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The p53 tumor suppressor is a transcription factor that plays a crucial role in the activation of genes in response to DNA damage. As a first step towards detailed structural studies of the molecule aimed at understanding its regulation, we have used 4D-TROSY triple resonance NMR spectroscopy to obtain nearly complete 1H(N), 15N, 13C(alpha), 13CO and 13C(beta) resonance assignments of a dimeric form of the protein comprising DNA-binding and oligomerization domains (67 kDa). A simple comparison of 4D spectra recorded on p53 molecules consisting of DNA-binding and oligomerization domains with and without the regulatory domain establishes that both constructs have essentially identical chemical shifts. Although the affinity of p53 for target DNA is decreased in constructs containing the regulatory domain, the chemical shift results reported here suggest that this decrease is not due to specific domain interactions involving the regulatory portion of the molecule, or alternatively, that such interactions require the presence of DNA.

The retinoid X receptor (RXR) is a prominent member of the nuclear receptor family of ligand-inducible transcription factors. Many proteins of this family exert their function as heterodimers with RXR as a common upstream partner. Studies of the DNA-binding domains of several nuclear receptors reveal differences in structure and dynamics, both between the different proteins and between the free- and DNA-bound receptor DBDs. We investigated the differences in dynamics between RXR free in solution and in complex with a 14 base-pair oligonucleotide, using (1)H and (15)N relaxation studies. Nano- to picosecond dynamics were probed on (15)N, employing Lipari-Szabo analysis with an axially symmetric tumbling model to estimate the exchange contributions to the transverse relaxation rates. Furthermore, milli- to microsecond dynamics were estimated qualitatively for (1)H and (15)N, using CPMG-HSQC and CPMG-T(2) measurements with differential pulse spacing. RXR shows hardly any nano- to picosecond time-scale internal motion. Upon DNA binding, the order parameters show a tiny increase. Dynamics in the milli- to microsecond time scale is more prevalent. It is localized in the first and second zinc fingers of the free RXR. Upon DNA-binding, exchange associated with specific/aspecific DNA-binding of RXR is observed throughout the sequence, whereas conformational flexibility of the D-box and the second zinc finger of RXR is greatly reduced. Since this DNA-binding induced folding transition occurs remote from the DNA in a region which is involved in protein-protein interactions, it may very well be related to the cooperativity of dimeric DNA binding.

High-alkaline serine proteases have been successfully applied as protein degrading components of detergent formulations and are subject to extensive protein engineering efforts to improve their stability and performance. Dynamics has been suggested to play an important role in determining enzyme activity and specificity and it is therefore of interest to establish how local changes in internal mobility affect protein stability, specificity and performance. Here we present the dynamic properties of the 269 residue serine proteases subtilisin PB92 (Maxacal(TM)) and subtilisin BLS (Savinase(TM)), secreted by Bacillus lentus, and an engineered quadruple variant, DSAI, that has improved washing performance. T1, T2 and heteronuclear NOE measurements of the 15N nuclei indicate that for all three proteins the majority of the backbone is very rigid, with only a limited number of residues being involved in local mobility. Many of the residues that constitute the S1 and S4 pockets, determining substrate specificity, are flexible in solution. In contrast, the backbone amides of the residues that constitute the catalytic triad do not exhibit any motion. Subtilisins PB92, BLS and DSAI demonstrate similar but not identical NMR relaxation rates. A detailed analysis of local flexibility indicates that the motion of residues Thr143 and Ala194 becomes more restricted in subtilisin BLS and DSAI. Noteworthy, the loop regions involved in substrate binding become more structured in the engineered variant as compared with the two native proteases, suggesting a relation between altered dynamics and performance. Similar conclusions have been established by X-ray crystallograpic methods, as shown in the accompanying paper., (Copyright 1998 Academic Press.)

Slow protein dynamics can be studied by 15N spin-echo (CPMG) and off-resonance rotating frame relaxation through the effective field dependence of the exchange-mediated relaxation contribution. It is shown that, by a combination of these complementary techniques, a more extended sampling of the microsecond time scale processes is achieved than by either method alone. 15N R2 and improved off-resonance R1 rho experiments [Mulder et al. (1998) J. Magn. Reson., 131, 351-357] were applied to the 9-cis-retinoic acid receptor DNA-binding domain and allowed the identification of 14 residues exhibiting microsecond time scale dynamics. Assuming exchange between two conformational substates, average lifetimes ranging from 37 to 416 microseconds, and chemical shift differences of up to 3 ppm were obtained. The largest perturbation of tertiary structure was observed for the second zinc finger region, which was found to be disordered in the solution structure [Holmbeck et al. (1998) J. Mol. Biol., 281, 271-284]. Since this zinc-coordinating domain comprises the principal dimerization interface for RXR in a wide repertoire of complexes with different hormone receptors to their cognate response elements, this finding has important implications for our understanding of nuclear receptor assembly on DNA direct repeats. The flexibility observed for the dimerization domain may explain how RXR, through the ability to adaptively interact with a wide variety of highly homologous partner molecules, demonstrates such a versatile DNA-binding repertoire.

The all-trans retinoic acid and 9-cis retinoic acid receptors (RAR and RXR, respectively) belong to a family of ligand inducible transcription factors, which exert their effect via binding to hormone response elements. Both are members of the class II sub-family of nuclear receptors, which bind DNA as dimers, on tandem repeats of a hexamer motif separated by a variable spacer. The variability in spacer length and the head-to-tail organization of the hormone response elements result in different protein-protein interactions in each of the complexes. We show that the zinc-coordinating loop regions of RXR and RAR DNA-binding domains exhibit dynamics on the millisecond to microsecond time scale. The highly dynamic second zinc finger of RXR constitutes the primary protein-protein interface in many nuclear receptor assemblies on DNA. Dynamics is also observed in the first and second zinc fingers of RAR, which are implicated in dimeric interactions with RXR on response elements with spacers of 5 base pairs and 1 base pair, respectively. The striking correspondence between the regions that exhibit conformational exchange and the dimer interfaces of the proteins complexed with DNA suggests a functional role for the dynamics. The observed flexibility may allow the proteins to adapt to various partners and with different orientations upon assembly on DNA. Furthermore, the more extensive dynamics observed for RXR may reflect the greater ability of this protein to modulate its interaction surface since it participates in a wide variety of receptor complexes.

The solution structure of photoactive yellow protein (PYP), a photosensory protein from Ectothiorhodospira halophila, has been determined by multidimensional NMR spectroscopy. The structure consists of an open, twisted, 6-stranded, antiparallel beta-sheet, which is flanked by four alpha-helices on both sides. The final set of 26 selected structures is well-defined for the regions spanning residues Phe6-Ala16, Asp24-Ala112, and Tyr118-Val125 and displays a root-mean-square deviation, versus the average, of 0.45 A for the backbone and 0.88 A for all heavy atoms. Comparison of the solution structure with an earlier published 1.4 A crystal structure (Borgstahl, G. E. O., Williams, D. R., and Getzoff, E. D. (1995) Biochemistry 34, 6278-6287) reveals a similarity with a root-mean-square deviation of 1.77 A for the backbone for the well-defined regions. The most distinct difference in the backbone with the crystal structure is found near the N-terminus, for residues Asp19-Leu23, which corresponds to an alpha-helix in the crystal structure and to one of the poorest defined regions in the solution structure. To characterize the dynamic behavior of PYP in solution, we undertook a 15N relaxation study and measurements of hydrogen/deuterium exchange. Determination of order parameters through the model-free Lipari-Szabo approach enabled the identification of several regions of enhanced dynamics. The comparison of atomic displacements in the backbone traces of the ensemble structures, with mobility measurements from NMR, show that the poorly defined regions feature fast internal motions in the nanosecond to picosecond time scale.

Light irradiation of photoactive yellow protein (PYP) induces a photocycle, in which red-shifted (pR) and blue-shifted (pB) intermediates have been characterized. An NMR study of the long-lived pB intermediate now reveals that it exhibits a large degree of disorder and exists as a family of multiple conformers that exchange on a millisecond time scale. This shows that the behavior of PYP in solution is different from what has been observed in the crystalline state. Furthermore, differential refolding to ground state pG is observed, whereby the central beta-sheet and parts of the helical structure are formed first and the region around the chromophore at a later stage.

Background: Research on high-alkaline proteases, such as serine protease PB92, has been largely inspired by their industrial application as protein-degrading components of washing powders. Serine protease PB92 is a member of the subtilase family of enzymes, which has been extensively studied. These studies have included exhaustive protein engineering investigations and X-ray crystallography, in order to provide insight into the mechanism and specificity of enzyme catalysis. Distortions have been observed in the substrate-binding region of subtilisin crystal structures, due to crystal contacts. In addition, the structural variability in the substrate-binding region of subtilisins is often attributed to flexibility. It was hoped that the solution structure of this enzyme would provide further details about the conformation of this key region and give new insights into the functional properties of these enzymes., Results: The three-dimensional solution structure of the 269-residue (27 kDa) serine protease PB92 has been determined using distance and dihedral angle constraints derived from triple-resonance NMR data. The solution structure is represented by a family of 18 conformers which overlay onto the average structure with backbone and all-heavy-atom root mean square deviations (for the main body of the molecule) of 0.88 and 1.21 A, respectively. The family of structures contains a number of regions of relatively high conformational heterogeneity, including various segments that are involved in the formation of the substrate-binding site. The presence of flexibility within these segments has been established from NMR relaxation parameters and measurements of amide proton exchange rates., Conclusions: The solution structure of the serine protease PB92 presents a well defined global fold which is rigid with the exception of a restricted number of sites. Among the limited number of residues involved in significant internal mobility are those of two pockets, termed S1 and S4, within the substrate-binding site. The presence of flexibility within the binding site supports the proposed induced fit mechanism of substrate binding.

We present here HSQC experiments with improved sensitivity for signals in the presence of exchange broadening. During periods of coherence transfer through scalar coupling the experiments employ CPMG-derived pulse trains to reduce loss of dephasing of spin coherence due to chemical exchange. (15)N-(1)H gradient CPMG-HSQC and SE-CPMG-HSQC experiments have been developed and applied to complexes of lac repressor headpiece with operator DNA. Improved sensitivity is demonstrated for many protein backbone and side-chain resonances in the complex, markedly for signals of protons located at the protein-DNA interface. In addition, a significant increase in intensity is observed for arginine guanidino groups undergoing conformational exchange.

Two high pressure liquid chromatographic methods, a straight and a reverse phase system, were developed and compared with the official (chemical) AOAC method for vitamin D concentrates. The effects of the systematic error and the reproducibility of using an internal or external standard were studied, as well as the effect of using peak height or peak height X retention time for calculating the potential vitamin D content. A method is given for determining the conversion factor to calculate previtamin D as vitamin D. Based on the results of the comparison, the following conditions were selected for collaborative study: straight phase, amyl alcohol-hexane mobile phase, external standard, and calculation of potency by peak height.

Further study of vitamin D methodology solved the discrepancy between the AOAC chemical method, 43.068-43.078, and the HPLC assay for vitamin D3 in resin containing dry powders. The discrepancy is caused by the difference in solubility of the vitamin D3 resin in benzene and in pentane. The method has been modified accordingly, and has been adopted official first action for vitamin D3 resins and vitamin D3 resin containing powders and aqueous dispersions.

Vitamin D is determined by high performance liquid chromatography (HPLC) in samples containing other fat-soluble vitamins. The vitamin D in the unsaponifiable residue is extracted and separated from interferences by straight phase chromatography, and the fraction corresponding to vitamin D3 is collected and quantitated using the AOAC official final action HPLC method for vitamin D3. Analysis of a synthetic mixture gave reasonable recoveries. The method measures potential vitamin D3 content in milkpowder samples containing 2 IU vitamin D/g in the presence of all known vitamin D3 isomers, vitamin A, and vitamin E.

The official first action method for determining vitamin D in multivitamin preparations was modified. The method was collaboratively studied by 7 laboratories, using 6 preparations in oil. The preparations consisted of vitamin D at various levels and at various ratios (in w/w) in vitamin A. Three samples contained cholecalciferol and 3 samples contained vitamin D3 from vitamin D3 resin. After outliers were eliminated by the Dixon test, data were analyzed and averages were compared with amounts of vitamin D known to be in each sample. For samples with vitamin D: vitamin A ratios of 1:0.5, 1:5, and 1:10, the mean vitamin D recoveries were 98.8, 94.6, and 90.7%, respectively. The method has been adopted as official final action.

Vitamin D is determined in preparations containing other fat-soluble vitamins by high performance liquid chromatography (HPLC). The unsaponifiable residue is extracted and separated from interferences by reverse phase chromatography; the fraction corresponding to vitamin D3 is collected and quantitated using normal phase chromatography (amylalcohol-n-hexane as mobile phase) by measuring the vitamin D3 and pre-vitamin D3 peaks at 254 nm. Previtamin D3 content is calculated as vitamin D3 with a conversion factor (determined on the equipment used). Application of the method to vitamin AD3 mixtures in oils gives 98-102% recovery. The reproducibility, using an external standard, is 2-3%, calculated as the coefficient of variation; with an internal standard, the coefficient of variation is 1-1.5%. The method measures potential vitamin D3 content in preparations containing greater than or equal to 200 IU/g in the presence of all known vitamin D3 isomers, vitamin A, and vitamin E.

A collaborative study was carried out which compared the official chemical method (43.B14-43.B24), the HPLC method according to Hofsass et al. including maleic anhydride treatment, and the HLPC procedure according to De Vries et al. for vitamin D concentrates. A total of 396 samples were distributed to 33 collaborators for analysis. Five laboratories performed both the chemical and the HPLC methods. Five laboratories performed the Hofsass method and 16 laboratories performed the De Vries method. The results for the chemical method agreed with the theoretical values for the samples, and the standard deviation was comparable to that obtained in previous AOAC collaborative studies. Collaborative results for the Hofsass method were low. In addition, incorrect use of a fixed conversion factor (1/0.586) and necessity of a double chromatogrpahic system on a non-treated and a treated vitamin D sample reduce the effectiveness of the method. There were no adverse reactions to the DE Vries HPLC method. It is recommended that the method be adopted official first action as an alternative procedure for determining vitamin D in concentrates, excluding powders containing irradiated 7-dehydrocholesterol.

In 1971, a chemical method for the assay of vitamin D in concentrates containing only vitamin D was collaboratively studied by 14 laboratories, using 6 different samples from 2 European manufacturers. On the basis of these results, the laboratories were divided into 2 groups: 5 with significant laboratory biases of greater than or equal to 2%, and 9 laboratories with nonsignificant bias. The 9 laboratories were subdivided into 2 groups which differed significantly as to reproducibility within laboratories. The reproducibility between laboratories, expressed as a standard deviation in per cent with 95% confidence limits, was 1.2% (confidence range 0.6-7.3) and 4.7% (confidence range 2.4-29.3) for 3 and 6 laboratories, respectively. A second collaborative test was performed in 1974, using 12 vitamin D resin samples in oil from 3 United States manufacturers, to compare 2 chemical vitamin D assay methods (with and without maleic anhydride) and to compare results from the chemical and biological methods; 9 laboratories participated in the chemical method study and 3 in the rat bioassay study. The correlation of results of the chemical method including maleic anhydride treatment and the rat bioassays was satisfactory. The reproducibility of the chemical method was about the same as that in the first collaborative test.

The reaction with maleic anhydride yielding Diels-Alder adducts is used to distinguish vitamin D isomers. Treatment at 100 degrees C for 3 hr eliminates the fast-reacting (tachysterol and trans-vitamin D) and slow-reacting (cis-vitamin D and previtamin D) isomers. However, isotachysterol is not eliminated. The procedure has been incorporated as a confirmation test for isotachysterol in the official final action method for the determination of vitamin D in concentrates, 43.B14-43.B24.

The HPLC method for determining vitamin D in multivitamin preparations was studied collaboratively. Samples were distributed to 43 laboratories in 10 countries. Twenty-four laboratories gave their results. The method specifies a reverse phase system for the cleanup and a straight phase system for the determination. Difficulties arise when laboratories are equipped with HPLC apparatus with a single column. Laboratories experienced in vitamin D analysis reported good results, even if they were equipped with a single column HPLC apparatus. Eleven of the 24 laboratories reported satisfactory results. For this rather complicated method, the coefficient of variation for a single assay is acceptable. The method has been adopted official first action as an alternative procedure to the chemical method for determining vitamin D in multivitamins.