Structural investigations of stereoselective profen binding by equine and leporine serum albumins

Serum albumin, the most abundant transport protein of mammalian blood, interacts with various nonsteroidal anti-inflammatory drugs (NSAIDs) affecting their disposition, metabolism, and excretion. A big group of chiral NSAIDs transported by albumin, profens, is created by derivatives of 2-arylpropionic acid. The chiral center in the structures of profens is adjacent to the carboxylate moiety and often determines different pharmacological properties of profen enantiomers. This study describes crystal structures of two albumins, isolated from equine and leporine serum, in complexes with three profens: ibuprofen, ketoprofen, and suprofen. Based on three-dimensional structures, the stereoselectivity of albumin is discussed and referred to the previously published albumin complexes with drugs. Drug Site 2 (DS2) of albumin, the bulky hydrophobic pocket of subdomain IIIA with a patch of polar residues, preferentially binds (S)-enantiomers of all investigated profens. Almost identical binding mode of all these drugs clearly indicates the stereoselectivity of DS2 towards (S)-profens in different albumin species. Also, the affinity studies show that DS2 is the major site that presents high affinity towards investigated drugs. Additionally, crystallographic data reveal the secondary binding sites of ketoprofen in leporine serum albumin and ibuprofen in equine serum albumin, both overlapping with previously identified naproxen binding sites: the cleft formed between subdomains IIIA and IIIB close to the fatty acid binding site 5 and the niche created between subdomains IIA and IIIA, called fatty acid site 6.     

重组人巨噬细胞集落刺激因子的结构与功能

重组人粒细胞──巨噬细胞集落刺激因子(rhGM-CSF) 已经在原核、真核细胞表达并得到纯品,为它的结构与功能研究提供了有利条件．目前国内外对于rhGM-CSF的结构与功能研究主要集中在晶体结构、化学修饰、溶液中构象和稳定性以及突变和分子设计方面．分子结构与功能的关系以及与GM-CSF受体作用机理研究也取得了突破性进展．     

Crystal structure of kindlin-2 PH domain reveals a conformational transition for its membrane anchoring and regulation of integrin activation

Kindlin-2 belongs to a subfamily of FERM domain containing proteins, which plays key roles in activating integrin transmembrane receptors and mediating cell adhesion. Compared to conventional FERM domains, kindlin-2 FERM contains an inserted pleckstrin homology (PH) domain that specifically binds to phosphatidylinositol (3,4,5) trisphosphate (PIP3) and regulates the kindlin-2 function. We have determined the crystal structure of kindlin-2 PH domain at 1.9 ? resolution, which reveals a conserved PH domain fold with a highly charged and open binding pocket for PIP3 head group. Structural comparison with a previously reported solution structure of kindlin-2 PH domain bound to PIP3 head group reveals that upon PIP3 insertion, there is a significant conformational change of both the highly positively charged loop at the entry of the PIP3 binding pocket and the entire β barrel of the PH domain. We propose that such “induced-fit” type change is crucial for the tight binding of PIP3 to anchor kindlin-2 onto the membrane surface, thereby promoting its binding to integrins. Our results provide important structural insight into kindlin-2-mediated membrane anchoring and integrin activation.     

Structures of human Bruton's tyrosine kinase in active and inactive conformations suggest a mechanism of activation for TEC family kinases

Bruton's tyrosine kinase (BTK), a member of the TEC family of kinases, plays a crucial role in B‐cell maturation and mast cell activation. Although the structures of the unphosphorylated mouse BTK kinase domain and the unphosphorylated and phosphorylated kinase domains of human ITK are known, understanding the kinase selectivity profiles of BTK inhibitors has been hampered by the lack of availability of a high resolution, ligand‐bound BTK structure. Here, we report the crystal structures of the human BTK kinase domain bound to either Dasatinib (BMS‐354825) at 1.9 Å resolution or to 4‐amino‐5‐(4‐phenoxyphenyl)‐7H‐pyrrolospyrimidin‐ 7‐yl‐cyclopentane at 1.6 Å resolution. This data provides information relevant to the development of small molecule inhibitors targeting BTK and the TEC family of nonreceptor tyrosine kinases. Analysis of the structural differences between the TEC and Src families of kinases near the Trp‐Glu‐Ile motif in the N‐terminal region of the kinase domain suggests a mechanism of regulation of the TEC family members.     

Divalent metal 1,3-phenylenediacetate coordination polymers with rigid or flexible dipyridyl tethers: Chains, layers, and interpenetrated networks

Hydrothermal synthesis has afforded four divalent metal 1,3-phenylenediacetate (1,3-phda) coordination polymers containing different dipyridyl-type ligands. {[Cu(1,3-phda)(dpa)(H₂O)]·H₂O}_n (1, dpa = 4,4′-dipyridylamine) exhibits a simple 2-D (4,4) rhomboid grid structure. {[Co(1,3-phda)(bpy)]·1.5H₂O}_n (2, bpy = 4,4′-bipyridine) also possesses a (4,4) layer structure, but with syn-syn bridged {Co₂(OCO)₂} dimeric kernels serving as 4-connected nodes. {[Co(H₂O)₄(3-bpmpH₂)](1,3-phda)₂·8H₂O}_n (3, 3-bpmp = bis(3-pyridylmethyl)piperazine) manifests cationic 1-D [Co(H₂O)₄(3-bpmpH₂)]_n⁴ⁿ⁺ chains linked into higher dimensionality by unligated 1,3-phda anions and curled tetrameric water molecule units. {[Ni(1,3-phda)(4-bpmp)(H₂O)₂]·2H₂O}_n (4, 4-bpmp = bis(4-pyridylmethyl)piperazine) has an underlying twofold interpenetrated 6⁵8 (cds) 3-D network topology. Variable temperature magnetic susceptibility studies revealed the presence of weak antiferromagnetic coupling and zero-field splitting (J = −1.65(4) cm⁻¹ and D = 30.9(7) cm⁻¹ with g = 2.20(1)) within the {Co₂(OCO)₂} dimers in 2.     

Copper(II) promoted imidazolidine ring formation and complexation: A unique reaction course

The reaction of Cu(II) ions with a sodium salt of new Schiff base ligand NaL¹, sodium N-2-methyl pyridine-2-imine benzoate, in alkaline medium produced an imine bond coupled ligand and a novel complex, Na₂[Cu(L³)₂], L³ = 2,5-di(2-benzoic acid)-4-(2-pyridine)-1-(2-methyl-2-pyridine)-imidazolidine. When the reduced form of the sodium salt of the Schiff base ligand, NaL², is employed, a simple hexacoordinated copper(II) complex, [Cu(L²)₂], [L²]⁻ = bis(N-(2-methylpyridine)-2-aminomethylbenzoate), was isolated. The compounds were characterized by spectroscopic methods and the molecular structures of [Cu(L²)₂] and Na₂[Cu(L³)₂] were determined by single-crystal X-ray diffraction methods. Reaction mechanism for the synthesis of, Na₂[Cu(L³)₂], copper(II) promoted imine bond coupling is proposed and discussed. The redox behavior of [Cu(L²)₂] and Na₂[Cu(L³)₂], studied using cyclic voltammetry and electron paramagnetic resonance spectroscopic methods, are also discussed.     

Crystal structure of Bordetella pertussis BugD solute receptor unveils the basis of ligand binding in a new family of periplasmic binding proteins

Periplasmic binding proteins of a new family particularly well represented in Bordetella pertussis have been called Bug receptors. One B.pertussis Bug protein is part of a tripartite tricarboxylate transporter while the functions of the other 77 are unknown. We report the first structure of a Bug receptor, BugD. It adopts the characteristic Venus flytrap motif observed in other periplasmic binding proteins, with two globular domains bisected by a deep cleft. BugD displays a closed conformation resulting from the fortuitous capture of a ligand, identified from the electron density as an aspartate. The structure reveals a distinctive alpha carboxylate-binding motif, involving two water molecules that bridge the carboxylate oxygen atoms to the protein. Both water molecules are hydrogen bonded to a common carbonyl group from Ala14, and each forms a hydrogen bond with one carboxylate oxygen atom of the ligand. Additional hydrogen bonds are found between the ligand alpha carboxylate oxygen atoms and protein backbone amide groups and with a threonine hydroxyl group. This specific ligand-binding motif is highly conserved in Bug proteins, indicating that they may all be receptors of amino acids or other carboxylated solutes, with a similar binding mode. The present structure thus unveils the bases of ligand binding in this large family of periplasmic binding proteins, several hundred members of which have been identified in various bacterial species.     

Vacuum packing: a model system for laboratory-scale silage fermentations

AIMS: To determine the utility of vacuum-packed polythene bags as a convenient, flexible and cost-effective alternative to fixed volume glass vessels for lab-scale silage studies. METHODS AND RESULTS: Using perennial ryegrass or red clover forage, similar fermentations (as assessed by pH measurement) occurred in glass tube and vacuum-packed silos over a 35-day period. As vacuum-packing devices allow modification of initial packing density, the effect of four different settings (initial packing densities of 0.397, 0.435, 0.492 and 0.534 g cm(-3)) on the silage fermentation over 16 days was examined. Significant differences in pH decline and lactate accumulation were observed at different vacuum settings. Gas accumulation was apparent within all bags and changes in bag volume with time was observed to vary according to initial packing density. CONCLUSIONS: Vacuum-packed silos do provide a realistic model system for lab-scale silage fermentations. SIGNIFICANCE AND IMPACT OF THE STUDY: Use of vacuum-packed silos holds potential for lab-scale evaluations of silage fermentations, allowing higher throughput of samples, more consistent packing as well as the possibility of investigating the effects of different initial packing densities and use of different wrapping materials.     

X-ray structure of Na-ASP-2, a pathogenesis-related-1 protein from the nematode parasite, Necator americanus, and a vaccine antigen for human hookworm infection

Human hookworm infection is a major cause of anemia and malnutrition of adults and children in the developing world. As part of on-going efforts to control hookworm infection, The Human Hookworm Vaccine Initiative has identified candidate vaccine antigens from the infective L3 larval stages of the parasite, including a family of pathogenesis-related (PR) proteins known as the Ancylostoma-secreted proteins (ASPs). A novel crystal structure of Na-ASP-2, a PR-1 protein secreted by infective larvae of the human hookworm Necator americanus, has been solved to resolution limits of 1.68 A and to an R-factor of 17% using the recombinant protein expressed in and secreted by Pichia pastoris. The overall fold of Na-ASP-2 is a three-layer alphabetaalpha sandwich flanked by an N-terminal loop and a short, cysteine-rich C terminus. Our structure reveals a large central cavity that is flanked by His129 and Glu106, two residues that are well conserved in all parasitic nematode L3 ASPs. Na-ASP-2 has structural and charge similarities to chemokines, which suggests that Na-ASP-2 may be an extra-cellular ligand of an unknown receptor. Na-ASP-2 is a useful homology model for NIF, a natural antagonistic ligand of CR3 receptor. From these modeling studies, possible binding modes were predicted. In addition, this first structure of a PR-1 protein from parasitic helminths may shed light on the molecular basis of host-parasite interactions.     

Synthesis and mesomorphic properties of glycosyl dialkyl- and diacyl-glycerols bearing saturated, unsaturated and methyl branched fatty acid and fatty alcohol chains. Part II. Mesomorphic properties

The biophysical properties of a series of glycosyl dialkyl- and diacyl-glycerols bearing unsaturated or chiral methyl branched chains in the tail, and di- and trisaccharide carbohydrate headgroups are described. Thermotropism was investigated by polarising microscopy, the lyotropism was investigated by small angle X-ray diffraction and by the contact preparation method, and the gel to liquid crystalline phase transition by FT-IR-spectroscopy. The compounds displayed thermotropic Smectic A (SmA), cubic and columnar phases, whereas in the lyotropic phase diagram lamellar, hexagonal and cubic phases are found. The introduction of unsaturated or methyl branched chains leads to liquid crystallinity at ambient temperature. The difference between the 1,3-oleyl-glycerol maltoside and the corresponding 1,2-oleoyl-glycerol maltoside is small.