Aquaporin structure-function relationships: water flow through plant living cells

Plant aquaporins play an important role in water uptake and movement-an aquaporin that opens and closes a gate that regulates water movement in and out of cells. Some plant aquaporins also play an important role in response to water stress. Since their discovery, advancing knowledge of their structures and properties led to an understanding of the basic features of the water transport mechanism and increased illumination to water relations. Meanwhile, molecular and functional characterization of aquaporins has revealed the significance of their regulation in response to the adverse environments such as salinity and drought. This paper reviews the structure, species diversity, physiology function, regulation of plant aquaporins, and the relations between environmental factors and plant aquaporins. Complete understanding of aquaporin function and regulation is to integrate those mechanisms in time and space and to well regulate the permeation of water across biological membranes under changing environmental and developmental conditions.     

Coulomb and overlap self-similarities: a comparative selectivity analysis of structure-function relationships for auxin-like molecules

Auxins are defined mainly by a set of physiological actions, but the structure-effect relationship still is based on chemical intuition. Currently a well-defined auxin molecular structure is not available. The existence of different auxin binding proteins and mechanisms of auxin action, the wide diversity of the auxin molecules, and the pleiotropic effects of auxin imply a completely different mechanism as described for the animal hormone concept. Here, we present a computational approach dealing with semiempirical optimizations of the auxin molecules themselves, which represent a number of about 250 different chemical structures. Our approach uses molecular quantum similarity measures and additional quantum variables for the analysis of auxin-like molecules. The finding of similarities in molecules by focusing basically on their electron structure results in new insights in the relationship of the different auxin groups. Additional statistical analysis allows the identification of relationships between similarity groups and their biological activity, respectively. It is postulated that the auxin-like molecular recognition depends more on specific molecular assembling states than on a specific ring system or side chain.     

13C-detection in RNA bases: revealing structure-chemical shift relationships

The chemical shifts of the unprotonated carbons in the proton-deficient nucleobases of RNA are rarely reported, despite the valuable information that they contain about base-pairing and base-stacking. We have developed 13C-detected 2D-experiments to identify the unprotonated 13C in the RNA bases and have assigned all the base nuclei of uniformly 13C,15N-labeled HIV-2 TAR-RNA. The 13C chemical shift distributions revealed perturbations correlated with the base-pairing and base-stacking properties of all four base-types. From this work, we conclude that the information contained in the chemical shift perturbations within the base rings can provide valuable restraint information for solving RNA structures, especially in conformational averaged regions, where NOE-based information is not available.     

Mutagenesis approaches to deduce structure-function relationships in terpene synthases

This review highlights mutagenesis studies of terpene synthases, specifically sesquiterpene synthases and oxidosqualene cyclases. Mutagenesis studies of these enzymes have provided mechanistic insights, structure-function relationships for specific enzymatic residues, novel terpene structures and enzymes with novel activities. The literature through 2002 is reviewed and 113 references cited.     

Identification of six new photoactive yellow proteins--diversity and structure-function relationships in a bacterial blue light photoreceptor

Photoactive yellow proteins (PYP) are bacterial photoreceptors with a Per-Arnt-Sim (PAS) domain fold. We report the identification of six new PYPs, thus nearly doubling the size of this protein family. This extends the taxonomic diversity of PYP-containing bacteria from photosynthetic to nonphotosynthetic bacteria, from aquatic to soil-dwelling organisms, and from Proteobacteria to Salinibacter ruber from the phylum Bacteriodetes. The new PYPs greatly increase the sequence diversity of the PYP family, reducing the most prevalent pair-wise identity from 45% to 25%. Sequence alignments and analysis indicate that all 14 PYPs share a common structure with 13 highly conserved residues that form the chromophore binding pocket. Nevertheless, the functional properties of the PYPs vary greatly--the absorbance maximum extends from 432 to 465 nm, the pK(a) of the chromophore varies from pH 2.8 to 10.2, and the lifetime of the presumed PYP signaling state ranges from 1 ms to 1 h. Thus, the PYP family offers an excellent opportunity to investigate how functional properties are tuned over a wide range, while maintaining the same overall protein structural fold. We discuss the implications of these results for structure-function relationships in the PYP family.     

Spinosyn g: proof of structure by semisynthesis

[reaction: see text] Spinosyn G was isolated in the late 1980s as a minor component from the broth of our potent, fermentation-derived insecticide spinosad. Its structure was then tentatively identified as 5' '-epispinosyn A (3) on the basis of (1)H and (13)C NMR data, but the 4' '-epi compound 4 could not be conclusively ruled out with the data available. Described herein are unambiguous syntheses of both 3 and 4, whereby 3 was proved identical to the natural product. Compound 4 was prepared from intact spinosyn A by a novel F-TEDA-promoted oxidative deamination to the 4' '-ketone 5, stereoselective reduction to the equatorial alcohol 6, and nitrogen incorporation via the axial azide 7. Compound 3 was obtained by coupling spinosyn A 17-pseudoaglycone (9) with the N-protected dihydropyran 16 derived from methyl l-ossaminide (14). This gave an approximately 2:1 mixture of anomeric products 17 with the desired equatorial glycoside predominating, which was then converted to 3 by N-deprotection and methylation.     

Two-photon absorption and first nonlinear optical properties of ionic octupolar molecules: structure-function relationships and solvent effects

We present a quantum-chemical analysis of the two-photon absorption properties and first hyperpolarizabilities of a series of ionic octupolar molecules and a comparison of their characteristics with corresponding neutral molecules. The molecular geometries are obtained via BL3YP/6-31G (d,p) level optimization including the SCRF/PCM approach, while the dynamic NLO and two-photon absorption properties are calculated with the ZINDO/CV method including solvent effects. The effects of donor or acceptor substitution and elongation of the conjugation path length are established to demonstrate the engineering guidelines for enhancing two-photon absorption cross section and molecular optical nonlinearities. It is found that the chain length dependence of the two-photon absorption and the first nonlinearity follow the same trend, displaying a saturation limit at n = 5. The solvent induced effect on the two-photon absorption and NLO properties are studied using the ZINDO/CV/SCRF method. It has been observed that two-photon absorption and the first nonlinearity peaks at epsilon approximately = 20 and then decreases slightly, approaching saturation. We also compare our theoretical findings with the experimental results wherever available in the literature.     

A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships

The rapid expansion of structural information for protein-ligand binding sites is potentially an important source of information in structure-based drug design and in understanding ligand cross reactivity and toxicity. We have developed a large database of ligand binding sites extracted automatically from the Protein Data Bank. This has been combined with a method for calculating binding site similarity based on geometric hashing to create a relational database for the retrieval of site similarity and binding site superposition. It contains an all-against-all comparison of binding sites and holds known protein-ligand binding sites, which are made accessible to data mining. Here we demonstrate its utility in two structure-based applications: in determining site similarity and in aiding the derivation of a receptor-based pharmacophore model. The database is available from http://www.bioinformatics.leeds.ac.uk/sb/.     

Exposure of hydrophobic sites in CA2+-binding proteins: Influence on chromatographic properties and structure-function relationships

Calmodulin and related Ca²⁺ -binding proteins were characterized using different labeling, chromatographic and spectroscopic techniques. Ca²⁺-binding to members of the so-called “EF-hand”- or “helix-loop-helix”-model protein family induced conformational changes, thereby exposing hydrophobic sites in some of them. These sites were identified using the photoreactive, carbene-generating, radioactive probe 3-(trifluoromethyl)-3-(m-[¹²⁵1]iodophenyl)diazirine, and characterized using different high performance liquid chromatography techniques. The influence of chemical modification of some of the amino acid residues on the properties of calmodulin were characterized using circular dichroism. A correlation between an increase of oxidized methionine residues of calmodulin and a decrease of Ca²⁺-induced helical content was observed.     

福建三尖杉碱及其类似物的半合成研究: 一个立体选择性反应的发现

从表台湾三尖杉碱(epiwilsonine)(3)合成福建三尖杉碱(cephalofortunaine)(4)时, 发现3在稀醋酸中子0℃加1:10溴-四氯化碳混合试剂能直接生成2-O-乙酰基福建三尖杉碱的一对2-C差向异构体1与2(9:1), 产率及两个产物比例随着温度而变化。同时报道了类似物5, 6, 10和11的半合成与这类化合物^1H NMR中质子的归属。     

一种核糖核酸酶构象稳定性的研究

Aspergillus niger SA-13-20核糖核酸酶是从突变株A.niger SA-13-20分泌的胞外酶中分离出的一种新的核糖核酸酶。采用紫外光谱、荧光光谱和红外光谱研究了A.niger SA-13-20核糖核酸酶在不同pH值条件下的构象稳定性。紫外光谱和荧光光谱结果均表明该酶蛋白在酸性和弱碱性pH值下构象较稳定,当pH值高于9.6时构象不稳定;红外光谱结合去卷积和曲线拟合技术对蛋白质酰胺Ⅰ带的测定和处理结果表明,在室温下,pH 5.0时该酶蛋白二级结构中α-螺旋、β-折叠、转角和无规结构所占的成分分别为13.28%、42.30%、26.48%和17.95%。测得该酶的热解链温度Tm、解链熵变ΔSm及解链焓变ΔHm分别为70.1℃、644 J.mol-1.K-1及22.1 kJ.mol-1,表明该酶属于耐热能力较强的核糖核酸酶。研究结果有助于揭示该酶结构与功能的关系,推动其在科研和生产等方面的应用。     

Future of interfacial electrochemistry: from structure-function relationships to better understanding of charge transfer reactions and (photo)electrocatalytic reactivity

Journal of Solid State Electrochemistry -     

BODIL: a molecular modeling environment for structure-function analysis and drug design

BODIL is a molecular modeling environment geared to help the user to quickly identify key features of proteins critical to molecular recognition, especially (1) in drug discovery applications, and (2) to understand the structural basis for function. The program incorporates state-of-the-art graphics, sequence and structural alignment methods, among other capabilities needed in modern structure–function–drug target research. BODIL has a flexible design that allows on-the-fly incorporation of new modules, has intelligent memory management, and fast multi-view graphics. A beta version of BODIL and an accompanying tutorial are available at http://www.abo.fi/fak/mnf/bkf/research/johnson/bodil.html     

High-field NMR studies of molecular recognition and structure-function relationships in antimicrobial piscidins at the water-lipid bilayer interface

High magnetic field solid-state NMR was performed on amphipathic cationic antimicrobial peptides from fish to characterize their secondary structure and orientation in hydrated phospholipid bilayers. High-resolution distance and orientational restraints on 13C- and 15N-labeled amidated piscidins 1 and 3 provided site-specific information establishing alpha-helicity and an orientation parallel to the membrane surface. Few membrane-bound natural peptides with this topology have been structurally studied at high resolution in the presence of hydrated lipid bilayers. This orientation was foreseen since the partitioning of amphipathic cationic antimicrobial peptides at the water-bilayer interface allows for favorable peptide-lipid interactions, and it may be related to the mechanism of action. The enhanced resolution obtained at 900 MHz evidences a determinant advantage of ultra-high-field NMR for the structural determination of multiple-labeled peptides and proteins.