of early origin firing in fission yeast., (Copyright © 2017 American Society for Microbiology.)

The alkali metal (M=Li, Na, and K) para-substituted (M-1), meta-substituted (M-2) or ortho-substituted (M-3) derivatives of phenylpentazole (PhN5) were studied using density functional theory. The substituted metals improve the energy barrier for decomposition of the N5 ring of PhN5 by 19.3 ∼ 65.0 kJ/mol. M-3 has the ionic N-M bond, which is not found for M-1 and M-2. M-1 and M-2 have similar electrostatic potentials and dispersion interactions between metal and N5 ring. The comparable intramolecular interactions of M-1 and M-2 lead to similar N5 ring stability. Compared to M-1 and M-2, M-3 has a more negative charge on N5 ring and stronger dispersion interaction. The stronger intramolecular interactions of M-3 result in the higher N5 ring stability. For M-1 and M-2, different metals have slight affects on N5 ring stability. For M-3, N5 ring stability decreases in the order of Li > Na > K. The substituted metal lowers E(g) of PhN5.

Contrary to the widespread view that hydrogen bonding and its entropy effect play a dominant role in protein folding, folding into helical and hairpin-like structures is observed in molecular dynamics (MD) simulations without hydrogen bonding in the peptide-solvent system. In the widely used point charge model, hydrogen bonding is calculated as part of the interaction between atomic partial charges. It is removed from these simulations by setting atomic charges of the peptide and water to zero. Because of the structural difference between the peptide and water, van der Waals (VDW) interactions favor peptide intramolecular interactions and are a major contributing factor to the structural compactness. These compact structures are amino acid sequence dependent and closely resemble standard secondary structures, as a consequence of VDW interactions and covalent bonding constraints. Hydrogen bonding is a short range interaction and it locks the approximate structure into the specific secondary structure when it is included in the simulation. In contrast to standard molecular simulations where the total energy is dominated by charge-charge interactions, these simulation results will give us a new view of the folding mechanism., (© 2015 The Protein Society.)

Heat shock transcription factor (HSF) regulates the expression of genes encoding molecular chaperones and stress-responsive proteins. Conversion of HSF from a monomer to a homotrimer or heterotrimer is essential for its binding to heat shock elements (HSEs) comprised of inverted repeats of the pentamer nGAAn. Here, we constructed various human HSF1 derivatives and analyzed their transcriptional activity through the continuously and discontinuously arranged nGAAn units. We identified a short stretch of amino acids that inhibits the activation ability of HSF1, especially through discontinuous HSEs. This stretch is conserved in HSFs of various organisms, interacts with the hydrophobic repeat regions that mediate HSF oligomerization, and impedes homotrimer formation and DNA binding. This conserved domain plays an important role in maintaining HSF in an inactive monomeric form., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Vertebrate ankyrin-B and ankyrin-G exhibit divergent subcellular localization and function despite their high sequence and structural similarity and common origin from a single ancestral gene at the onset of chordate evolution. Previous studies of ankyrin family diversity have focused on the C-terminal regulatory domain. Here, we identify an ankyrin-B-specific linker peptide connecting the ankyrin repeat domain to the ZU52-UPA module that inhibits binding of ankyrin-B to membrane protein partners E-cadherin and neurofascin 186 and prevents association of ankyrin-B with epithelial lateral membranes as well as neuronal plasma membranes. The residues of the ankyrin-B linker required for autoinhibition are encoded by a small exon that is highly divergent between ankyrin family members but conserved in the ankyrin-B lineage. We show that the ankyrin-B linker suppresses activity of the ANK repeat domain through an intramolecular interaction, likely with a groove on the surface of the ANK repeat solenoid, thereby regulating the affinities between ankyrin-B and its binding partners. These results provide a simple evolutionary explanation for how ankyrin-B and ankyrin-G have acquired striking differences in their plasma membrane association while maintaining overall high levels of sequence similarity.

Five 8-(4-R-phenyl)-1-naphthol derivatives were prepared by PdCl(2)-catalysed electrophilic aromatic substitution. The pK(a)' values for these 1,8-disubstituted arene naphthols have been measured in acetonitrile/water (R = NO(2), 8.42; R = Cl, 8.52; R = H, 8.56; R = Me 8.68; and R = OMe, 8.71) and indicate a correlation with the electronic nature of the arene substituent, as determined through LFER analysis. Contributions to the relative pK(a)' values have been interpreted, using M06-2X DFT calculations, as consisting of two components: A small contribution from initial OH-π bonding in the starting materials and a larger contribution from anion-π interactions in the products. Such effects have implications for a range of other systems.