Influence of Medium and Long Range Interactions in (α/β)8 Barrel Proteins

The residue-residue contacts and the role of medium and long rangeinteractions in 36 (/)₈ barrel proteins have beenanalysed. The influence of long range contacts in the formation ofphysico-chemically similar clusters, and the preference of amino acidresidues towards long range contacts have also been studied. Theresults reveal a nearly uniform level of medium and long rangecontacts in most of the proteins. The residues Gln and Ala havehighest medium range contacts and the residue Pro has the lowestmedium range contacts. The residue Cys has the highest long rangecontact followed by other hydrophobic residues namely Val, Ile andLeu. In the physico-chemically similar clusters identified in theseproteins, 25–40 percent residues are influenced by long rangecontacts, and the residues Cys, Ile, Val and Met are the mostpreferred ones.     

Protein Design through Systematic Catalytic Loop Exchange in the (β/α)8 Fold

Protein engineering by directed evolution has proven effective in achieving various functional modifications, but the well-established protocols for the introduction of variability, typically limited to random point mutations, seriously restrict the scope of the approach. In an attempt to overcome this limitation, we sought to explore variant libraries with richer diversity at regions recognized as functionally important through an exchange of natural components, thus combining design with combinatorial diversity. With this approach, we expected to maintain interactions important for protein stability while directing the introduction of variability to areas important for catalysis.Our strategy consisted in loop exchange over a (β/α)₈ fold. Phosphoribosylanthranilate isomerase was chosen as scaffold, and we investigated its tolerance to loop exchange by fusing variant libraries to the chloramphenicol acetyl transferase coding gene as an in vivo folding reporter. We replaced loops 2, 4, and 6 of phosphoribosylanthranilate isomerase with loops of varied types and sizes from enzymes sharing the same fold.To allow for a better structural fit, saturation mutagenesis was adopted at two amino acid positions preceding the exchanged loop. Our results showed that 30% to 90% of the generated mutants in the different libraries were folded. Some variants were selected for further characterization after removal of chloramphenicol acetyl transferase gene, and their stability was studied by circular dichroism and fluorescence spectroscopy. The sequences of 545 clones show that the introduction of variability at “hinges” connecting the loops with the scaffold exhibited a noticeable effect on the appearance of folded proteins. Also, we observed that each position accepted foreign loops of different sizes and sequences.We believe our work provides the basis of a general method of exchanging variably sized loops within the (β/α)₈ fold, affording a novel starting point for the screening of novel activities as well as modest diversions from an original activity.     

Experimental Evidence for the Existence of a Stable Half-Barrel Subdomain in the (β/α)8-Barrel Fold

The (β/α)₈-barrel is one of the most common folds functioning as enzymes. The emergence of two (β/α)₈-barrel enzymes involved in histidine biosynthesis, each of which has a twofold symmetric structure, has been proposed to be a consequence of tandem duplication and fusion of a (β/α)₄-half-barrel. However, little evidence has been found for the existence of an ancestral half-barrel in the evolution of other (β/α)₈-barrel proteins. In order to detect remnants of an ancestral half-barrel in the (β/α)₈-barrel structure of Escherichia coli N-(5′-phosphoribosyl)anthranilate isomerase, we engineered three potential half-barrel units, (β/α)_1-4, (β/α)_3-6, and (β/α)_5-8. Among these three arrangements, only (β/α)_3-6 is stable; it exists in equilibrium between monomeric and dimeric forms. Thus, the central segment of N-(5′-phosphoribosyl)anthranilate isomerase from E. coli can serve as a half-barrel precursor. A tandem duplication of (β/α)_3-6 yielded predominantly monomeric structures that were quite stable. This result exemplified that the structural characteristics of noncovalently assembled half-barrels could be improved by duplication and fusion. Moreover, our results may provide information regarding the local structural units that encompass interactions important for the early folding events of this ubiquitous protein conformation.     

Thallium(III) complexes of the metalloligands [Pt2(μ-S)2(PPh3)4] and [Pt2(μ-Se)2(PPh3)4]

Reactions of [Pt₂(μ-S)₂(PPh₃)₄] with the diarylthallium(III) bromides Ar₂TlBr [Ar = Ph and p-ClC₆H₄] in methanol gave good yields of the thallium(III) adducts [Pt₂(μ-S)₂(PPh₃)₄TlAr₂]⁺, isolated as their salts. The corresponding selenide complex [Pt₂(μ-Se)₂(PPh₃)₄TlPh₂]BPh₄ was similarly synthesised from [Pt₂(μ-Se)₂(PPh₃)₄], Ph₂TlBr and NaBPh₄. The reaction of [Pt₂(μ-S)₂(PPh₃)₄] with PhTlBr₂ gave [Pt₂(μ-S)₂(PPh₃)₄TlBrPh]⁺, while reaction with TlBr₃ gave the dibromothallium(III) adduct [Pt₂(μ-S)₂(PPh₃)₄TlBr₂]⁺[TlBr₄]⁻. The latter complex is a rare example of a thallium(III) dihalide complex stabilised solely by sulfur donor ligands. X-ray crystal structure determinations on the complexes [Pt₂(μ-S)₂(PPh₃)₄TlPh₂]BPh₄, [Pt₂(μ-S)₂(PPh₃)₄TlBrPh]BPh₄ and [Pt₂(μ-S)₂(PPh₃)₄TlBr₂][TlBr₄] reveal a greater interaction between the thallium(III) centre and the two sulfide ligands on stepwise replacement of Ph by Br, as indicated by shorter Tl-S and Pt?Tl distances, and an increasing S-Tl-S bond angle. Investigations of the ESI MS fragmentation behaviour of the thallium(III) complexes are reported.     

Dynamic properties of the fluxional Rh2H(μ-PPh2)2(PPh3)3 complex

The rhodium dimer [Rh₂H(PPh₂)₂(PPh₃)₃]⁻ was prepared from RhCl(PPh₃)₃ and K₄Sn₉ in the presence of 2,2,2-cryptand in ethylenediamine/toluene solvent mixtures. The [K(2,2,2-crypt)]⁺ salt was isolated and characterized via NMR and X-ray diffraction studies. The solid state structure reveals a binuclear, diphenylphosphido-bridged, 32 electron Rh(I)-Rh(I) complex with edge-shared tetrahedral and square planar Rh centers with overall C_s point symmetry. 1-D and 2-D ¹H, ³¹P, and ³¹P{¹H} NMR experiments were used to characterize the complex.     

Synthesis of some pentanuclear platinum clusters [Pt5(CO)6(L)4]. The X-ray structure of [Pt5(μ-CO)5(CO)(PCy3)4]

[Pt₅(μ-CO)₅(CO)L₄] (L = PPh₃1, PPh₂Bz 2, AsPh₃3, PEt₃4, PCy₃5) have been synthesized by reacting [Pt₃(μ-CO)₃(PR₃)₃] with H₂O₂ (1 and 2), by reduction of cis-[PtCl₂(CO)(PEt₃)] with Zn dust (4), and by the Zn reduction of [Pt₃(μ-CO)₃(PCy₃)₃] in the presence of [PtCl₂(CH₃CN)₂] (5). Complex 5 has not been observed previously and has been characterized by X-ray crystallography. Oxidation of the phosphine ligands with H₂O₂ is a new way to synthesize 1 and 2. The first complete NMR characterization of these complexes has also been achieved, and showed that these pentanuclear cluster complexes exhibit similar stereochemistries in solution and in the solid state. The observed ¹J_Pt-Pt values do not have any correlation with the corresponding bond lengths, again pointing out the irregular behaviour of such parameter in Pt complexes.     

The arylation of [Pt2(μ-S)2(PPh3)4]

Routes to the synthesis of the mixed sulfide-phenylthiolate complex [Pt₂(μ-S)(μ-SPh)(PPh₃)₄]⁺ have been explored; reaction of [Pt₂(μ-S)₂(PPh₃)₄] with excess Ph₂IBr proceeds readily to selectively produce this complex, which was structurally characterised as its PF₆⁻ salt. Reactions of [Pt₂(μ-S)₂(PPh₃)₄] with other potent arylating reagents (1-chloro-2,4-dinitrobenzene and 1,5-difluoro-2,4-dinitrobenzene) also produce the corresponding nitroaryl-thiolate complexes [Pt₂(μ-S){μ-SC₆H₂(NO₂)₂X}(PPh₃)₄]⁺ (X = H, F). The complex [Pt₂(μ-S)(μ-SPh)(PPh₃)₄]⁺ reacts with Me₂SO₄ to produce the mixed alkyl/aryl bis-thiolate complex [Pt₂(μ-SMe)(μ-SPh)(PPh₃)₄]²⁺, but corresponding reactions with the nitroaryl-thiolate complexes are plagued by elimination of the nitroaryl group and formation of [Pt₂(μ-SMe)₂(PPh₃)₄]²⁺. [Pt₂(μ-S)(μ-SPh)(PPh₃)₄]⁺ also reacts with Ph₃PAuCl to give [Pt₂(μ-SAuPPh₃)(μ-SPh)(PPh₃)₄]²⁺.     

Reduction chemistry of the mixed ligand metallocene [(C5Me5)(C8H8)U]2(μ-C8H8) with bipyridines

The U⁴⁺ cyclooctatetraenyl complex, [(C₅Me₅)(C₈H₈)U]₂(μ-C₈H₈), 1, reacts with two equiv of 4,4′-dimethyl-2,2′-bipyridine (Me₂bipy) and 2 equiv of 2,2′-bipyridine (bipy) to form 2 equiv of (η⁵-C₅Me₅)(η⁸-C₈H₈)U(Me₂bipy-κ²N,N′) and (η⁵-C₅Me₅)(η⁸-C₈H₈)U(bipy-κ²N,N′), respectively. X-ray crystallography, infrared spectroscopy, and density functional theory calculations indicate that the products are best described as U⁴⁺ complexes of bipyridyl radical anions. Hence, only one of the (C₈H₈)²⁻ ligands in 1 acts as a reductant and delivers 2 electrons per equiv of 1. Since the reduction potentials of uncomplexed (C₈H₈)²⁻, Me₂bipy, and bipy are −1.86, −2.15, and −2.10 V vs SCE, respectively, it is likely that prior coordination of the bipyridine reagents enhances the electron transfer.     

Extending the coordination chemistry of cobalt with the metalloligand [Pt2(μ-S)2(PPh3)4]: Synthesis of the first cobalt(III) derivatives

The coordination chemistry of the metalloligand [Pt₂(μ-S)₂(PPh₃)₄] towards cobalt(II) and cobalt(III) centres has been explored using an electrospray ionisation mass spectrometry (ESI MS)-directed methodology. Reaction of [Pt₂(μ-S)₂(PPh₃)₄] with CoCl₂·6H₂O in methanol gave a green-yellow suspension of the known adduct [Pt₂(μ-S)₂(PPh₃)₄CoCl₂], and the CoBr₂ adduct could be similarly prepared. When in situ-generated [Pt₂(μ-S)₂(PPh₃)₄CoCl₂] is reacted with 8-hydroxyquinoline (HQ) and base, the initial product is the cobalt(II) adduct [Pt₂(μ-S)₂(PPh₃)₄CoQ]⁺, which is then converted in air to the cobalt(III) adduct [Pt₂(μ-S)₂(PPh₃)₄CoQ₂]⁺, isolated as its hexafluorophosphate salt. The corresponding picolinate (Pic) derivative [Pt₂(μ-S)₂(PPh₃)₄Co(Pic)₂]⁺ was similarly prepared, however reaction of [Pt₂(μ-S)₂(PPh₃)₄], CoCl₂·6H₂O and 8-(tosylamino)quinoline (HTQ) produced only the cobalt(II) adduct [Pt₂(μ-S)₂(PPh₃)₄CoTQ]⁺. Reactions of [Pt₂(μ-S)₂(PPh₃)₄], CoCl₂·6H₂O and dithiocarbamates gave cobalt(III) complexes [Pt₂(μ-S)₂(PPh₃)₄Co(S₂CNR₂)₂]⁺ [R = Et or R₂ = (CH₂)₄], and proceeded much more rapidly, consistent with the known ability of the dithiocarbamate ligand to stabilize cobalt in higher oxidation states. A study of the fragmentation of cobalt(III) adducts by positive-ion ESI mass spectrometry indicated that [Pt₂(μ-S)₂(PPh₃)₄CoQ₂]⁺ fragments to form the radical cation [Pt₂(μ-S)₂(PPh₃)₄]⁺, which could also be generated by ESI MS analysis of [Pt₂(μ-S)₂(PPh₃)₄] in methanol-NaOH solution. In contrast, the corresponding indium(III) derivative [Pt₂(μ-S)₂(PPh₃)₄InQ₂]⁺, and the cobalt(III) dithiocarbamate [Pt₂(μ-S)₂(PPh₃)₄Co(S₂CN(CH₂)₄)₂]⁺ are much more reluctant to fragment under analogous conditions, and the differences are discussed in terms of cobalt(III) redox chemistry.     

A versatile entry into aqueous niobium chemistry: isolation and structure of the intermediate Nb4(μ2-O)2(μ2-OC2H5)4Cl4(OC2H5)4(HOC2H5)4

The reduction of ethanolic solutions of niobium pentachloride with zinc, followed by treatment with aqueous acids serves as a versatile entry into the aqueous solution chemistry of niobium. From the zinc-reduced solution, the major intermediate, Nb₄(μ₂-O)₂(μ₂-OC₂H₅)₄Cl₄(OC₂H₅)₄(HOC₂H₅)₄, was isolated and the crystal structure determined by X-ray crystallography. The complex crystallizes in the orthorhombic space group Pccn, with Z=4, a=21.0105(9), b=11.0387(5), c=19.1389(8), V=4438.9(3) ų, M_r=1090.19,R₁=0.0327 and wR₂=0.0876. The structure revealed a centrosymmetric tetrameric Nb(IV) complex, consisting of a pair of edge-sharing bi-octahedral Nb₂(μ₂-OC₂H₅)₄Cl₂(OC₂H₅)₂(HOC₂H₅)₂ units that are joined by two axial oxo ligands. The Nb-Nb distance of 2.7458(3) Å is consistent with a single metal-metal bond.     

Further studies on the coordination chemistry of [Pt2(μ-S)2(PPh3)4] towards indium(III) substrates

The reactivity of the metalloligand [Pt₂(μ-S)₂(PPh₃)₄] towards a variety of indium(III) substrates has been explored. Reaction with excess In(NO₃)₃ and halide (KBr or NaI) gave the four-coordinate adducts [Pt₂(μ-S)₂(PPh₃)₄InX₂]⁺[InX₄]⁻ (X = Br, I). An X-ray structure determination on the iodo complex revealed a slightly distorted tetrahedral coordination geometry at indium. In contrast, reaction of [Pt₂(μ-S)₂(PPh₃)₄] with indium(III) chloride was more complex; the ion [Pt₂(μ-S)₂(PPh₃)₄InCl₂]⁺ was initially observed in solution (using ESI mass spectrometry), and isolated as its BPh₄⁻ salt. Analysis of [Pt₂(μ-S)₂(PPh₃)₄InCl₂]⁺[BPh₄]⁻ by ESI MS showed the parent cation when analysed in MeCN solution. However in solutions containing methanol, partial solvolysis occurred to give the di-indium species [{Pt₂(μ-S)₂(PPh₃)₄InCl(OMe)}₂]²⁺ (proposed to contain an In₂(μ-OMe)₂ unit with five-coordinate indium) and its fragment ion [Pt₂(μ-S)₂(PPh₃)₄InCl(OMe)]⁺. Reaction of [Pt₂(μ-S)₂(PPh₃)₄] with InCl₃·3H₂O, 8-hydroxyquinoline (HQ) and trimethylamine in methanol gave the adduct [Pt₂(μ-S)₂(PPh₃)₄InQ₂]⁺, isolated as its PF₆⁻ salt. The same cationic complex is formed when [Pt₂(μ-S)₂(PPh₃)₄] is reacted with InQ₃ in methanol, but in this case the product is contaminated with the mononuclear complex [(Ph₃P)₂PtQ]⁺ formed by disintegration of the trinuclear complex [Pt₂(μ-S)₂(PPh₃)₄InQ₂]⁺ with byproduct Q⁻. [(Ph₃P)₂PtQ]⁺BPh₄⁻ was independently prepared from cis-[PtCl₂(PPh₃)₂] and HQ/Me₃N, and is the first example of a platinum 8-hydroxyquinolinate complex containing phosphine ligands.     

VICMpred： An SVM-based Method for the Prediction of Functional Proteins of Gram-negative Bacteria Using Amino Acid Patterns and Composition

In this study, an attempt has been made to predict the major functions of gramnegative bacterial proteins from their amino acid sequences. The dataset used for training and testing consists of 670 non-redundant gram-negative bacterial proteins （255 of cellular process, 60 of information molecules, 285 of metabolism, and 70 of virulence factors）. First we developed an SVM-based method using amino acid and dipeptide composition and achieved the overall accuracy of 52.39% and 47.01%, respectively. We introduced a new concept for the classification of proteins based on tetrapeptides, in which we identified the unique tetrapeptides significantly found in a class of proteins. These tetrapeptides were used as the input feature for predicting the function of a protein and achieved the overall accuracy of 68.66%. We also developed a hybrid method in which the tetrapeptide information was used with amino acid composition and achieved the overall accuracy of 70.75%. A five-fold cross validation was used to evaluate the performance of these methods. The web server VICMpred has been developed for predicting the function of gram-negative bacterial proteins （http：//www.imtech.res.in/raghava/vicmpred/）.     

Importance of long-range interactions in (α/β)8 barrel fold

Protein structures are stabilized by both local and long-range interactions. In this work, we analyzed the importance of long-range interactions in (α/β)₈ barrel proteins in terms of residue distances. We found that the residues occurring in the range of 21–30 residues apart contribute more toward long-range contacts. Indeed, about 50% of successive strands in these proteins are found to occur at a sequential distance of 21–30 residues. The aromatic amino acid residues Phe, Trp, and Tyr prefer the 4–10 range and all other residues prefer the 21–30 range. Hydrophobic-hydrophobic resideu pairs are the most preferred ones for long-range interactions and they may play a key role in the folding and stabilization of (α/β)₈ barrel proteins.     

Characterisation of α3β1 and αvβ3 integrin N-oligosaccharides in metastatic melanoma WM9 and WM239 cell lines

It is well documented that glycan synthesis is altered in some pathological processes, including cancer. The most frequently observed alterations during tumourigenesis are extensive expression of β1,6-branched complex type N-glycans, the presence of poly-N-acetyllactosamine structures, and high sialylation of cell surface glycoproteins. This study investigated two integrins, α₃β₁ and α_vβ₃, whose expression is closely related to cancer progression. Their oligosaccharide structures in two metastatic melanoma cell lines (WM9, WM239) were analysed with the use of matrix-assisted laser desorption ionisation mass spectrometry. Both examined integrins possessed heavily sialylated and fucosylated glycans, with β1,6-branches and short polylactosamine chains. In WM9 cells, α₃β₁ integrin was more variously glycosylated than α_vβ₃; in WM239 cells the situation was the reverse. Functional studies (wound healing and ELISA integrin binding assays) revealed that the N-oligosaccharide component of the tested integrins influenced melanoma cell migration on vitronectin and α₃β₁ integrin binding to laminin-5. Additionally, more variously glycosylated integrins exerted a stronger influence on these parameters. To the best of our knowledge, this is the first report concerning structural characterisation of α_vβ₃ integrin glycans in melanoma or in any cancer cells.     

[Ir(acac)(η-C8H14)2]: A precursor in the synthesis of cyclometalated iridium(III) complexes

A new convenient synthesis and the crystallographic characterization of [Ir(acac)(coe)₂] (2, acac = acetylacetonato; coe = cis-cyclooctene) are described. The title compound crystallized from THF/ethanol in two modifications (monoclinic P2₁/c, 2a, and triclinic , 2b). Complex 2 represents an efficient starting material in the synthesis of mononuclear iridium(III) complexes containing cyclometalated 2-phenylpyridinato ligands using oxidative addition reactions of the corresponding ligands towards 2. Thus [Ir(acac)(ppy)₂] (3, ppy = 2-phenylpyridinato) and [Ir(ppy)₃] (4) (mer, 4a; fac, 4b) were prepared in excellent yields and short reaction times in a kind of one-pot procedure starting from [{Ir(μ-Cl)(coe)₂}₂] (1). Furthermore a convenient synthesis of [{Ir(μ-Cl)(ppy)₂}₂] (5) from 1 and Hppy is described.     

An electrospray mass spectrometry-directed survey of the coordination chemistry of the metalloligand [Pt2(μ-S)2(PPh3)4] with platinum(II) and palladium(II) chloride substrates: influence of metal-ligand lability on product type

The reactivity of the metalloligand [Pt₂(μ-S)₂(PPh₃)₄] towards a wide range of platinum(II) and palladium(II) chloride complex substrates [L₂MCl₂] has been explored, using the technique of electrospray ionisation mass spectrometry to directly analyse reaction solutions. In the majority of cases, products are formed by addition of the ML₂²⁺ fragment to the {Pt₂S₂} core, giving trinuclear species [Pt₂(μ-S)₂(PPh₃)₄ML₂]²⁺. The adducts with Pt(diene) [diene=cyclo-octa-1,5-diene (cod), norbornadiene], Pd(cod), Pd(bipy) (bipy=2,2^′-bipyridine), Pt(PMe₃)₂ and Pt(PTA)₂ (PTA=phosphatriaza-adamantane) moieties were synthesised and characterised on the macroscopic scale, with [Pt₂(μ-S)₂(PPh₃)₄Pt(cod)] (BF₄)₂ and [Pt₂(μ-S)₂(PPh₃)₄Pd(bipy)] (PF₆)₂ also characterised by X-ray diffraction studies. No metal scrambling was found to occur, as has been observed in some previous cases involving the related complexes [Pt₂(μ-Se)₂(PPh₃)₄] and [Pt₂(μ-S)₂(dppe)₂] (dppe=Ph₂PCH₂CH₂PPh₂). With cis-[PtCl₂(SOMe₂)₂] the species [Pt₂(μ-S)₂(PPh₃)₄PtCl(SOMe₂)]⁺ was formed, as a result of the lability of the SOMe₂ ligand. With palladium(II)-phosphine systems, the observed product species is dependent on the phosphine; the bulky PPh₃ ligand in [PdCl₂(PPh₃)₂] leads primarily to the analogous known species [Pt₂(μ-S)₂(PPh₃)₄PdCl(PPh₃)]⁺, and a small amount of the metal-scrambled species [PtPd₂S₂(PPh₃)₅Cl]⁺. In contrast, [PdCl₂(PTA)₂], containing the small PTA ligand gave [Pt₂(μ-S)₂(PPh₃)₄Pd(PTA)₂]²⁺.     

Synthesis and characterisation of [Pt2(μ-S)(μ-I)(PPh3)4] - A cationic iodo analogue of the metalloligand [Pt2(μ-S)2(PPh3)4]

Reaction of [Pt₂(μ-S)₂(PPh₃)₄] with a number of transition metal-iodo complexes leads to the formation of the cationic iodo analogue [Pt₂(μ-S)(μ-I)(PPh₃)₄]⁺, identified using electrospray ionisation mass spectrometry (ESI MS). Synthetic routes to this complex were developed, using the reaction of [Pt₂(μ-S)₂(PPh₃)₄] with either [PtI₂(PPh₃)₂] or elemental iodine. The complex was characterised by NMR spectroscopy, ESI MS and an X-ray structure determination, which reveals the presence of a planar, disordered {Pt₂SI}⁺ core. Monitoring the iodine reaction by ESI MS allows the identification of various iodine species, including the short-lived intermediate [Pt₂(μ-S)₂(PPh₃)₄I]⁺, which allows a mechanism for the reaction to be proposed.