Experimental characterization of the association of ß-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds.

We investigate the binding of native ß-cyclodextrin (ß-CD) and eight novel ß-CD derivatives with two different guest compounds, using isothermal calorimetry and 2D NOESY NMR. In all cases, the stoichiometry is 1:1 and binding is exothermic. Overall, modifications at the 3' position of ß-CD, which is at the secondary face, weaken binding by several kJ/mol relative to native ß-CD, while modifications at the 6' position (primary face) maintain or somewhat reduce the binding affinity. The variations in binding enthalpy are larger than the variations in binding free energy, so entropy-enthalpy compensation is observed. Characterization of the bound conformations with NOESY NMR shows that the polar groups of the guests may be situated at either face, depending on the host molecule, and, in some cases, both orientations are populated. The present results were used in the SAMPL7 blinded prediction challenge whose results are detailed in the same special issue of JCAMD.

Gait in ducks (Anas platyrhynchos) and chickens (Gallus gallus) - similarities in adaptation to high growth rate.

Genetic selection for increased growth rate and muscle mass in broiler chickens has been accompanied by mobility issues and poor gait. There are concerns that the Pekin duck, which is on a similar selection trajectory (for production traits) to the broiler chicken, may encounter gait problems in the future. In order to understand how gait has been altered by selection, the walking ability of divergent lines of high- and low-growth chickens and ducks was objectively measured using a pressure platform, which recorded various components of their gait. In both species, lines which had been selected for large breast muscle mass moved at a slower velocity and with a greater step width than their lighter conspecifics. These high-growth lines also spent more time supported by two feet in order to improve balance when compared with their lighter, low-growth conspecifics. We demonstrate that chicken and duck lines which have been subjected to intense selection for high growth rates and meat yields have adapted their gait in similar ways. A greater understanding of which components of gait have been altered in selected lines with impaired walking ability may lead to more effective breeding strategies to improve gait in poultry.

Potential bias in NMR relaxation data introduced by peak intensity analysis and curve fitting methods.

We present an evaluation of the accuracy and precision of relaxation rates calculated using a variety of methods, applied to data sets obtained for several very different protein systems. We show that common methods of data evaluation, such as the determination of peak heights and peak volumes, may be subject to bias, giving incorrect values for quantities such as R1 and R2. For example, one common method of peak-height determination, using a search routine to obtain the peak-height maximum in successive spectra, may be a source of significant systematic error in the relaxation rate. The alternative use of peak volumes or of a fixed coordinate position for the peak height in successive spectra gives more accurate results, particularly in cases where the signal/noise is low, but these methods have inherent problems of their own. For example, volumes are difficult to quantitate for overlapped peaks. We show that with any method of sampling the peak intensity, the choice of a 2- or 3-parameter equation to fit the exponential relaxation decay curves can dramatically affect both the accuracy and precision of the calculated relaxation rates. In general, a 2-parameter fit of relaxation decay curves is preferable. However, for very low intensity peaks a 3 parameter fit may be more appropriate.

SANE (Structure Assisted NOE Evaluation): an automated model-based approach for NOE assignment.

A reliable automated approach for assignment of NOESY spectra would allow more rapid determination of protein structures by NMR. In this paper we describe a semi-automated procedure for complete NOESY assignment (SANE, Structure Assisted NOE Evaluation), coupled to an iterative procedure for NMR structure determination where the user is directly involved. Our method is similar to ARIA [Nilges et al. (1997) J. Mol. Biol., 269, 408-422], but is compatible with the molecular dynamics suites AMBER and DYANA. The method is ideal for systems where an initial model or crystal structure is available, but has also been used successfully for ab initio structure determination. Use of this semi-automated iterative approach assists in the identification of errors in the NOE assignments to short-cut the path to an NMR solution structure.

Inherent flexibility in a potent inhibitor of blood coagulation, recombinant nematode anticoagulant protein c2.

Nematode anticoagulant proteins (NAPs) from the hematophagous nematode Ancylostoma caninum inhibit blood coagulation with picomolar inhibition constants, and have been targeted as novel pharmaceutical agents. NAP5 and NAP6 inhibit factor Xa by binding to its active site, whereas NAPc2 binds to factor Xa at a different, as yet unidentified, site and the resultant binary complex inhibits the tissue factor-factor VIIa complex. We have undertaken NMR studies of NAPc2, including the calculation of a solution structure, and found that the protein is folded, with five disulfide bonds, but is extremely flexible, especially in the acidic loop. The Halpha secondary shifts and 3JHNHalpha coupling constants indicate the presence of some beta structure and a short helix, but the intervening loops are highly conformationally heterogeneous. Heteronuclear NOE measurements showed the presence of large amplitude motions on a subnanosecond timescale at the N-terminus and C-terminus and in the substrate-binding loop, indicating that the conformational heterogeneity observed in the NMR structures is due to flexibility of the polypeptide chain in these regions. Flexibility may well be an important factor in the physiological function of NAPc2, because it must interact with other proteins in the inhibition of blood coagulation. We suggest that this inhibitor is likely to become structured on binding to factor Xa, because the inhibition of the tissue factor-factor VIIa complex requires both NAPc2 and factor Xa.

Conformational dynamics of thyroid hormones by variable temperature nuclear magnetic resonance: the role of side chain rotations and cisoid/transoid interconversions.

1H NMR spectra of the thyroid hormone thyroxine recorded at low temperature and high field show splitting into two peaks of the resonance due to the H2,6 protons of the inner (tyrosyl) ring. A single resonance is observed in 600 MHz spectra at temperatures above 185 K. An analysis of the line shape as a function of temperature shows that the coalescence phenomenon is due to an exchange process with a barrier of 37 kJ mol-1. This is identical to the barrier for coalescence of the H2',6' protons of the outer (phenolic) ring reported previously for the thyroid hormones and their analogues. It is proposed that the separate peaks at low temperature are due to resonances for H2,6 in cisoid and transoid conformers which are populated in approximately equal populations. These two peaks are averaged resonances for the individual H2 and H6 protons. Conversion of cisoid to transoid forms can occur via rotation of either the alanyl side chain or the outer ring, from one face of the inner ring to the other. It is proposed that the latter process is the one responsible for the observed coalescence phenomenon. The barrier to rotation of the alanyl side chain is > or = 37 kJ mol-1, which is significantly larger than has previously been reported for Csp2-Csp3 bonds in other Ph-CH2-X systems. The recent crystal structure of a hormone agonist bound to the ligand-binding domain of the rat thyroid hormone receptor (Wagner et al. Nature 1995, 378, 690-697) shows the transoid form to be the bound conformation. The significant energy barrier to cisoid/transoid interconversion determined in the current study combined with the tight fit of the hormone to its receptor suggests that interconversion between the forms cannot occur at the receptor site but that selection for the preferred bound form occurs from the 50% population of the transoid form in solution.

1H and 13C NMR relaxation studies of molecular dynamics of the thyroid hormones thyroxine, 3,5,3'-triiodothyronine, and 3,5-diiodothyronine.

1H and 13C NMR spin-lattice relaxation times and 13C{1H} nuclear Overhauser enhancement factors have been measured for the thyroid hormones thyroxine, 3,5,3'-triiodothyronine, and 3,5-diiodothyronine, with the aim of determining the internal molecular dynamics in these molecules. Spin-lattice relaxation times of protons on the two aromatic rings of these hormones show remarkable differences, with values for the hydroxyl-bearing ring being a factor of 4-12 times larger than those for the alanyl-bearing ring. This difference is not mirrored in the 13C relaxation times, which are identical within experimental error for the two rings. The 13C data show that the mobility of the two rings is similar, and therefore the difference in proton spin-lattice relaxation times arises because the protons of the alanyl-bearing ring are efficiently relaxed by interactions with neighboring protons on the side chain. Quantitative analysis of the 13C relaxation data shows that there must be a significant degree of internal flexibility in the thyroid hormone molecules. The NMR data suggest that in methanol the molecules tumble with an overall correlation time of approximately 0.35 ns, but that rapid internal motion (in the form of jumps between two stable conformations) occurs on a 30-fold faster time scale. When combined with previous variable temperature NMR studies that show interconversion between proximal and distal forms of the outer ring on the microsecond time scale, the results provide a complete description of the conformations and both fast and slow internal motions in the thyroid hormones. The findings suggest that modeling studies of thyroid hormone interactions with receptor proteins should take into account the possibility that these internal motions are present. In effect, the thyroid hormones may likely populate a larger range of conformations in the bound state than might be inferred from just the lowest energy forms seen in the crystal and solution states.

Synthesis and structural characterisation of analogues of the potassium channel blocker charybdotoxin.

Charybdotoxin is a 37-residue polypeptide toxin from scorpion venom, which acts by blocking voltage-gated and Ca(2+)-activated K+ channels. We have synthesized charybdotoxin and three mono-substituted analogues using an Fmoc-tBu protocol. The Phe-2 --> Tyr analogues was chosen to introduce a site for Tyr iodination which was distinct from the K+ channel binding surface, while the Glu-12 --> Gln and Arg-19 --> His analogues were studied to probe the roles of charged residues at these positions in the structure and activity of the toxin. The synthetic native molecule was equipped with natural toxin in inhibiting the human erythrocyte Ca(2+)-dependent K+ channel. The affinities of all three analogues for the erythrocyte K+ channel were slightly reduced, with the Arg-19 --> His analogue showing the greatest increase in IC50 (2.30-fold). Two-dimensional 1H-NMR studies of these analogues showed that the Glu-12 to Gln substitution, which appeared to destabilise the N-terminal half of the alpha-helix, possibly due to the weakening of an N-terminal helix capping interaction which is apparent from our NMR data. His-21 has a pKa more than one unit below the value for a non-interacting histidine. Possible reasons for this are that the imidazolium side chain is partly buried and is located near positively charged moieties. Thus, His-21 would be neutral at physiological pH, where charybdotoxin binds to the potassium channel.

Three-dimensional structure in solution of the calcium channel blocker omega-conotoxin.

The 27 amino acid residue polypeptide omega-conotoxin GVIA, from venom of the cone shell Conus geographus, blocks neuronal voltage-activated calcium channels at picomolar concentrations. The three-dimensional structure in aqueous solution of synthetic omega-conotoxin has been determined from two-dimensional 1H n.m.r. data recorded at 600 MHz. Structural constraints consisting of interproton distances inferred from NOEs and dihedral angles from spin-spin coupling constants were used as input for distance geometry calculations with the program DSPACE. The structures were then refined using back-calculation of NOESY spectra. The family of structures obtained in this way is well defined by the n.m.r. data, the best 12 structures having pairwise root-mean-square differences of 0.68 (+/- 0.15) A over the backbone heavy atoms (N, C alpha and C) and 1.15 (+/- 0.17) A over all heavy-atoms. The molecule adopts a compact structure consisting of a small, triple-stranded, anti-parallel beta-sheet and several reverse turns. All three tyrosine residues are located on the molecular surface, which is noteworthy for its abundance of side-chain hydroxyl groups. There is no negatively charged group in conotoxin, but the five positively charged groups are distributed in three small patches on the surface, one of which, made up of the ammonium moieties of the N terminus and Lys2, may contribute to the receptor-binding surface of the molecule. An isomer of conotoxin with the same amino acid sequence, but different disulfide pairings, has also been investigated. Its structure is less well ordered than that of native conotoxin and it shows significant heterogeneity, probably as a result of cis-trans isomerism preceding hydroxyproline residues.