Protein fold recognition

Summary An important, yet seemingly unattainable, goal in structural molecular biology is to be able to predict the native three-dimensional structure of a protein entirely from its amino acid sequence. Prediction methods based on rigorous energy calculations have not yet been successful, and best results have been obtained from homology modelling and statistical secondary structure prediction. Homology modelling is limited to cases where significant sequence similarity is shared between a protein of known structure and the unknown. Secondary structure prediction methods are not only unreliable, but also do not offer any obvious route to the full tertiary structure. Recently, methods have been developed whereby entire protein folds are recognized from sequence, even where little or no sequence similarity is shared between the proteins under consideration. In this paper we review the current methods, including our own, and in particular offer a historical background to their development. In addition, we also discuss the future of these methods and outline the developments under investigation in our laboratory.     

An alternative sampling algorithm for use in liquid chromatography/tandem mass spectrometry experiments

In liquid chromatography/tandem mass spectrometry (LC/MS/MS) analyses of complex peptide mixtures, dynamic exclusion functions are used to minimize repeat selections of identical precursors for collision induced dissociation (CID). We describe a new algorithm for the dynamic exclusion of m/z values during LC/MS/MS. Full-scan based peak exclusion (Fulspec) uses a simplified model of chromatographic peak formation to detect and exclude contaminants present throughout the run or that lead to broad peaks. Therefore, instead of excluding peptides from fragment analysis according to a rigidly predefined time window, the chromatographic properties of the detected analytes are used. The algorithm was tested on two datasets derived from previously published experiments. Fulspec achieves a distribution of CID spectra with minimal tailing on the retention time axis, without resorting to rigid exclusion of m/z values. The procedure further excludes intensities with a bias towards low-quality CID spectra. This combination frees up valuable analytical capacity. The underlying intensity vs. quality analyses challenge the assumption that abundant precursors automatically give the best identifications. Further validation of the algorithm will require its incorporation by equipment manufacturers into the instrument control programs.     

Synthese,Struktur und einige Reaktionen [N-(N′,N′,N″,N″-tetramethyl)-guanidinyl]-substituierter Phosphorylverbindungen

Synthesis, Structure, and some Reactions of N-(N′,N′,N″,N″-tetramethyl)guanidinyl-substituted Phosphoryl Compounds The tetramethylguanidinyl-substituted phosphoryl compounds 1 – 10 were prepared in the reaction of the appropriate chlorophosphoryl compounds with either N′,N′,N″,N″-tetramethylguanidine (HTMG) or N-trimethylsilyl-(N′,N′,N″,N″-tetramethyl)guanidine (TMSTMG). With methyl iodide 1 reacted with N-alkylation to give the ammonium salt 11. 1 reacted with BF₃ · Et₂O at both imino nitrogen atoms with formation of the bis-BF₃-adduct 12 . The X-ray structure determination of phenylphosphonic acid-bis(N′,N′,N″,N″-tetramethylguanidinide) 3 shows shortened PN-bonds and widened PNC-angles, consistent with the partial double bond character of the PN-bond.     

Reactions of Ru3(CO)12 with Diphosphenes — A New Route to 50‐Electron Ru3P2 nido‐Clusters

The reaction of the symmetric diphosphene 2, 4, 6‐(CF₃)₃‐C₆H₂‐P=P‐C₆H₂‐2, 4, 6‐(CF₃)₃ 4 with Ru₃(CO)₁₂ led to the 50‐electron Ru₃P₂ nido‐cluster Ru₃(CO)₉[μ‐P‐C₆H₂‐2, 4, 6‐(CF₃)₃]₂ 5 , which in solution at room temperature displays hindered rotation of the aromatic rings about the C(aryl)—P bonds. The structure of 5 was determined by X‐ray crystal structure analysis; its Ru₃P₂ centre forms a distorted square pyramid with one ruthenium atom at the apex. One of the two C₆H₂(CF₃)₃ groups is also appreciably distorted. Temperature‐dependent ¹⁹F NMR studies of the [A₃M₃X]₂ spin system (A = M = CF₃, X = ³¹P) of 5 indicated a rotational barrier ΔG^≠ of 82.3 kJ mol^‐1 at 141 °C. The same Ru₃P₂ core was obtained by the reaction of the unsymmetric diphosphene Mes*‐P=P‐Mes 11 with Ru₃(CO)₁₂; hindered rotation about the C(aryl)—P bonds was also observed, in this case.     

Novel nucleophilic substitution of alkyl bromo-2(1H)-pyridones

Nucleophilic substitution of certain alkyl bromo-2(1H)-pyridones gave some unexpected products where the alkyl group is substituted and the ring bromine is replaced by hydrogen. The expected ring substituted product is also formed, but only as the minor product in most cases. Many reactions are cited with various nucleophiles, and a plausible mechanism is also presented.     

A novel photoaddition of 2-phenylbenzimidazole

Irradiation of 2-phenylbenzimidazole ( 3 ) in the presence of methyl acrylate (20 equivalents) using a medium pressure mercury lamp gives methyl 2-(2-phenylbenzimidazol-1-yl)propionate ( 4 ) (75%) whose structure has been confirmed by an X-ray analysis. A similar reaction using acrylonitrile gave only a low yield (1%) of the corresponding propionitrile derivative 5 . A mechanism involving photoexcitation of 2-phenylbenzimidazole ( 3 ) followed by sequential single electron transfer, proton transfer and radical coupling is proposed to account for the formation of the novel photoadducts 4 and 5 .     

Polysulfonylamine. CLX [1] Kristallstrukturen von Metall‐di(methansulfonyl)amiden. 10 [2] Die dreidimensionalen Koordinationspolymere M[(CH3SO2)2N] mit M = Kalium,Rubidium, Caesium (isotype Strukturen für M = K,Rb)

Polysulfonylamines. CLX. Crystal Structures of Metal Di(methanesulfonyl)amides. 10. The Three‐Dimensional Coordination Polymers M[(CH₃SO₂)₂N], where M is Potassium, Rubidium, Cesium (Isotypic Structures for M = K, Rb) Low‐temperature X‐ray crystal structures are reported for KA (monoclinic, space group P2₁/c, Z′ = 1), RbA (isotypic and isostructural with KA), and CsA (monoclinic, P2₁/n, Z′ = 1), where A^— denotes the anion obtained by deprotonation of the strong nitrogen acid (MeSO₂)₂NH. In KA and RbA, the anion is distorted into a rare C₁ conformation, whereas the standard C₂ conformation is retained in the cesium complex. The structures consist of three‐dimensional coordination networks, in which each cation adopts an irregular (O₆N)‐heptacoordination by forming close contacts to one (O, N)‐chelating, one (O, O)‐chelating and three κ¹O‐bonding ligands; however, the coordination number for Cs⁺ is effectively increased to 8 by a very short Cs···Cs contact distance of 422.5 pm. The crystal packings of the isotypic compounds KA and RbA display lamellar layer substructures that involve six independent ligand‐metal bonds and comprise an internal cation lamella and peripheral regions built up from anion monolayers; the 3D framework is completed by one independent M—O bond cross‐linking the layer substructures. In contrast, CsA features anion monolayers that intercalate planar zigzag chains of cations (Cs···Cs alternatingly 422.5 and 487.5 pm, Cs···Cs···Cs 135.7°), whereby each chain is surrounded and coordinated by four anion stacks and each anion stack connects two cation chains. All structures exhibit close C—H···A interanion contacts consistent with weak hydrogen bonding.     

Swelling and network parameters of crosslinked thermoreversible hydrogels of poly(N-ethylacrylamide)

Samples of Poly(N-ethylacrylamide) (PEA) have been synthesized by free radical polymerization in water using N,N′-methylene bis-acrylamide (BIS) as crosslinker. Hydrogels obtained by swelling them in water, 15 wt% KCl and 1 wt% sodium dodecyl sulphate (SDS) were examined by gravimetric, dimensional and compression-strain measurements to afford values of swelling ratio, polymer-solvent interaction parameters, elastic moduli and effective crosslinking density ν_e. Crosslinking inefficiency is evidenced by the low value (0.23) of ν_e relative to the theoretical crosslinking density ν_t based on the content of BIS in the synthesis. A small but finite extrapolated value of ν_e at ν_t = 0 is indicative of hydrophobic physical interactions. In water at 298 K increasing the content of BIS leads to a decrease in swelling and increases in values of elastic moduli and polymer-water interaction parameter. At a fixed content of BIS the values of ν_e and the elastic moduli exhibit an unusual increase with temperature, the crosslinking thus being thermally reversible. It is proposed that this results from a balance between hydrophobic interaction and breakage of hydrophilic hydrogen bonding. Although KCl in the medium decreases the swelling compared with that in water, the opposite effect occurs on incorporation of SDS, which is assumed to confer some polyelectrolyte character to the PEA chains. The finding, that these two swelling media reduce the values of ν_e and elastic moduli cf the value in water, has not been resolved satisfactorily.