Coordination polymers with macrocyclic cages and pockets within their backbones

The reaction between the flexible ligand (1,4-bis(pyridine-2-yl-methanethio)benzene) and Ag+ produces two novel coordination polymers with macrocyclic cages or pockets contained within their backbones, depending upon the ratio of starting materials.     

Evidence from Chlamydomonas on the photoactivation of rhodopsins without isomerization of their chromophore

Attachment of retinal to opsin forms the chromophore N-retinylidene, which isomerizes during photoactivation of rhodopsins. To test whether isomerization is crucial, custom-tailored chromophores lacking the β-ionone ring and any isomerizable bonds were incorporated in?vivo into the opsin of a blind mutant of the eukaryote Chlamydomonas reinhardtii. The analogs restored phototaxis with the anticipated action spectra, ruling out the need for isomerization in photoactivation. To further elucidate photoactivation, responses to chromophores formed from naphthalene aldehydes were studied. The resulting action spectral shifts suggest that charge separation within the excited chromophore leads to electric field-induced polarization of nearby amino acid residues and altered hydrogen bonding. This redistribution of charge facilitates the reported multiple bond rotations and protein rearrangements of rhodopsin activation. These results provide insight into the activation of rhodopsins and related GPCRs.     

Modified Gaussian functions and their use in quantum chemistry. I. Integrals

A modified Gaussian function g(u, v, w, a, R ) = const s(a, R ) is considered where l = u + v + w, s (a, R ) is a 1s-type Gaussian function centered at R , a is the coefficient in the exponent of the 1 s Gaussian function and X, Y, Z are components of R . General formulae are derived for overlap integrals, kinetic energy integrals, nuclear attraction integrals, and electron repulsion integrals, valid for any l. The formulae are much simpler than those derived by Huzinaga for Cartesian Gaussian functions.     

Landscapes and their correlation functions

Fitness landscapes are an important concept in molecular evolution. Many important examples of landscapes in physics and combinatorial optimization, which are widely used as model landscapes in simulations of molecular evolution and adaptation, are elementary, i.e., they are (up to an additive constant) eigenfunctions of a graph Laplacian. It is shown that elementary landscapes are characterized by their correlation functions. The correlation functions are in turn uniquely determined by the geometry of the underlying configuration space and the nearest neighbor correlation of the elementary landscape. Two types of correlation functions are investigated here: the correlation of a time series sampled along a random walk on the landscape and the correlation function with respect to a partition of the set of all vertex pairs.     

Molecules and their functions in autophagy

Autophagy is a self-degradation system of cellular components through an autophagosomal-lysosomal pathway. Over the last 15 yr, yeast genetic screens led to the identification of a number of genes involved in the autophagic pathway. Most of these autophagy genes are present in higher eukaryotes and regulate autophagy process for cell survival and homeostasis. Significant progress has recently been made to better understand the molecular mechanisms of the autophagy machinery. Especially, autophagy process, including the regulation of autophagy induction through mTOR and the nucleation and elongation in autophagosome formation through class III phosphatidylinositol 3-kinase complex and ubiquitin-like conjugation systems, became evident. While many unanswered questions remain to be answered, here, we summarize the recent process of autophagy with emphasis on molecules and their protein complexes along with advanced molecular mechanisms that regulate the autophagy machinery.     

Exhaustive syntheses of naphthofluoresceins and their functions

Naphthofluorescein and/or seminaphthofluorescein derivatives possessing the additional benzene units to one or both sides of fluorescein were exhaustively constructed through Friedel-Crafts type reactions between corresponding aroylbenzoic acids and dihydroxynaphthalenes. Compound 4 works as a one-dye pH indicator, which shows red in strong acid condition and blue in basic solution. Compound 23 (diacetate of compound 4) shows good transitivity to the HEK 293 cells and acts as a fluorescent pigment for the living cell imaging. Compounds 5, 6, and 9 show fluorescent emission in the NIR region (>700 nm) and imply the potentialities of NIR fluorescent probes.     

Transition metal bonding functions and their application in adsorptions and catalytic reactions: Part I: Theoretical model

A new method has been proposed for rapidly and chemically-intuitively giving correct information on the relative abilities or relative data (binding energy, bond structure, bond strength, vibration frequencies of surface species, etc.) of chemisorptions, dissociation and reactions on various transition metals, and the effects caused by the Metal-Promoter (or -Support) Interactions. In order to achieve this purpose, the LCAO method is first used to derive the wave function of the mono-transition-metal atom, represented by the combination of molecular orbital (M.O.) bands, where each M.O. is described as the linear combination of s and d orbitals. Second, based on various electronic spectra before and after adsorption, we assume that the adsorption and reaction occur chiefly on the valence band around the Fermi level. The valence band consists of three M.O. Groups (MOGs): the vacant MOG at the bottom of the s band, the vacant or fractional half-occupied MOG of the d band and the occupied MOG at the top of the occupied d band near the Fermi level, denoted as Ψ(Mi, Vs), Ψ(Mi, Vd) and Ψ(Mi, d_occ), respectively. Assuming that the M.O.'s energy distribution is even, the concept of mean energy and mean chemisorption binding energy is employed, and the three MOGs can be simplified as three representative M.O.s. According to the principle of Bloch energy band formation, the concept of d-s band overlap and the probability theory, some simple formulas with the parameters of metal band structure such as the width of the d band, the atomic orbital effective exponents and the total electron number of the s and d orbitals have been derived to calculate coefficients of the s and d orbitals of the three representative M.O.s. The interaction between metal and adsorbate is characterized by bonding functions which depend on three factors: the overlap integral between the wave function of three representative M.O.s and the adsorbate, the thermodynamic potential and the ability of electron transfer. The bonding functions D, A, B and AB have been proposed to characterize the bonds involved in metal electron donation, metal electron acceptance, d electron back-donation and σ-π coordination, respectively. Our model involves intuitive chemical localized bonds and represents the delocalized effects of energy bands. Its advantages (relatively realistic, intuition, rapidity, convenience and practice) and drawbacks (the inability to obtain the absolute amounts of surface bond strength, electron charge distribution and detailed energy levels) were discussed in comparison with the EHMO, CNDO, X_α-SW, LDF, GVB and EMT methods.     

Auxiliary functions for molecular integrals with Slater‐type orbitals. I. Translation methods

Many types of molecular integrals involving Slater functions can be expressed, with the ζ‐function method in terms of sets of one‐dimensional auxiliary integrals whose integrands contain two‐range functions. After reviewing the properties of these functions (including recurrence relations, derivatives, integral representations, and series expansions), we carry out a detailed study of the auxiliary integrals aimed to facilitate both the formal and computational applications of the ζ‐function method. The usefulness of this study in formal applications is illustrated with an example. The high performance in numerical applications is proved by the development of a very efficient program for the calculation of two‐center integrals with Slater functions corresponding to electrostatic potential, electric field, and electric field gradient. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Deubiquitinating enzymes: their functions and substrate specificity

Conjugation of one or more molecules of ubiquitin to target proteins can signify one of several fates, including degradation by the 26S proteasome, or trafficking via the secretory or endocytic pathways. Whereas much attention in recent years has focussed on the mechanisms of forming these different ubiquitin conjugates, far less is known about the removal of ubiquitin, which is performed by deubiquitinating enzymes (DUBs). While it has been appreciated for some 10 years that DUBs constitute large gene families in eukaryotes, and known for much longer that ubiquitination is a reversible process, information on the exact role of DUBs has been slow in coming. This review will attempt to summarise results from the last few years that shows that DUBs are an essential regulatory step of both protein degradation by the proteasome, and of other ubiquitin-dependent processes, by virtue of their ability to regulate protein ubiquitination in a target-specific manner.     

Enzymes catalyzing protein folding and their cellular functions

In live cells, protein folding often cannot occur spontaneously, but requires the participation of helper proteins - molecular chaperones and foldases. The mechanisms employed by chaperones markedly increase the effectiveness of protein folding, but have no bearing on the rate of this process, whereas foldases actually accelerate protein folding by exerting a direct influence on the rate-limiting steps of the overall reaction. Two types of foldases are known, using different principles of action. Peptidyl-prolyl cis/trans isomerase and protein-disulfide isomerase catalyze the folding of every protein that needs isomerization of prolyl peptide bonds or formation and isomerization of disulfide bonds for proper folding. By contrast, some foldases operating in the periplasm of bacterial cells are specifically designed to help in the folding of substrate proteins whose primary structure does not contain sufficient information for correct folding. In this review, we discuss recent data on the catalytic mechanisms of both types of foldases, focusing specifically on how a catalyst provides the structural information required for the folding of a target protein. Comparative analysis of the mechanisms employed by two different periplasmic foldases is used to substantiate the notion that combinations of a protein which is unable to fold independently and a specific catalyst delivering the necessary steric information are probably designed to achieve some particular biological purposes. The review also covers the problem of participation of peptidyl-prolyl cis/trans isomerase in different cellular functions, highlighting the role of this enzyme in conformational rearrangements of folded native proteins.     

Carotenoids and their cleavage products: biosynthesis and functions

This review focuses on plant carotenoids, but it also includes progress made on microbial and animal carotenoid metabolism to better understand the functions and the evolution of these structurally diverse compounds with a common backbone. Plants have evolved isogenes for specific key steps of carotenoid biosynthesis with differential expression profiles, whose characteristic features will be compared. Perhaps the most exciting progress has been made in studies of carotenoid cleavage products (apocarotenoids) with an ever-expanding variety of novel functions being discovered. This review therefore covers structural, molecular genetic and functional aspects of carotenoids and apocarotenoids alike. Apocarotenoids are specifically tailored from carotenoids by a family of oxidative cleavage enzymes, but whether there are contributions to their generation from chemical oxidation, photooxidation or other mechanisms is largely unknown. Control of carotenoid homeostasis is discussed in the context of biosynthetic and degradative reactions but also in the context of subcellular environments for deposition and sequestration within and outside of plastids. Other aspects of carotenoid research, including metabolic engineering and synthetic biology approaches, will only be covered briefly.     

A theoretical case study of type I and type II beta-turns

NMR chemical shielding anisotropy tensors have been computed by employing a medium size basis set and the GIAO-DFT(B3LYP) formalism of electronic structure theory for all of the atoms of type I and type II beta-turn models. The models contain all possible combinations of the amino acid residues Gly, Ala, Val, and Ser, with all possible side-chain orientations where applicable in a dipeptide. The several hundred structures investigated contain either constrained or optimized phi, psi, and chi dihedral angles. A statistical analysis of the resulting large database was performed and multidimensional (2D and 3D) chemical-shift/chemical-shift plots were generated. The (1)H(alpha-13)C(alpha), (13)C(alpha-1)H(alpha-13)C(beta), and (13)C(alpha-1)H(alpha-13)C' 2D and 3D plots have the notable feature that the conformers clearly cluster in distinct regions. This allows straightforward identification of the backbone and side-chain conformations of the residues forming beta-turns. Chemical shift calculations on larger For-(L-Ala)(n)-NH(2) (n=4, 6, 8) models, containing a single type I or type II beta-turn, prove that the simple models employed are adequate. A limited number of chemical shift calculations performed at the highly correlated CCSD(T) level prove the adequacy of the computational method chosen. For all nuclei, statistically averaged theoretical and experimental shifts taken from the BioMagnetic Resonance Bank (BMRB) exhibit good correlation. These results confirm and extend our previous findings that chemical shift information from selected multiple-pulse NMR experiments could be employed directly to extract folding information for polypeptides and proteins.     

Spin-adapted wave functions of the serber type and time reversal

A procedure is proposed for generating Serber-type spin eigenfunctions withM _s = 0. The procedure uses the time-reversal invariance of these functions to increase the efficiency and to reduce the storage requirements. Simplifications in calculating the matrix elements of an observable operator which follow from the use of the time-reversal symmetry are briefly discussed.     

Asymmetric synthesis of pentenomycin I, epipentenomycin I, and their analogs

The synthetic utility of the intramolecular acylation of α-sulfinyl carbanions as an efficient and general synthetic approach for the preparation of (−)-pentenomycin I (1) and (−)-epipentenomycin I (5) and their enantiomers (ent-1 and ent-5), starting from chiral (2S,5S,6S)-ester 6 and ent-6, respectively, has been demonstrated. Easy accesses to pentenomycin analogs have also been demonstrated through the Pummerer, Suzuki-Miyaura, and Sonogashira reactions.     

Development of new chiral phosphine-salen type ligands and their application in the Cu(I)-catalyzed enantioselective Henry reaction

Chiral phosphine-salen type ligand L4 prepared from (R)-2-(diphenylphosphino)-1,1′-binaphthyl-2′-amine was found to be a fairly effective chiral ligand for Cu(I)-promoted enantioselective Henry reactions of arylaldehydes with nitromethane to give the corresponding adducts in moderate enantioselectivities and moderate to good yields.     

The distinct signaling mechanisms of microbial sensory rhodopsins in Archaea, Eubacteria and Eukarya

Most of the known archaeal-type microbial rhodopsins are retinal-binding ion transporters, such as bacteriorhodopsin (BR) and proteorhodopsin (PR). Their identification is the result of extensive studies of their photochemical and biophysical properties. The cells containing these pigments, however, use other microbial rhodopsins as photosensors to monitor environmental light signals. From the early studies of sensory rhodopsin I (HsSRI) in Halobacterium salinarum and sensory rhodopsin II (NpSRII) in Natronomonas pharaonis, we now know that several microbial sensory rhodopsins in the other major domain of life relay information on light intensity and quality to the cell. Three of the most studied photosensory transduction mechanisms of these microbial rhodopsins are dealt with in this review. We discuss recent progress in the understanding of genomic organization, photochemical properties and photosignaling mechanisms with respect to biological function.     

Modified Cartesian Gaussian functions and their use in quantum chemistry

The general formula for the electron-electron repulsion integral in the modified Cartesian Gaussian basis set derived in Ref. [1] is simplified. A general relation between the standard and modified CG functions is given. A possible use of the modified CG functions to quantum chemical calculations which include the correlation factor r_ij² is indicated.     

Analysis of exponent values in Gaussian‐type functions for development of protonic and deuteronic basis functions

We analyzed the exponent (α) values in Gaussian‐type functions (GTF) for protons and deuterons in BH₃, CH₄, NH₃, H₂O, HF, and their deuterated molecules for the development of nuclear basis functions, which are used for molecular orbital (MO) calculations that directly include nuclear quantum effects. The optimized α (α_opt) value in the single s‐type ([1s]) GTF for protons is changed due to the difference in flexibility of the electronic basis sets. The difference between the energy obtained by using the α_opt value for each molecule and that obtained by using the average α (α_ave) value for these exponents with the 6‐31G(d,p) electronic basis function is only 2 × 10^?5 a.u. The α_ave values of protonic and deuteronic [1s] GTFs by the present calculation are 24.1825 and 35.6214, respectively. We found that the α_ave values enable the evaluation of the total energy and the geometrical changes in hydrogen bonding, such as O…H? O, O…H? N, and O…H? C, while the α_opt value became small by forming a hydrogen bond. The result using only the [1s] GTF for the protonic and deuteronic basis functions is sufficient to explain the differences of energy and geometry induced by the H/D isotope effect, although the total energy of ～5 × 10^?4 a.u. was improved by using the s‐, p‐, and d‐type ([1s1p1d]) GTFs for protons and deuterons. We clearly demonstrate that the protonic and deuteronic basis functions based on the α_ave value enable us to apply the method to other sample molecules (glycine, malonaldehyde, and formic acid dimer). The protonic and deuteronic basis functions we developed treat the quantum effects of protons and deuterons effectively and extend the application range of the MO calculation to include nuclear quantum effects. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006