Visible‐Light‐Induced Photodimerization of a Photoactive Yellow Protein (PYP) Chromophore Model in a Single Crystal

The chromophore of the photoactive yellow protein (PYP), the photoreceptor in the photomotility of the bacterium Halorhodospira halophila, is a deprotonated para‐coumaric thioester linked to the side residue of a cysteine residue. The photophysics of the PYP chromophore is conveniently modeled with para‐hydroxycinnamic thiophenyl esters. Herein, we report the first direct evidence, obtained with X‐ray diffraction, of photodimerization of a para‐hydroxycinnamic thiophenyl ester in single crystalline state. This result represents the first direct observation of [2+2] dimerization of a model PYP chromophore, and demonstrates that even very weak light in the visible region is capable of inducing parallel radical reactions in PYP from the excited state of the chromophore, in addition to the main reaction pathway (trans–cis isomerization). This PYP model system adds an interesting example to the known solid‐state photodimerizations, because unlike the anhydrous crystal (which is not capable of sustaining the stress and disintegrates in the course of photodimerization), a single water molecule “dilutes” the structure to the extent sufficient for single‐crystal‐to‐single‐crystal reaction.     

人工金属酶分子设计新进展:肌红蛋白研究实例分析

金属酶在生物体中发挥着多种至关重要的作用,而人工金属酶的分子设计能够调控和拓展天然金属酶的功能,甚至创造出功能更为优越的新型酶分子。肌红蛋白（Mb）是作为血红素蛋白或其他金属蛋白分子设计的理想蛋白模型。近些年,基于Mb蛋白骨架的人工金属酶的分子设计逐渐发展了多种研究策略,包括设计氢键网络、金属结合位点、分子内二硫键、利用蛋白翻译后修饰、引入非天然氨基酸和非天然辅基等。本文着重综述这些方面的最新研究进展,可以帮助我们深刻认识金属酶的结构与功能关系,同时掌握人工金属酶分子设计的思路与方法,从而有助于推动这一领域的快速发展。     

Rational Heme Protein Design: All Roads Lead to Rome

Heme proteins are among the most abundant and important metalloproteins, exerting diverse biological functions including oxygen transport, small molecule sensing, selective C? H bond activation, nitrite reduction, and electron transfer. Rational heme protein designs focus on the modification of the heme‐binding active site and the heme group, protein hybridization and domain swapping, and de novo design. These strategies not only provide us with unique advantages for illustrating the structure–property–reactivity–function (SPRF) relationship of heme proteins in nature but also endow us with the ability to create novel biocatalysts and biosensors.     

Rational Topological Design for Fluorescence Enhancement upon Aggregation of Distyrylfuran Derivatives

A series of 2,5‐distyrylfuran derivatives bearing pentafluorophenyl‐ and cyanovinyl units have been synthesized for aggregation‐induced emission (AIE). The effect of the type and extent of the supramolecular connections on the AIE of the furan derivatives were examined and correlated with their X‐ray crystal structures. It was found that the simultaneous presence of cyano and perfluorophenyl units strongly enhances the fluorescence upon aggregation. Single‐crystal X‐ray diffraction analysis confirmed that C?H???F, F???F, C?H???nitrile, Ar???Ar_F (Ar=aryl, Ar_F=fluoroaryl), and nitrile???Ar_F intra‐ and intermolecular interactions drive the topology of the molecule and that solid‐state supramolecular contacts favor AIE of the furan derivatives.     

Antifreeze Protein‐Induced Selective Crystallization of a New Thermodynamically and Kinetically Less Preferred Molecular Crystal

The formation of a new, dihydrate crystalline form of 5‐methyluridine (m⁵U) was selectively induced by a protein additive, antifreeze protein (AFP) in a highly efficient manner (in 10^?6 molar scale, whereas known kinetic additives need 0.1 molar scale). The hemihydrate form (form I, the only previously known crystalline form of m⁵U) and the dihydrate form of m⁵U (form II) obtained herein were characterized using X‐ray crystallography and differential scanning calorimetry (DSC). Compared to form I, remarkably, form II is thermodynamically and kinetically less preferred. The presence of AFP can selectively inhibit the appearance of form I and hence allows the growth of form II, the pure form of which cannot grow directly from m⁵U supersaturated solutions under the same conditions. An explanation supported by both experimental and theoretical results is provided for the AFP‐induced selection process. Implications on AFP‐induced ice shape changes are also discussed. Control of crystallization from supersaturated solutions is of great interest in both fundamental research and practical applications in fields like chemistry, pharmacology and materials science. These findings suggest that crystallization processes with AFPs could be valuable for selective growth of hydrates and polymorphs of important pharmaceutical compounds.     

Crystallographic analysis of metal-ion binding to human ubiquitin

The metal-binding ability of human ubiquitin (hUb) towards a selection of biologically relevant metal ions and complexes has been probed. Different techniques have been used to obtain crystals suitable for crystallographic analysis. In the first type of experiments, crystals of hUb have been soaked in solutions containing copper(II) acetate and two metallodrugs, Zeise salt (K[PtCl(3)(η(2)-C(2)H(4))]·H(2)O) and cisplatin (cis-[PtCl(2)(NH(3))(2)]). The Zeise salt is used in a test for hepatitis, whereas cisplatin is one of the most powerful anticancer drugs in clinical use. The Zeise salt readily reacts with hUb crystals to afford an adduct with three platinum residues per protein molecule, Pt(3)-hUb. In contrast, copper(II) acetate and cisplatin were found to be unreactive for contact times up to one hour and to cause degradation of the hUb crystals for longer times. In the second type of experiments, hUb was cocrystallized with a solution of copper(II) or zinc(II) acetate or cisplatin. Zinc(II) acetate gives, at low metal-to-protein molar ratios (8:1), crystals containing one metal ion per three molecules of protein, Zn-hUb(3) (already reported in previous work), whereas at high metal-to-protein ratios (70:1) gives crystals containing three Zn(II) ions per protein molecule, Zn(3)-hUb. In contrast, once again, copper(II) acetate and cisplatin, even at low metal-to-protein ratios, do not give crystalline material. In the soaking experiment, the Zeise anion leads to simultaneous platination of His68, Met1, and Lys6. Present and previous results of cocrystallization experiments performed with Zn(II) and other Group 12 metal ions allow a comprehensive understanding of the metal-ion binding properties of hUb with His68 as the main anchoring site, followed by Met1 and carboxylic groups of Glu16, Glu18, Glu64, Asp21, and Asp32, to be reached. In the case of platinum, Lys6 can also be a binding site. The amount of bound metal ion, with respect to that of the protein, appears to be a relevant parameter influencing crystal packing.     

Facile synthesis of pyridinium aryltetrachlorotellurates: crystal and molecular structure of [C5H6N][RTeCl4] (R = m‐O2NC6H4, p‐NCC6H4)

Arylation of TeCl₄ with arylboroxine–pyridine complexes [(RBO)₃·C₅H₅N, where R = m‐O₂NC₆H₄ ( 1 ), p‐O₂NC₆H₄ ( 2 ), m‐NCC₆H₄ ( 3 ), p‐NCC₆H₄ ( 4 )] and advantageous moisture provided good yields of the pyridinium aryltetrachlorotellurates [C₅H₆N][RTeCl₄] [R = m‐O₂NC₆H₄ ( 5 ), p‐O₂NC₆H₄ ( 6 ), m‐NCC₆H₄ ( 7 ), p‐NCC₆H₄ ( 8 )]. Compounds 5 and 8 have been investigated by X‐ray crystallography. Key features of both crystal structures are intermolecular secondary Te???Cl interactions between the aryltetrachlorotellurate anions and weak association of the cations and anions. Electrospray mass spectra of compound 5 reveal that the associative interactions also play a role in solution. Copyright © 2005 John Wiley & Sons, Ltd.     

Precise Design of Artificial Cofactors for Enhancing Peroxidase Activity of Myoglobin: Myoglobin Mutant H64D Reconstituted with a “Single‐Winged Cofactor” Is Equivalent to Native Horseradish Peroxidase in Oxidation Activity

H64D myoglobin mutant was reconstituted with two different types of synthetic hemes that have aromatic rings and a carboxylate‐based cluster attached to the terminus of one or both of the heme‐propionate moieties, thereby forming a “single‐winged cofactor” and “double‐winged cofactor,” respectively. The reconstituted mutant myoglobins have smaller K_m values with respect to 2‐methoxyphenol oxidation activity relative to the parent mutant with native heme. This suggests that the attached moiety functions as a substrate‐binding domain. However, the k_cat value of the mutant myoglobin with the double‐winged cofactor is much lower than that of the mutant with the native heme. In contrast, the mutant reconstituted with the single‐winged cofactor has a larger k_cat value, thereby resulting in overall catalytic activity that is essentially equivalent to that of the native horseradish peroxidase. Enhanced peroxygenase activity was also observed for the mutant myoglobin with the single‐winged cofactor, thus indicating that introduction of an artificial substrate‐binding domain at only one of the heme propionates in the H64D mutant is the optimal engineering strategy for improving the peroxidase activity of myoglobin.     

The Structure of 2‐[(1S)‐(+)‐10‐camphorsulfonamino]‐6‐aminopyridine in the Solid State and in Solution; Unprecedented Cocrystallization of Four Stereoisomers

The solid and solution structures of a new optically active aminopyridine compound, 2‐[(1S)‐(+)‐10‐camphorsulfonamino]‐6‐aminopyridine [(S)‐csaap], 1 , are reported. Crystal data: space group P2₁, a = 8.9729 (5), b = 10.9447 (6), c = 36.693 (2) Å, β = 96.435 (1)°, V = 3580.8 (3) ų, Z = 8, R₁ = 0.0673 and wR₂ = 0.1600 with I > 2σ(I). This chiral compound shows an unprecedented cocrystallization of four stereoisomers, which are characterized by X‐ray crystallography and NMR spectroscopy.     

Phase Behavior of a Designed Cyclopropyl Analogue of Monoolein: Implications for Low‐Temperature Membrane Protein Crystallization

Lipidic cubic phases (LCPs) are used in areas ranging from membrane biology to biodevices. Because some membrane proteins are notoriously unstable at room temperature, and available LCPs undergo transformation to lamellar phases at low temperatures, development of stable low‐temperature LCPs for biophysical studies of membrane proteins is called for. Monodihydrosterculin (MDS) is a designer lipid based on monoolein (MO) with a configurationally restricted cyclopropyl ring replacing the olefin. Small‐angle X‐ray scattering (SAXS) analyses revealed a phase diagram for MDS lacking the high‐temperature, highly curved reverse hexagonal phase typical for MO, and extending the cubic phase boundary to lower temperature, thereby establishing the relationship between lipid molecular structure and mesophase behavior. The use of MDS as a new material for LCP‐based membrane protein crystallization at low temperature was demonstrated by crystallizing bacteriorhodopsin at 20 °C as well as 4 °C.     

NMR Spectroscopy and X‐Ray Characterisation of Cationic N‐Heteroaryl‐Pyridylamido ZrIV Complexes: A Further Level of Complexity for the Elusive Active Species of Pyridylamido Olefin Polymerisation Catalysts

New [(N^?,N,N^?)ZrR₂] dialkyl complexes (N^?,N,N^?=pyrrolyl‐pyridyl‐amido or indolyl‐pyridyl‐amido; R=Me or CH₂Ph) have been synthesised and tested as pre‐catalysts for ethene and propene polymerisation in combination with different activators, such as B(C₆F₅)₃, [Ph₃C][B(C₆F₅)₄], [HNMe₂Ph][B(C₆F₅)₄] or solid AlMe₃‐depleted methylaluminoxane (DMAO). Polyethylene (M_w>2 MDa and M_w/M_n = 1.3–1.6) has been produced if pre‐catalysts were activated with 1000 equivalents of DMAO (based on Al) [activity >1000 kg_PE (mol_[Zr] h mol atm)^?1] or by using a higher pre‐catalyst concentration and a mixture of [HNPhMe₂][B(C₆F₅)₄] (1 equiv) and AliBu₂H (60 equiv). In the case of propene polymerisation, activity has been observed only if pre‐catalysts were treated with an excess of AliBu₂H prior to addition of DMAO, which led to highly isotactic polypropylene ([mmmm]>95 %). Neutral pre‐catalysts and ion pairs derived from their activation have been characterised in solution by using advanced 1D and 2D NMR spectroscopy experiments. The detection and rationalisation of intercationic NOEs clearly showed the formation of dimeric species in which some pyrrolyl or indolyl π‐electron density of one unit is engaged in stabilising the metal centre of the other unit, which relegates the counterions in the second coordination sphere. The solid‐state structure of the dimeric indolyl‐pyridyl‐amidomethylzirconium derivative, determined by X‐ray diffraction studies, points toward a weak Zr???η³‐indolyl interaction. It can be hypothesised that the formation of dimeric cationic species hampers monomer coordination (especially of less reactive α‐olefins) and that addition of AliBu₂H is crucial to split the homodimers.     

New Structural Motif for Carboxylic Acid Perhydrolases

Some serine hydrolases also catalyze a promiscuous reaction— reversible perhydrolysis of carboxylic acids to make peroxycarboxylic acids. Five X‐ray crystal structures of these carboxylic acid perhydrolases show a proline in the oxyanion loop. Here, we test whether this proline is essential for high perhydrolysis activity using Pseudomonas fluorescens esterase (PFE). The L29P variant of this esterase catalyzes perhydrolysis 43‐fold faster (k_cat comparison) than the wild type. Surprisingly, saturation mutagenesis at the 29 position of PFE identified six other amino acid substitutions that increase perhydrolysis of acetic acid at least fourfold over the wild type. The best variant, L29I PFE, catalyzed perhydrolysis 83‐times faster (k_cat comparison) than wild‐type PFE and twice as fast as L29P PFE. Despite the different amino acid in the oxyanion loop, L29I PFE shows a similar selectivity for hydrogen peroxide over water as L29P PFE (β₀=170 vs. 160 M ^?1), and a similar fast formation of acetyl‐enzyme (140 vs. 62 U mg^?1). X‐ray crystal structures of L29I PFE with and without bound acetate show an unusual mixture of two different oxyanion loop conformations. The type II β‐turn conformation resembles the wild‐type structure and is unlikely to increase perhydrolysis, but the type I β‐turn conformation creates a binding site for a second acetate. Modeling suggests that a previously proposed mechanism for L29P PFE can be extended to include L29I PFE, so that an acetate accepts a hydrogen bond to promote faster formation of the acetyl‐enzyme.     

Characterization of trace embedded impurities in thin multilayer structures using synchrotron X‐ray standing waves

X‐ray standing wave (XSW) field generated under Bragg reflection condition in a periodic Mo/Si multilayer structure has been used to determine the concentration and location of various trace element contaminants embedded in different layers of that multilayer structure. We have used intense synchrotron X rays for XSW analysis. It is observed that various trace element impurities such as Cr, Fe, Ni and W get embedded unintentionally in the multilayer structure during the deposition process. Consequences of such impurity incorporation on the optical properties of the multilayer structure are discussed in hard and soft X‐ray regions. Present measurements are important in order to optimize the deposition methods on one hand and to better correlate the measured optical properties of a multilayer structure with theoretical models on the other. Copyright © 2010 John Wiley & Sons, Ltd.     

Synthesis of the First Tellurium‐Derivatized Oligonucleotides for Structural and Functional Studies

We report here the first synthesis of Te‐nucleoside phosphoramidites and Te‐modified oligonucleotides. We protected the 2′‐tellurium functionality by alkylation and found that the Te functionality is compatible with solid‐phase synthesis and that the Te oligonucleotides are stable during deprotection and purification. In addition, the redox properties of the Te functionalities have been explored. We found that the telluride and telluoxide DNAs are interchangeable by redox reactions. At elevated temperature, the Te‐DNA can also be site‐specifically fragmented oxidatively or reductively when 2′‐TePh functionality is present, whereas elimination of the nucleobase is observed in the presence of 2′‐TeMe. Moreover, the stability of the DNA duplexes derivatized with the Te functionalities has been investigated. Our Te derivatization of nucleic acids provides a novel approach for investigating DNA damage as well as for structure and function studies of nucleic acids and their protein complexes.     

Cyclic Hydroboration – The Structure of Perhydro‐9b‐boraphenalenes

Complete hydroboration of cyclododecatrienes was reported to give two isomers, depending on conditions. The assignment of their structure had been attempted without unequivocal proofs. We have now used NMR spectroscopy (¹¹B, ¹³C, ¹⁵N and ²³Na NMR) to study the sodium amides of these two polycyclic boranes. In addition, one of the isomeric borates could be crystallized, and the X‐ray analysis revealed a cis‐,cis‐,trans configuration of the six‐membered rings reversing the original structural assignment.