Structural and kinetic studies on adenylosuccinate lyase from Mycobacterium smegmatis and Mycobacterium tuberculosis provide new insights on the catalytic residues of the enzyme

Adenylosuccinate lyase (ASL), an enzyme involved in purine biosynthesis, has been recognized as a drug target against microbial infections. In the present study, ASL from Mycobacteriumsmegmatis (MsASL) and Mycobacteriumtuberculosis (MtbASL) were cloned, purified and crystallized. The X-ray crystal structure of MsASL was determined at a resolution of 2.16 angstrom. It is the first report of an apo-ASL structure with a partially ordered active site C3 loop. Diffracting crystals of MtbASL could not be obtained and a model for its structure was derived using MsASL as a template. These structures suggest that His149 and either Lys285 or Ser279 of MsASL are the residues most likely to function as the catalytic acid and base, respectively. Most of the active site residues were found to be conserved, with the exception of Ser148 and Gly319 of MsASL. Ser148 is structurally equivalent to a threonine in most other ASLs. Gly319 is replaced by an arginine residue in most ASLs. The two enzymes were catalytically much less active compared to ASLs from other organisms. Arg319Gly substitution and reduced flexibility of the C3 loop might account for the low catalytic activity of mycobacterial ASLs. The low activity is consistent with the slow growth rate of Mycobacteria and their high GC containing genomes, as well as their dependence on other salvage pathways for the supply of purine nucleotides. Structured digital abstract andby()

Do we see what we should see? Describing non-covalent interactions in protein structures including precision

The power of X-ray crystal structure analysis as a technique is to `see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this `seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and alpha-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.

Iso-specific Ziegler-Natta polymerization of α-olefins with a single-component organoyttrium catalyst

The synthesis of a sterically tailored ligand array (M)_2((C_5H_2-2-Si(CH_3)_3-4-C(CH_3)_3)S_2i(CH_3)_2]("M_2Bp") (M = Li, 16; K, 19) is described. Transmetallation of Li_2Bp with YCl_3(THF)_3 affords exclusively the C_2 symmetric product rac-[BpY(µ_2-Cl)_2Li(THF)_2], 20. A X-ray crystal structure of 20 has been determined; triclinic, P1, a= 13.110 (8), b = 17.163 (15), c = 20.623 (14) Å, α = 104.02 (7), β = 99.38 (5), γ = 100.24 (6)° , Z = 4, R = 0.056. Transmetallation of K_2Bp with YCl_3(THF)_3 affords the halide free complex rac-BpYCl, 23. The corresponding rac-BpLaCl, 28, is prepared in an anlogous manner. In all cases the achiral meso isomer is not obtained since only for the racemic isomers are the unfavorable steric interactions between the Si(CH3)_3 groups in the narrow portion of the [Cp-M'-Cp] wedge avoided. Alkylation of 20 or 23 with LiCH(Si(CH_3)_3)_2 affords rac-BpYCH(Si(CH_3)_3)_2, 26 in good yield. Alkylation of 28 with LiCH(Si(CH_3)_3)_2 affords rac-BpLaCH(Si(CH_3)_3)_2 29. Hydrogenation of 26 cleanly affords the bridging hydride species [BpY(µ_2-H)]_2, 27, as the homochiral (R,R) and (S,S) dimeric pairs. 26 is an efficient initiator for the polymerization of ethylene to high molecular weight linear polyethylene. 27 catalyzes the polymerization of propylene (25% v/v in methylcyclohexane) and neat samples of 1-butene, 1-pentene, 1-hexene to moderately high molecular weight polymers: polypropylene (M_n = 4,200, PDI 2.32, T_m 157 °C); poly-1-butene (M_n = 8,500, PDI 3.44, T_m 105 °C); poly-1-pentene (M_n = 20,000, PDI 1.99, T_m 73 °C); poly-1-hexene (M_n = 24,000, PDI 1.75, T_m < 25 °C). ^(13)C NMR spectra at the pentad analysis level indicates that the degree of isotacticity is 99% mmmm for all polymer samples. 27 is the first single component iso-specific α-olefin polymerization catalyst. The presumed origins of the high isospecificity are presented.

Synthetic and structural studies of permethylscandocene and permethyltantalocene derivatives

Cp*_2Sc-H reacts with H_2 and CO at -78°C to yield Cp*_2ScOCH_3. A stepwise reduction of CO to an alkoxide is observed when CO reacts with Cp*_2ScC_6H_4CH_3-p to give the η^2-acyl Cp*_2Sc(CO)C_6H_4CH_3-p, which then reacts with H_2 to produce Cp*_2ScOCH_2C_6H_4CH_3-p. Cp*_2ScCH_3 and Cp*_2ScH(THF) react with CO to give unchar- uncharacterizable products. Cp*_2ScH and Cp*_2ScCH_3 react with Cp_2MCO (M = Mo, W) to give scandoxycarbenes, Cp_2M=C(CH_3)OScCp*_2, while a wide variety of Cp*_2ScX (X = H, CH_3, N(CH_3)_2, CH_2CH_2C_6H_5) reacts with CpM(CO)_2 (M = Co, Rh) to yield similar carbene complexes. An x-ray crystal structure determination of Cp(CO)Co=C(CH_3)- OScCp*_2 revealed a µ^2: η^1, η^1 carbonyl interaction between the Co-CO and Sc.

CO_2 inserts cleanly into Sc-phenyl bonds at -78°C to produce a carboxylate complex, Cp*_2Sc(O_2C)C_6H_4CH_3-p. The structure of this compound was determined by x-ray crystallographic techniques.

Excess C_2H_2 reacts with Cp*_2ScR (R = H, alkyl, aryl, alkenyl, alkynyl, amide) at temperatures below -78°C to form the alkynyl species Cp*_2Sc-C≡C-H, which then reacts with the remaining acetylene to form polyacetylene. Cp*_2Sc-C≡C-H further reacts to yield Cp*_2sc-C≡C-ScCp*_2. This unusual C_2 bridged dimer was characterized by x-ray crystallography.

Attempts were made to model the C-N bond breaking step of hydrodenitrogenation by synthesizing Cp*_2TaH(η^2-H_2C=N(C_6H_4X)) and studying its rearrangement to Cp*_2Ta(=N(C_6H_4X))(CH_3). The 1,2 addition/elimination reactions of Cp*_2Ta(η^2- H_2C=N(CH_3)H and Cp*_2Ta(=X)H (X=O, S, NH, N(C_6H_5)) were investigated. Cp*_2Ta(=NH)H was found to react with D_2 to give Cp*_2Ta(=ND)H, implying a nonsymmetric amide-dihydride intermediate for the addition/elimination process. Cp*_2Ta(=S)H and H_2O equilibrate with Cp*_2Ta(=O)H and H_2S, which allowed determination of the difference in bond strengths for Ta=O and Ta=S. Ta=O was found to be approximately 41 kcals/mole stronger than Ta=S.

Structural and Biophysical Characterization of Variants of the Mechanosensitive Channel of Large Conductance (MSCL)

The ability to sense mechanical force is vital to all organisms to interact with and respond to stimuli in their environment. Mechanosensation is critical to many physiological functions such as the senses of hearing and touch in animals, gravitropism in plants and osmoregulation in bacteria. Of these processes, the best understood at the molecular level involve bacterial mechanosensitive channels. Under hypo-osmotic stress, bacteria are able to alleviate turgor pressure through mechanosensitive channels that gate directly in response to tension in the membrane lipid bilayer. A key participant in this response is the mechanosensitive channel of large conductance (MscL), a non-selective channel with a high conductance of ~3 nS that gates at tensions close to the membrane lytic tension.

It has been appreciated since the original discovery by C. Kung that the small subunit size (~130 to 160 residues) and the high conductance necessitate that MscL forms a homo-oligomeric channel. Over the past 20 years of study, the proposed oligomeric state of MscL has ranged from monomer to hexamer. Oligomeric state has been shown to vary between MscL homologues and is influenced by lipid/detergent environment. In this thesis, we report the creation of a chimera library to systematically survey the correlation between MscL sequence and oligomeric state to identify the sequence determinants of oligomeric state. Our results demonstrate that although there is no combination of sequences uniquely associated with a given oligomeric state (or mixture of oligomeric states), there are significant correlations. In the quest to characterize the oligomeric state of MscL, an exciting discovery was made about the dynamic nature of the MscL complex. We found that in detergent solution, under mild heating conditions (37 °C – 60 °C), subunits of MscL can exchange between complexes, and the dynamics of this process are sensitive to the protein sequence.

Extensive efforts were made to produce high diffraction quality crystals of MscL for the determination of a high resolution X-ray crystal structure of a full length channel. The surface entropy reduction strategy was applied to the design of S. aureus MscL variants and while the strategy appears to have improved the crystallizability of S. aureus MscL, unfortunately the diffraction qualities of these crystals were not significantly improved. MscL chimeras were also screened for crystallization in various solubilization detergents, but also failed to yield high quality crystals.

MscL is a fascinating protein and continues to serve as a model system for the study of the structural and functional properties of mechanosensitive channels. Further characterization of the MscL chimera library will offer more insight into the characteristics of the channel. Of particular interest are the functional characterization of the chimeras and the exploration of the physiological relevance of intercomplex subunit exchange.

Biochemical and Biophysical Characterization of Huntingtin

Huntington’s disease (HD) is a fatal autosomal dominant neurodegenerative disease. HD has no cure, and patients pass away 10-20 years after the onset of symptoms. The causal mutation for HD is a trinucleotide repeat expansion in exon 1 of the huntingtin gene that leads to a polyglutamine (polyQ) repeat expansion in the N-terminal region of the huntingtin protein. Interestingly, there is a threshold of 37 polyQ repeats under which little or no disease exists; and above which, patients invariably show symptoms of HD. The huntingtin protein is a 350 kDa protein with unclear function. As the polyQ stretch expands, its propensity to aggregate increases with polyQ length. Models for polyQ toxicity include formation of aggregates that recruit and sequester essential cellular proteins, or altered function producing improper interactions between mutant huntingtin and other proteins. In both models, soluble expanded polyQ may be an intermediate state that can be targeted by potential therapeutics.

In the first study described herein, the conformation of soluble, expanded polyQ was determined to be linear and extended using equilibrium gel filtration and small-angle X-ray scattering. While attempts to purify and crystallize domains of the huntingtin protein were unsuccessful, the aggregation of huntingtin exon 1 was investigated using other biochemical techniques including dynamic light scattering, turbidity analysis, Congo red staining, and thioflavin T fluorescence. Chapter 4 describes crystallization experiments sent to the International Space Station and determination of the X-ray crystal structure of the anti-polyQ Fab MW1. In the final study, multimeric fibronectin type III (FN3) domain proteins were engineered to bind with high avidity to expanded polyQ tracts in mutant huntingtin exon 1. Surface plasmon resonance was used to observe binding of monomeric and multimeric FN3 proteins with huntingtin.

Synthesis and structural characterisation of [Cu2[(PDC)2(bpa)(H2O)2]•nH2O•mDMF (n=3 and m=1 for 1, n=7 and m=0 for 2, PDC=2,5-pyrindinedicarboxylate and bpa= 1,2-di(4-pyridil)ethane))

[EN] Combination of polycarboxylate anions and dipyridyl ligands is an effective strategy to produce solid coordination frameworks (SCF) which are crystalline materials based on connections between metal ions through organic ligands. In this sense, combination of polycarboxylate anions and dipyridyl ligands is an effective strategy to produce extended structures. In this context, this work is focused on two novel CuII-based SCFs exhibiting PDC (2,5-pyridinedicarboxylate) and bpa (1,2-di(4-pyridyl)ethane), being the first structures reported in literature containing both ligands. Chemical formula are [Cu2[(PDC)2(bpa)(H2O)2]•3H2O•DMF (1), and [Cu2(PDC)2(bpa)(H2O)2]•7H2O (2), where DMF is dimethylformamide. Compounds 1 and 2 have been characterized by means of XRD, IR, TG/DTG, and DTA analysis.

Rare-earth-metal mixed hydride/aryloxide complexes bearing mono(cyclopentadienyl) ligands. Synthesis, CO2 fixation, and catalysis on copolymerization of CO2 with cyclohexene oxide

Hydrogenolysis of mono(cyclopentadienyl)-ligated rare-earth-metal bis(alkyl) complexes Cp'Ln-(CH2SiMe3)2(THF) (Ln = Y (1a), Dy (1b), Lu (1c); Cp' = C5Me4SiMe3) with PhSiH3 afforded the mixed hydride/alkyl complexes [Cp'Ln(mu-H)(CH2SiMe3)(THF)](2) (Ln = Y (2a), Dy (2b), Lu (2c)). The overall structure of complexes 2a-c is a C-2-symmetric dimer containing a planar symmetric Ln(2)H(2) core at the center of the molecule. Deprotonation of ArOH (Ar = C6H2-Bu-t(2)-2,6-Me-4) by the metal alkyl group of 2a-c led to formation of the mixed hydride/aryloxide derivatives [Cp'Ln(mu-H)(OAr)](2) (Ln = Y (3a), Dy (3b), Lu (3c)), which adopt the dimeric structure through hydride bridges with trans-accommodated terminal aryloxide groups.

Magnetic Coupling between Copper(II) Ions Mediated by Hydrogen-Bonded (Neutral) Water Molecules

A new hydrogen-bonded dinuclear copper(II) coordination compound has been synthesized from the Schiff-base ligand 6-(pyridine-2-ylhydrazonomethyl)phenol (Hphp). The molecular structure of [Cu-2(php)(2)(H2O2)(2)(ClO4)](ClO4)- (H2O) (1), determined by single-crystal X-ray diffraction, reveals the presence of two copper(II) centers held together by means of two strong hydrogen bonds, with O center dot O contacts of only 2.60-2.68 angstrom. Temperature-dependent magnetic susceptibility measurements down to 3 K show that the two metal ions are antiferromagnetically coupled (J = -19.8(2) cm(-1)). This exchange is most likely through two hydrogen-bonding pathways, where a coordinated water on the first Cu, donates a H bond to the O atoms of the coordinated php at the other Cu. This strong O center dot H (water) bonding interaction has been clearly evidenced by theoretical calculations. In the relatively few related cases from the literature, this exchange path, mediated by a (neutral) coordinated water molecule, was not recognized.

New titanium complexes with two beta-enaminoketonato chelate ligands: Syntheses, structures, and olefin polymerization activities

New titanium complexes with two nonsymmetric bidentate beta-enaminoketonato (N,O) ligands (4a-e), [(Ph)NC(R-2)C(H)C(R-1)O](2)TiCl2, have been synthesized. X-ray crystal structure reveals that complex 4a has a C-2-symmetric conformation with a distorted octahedral geometry around the titanium center. With modified methylaluminoxane (MMAO) as a cocatalyst, complexes 4a-e are active catalysts for ethylene polymerization at room temperature, producing high molecular weight polyethylenes bearing linear structures. The 4a,b/MMAO catalyst systems exhibit the characteristics of a quasi-living polymerization of ethylene, producing polyethylenes with narrow molecular weight distributions. Moreover, the 4a-d/MMAO catalyst systems are also capable of promoting the quasi-living copolymerization of ethylene with norbornene at room temperature, yielding high molecular weight alternating copolymers with narrow molecular weight distributions. The quasi-living nature of the catalysts allows the synthesis of new A-B polyethylene-block-poly(ethylene-conorbornene) diblock copolymer.

Tetra-mu-L-isoleucine-bis[tetraapuasamarium(III)] hexaperchlorate

The title complex, [Sm-2(C6H13NO2)(4)(H2O)(8)](ClO4)(6), contains dimeric [Sm-2(Ile)(4)(H2O)(8)](6+) cations (Ile is L-isoleucine) and perchlorate anions. The two Sm3+ cations lie on a crystallographic twofold rotation axis. The four isoleucine molecules act as bridging ligands, linking two Sm3+ ions through their carboxyl O atoms. Each Sm3+ ion is also coordinated by four water molecules to complete eightfold coordination in a square antiprismatic fashion. One of the three perchlorate anions in the asymmetric unit is disordered.

Phenylthiolate as a sigma- and pi-donor ligand: synthesis of a 3-D organometallic coordination polymer [K2Fe(SPh)(4)](n)

The synthesis and crystal structure of the first mixed-metal organometallic polymer network containing phenylthiolato ligands, [K2Fe(SPh)(4)](n), are investigated. The simple phenyl-thiolate acts as a sigma- and pi-donor ligand to give a 3-D potassium iron coordination polymer with both metal-carbon and metal-sulfur coordination interactions.

Solvent-dependent formation of di- and trinuclear rhodiurn and iridium complexes bridged by N,N '-donor ligands

Reactions of Rh and Ir hydrido complexes. [Rh(H)(2)(PPh3)(2)(solv)(EtOH)]ClO4 (solv = Me2CO, 1a; EtOH, 1b) and [Ir(H)(2)(PPh3)(2)(Me2CO)(2)]BF4 (2), with various N,N'-donor bridging ligands, such as pyrazine (pyz), 4,4'-trimethylenedipyridine (tmdp) and di(4-pyridyl) disulfide (dpds), in some solvents were examined, and their reaction products were characterized by X-ray crystal structure analysis. IR, H-1 NMR and UV-vis spectra. Rh hydrido complexes, la or 1b, formed a dinuclear Rh complex, [Rh-2(PPh3)(2) {(eta(6)-C6H5PPh2}(2)] (ClO4)(2).6CH(2)Cl(2) (3.6CH(2)Cl(2)), in dichloromethane with a reductive elimination of hydrogen. The reactions of 1a or 1b with the pyz ligand in dichloromethane and tetrahydrofuran gave triangular Rh-3 complexes, [Rh-3(PPh3)(6)(pyz)(3)](ClO4)(3).CH2Cl2 (5.CH2Cl2) and [Rh-3(PPh3)(6)(pyz)(3)](ClO4)(3).EtOH (5.EtOH), respectively, in contrast to the formation of a dinuclear Rh hydrido complex, [Rh-2(H)(4)(PPh3)(4)(Me2CO)(2)(pyz)](ClO4)(2).EtOH A-EtOH). in acetone. The reactions of la or 1b with the tmdp ligand in dichloromethane and 3-methyl-2-butanone also afforded dinuclear Rh complexes, [Rh-2(PPh3)(4)(tmdp)(2)](ClO4)(2) (6) and [Rh-2(PPh3)(4)(tmdp)(2)](ClO4)(2).4MeCOCHMe(2) (6.4MeCOCHMe(2)), respectively. On the other hand, Ir hydrido complex 2 reacted with pyz and dpds ligands in dichloromethane to afford dinuclear Ir complexes, [Ir-2(H)(4)(PPh3)(4)(Me2CO)(2)(pyz)]- (BF4)(2).3CH(2)Cl(2) (7.3CH(2)Cl(2)) and [Ir-2(H)(4)(PPh3)(4)(dpds)(2)](BF4)(2).3CH(2)Cl(2).H2O (8.3CH(2)Cl(2).H2O), respectively, without any reductive elimination of hydrogen. Based on structural studies in solution and in the solid state. it was demonstrated that various Rh and Ir complexes were selectively produced depending on the choice of solvents and N,N'-donor bridging ligands.

Synthesis and characterization of tris(cyclopentylcyclopentadienyl)lanthanide complexes (C5H9C5H4)(3)NdBrLi(THF)(3) and (C5H9C5H4)(3)SmTHF

(C5H9C5H4)(3)NdBrLi(THF)(4)(1)(C5H9=cyclopentyl) was obtained from the reaction of NdCl3 with C5H9C5H4Na and LiBr (Nd:Na:Li=1:2:1 molar ratio) in THE X-ray crystallography showed that the ten-coordinated neodymium atom is bonded to three cyclopentylcyclopentadienyl(eta(5)) rings and a single bromine atom bridging a lithium which is bonded to three THF molecules. Complex 1 is triclinic, P1 space group with unit dimensions of a= 12.048(2), b= 13.498(3), c= 13.831(3)Angstrom, a = 104.16(3), beta = 104.07(3), gamma =95.96(3)degrees, V=2083.3(7)Angstrom(3), Z=2, D-c=1.35Mg/m(3) and F(000)=874. (C5H9C5H4)(3)SmTHF (2) was synthesized by reaction of anhydrous SmCl3 with C5H9C5H4Na at a molar ratio of 1:3. The structure was determined by X-ray crystallography. The ten-coordinated samarium atom is bonded to three cycloperrtylcyclopentadienyl rings and one oxygen of THF molecule to form a pseudo-tetrahedron. Complex 2 is orthorhombic, Fdd2 space group with unit cell dimensions of a =28.175(5)Angstrom, b =46.24(2) Angstrom, c =9.167(4) Angstrom(3), V=11943(8)Angstrom(3), Z= 16, D-c = 1.38Mg/m(3) and F(000)=5136.

Synthesis and characterization of polynuclear half-sandwich lanthanoid complexes [Na(THF)(6)](2)[(Cp6Sm6Se13)-Sm-t] and [Li(LHF4](2)[Cp6Nd6Se13]

The half-sandwich tert-butyl cyclopentadienyl lanthanoid complexes {[Cp ' Ln(THF)](2)(mu (2)-Cl)(2)(mu (3)-Cl)(3)Na(THF)}(n) [Cp ' = eta (5)-' BuC5H4; Ln = Nd (1a), Sm (1b), Gd (1c), Yb (1d)] are prepared by the reaction of anhydrous lanthanoid trichloride, LnCl(3), with NaCp ' in THF solution. Complex 1b reacts with Na2Se5 to give hexanuclear samarium polyselenide complexes [Na(THF)(6)](2)[Cp-6' SM6(mu (6)-Se)(mu -Se-2)(6)] (2). An analogous cyclopentadienyl neodymium polyselenide complex [Li(THF)(4)](2)[Cp6Nd6(mu (6)-Se)(mu -Se-2)(6)] (3) is synthesized by the reaction of [CpNdCl2. 2LiCl . 5THF] with Na2Se5 in THF solution. The molecular structures of 1a and 2 were determined by X-ray crystal structure analysis. Complex 2 contains an interstitial selenium atom which is coordinated with six samarium atoms. (C) 2001 Elsevier Science BN. All rights reserved.