Molecular recognition between protein and nicotinamide dinucleotide in intact, proton-translocating transhydrogenase studied by ATR-FTIR Spectroscopy

Nicotinamide dinucleotide binding to transhydrogenase purified from Escherichia coli was investigated by attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. Detergent-free transhydrogenase was deposited as a thin film on an ATR prism, and spectra were recorded during perfusion with buffers in the presence and absence of dinucleotide (NADP(+), NADPH, NAD(+), or NADH) in both H(2)O and D(2)O media. IR spectral changes were attributable to the bound dinucleotides and to changes in the protein itself. The dissociation constant of NADPH was estimated to be approximately 5 muM from a titration of the magnitude of the IR changes against the nucleotide concentration. IR spectra of related model compounds were used to assign principle bands of the dinucleotides. This information was combined with IR data on amino acids and with protein crystallographic data to identify interactions between specific parts of the dinucleotides and their binding sites in the protein. Several IR bands of bound nucleotide were sharpened and/or shifted relative to those in aqueous solution, reflecting a restriction to motion and a change in environment upon binding. Alterations in the protein secondary structure indicated by amide I/II changes were distinctly different for NADP(H) and for NAD(H) binding. The data suggest that NADP(H) binding leads to perturbation of a deeply buried part of the polypeptide backbone and to protonation of a carboxylic acid residue.     

Infrared spectroscopy of phenylalanine Ag(I) and Zn(II) complexes in the gas phase

Infrared multiple-photon dissociation (IR-MPD) spectroscopy has been applied to singly-charged complexes involving the transition metals Ag(+) and Zn(2+) with the aromatic amino acid phenylalanine. These studies are complemented by DFT calculations. For [Phe+Ag](+) the calculations favor a tridentate charge solvation N/O/ring structure. The experimental spectrum strongly supports this as the predominant binding geometry and, in particular, rules out a significant presence of the salt-bridge conformation. Zn(2+) forms a deprotonated dimer complex with Phe, [Zn+Phe(2)-H](+), in which the +2 oxidation state serves as a useful biomimetic model for zinc protein sites. A number of low-energy conformations were located, of which the lowest-energy conformer predicted by the calculations involves a Phe ligand deprotonated on the carboxylic acid, while the other Phe ligand is in the tridentate charge solvation conformation. The calculated IR spectrum of this conformer gives a close fit to the experimental spectrum, strongly supporting this as the predominant binding geometry. This most stable calculated complex is characterized by N/ O/ring metal chelation with a tetrahedral-type coordination core of Zn(2+) to N and O of both ligands. Another similar tightly chelated structure shows a square-planar-type coordination core, but this structure is computed to be less stable and gives a less satisfactory match to the experimental spectrum. This preference for the tetrahedral geometry of the Lewis-basic atomic ligands parallels the common Zn(II) coordination geometry in proteins. The number of clearly identifiable peaks resolved in the IR-MPD spectra as well as the much-improved matches between the observed spectra and the DFT-calculated spectra of the most stable geometries compared to previous studies are noteworthy for systems of this size and complexity. These results demonstrate that IR spectroscopy of transition metal-amino acid complexes in combination with DFT calculations is a very powerful structural tool, readily applicable to biomimetic systems that model, for example, the reaction centers of proteins in the solvent-free environment. In addition, we present a novel ion-capturing method for Fourier transform ion cyclotron resonance mass spectrometry which removes the necessity of a buffer gas pulse, while allowing ion trapping at moderate voltages with apparently reduced collisional excitation of the ions.     

Asymmetric organotellurides as potent antioxidants and building blocks of protein conjugates

New asymmetric organotellurides exhibiting good antioxidant properties in vitro and in cell culture can be attached to human serum albumin.     

Formation of protein-coated iron minerals

The ability of iron to cycle between Fe(2+) and Fe(3+) forms has led to the evolution, in different forms, of several iron-containing protein cofactors that are essential for a wide variety of cellular processes, to the extent that virtually all cells require iron for survival and prosperity. The redox properties of iron, however, also mean that this metal is potentially highly toxic and this, coupled with the extreme insolubility of Fe(3+), presents the cell with the significant problem of how to maintain this essential metal in a safe and bioavailable form. This has been overcome through the evolution of proteins capable of reversibly storing iron in the form of a Fe(3+) mineral. For several decades the ferritins have been synonymous with the function of iron storage. Within this family are subfamilies of mammalian, plant and bacterial ferritins which are all composed of 24 subunits assembled to form an essentially spherical protein with a central cavity in which the mineral is laid down. In the past few years it has become clear that other proteins, belonging to the family of DNA-binding proteins from starved cells (the Dps family), which are oligomers of 12 subunits, and to the frataxin family, which may contain up to 48 subunits, are also able to lay down a Fe(3+) mineral core. Here we present an overview of the formation of protein-coated iron minerals, with particular emphasis on the structures of the protein coats and the mechanisms by which they promote core formation. We show on the one hand that significant mechanistic similarities exist between structurally dissimilar proteins, while on the other that relatively small structural differences between otherwise similar proteins result in quite dramatic mechanistic differences.     

Separation of inorganic anions by unsuppresed ion chromatography

The elution behaviour of 11 inorganic anions is investigated by unsuppressed ion chromatography with PRP-X100 a macroporous poly(styrene-divinylbenzene) strong-base anion-exchanger. Weak acids (cyanide and sulfide) can be separated and detected at pH 9 with sodium p-hydroxybenzoate as the eluent.     

Scalar network analysers operating at Ka- and W-bands

Scalar network analysers measuring the amplitude of the reflection/transmission coefficients of waveguide structures have been realised at Ka- and W-bands. Their accuracy derived by using standard mismatches is excellent at Ka- band and fairly good at W-band. To our knowledge this is the first instance where the accuracy of measurements obtained from a scalar network analyser was checked over full waveguide bands with the aid of standard mismatches. The reported reflectometers are precursors of vector network analysers based on six-port reflectometers. Methods aimed at increasing the signal-to-noise ratio (SNR) of the measurements have been developed, while proposals for improving the dynamic range of these network analysers are put forward.     

A note on using alternative second-order models for the subproblems arising in barrier function methods for minimization

Summary. Inequality constrained minimization problems are often solved by considering a sequence of parameterized barrier functions. Each barrier function is approximately minimized and the relevant parameters subsequently adjusted. It is common for the estimated solution to one barrier function problem to be used as a starting estimate for the next. However, this has unfortunate repercussions for the standard Newton-like methods applied to the barrier subproblem. In this note, we consider a class of alternative Newton methods which attempt to avoid such difficulties. Such schemes have already proved of use in the Harwell Subroutine Library quadratic programming codes {\tt VE14} and {\tt VE19}. Received May 2, 1993/Revised form received February 12, 1994     

Stereoselective synthesis of the tetrahydropyran core of polycarvernoside A

[reaction: see text] A concise and stereoselective synthesis of the tetrasubstituted tetrahydropyran core of polycavernoside A was achieved in 55% overall yield from 3-benzyloxypropanal. A stereoselective allyl transfer reaction was used in the synthesis of enol ether 18 followed by a TFA-mediated cyclization to create the three new asymmetric centers in the tetrahydropyran with complete stereocontrol in a single-pot process.     

Preprocessing for quadratic programming

Techniques for the preprocessing of (not-necessarily convex) quadratic programs are discussed. Most of the procedures extend known ones from the linear to quadratic cases, but a few new preprocessing techniques are introduced. The implementation aspects are also discussed. Numerical results are finally presented to indicate the potential of the resulting code, both for linear and quadratic problems. The impact of insisting that bounds of the variables in the reduced problem be as tight as possible rather than allowing some slack in these bounds is also shown to be numerically significant.Mathamatics Subject Classification (2000): 20E28, 20G40, 20C20To Roger Fletcher, friend, mentor and inspiration, for his 65th birthday