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Highlights: [•] FT-IR, FT-Raman spectral investigation of thiophene-2-carbohydrazide performed. [•] The redistribution of electron density has been discussed. [•] The HOMO and LUMO energy gap show that charge transfer occurs within the molecule. [•] The calculated 3D MESP contour map is confirm an electrophilic and nucleophilic region. [•] Variation of dipole moment, polarizability is more in TCH1 than TCH2. [Copyright &y& Elsevier]

Abstract: To investigate the relationship between structures and piezochromic luminescence behavior and to develop excellent materials for efficient light-emitting electrochemical cells, a series of iridium(III) complexes with different length of alkyl chains have been designed and synthesized. The results show that all complexes exhibit not only naked-eye visible and reversible piezochromic behavior, but chain length-dependent emission properties: the shorter the alkyl chain is, the more remarkable mechanochromic behavior and higher recrystallization temperature will be. In light of powder X-ray diffractometry and differential scanning calorimetric data, the interconversion between crystalline and amorphous states upon external stimuli is response for the present piezochromism. Additionally, these complexes show high quantum yields of 55–65% in neat films as well as excellent redox reversibility. Despite changed alkyl chains are introduced into these complexes, the negligible effect on emitting colors and excited-state characters of them in both solutions and neat films have been observed. Such photophysical properties are also interpreted with the help of theoretical calculations. Moreover, the theoretical results suggest that the intrinsic intramolecular π–π stacking confirmed by the crystal structures can effectively restrict the opening of the structures in metal-centered excited-state, demonstrating their stability. The structure–property relationships and the results demonstrated here will help researchers develop and design more promising iridium(III)-based piezochromic materials and attractive phosphors for optical devices. [Copyright &y& Elsevier]

STIM1 (stromal interactionmolecule 1) is one of the key elements that mediate store-operated Ca2+ entry via CRAC (Ca2+ - releaseactivated Ca2+) channels in immune and non-excitable cells. Under physiological conditions, the intramolecular auto-inhibitions in STIM1 C- and STIM1 N-termini play essential roles in keeping STIM1 in an inactive state. However, the auto-inhibitory mechanism of the STIM1 C-terminus is still unclear. In the present study, we first predicted a short inhibitory domain (residues 310-317) in human STIM1 that might determine the different localizations of human STIM1 from Caenorhabditis elegans STIM1 in resting cells. Next, we confirmed the prediction and further identified an aromatic amino acid residue, Tyr316, that played a crucial role in maintaining STIM1 in a closed conformation in quiescent cells. Full-length STIM1-Y316A formed constitutive clusters near the plasma membrane and activated the CRAC channel in the resting state when co-expressed with Orai1. The introduction of a Y316A mutation caused the higher-order oligomerization of the in vitro purified STIM1 fragment containing both the auto-inhibitory domain andCAD(CRAC-activating domain).We propose that the Tyr316 residue may be involved in the auto-inhibitory mechanism of the STIM1 C-terminus in the quiescent state. This inhibition could be achieved either by interactingwith the CADusing hydrogen and/or hydrophobic bonds, or by an intermolecular interaction using repulsive forces, which maintained a dimeric STIM1. [ABSTRACT FROM AUTHOR]

Abstract: 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 &y& Elsevier]

Highlights: [•] The juxtamembrane domain (JMD) of the receptor kinase ACR4 contains 2 phosphosites. [•] Naïve and phosphorylated JMD peptides were panned against a phage-peptide library. [•] The consensus sequence LxSLL is recognized by the phosphorylated (pJMD) peptides. [•] pJMD peptides bind specifically to ACR4 kinase domain containing the LxSLL motif. [•] An intramolecular interaction is suggested between the JM and kinase domain of ACR4. [ABSTRACT FROM AUTHOR]

Abstract: Even though a bond path and the corresponding bond critical point were found for the intramolecular XO (X=Cl,Br) interaction in 3-halogenopropenal, thus according to QTAIM suggesting the stabilizing nature of this interaction, it was shown that this contact is repulsive. In order to utilize the well-defined energy of the intermolecular interaction, a dimer model was used. The C–XOt from the ZZ conformer of 3-halogenopropenal was preserved with its original geometrical arrangement. Such approach leads to the conclusion according to which the presence of a bond path and the corresponding bond critical point do not necessarily indicate a stabilizing interaction between a pair of atoms, but rather is a direct consequence of a large accumulation of the electron density between atoms. Values of QTAIM parameters characterizing both BCP of XO and RCP remain rather unchanged if the C–XOt with its preserved geometry is embedded in a dimer. It was also shown that atoms X and O are interacting by negative surfaces of the molecular electrostatic potential. Also the charge transfer between interacting fragments is opposite to expected. [Copyright &y& Elsevier]

Several trisamides of N,N-bis(2-aminoethyl)ethane-1,2-amine are prepared as potential saccharide receptors. Surprisingly low or even nil affinity to n-octyl-glucose is found by 1H NMR titration, and explained as a consequence of intramolecular hydrogen bonds of trisamides, (RCONHC2H4)3N. The hydrogen bonds are identified by combination of 1H NMR and infrared spectra, and 1H NMR temperature coefficients. Results demonstrate that even small molecule can has a rather strong secondary structure, which can cause their malfunctioning in certain applications. Results also point out that the amide temperature coefficients should not be used as the only parameter for the consideration a hydrogen bond is intermolecular or intramolecular, particularly, in the case of furcated hydrogen bonds, and in the cases were a couple of signals are averaged. [ABSTRACT FROM AUTHOR]

A comprehensive molecular dynamics simulation study of n-alkanes using the optimized potential for liquid simulation with all-atoms (OPLS-AA) force field at ambient condition has been performed. Our results indicate that while simulations with the OPLS-AA force field accurately predict the liquid state mass density for n-alkanes with carbon number equal or less than 10, for n-alkanes with carbon number equal or exceeding 12, the OPLS-AA force field with the standard scaling factor for the 1-4 intramolecular Van der Waals and electrostatic interaction gives rise to a quasi-crystalline structure. We found that accurate predictions of the liquid state properties are obtained by successively reducing the aforementioned scaling factor for each increase of the carbon number beyond n-dodecane. To better understand the effects of reducing the scaling factor, its influence on the torsion potential profile, and the corresponding gauche-trans conformer distribution, heat of vaporization, melting point, and self-diffusion coefficient for n-dodecane were investigated. This relatively simple procedure enables more accurate predictions of the thermo-physical properties of longer n-alkanes. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

We have developed a space-restricted wave function (SRW) method for the analysis of various types of intramolecular interactions. In this study, we demonstrate the applicability of our SRW method to the analysis of the nature of the PO bond in phosphine oxide (R3PO), one of the hypervalent molecules. An interesting character of this bond has been extensively studied by focusing on the negative hyperconjugation of the O lone pair (nO) with the R3P group. We reinvestigated the nature of the bond in terms of a change in total energy to produce evidence for the validity of our method. The electronic states without the interaction involving three nO orbitals (R3P+−O−) produced by the method were used as reference states in the assessment of the effects of this nO-R3P interaction. The result confirms that this interaction plays an essential role in the nature of the bond and occurs between the nO orbitals and the PR antibonding orbitals, in agreement with previous studies. A molecular orbital (MO)-pair analysis technique shows that the nO-R3P interaction is decomposed into the negative hyperconjugation and the Pauli repulsion. Considering a reference state where the PO bond is completely broken (R3P2+···O2−) at an interacting distance, PO bond formation is attributed to one σ bond plus two 0.5 π bonds. This is equivalent to three banana bonds highly polarized to the O atom. Consequently, the SRW method suggested improved explanations of the nature of the PO bond. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

A cyclic chlorophyll hetero-dyad 1-HH, prepared by double ester linking of two structurally different pyropheophorbide- a moieties through 3-CHOCO-13′ and 17-COOCH-3′, was metallated with zinc and copper to give mono and di-metallated complexes 1-MH or 1-HM and 1-MM. The metallation proceeded stepwise and regioselectively, with predominant synthesis of one of the two mono-metallated complexes 1-MH as intermediate. The di-zinc complex produced, 1-ZnZn, was demetallated exclusively via the same mono-zinc complex 1-ZnH as was the major intermediate during metallation. Visible and/or circular dichroism spectra of 1-HH, 1-MH, 1-HM, and 1-MM (M = Ni, Cu, or Zn) were measured in organic solvents. Intramolecular interaction of chlorin chromophores is discussed and compared with that of the corresponding monomeric species. [ABSTRACT FROM AUTHOR]

Abstract: The type I diacylglycerol kinase (DGK) isozymes (α, β and γ) contain a shared recoverin homology (RVH) domain, a tandem repeat of Ca2+-binding EF-hand motifs, two cysteine-rich C1 domains, and the catalytic domain. We previously reported that a DGKα mutant lacking the RVH domain and EF-hands was constitutively active, implying that the N-terminal region (NTR) of DGKα, consisting of the RVH domain and EF-hand motifs, intramolecularly interacts with and masks the activity of the C-terminal region (CTR), containing the C1 and catalytic domains. In this study, we demonstrate that a glutathione S-transferase (GST)-fused DGKα-NTR construct physically binds to a green fluorescent protein (GFP)-fused DGKα-CTR construct. Moreover, co-precipitation of GFP-DGKα-CTR with GST-DGKα-NTR was clearly attenuated by the addition of 1μM Ca2+. This result indicates that Ca2+ induces dissociation of the physical interaction between DGKα-NTR and DGKα-CTR. In addition to previously reported calcium-dependent changes in the hydrophobicity and net surface charge, Ca2+ also appeared to induce a decrease in the α-helical content of DGKα-NTR. These results suggest that Ca2+-induced conformational changes in the NTR release the intramolecular association between the NTR and the CTR of DGKα. [Copyright &y& Elsevier]

We present a new method that produces a variationally determined zeroth-order wave function for the analysis of intramolecular interactions between the fragments of a molecule. In our method, called the space-restricted wave function (SRW) method, this wave function is defined with nonorthogonal orbitals, which are obtained using the appropriately restricted variational spaces. The wave function thus obtained represents the electronic state with the target interactions deactivated, and it is constructed without unnecessarily breaking bonds, in contrast to some of the existing methods. Furthermore, we can perform energy decomposition analysis of intramolecular interactions using the zeroth-order functions that the SRW method yields. The validity of the SRW method is demonstrated in the analysis of the resonance energy and the rotational barrier of the C-N bond in formamide and its analogs. This method gives energy components that are different from those given by existing methods. With these components, we elucidate the origin of the rotational barrier from another point of view. Our SRW method gives meaningful results for the investigation of electron behavior and the nature of the molecular system. [ABSTRACT FROM AUTHOR]

We have explored the geometric and electronic structures, band gap, thermodynamic properties, density, detonation velocity and detonation pressure of aminopolynitropyrazoles using the density functional theory (DFT) at the B3LYP/aug-cc-pVDZ level. The calculated detonation velocity and detonation pressure, stability and sensitivity of model compounds appear to be promising compared to the known explosives 3,4-dinitro-1 H-pyrazole (3,4-DNP), 3,5-dinitro-1 H-pyrazole (3,5-DNP), hexahydro-1,3,5-trinitro-1,3,5-triazinane (RDX) and octahydro-1,3,5,7-tetranitro-l,3,5,7-tetraazocane (HMX). The position of NH group in the polynitropyrazoles presumably determines the structure, stability, sensitivity, density, detonation velocity and detonation pressure. [ABSTRACT FROM AUTHOR]

Abstract: Reactions of (2-formylphenyl)mercury(II) bromide 10 with primary amines give mono-, bis- and tris- Schiff base derivatives (11–18). Structures of the synthesized compounds show the presence of five-membered intramolecular Hg⋯N interaction. Luminescence studies of the compounds have been performed. Attempts to use the synthesized compounds for binding neutral donor molecules or fluoride ions were unsuccessful. [Copyright &y& Elsevier]

Abstract: [D(CH2CH2S)2]M(XCH2CH2Y) 1–8 (M=Ge, Sn; D=O, S; X=Y=S, O and X=S, Y=O) spirocycles were synthesized to analyze the influence of the metal center replacement and the donor atom hardness on the strength of the transannular bond and the hypercoordination phenomena. The compounds were characterized by IR, Raman and NMR (1H, 13C and 119Sn) spectroscopy, E.I. mass spectrometry and elemental analysis. The molecular and crystal structures of compounds 3, 4, 6–8 and Ge(SCH2CH2S)2 (9) were obtained by X-ray diffraction analyses. They all exhibit five-coordinate central atoms due to transannular metal coordination (MD) except 4, which displays a dimeric structure formed by the fusion of two five-membered rings resulting in a cyclic-distannoxane unit, {[O(CH2CH2S)2]Sn(SCH2CH2O)}2. The relationship between the nature of the metal center and the differences found between the two germanium and tin series are discussed. [Copyright &y& Elsevier]

Abstract: In this study, 3,4,5-trinitro-1H-pyrazole (R20), 3,4,5-trinitro-1H-pyrazol-1-amine (R21), 1-methyl-3,4,5-trinitro-1H-pyrazole (R22), and 1,3,4,5-tetranitro-1H-pyrazole (R23) have been considered as potential candidates for high-energy density materials by quantum chemical treatment. The geometric and electronic structures, band gap, thermodynamic properties, crystal density and detonation properties were studied using density functional theory at the B3LYP/aug-cc-pVDZ level. The calculated energy of explosion, density, and detonation performance of model compounds are comparable to 1,3,5-trinitro-1,3,5-triazinane (RDX), and 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX). Atoms-in-molecules (AIM) analyses have also been carried to understand the nature of intramolecular interactions and the strength of trigger bonds. [Copyright &y& Elsevier]

Abstract: A theoretical study supported by calculations at the B3LYP/6-31+G and B3LYP/6-311++G(d,p) levels demonstrated that an attractive interaction involving a hydrogen bond between a hydroxyl group and an acceptor halogen atom (O–H⋯Cl) is present in 2,3-dihydro-2-hydroxy-2-chloromethylimidazo[1,2-a]pyridinium salts, which have an hemiaminal structure. However, the conformers obtained from a dihedral angle analysis performed upon these hemiaminal structures showed relatively small differences in energy among them, indicating that the hydrogen bonding interaction is not entirely responsible for preventing the aromatization process. Calculations were carried out on the gas phase of the hemiaminal cation 6b and the corresponding fully aromatic heterocycle cation 8b. It was found that the difference in energy between the two species is rather small, suggesting that other factors must be contributing to the hemiaminal isolation. The fact that a hydrogen bond is a stabilizing element of the hemiaminal suggests that the formation process of this compound should be favored in aprotic solvents. Accordingly, the condensation of several 2-aminopyridines with 3-bromo-1,1,1-trifluoroacetone was revised. The reaction performed in dry acetone (a non-competing hydrogen bond solvent) proceeded to the hemiaminal derivative, thus confirming the prediction made by theoretical calculations. [ABSTRACT FROM AUTHOR]

IR Fourier spectroscopy methods have been adopted to study intramolecular interactions that occur in CCl4 solutions of antiviral derivatives of aminophenol. Analysis of the IR spectra showed that intramolecular bonds O–H···N, O–H···O=C, N–H···O=S=O, and O–H···O=S=O can occur in these compounds depending on the substituent on the amino group. Not only the presence of intramolecular O–H···N, O–H···O=S=O, and N– H···O=S=O hydrogen bonds in 2-amino-4,6-di-tert-butylphenol derivatives containing a sulfonamide fragment but also conformational equilibrium among these types of intramolecular interactions are essential for the manifestation of high efficiency in suppressing HIV-infection in cell culture. [ABSTRACT FROM AUTHOR]

IR-Fourier spectroscopy methods are adopted to the study of intramolecular interactions occurring in CCl4 solutions of antivirally active derivatives of N-(3,5-di- tert-butyl-2-hydroxyphenyl)acetamide. Analysis of IR spectra has shown that intramolecular H-bonds O–H···O=C and N–H···O=C are formed in solutions of these compounds. The O–H···O=C and N–H···O=C bond strengths and the direction of the equilibrium shift between the two types of conformers depend on the type of carbonyl group substituent. An intramolecular O–H···O=C H-bond is characteristic of highly active derivatives of N-(3,5-di- tert-butyl-2-hydroxyphenyl)acetamide. [ABSTRACT FROM AUTHOR]

Abstract: The plant plasma membrane H+-ATPase is kept at a low activity level by its C-terminal domain, the inhibitory function of which is thought to be mediated by two regions (region I and II) interacting with cytoplasmic domains essential for the catalytic cycle. The activity of the enzyme is well known to be regulated by 14-3-3 proteins, the association of which requires phosphorylation of the penultimate H+-ATPase residue, but can be abolished by phosphorylation of residues close-by. The current knowledge about H+-ATPase regulation is briefly summed up here, combined with data that query some of the above statements. Expression of various C-terminal deletion constructs of PMA2, a H+-ATPase isoform from Nicotiana plumbaginifolia, in yeast indicates that three regions, which do not correspond to regions I or II, contribute to autoinhibition. Their individual and combined action can be abolished by (mimicking) phosphorylation of three threonine residues located within or close to these regions. With respect to the wild-type PMA2, mimicking phosphorylation of two of these residues increases enzyme activity. However, constitutive activation of wild-type PMA2 requires 14-3-3 association. Altogether, the data suggest that regulation of the plant H+-ATPase occurs in progressive steps, mediated by several protein kinases and phosphatases, thus allowing gradual as well as fine-tuned adjustment of its activity. Moreover, mating-based split ubiquitin assays indicate a complex interplay between the C-terminal domain and the rest of the enzyme. Notably, their tight contact does not seem to be the cause of the inactive state of the enzyme. [Copyright &y& Elsevier]

Abstract: A series of flexible multidentate ligands containing N,P-donor, 2-[N-(diphenylphosphino)methyl]amino-pyridine (L1 ), 2-[N-bi-(diphenylphosphino) methyl]amino-pyridine (L2 ), 2-[N-(diphenylphosphino)methyl]amino-7-methyl-1,8-naphthyridine (L3 ) and 4-[(N-diphenylphosphino)methyl]amino-pyridine) (L4 ) have been synthesized. The mono- and dinuclear cyclometalated platinum(II) complexes [Pt(C^N^N)L1]ClO4 (HC^N^N=6-phenyl-2,2′-bipyridine), [Pt2(C^N^N)2L1](ClO4)2, [Pt2(C^N^N)2L2](ClO4)2, [Pt(C^N^N)L3]ClO4 and [Pt2(C^N^N)2L4](ClO4)2 were prepared and their structures determined by X-ray crystal analysis. These complexes exhibit long-lived bright orange emissions ranging from 560 to 610nm in the solid state at room temperature. In solution, dinuclear complexes have emissions with higher quantum yields than mononuclear complexes. This can be attributed to intramolecular interaction of free functional group with Pt(II) at axial position, resulting in the quenching of phosphorescence for platinum(II) complexes in the 3MLCT excited state. [Copyright &y& Elsevier]

We have used Fourier transform IR (FTIR) spectroscopy to study intramolecular interactions in solutions of 4,6-di- tert-butyl-2-aminophenol in n-hexane. When the hydroxyl group in the molecule is ortho to the amino group, an O―H⋅⋅⋅N intramolecular hydrogen bond is formed in the 4-6-di- tert-butyl-2-aminophenol derivatives, where the strength of the hydrogen bond depends on the type of substituent at the para position of the phenyl ring. If there are electron-donor groups on the phenyl ring, then a stronger O―H⋅⋅⋅N bond is formed in the 4,6-di- tert-butyl-2-aminophenol derivatives than in molecules containing electron-acceptor Cl and Br atoms. Formation of the above-indicated intramolecular hydrogen bond affects the course of radiation-induced reactions occurring in n-hexane with participation of these compounds and also affects their antiviral activity. [ABSTRACT FROM AUTHOR]

Abstract: FOXO3a, a forkhead transcription factor and member of the forkhead box class O (FOXO) subfamily, has been shown to promote the translocation of p53 to the cytoplasm, thereby inducing the mitochondria-associated apoptotic pathway. However, the binding sites that mediate this interaction between FOXO3a and p53 have not been identified. Here, we show that two regions within FOXO3a, the forkhead (FH) DNA binding domain and a conserved C-terminal transactivation domain (CR3), interact with the DNA binding domain of p53, with affinities in the low millimolar range and low micromolar range, respectively. Our data further suggest that within the FOXO3a molecule, the FH and CR3 domains engage in an intramolecular interaction with low micromolar affinity. Moreover, we used NMR to determine the solution structure of the FH domain. This enabled us to map the binding site for the CR3, which overlaps with the DNA binding site. We demonstrate that an intrinsically disordered linker between the FH and CR3 domains is required for full p53 binding activity. We also show that p53 disrupts the intramolecular interaction between FH and CR3. These results provide evidence for interplay of the FH and CR3 domains in association with p53. [Copyright &y& Elsevier]

A model for intramolecular polarization is presented. It is used to describe the changes in the molecular charge distribution occurring as a response to changes of dihedral angles in the molecule. The model is based on a multicenter multipole distribution of the molecular charge distribution. The electric field from this charge distribution induce dipole moments in the same molecule. The model contains atom type parameters to describe the damping of the electric field. A total of four atom types are used. The parameters are fitted to a calibration set with various functional groups, and tested against a validation set. The error obtained for the calibration set is reduced by 92% and by 88% for the validation set, if compared to an accurate state-of-the-art force field. It is shown that rotating the non-polarizable multicenter multipole distribution for the equilibrium geometry gives too large dipole moments for dihedral angles deviating from the equilibrium geometry. This will lead to too large long-range attractions in simulations. This problem is overcome by using the dipole polarizability correction suggested here, which gives dipole moments very close to the Hartree-Fock dipole moments obtained from reference calculations. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [ABSTRACT FROM AUTHOR]

FTIR methods were used to study intramolecular and intermolecular interactions in solutions and the solid state of the biologically active aminophenols 2-anilino-4,6-di-tert-butylphenol, N-(3,5-di-tert-butyl-2-methoxyphenyl)aniline, and 2,4-di-tert-butyl-10H-1-phenothiazinol. An analysis of the IR spectra has shown that intramolecular interactions between the OH and NH groups occur in solutions of 2-anilino-4,6-di-tertbutylphenol in CCl4 to form O-H⋯N hydrogen bonds. The NH groups in solutions of N-(3,5-di-tert-butyl-2-methoxyphenyl)aniline in CCl4 are present in the non-associated state because of the absence of hydroxyl groups in the molecular structure. The OH and NH groups in solutions of 2,4-di-tert-butyl-10H-1-phenothiazinol in CCl4 do not interact within the molecule due to a decrease in the conformational mobility of the molecular fragments due to the presence of the rigid CAr-S-CAr molecular bond in this compound. Intermolecular interactions involving the NH groups occur in the solid state of these compounds. [ABSTRACT FROM AUTHOR]

In response to Van Mourik's comments on our paper (J Comput Chem 2007, 28, 1208.) we present an extended version of our rotation method. We also prove that intramolecular interaction energies as well the basis set superposition errors calculated with our rotation method are comparable with those obtained by the counterpoise method of Boys and Bernardi (Mol Phys 1970, 19, 533). In intramolecular interaction energy calculations, if the interacting groups are in proximity, our rotation method is recommended to avoid artificial interactions, which can be induced by fragmentation. © 2007 Wiley Periodicals, Inc.J Comput Chem, 2008 [ABSTRACT FROM AUTHOR]

Abstract: PTK6 (also known as Brk) is an intracellular tyrosine kinase that contains SH3, SH2, and tyrosine kinase catalytic (Kinase) domains. The SH3 domain of PTK6 interacts with the N-terminal half of the linker (Linker) region between the SH2 and Kinase domains. Site-directed mutagenesis and surface plasmon resonance studies showed that a tryptophan residue (Trp44) in the SH3 domain and proline residues in the Linker region, in the order of Pro177, Pro175, and Pro179, contribute to the interaction. The three-dimensional modeled structure of the SH3–Linker complex was in agreement with the biochemical data. Disruption of the intramolecular interaction between the SH3 domain and the Linker region by mutation of Trp44, Pro175, Pro177, and Pro179 markedly increased the catalytic activity of PTK6 in HEK 293 cells. These results demonstrate that Trp44 in the SH3 domain and Pro177, Pro175, and Pro179 in the N-terminal half of the Linker region play important roles in the SH3–Linker interaction to maintain the protein in an inactive conformation along with the phosphorylated Tyr447-SH2 interaction. [Copyright &y& Elsevier]

We have used IR Fourier spectroscopy to study intramolecular interactions in solutions of aminophenols in n-hexane. When the hydroxyl group in the molecule is ortho to the amino group, O-H⋯N and N-H⋯O intramolecular hydrogen bonds are formed in the aminophenols. Adding two tert-butyl groups to the benzene ring of ortho-aminophenols strengthens the O-H⋯N bond in the molecules, and prevents formation of an N-H⋯O bond. Additional acylation of the amino group in ortho-aminophenols leads to formation of an O-H⋯O=C intramolecular hydrogen bond. Formation of the above-indicated intramolecular hydrogen bonds in aminophenols affects the course of radiation-induced reactions occurring in n-hexane with participation of these compounds. The antioxidant properties of the aminophenols are enhanced when the hydroxyl groups in the molecules are found in the free state, and are diminished when strong O-H⋯N or O-H⋯O=C intramolecular hydrogen bonds are formed. [ABSTRACT FROM AUTHOR]

Abstract: Experimental (single-crystal X-ray diffraction) and computational evidence shows that there is short intramolecular distance between two phosphorus atoms in 1,2-(diphenylphosphino)-1,2-dicarba-closo-dodecaborane. In the optimized structure at the B3LYP/6-31G∗ level of theory the interaction was analyzed by quantum theory – atoms-in-molecules and natural bonding orbitals methods. Both methods established the interaction. The former method indicates direct P⋯P interaction, while the latter describes it as donor–acceptor interaction between phosphorus electron lone pair and adjacent antibonding P–C(phenyl) orbital. [Copyright &y& Elsevier]

Abstract: We have previously shown that domains involved in binding of protein kinase C (PKC) isozymes to their respective anchoring proteins (RACKs) and short peptides derived from these domains are PKC isozyme-selective antagonists. We also identified PKC isozyme-selective agonists, named ψRACK peptides, derived from a sequence within each PKC with high homology to its respective RACK. We noted that all the ψRACK sequences within each PKC isozyme have at least one non-homologous amino acid difference from their corresponding RACK that constitutes a charge change. Based on this information, we have devised here a new approach to design an isozyme-selective PKC antagonist, derived from the ψRACK sequence. We focused on εPKC ψRACK peptide, where the pseudo-εRACK sequence (ψεRACK; H D APIGYD; corresponding to εPKC85-92) is different in charge from the homologous RACK-derived sequence (N N VALGYD; corresponding to εRACK285-292) in the second amino acid. Here we show that changing the charge of the ψεRACK peptide through a substitution of only one amino acid (aspartate to asparagine) resulted in a peptide with an opposite activity on the same cell function and a substitution for aspartate with an alanine resulted in an inactive peptide. These data support our hypothesis regarding the mechanism by which pseudo-RACK peptide activates PKC in heart cells and suggest that this approach is applicable to other signaling proteins with inducible protein–protein interactions. [Copyright &y& Elsevier]

Abstract: The reaction of RN(CH2CH2OH)CHR1CR2R3OH (1–8) with a stoichiometric amount of tetrachloro(bromo)germane leads to the corresponding RN(CH2CH2O)(CHR1CR2R3O)GeHal2 (9–21). Difluorenylgermocane 22 was prepared by treatment of diethoxydifluorenylgermane with N-methyldiethanolamine. Different dialkanolamines were found to be successive precursors of dimethylgermocanes, RN(CH2CH2O)(CHR1CR2R3O)GeMe2 (23–26). The chemical properties of simple and easy to access germocanes RN(CH2CH2O)2GeX2 [X=OH, Br (28), Cl (29)] were studied and the difluoro (27), haloalkoxy (30–32), and dialkoxy (33, 34) derivatives were prepared. The structures of the compounds 16, 20–22, and 26 were confirmed by X-ray diffraction and the structural features in solution of 23 and 26 were studied by NMR spectroscopy (NOEs). The relationship between the nature of substituents at different positions of the germocane skeleton and the strength of the intramolecular Ge←N bond is discussed. [Copyright &y& Elsevier]

Abstract: The Ras-specific guanine nucleotide exchange region of hSos1 consists of two consecutive domains: the catalytic core (residues 742–1024) contains all residues binding to Ras, including the catalytic hairpin, and an upstream REM domain (residues 553–741), so called because it contains an evolutionary conserved Ras Exchange Motif (REM). We functionally define the boundaries of the REM domain through a combination of in vivo and in vitro assays. We show that an intra-REM domain interaction, mediated by phenylalanine 577, is required to allow interaction of the REM domain with the catalytic core, constraining it in the active conformation. [Copyright &y& Elsevier]

The N terminus of the c-Myc oncoprotein interacts with Bin1, a ubiquitously expressed nucleocytoplasmic protein with features of a tumor suppressor. The c-Myc/Bin1 interaction is dependent on the highly conserved Myc Box 1 (MB1) sequence of c-Myc. The c-Myc/Bin1 interaction has potential regulatory significance as c-Myc-mediated transformation and apoptosis can be modulated by the expression of Bin1. Multiple splicing of the Bin1 transcript results in ubiquitous, tissue-specific and tumor-specific populations of Bin1 proteins in vivo. We report on the structural features of the interaction between c-Myc and Bin1, and describe two mechanisms by which the binding of different Bin1 isoforms to c-Myc may be regulated in cells. Our findings identify a consensus class II SH3-binding motif in c-Myc and the C-terminal SH3 domain of Bin1 as the primary structure determinants of their interaction. We present biochemical and structural evidence that tumor-specific isoforms of Bin1 are precluded from interaction with c-Myc through an intramolecular polyproline–SH3 domain interaction that inhibits the Bin1 SH3 domain from binding to c-Myc. Furthermore, c-Myc/Bin1 interaction can be inhibited by phosphorylation of c-Myc at Ser62, a functionally important residue found within the c-Myc SH3-binding motif. Our data provide a structure-based model of the c-Myc/Bin1 interaction and suggest a mode of regulation that may be important for c-Myc function as a regulator of gene transcription. [Copyright &y& Elsevier]

Type IIB Ca2+-ATPases have a terminal auto-inhibitory, domain the action of which is suppressed by calmodulin (CaM) binding. Here, we show that a peptide (6His-1M-I116) corresponding to the first 116 aminoacids (aa) of At-ACA8, the first cloned isoform of Arabidopsis thaliana plasma membrane Ca2+-ATPase, inhibits the activity of the enzyme deprived of the N-terminus by controlled trypsin treatment 10-fold more efficiently than a peptide (41I-T63) corresponding only to the CaM-binding site. A peptide (268E-W348) corresponding to 81 aa of the small cytoplasmic loop of At-ACA8 binds peptide 6His-1M-I116 immobilized on Ni–NTA agarose. Peptide 268E-W348 stimulates Ca2+-ATPase activity. Its effect is not additive with that of CaM and is suppressed by tryptic cleavage of the N-terminus. These results provide the first functional identification of a site of intramolecular interaction with the terminal auto-inhibitory domain of type IIB Ca2+-ATPases. [Copyright &y& Elsevier]

This study shows that intramolecular hydrogen bonding in proteins depends on the accessibility of donors and acceptors to water molecules. The frequency of occurrence of H-bonded side chains in proteins is inversely proportional to the solvent accessibility of their donors and acceptors. Estimates of the notional free energy of hydrogen bonding suggest that intramolecular hydrogen-bonding interactions of buried and half-buried donors and acceptors can contribute favorably to the stability of a protein, whereas those of solvent-exposed polar atoms become less favorable or unfavorable. [Copyright &y& Elsevier]

Starch retrogradation property is critical for developing functional foods with desirable nutritional and textural attributes, while its nature currently remains elusive. The current study investigated the relations between starch chain-length distributions (CLDs) and interaction patterns (i.e. intermolecular versus intramolecular interactions) of starch molecules during the retrogradation process. CLDs for different waxy potato and sago starch mixtures were characterized by size-exclusion chromatography, and molecular interactions were characterized by differential scanning calorimetry and small amplitude oscillatory shear rheological test. Results for the first time showed that amylose molecules were involved in the formation of short-range intermolecular interactions with amylopectin molecules. Most intermolecularly heterogenous double helices were formed at the 1 : 1 mixing ratio of waxy potato to sago starch. Although the addition of waxy potato starch to sago starch increased the overall amount of short-range double helices, the amount of short-range intermolecular double helices was decreased. It suggests that there was an antagonistic effect between the formation of short-range inter- and intramolecular double helices. These results help a better understanding of the interaction patterns of amylose and amylopectin molecules during the retrogradation process. • Amylose was largely involved in forming short-range intermolecular interactions. • More amylose increased the amount of short-range intermolecular double helices. • More amylose decreased the amount of short-range intramolecular double helices. [ABSTRACT FROM AUTHOR]