Crystal structures of cellular retinoic acid binding proteins I and II in complex with all-trans-retinoic acid and a synthetic retinoid

Kleywegt, Gerard J.; Bergfors, Terese; Senn, Hans; Motté, Philippe; Gsell, Bernard; Shudo, Koichi; Jones, T. Alwyn

doi:10.1016/s0969-2126(94)00125-1

Cited by 205 publications

(227 citation statements)

References 69 publications

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“…In the typical application we present the results obtained by SFCHECK for the cellular retinoic acid binding protein (Kleywegt et al, 1994; PDB code 1CBS), representing an example of a good-quality model derived from high-quality data at high resolution (1.8 A Ê ), and for the structure of the HIN recombinase (DNA-binding domain C)±DNA complex (Feng et al, 1994; PDB code 1HCR), taken as an example of a poorer quality structure still in the process of being re®ned.…”

Section: Resultsmentioning

confidence: 99%

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SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model

Vaguine¹,

Richelle²,

Wodak³

1999

Acta Crystallogr D Biol Crystallogr

888

701

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In this paper we present SFCHECK, a stand-alone software package that features a uni®ed set of procedures for evaluating the structure-factor data obtained from X-ray diffraction experiments and for assessing the agreement of the atomic coordinates with these data. The evaluation is performed completely automatically, and produces a concise PostScript pictorial output similar to that of PROCHECK [Laskowski, MacArthur, Moss & Thornton (1993). J. Appl. Cryst. 26, 283±291], greatly facilitating visual inspection of the results. The required inputs are the structure-factor amplitudes and the atomic coordinates. Having those, the program summarizes relevant information on the deposited structure factors and evaluates their quality using criteria such as data completeness, structure-factor uncertainty and the optical resolution computed from the Patterson origin peak. The dependence of various parameters on the nominal resolution (d spacing) is also given. To evaluate the global agreement of the atomic model with the experimental data, the program recomputes the R factor, the correlation coef®cient between observed and calculated structure-factor amplitudes and R free (when appropriate). In addition, it gives several estimates of the average error in the atomic coordinates. The local agreement between the model and the electron-density map is evaluated on a per-residue basis, considering separately the macromolecule backbone and side-chain atoms, as well as solvent atoms and heterogroups. Among the criteria are the normalized average atomic displacement, the local density correlation coef®cient and the polymer chain connectivity. The possibility of computing these criteria using the omit-map procedure is also provided. The described software should be a valuable tool in monitoring the re®nement procedure and in assessing structures deposited in databases.

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Section: Resultsmentioning

confidence: 99%

“…This information is given in the Structure Factors panel in Fig. 2(a), which displays the ®rst page of the SFCHECK output for the cellular retinoic acid binding protein T (Kleywegt et al, 1994) …”

Section: Analysis Of the Structure-factor Datamentioning

confidence: 99%

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model

Vaguine¹,

Richelle²,

Wodak³

1999

Acta Crystallogr D Biol Crystallogr

888

701

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show abstract

“…deviations always less than 0.6 Å but generally around 0.2 Å. A conservative estimate of the average coordinate error is about 0.47 Å, obtained from a Luzzati plot with the R free rather than the R factor as one of the variables (41). (e) Finally, the use of the solvent correction systematically increased the average B factor of protein (ϩ6 Å 2 ) and oleate (ϩ7 Å 2 ) atoms but decreased that for bound solvent (Ϫ5 Å 2 ) compared with a trial refinement using just the 5-2.3-Å data.…”

Section: Model and Map-mentioning

confidence: 91%

The Crystal Structure of the Liver Fatty Acid-binding Protein

Thompson

Winter

Terwey

et al. 1997

Journal of Biological Chemistry

253

274

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The crystal structure of the recombinant form of rat liver fatty acid-binding protein was completed to 2.3 Å and refined to an R factor of 19.0%. The structural solution was obtained by molecular replacement using superimposed polyalanine coordinates of six intracellular lipid-binding proteins as a search probe. The entire amino acid sequence of rat liver fatty acid-binding protein along with an amino-terminal formyl-methionine was modeled in the crystal structure. In addition, the crystal was obtained in the presence of oleic acid, and the initial electron density clearly showed two fatty acid molecules bound within a central cavity. The carboxylate of one fatty acid molecule interacts with arginine 122 and is shielded from free solvent. It has an overall bent conformation. The more solvent-exposed carboxylate of the other oleate is located near the helix-turnhelix that caps one end of the ␤-barrel, while the acyl chain lies in the interior. The cavity contains both polar and nonpolar residues but also shows extensive hydrophobic character around the nonpolar atoms of the ligands. The primary and secondary oleate binding sites appear to be totally interdependent, mainly because favorable hydrophobic interactions form between both aliphatic chains.

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“…The first restriction (1) above reflects the fact that there are 107 backbone amide hydrogen atoms protected (H-bonded) in the native state of both apo-and holo-forms of CRABP I according to available crystal structures [15,38]. This can be demonstrated using ESI-MS by allowing exchange to occur under conditions where the intrinsic amide exchange rate is significantly lower and hence an initial time point can be measured more readily.…”

Section: Protein Dynamics and Ligand Binding-hdx Measurements At Neutmentioning

confidence: 99%

“…Importantly, the native ligand all-trans retinoic acid (ATRA), binds CRABP I predominantly by hydrophobic interactions, as the ligand forms ten contacts with non-polar side chains and only one salt bridge [15]. The overall contribution to the free energy of the protein-ligand complex formation in solution was estimated to be in the range of 5-6 kcal/mol [16].…”

mentioning

confidence: 99%

Indirect assessment of small hydrophobic ligand binding to a model protein using a combination of ESI MS and HDX/ESI MS

Kaltashov

Eyles

2003

J. Am. Soc. Mass Spectrom.

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Direct mass spectrometric characterization of interactions between proteins and small hydrophobic ligands often poses a serious problem due to the complex instability in the gas phase. We have developed a method that probes the efficacy of ligand-protein interactions indirectly by monitoring changes in protein flexibility. The latter is assessed quantitatively using a combination of charge state distribution analysis and amide hydrogen exchange under both native and mildly denaturing conditions. The method was used to evaluate binding of a model protein cellular retinoic acid binding protein I to its natural ligand all-trans retinoic acid (RA), isomers 13-cis-and 9-cis-RA, and retinol, yielding the following order of ligand affinities: All-trans RA Ͼ 9-cis RA Ͼ 13-cis RA, with no detectable binding of retinol. This order is in agreement with the results of earlier fluorimetric titration studies. Furthermore, binding energy of the protein to each of retinoic acid isomers was determined based on the measured hydrogen exchange kinetics data acquired under native conditions. (J Am Soc Mass Spectrom 2003, 14, 506 -515)

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Crystal structures of cellular retinoic acid binding proteins I and II in complex with all-trans-retinoic acid and a synthetic retinoid

Cited by 205 publications

References 69 publications

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model

The Crystal Structure of the Liver Fatty Acid-binding Protein

Indirect assessment of small hydrophobic ligand binding to a model protein using a combination of ESI MS and HDX/ESI MS

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