Structure of pig plasma retinol-binding protein at 1.65 Å resolution

Zanotti, Giuseppe; Panzalorto, Manuela; Marcato, Andrea; Malpeli, Giorgio; Folli, Claudia; Berni, Rodolfo

doi:10.1107/s0907444998002303

Cited by 27 publications

(22 citation statements)

References 9 publications

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“…This lower degree of sequence conservation is reflected in the larger average fluctuations, represented graphically in Figure 1b, found in the distance between the equivalent alpha carbons of the porcine OBP model compared with the two subunits of the bovine OBP dimer 11. Notice how the porcine32 and bovine RBP33 models are so extremely similar to each other throughout the entire polypeptide chain. In the case of the OBPs compared, on the other hand, the fluctuations are found to be on the average even higher in the final portion of the chain, i.e., in the region of the monomer that in the bovine OBP dimer is swapped.…”

Section: Resultsmentioning

confidence: 96%

Crystal structure of a truncated form of porcine odorant-binding protein

et al. 2000

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Section: Resultsmentioning

confidence: 96%

Crystal structure of a truncated form of porcine odorant-binding protein

et al. 2000

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“…The ratio of hydrophobic to total area is then obtained as a function of the distance from the binding site center and this function is averaged over 27 different centers placed on a 2 ϫ 2 ϫ 2 Å grid around the initial center. This type of calculation was carried out for the binding sites of retinol binding protein (RBP), human thrombin, bovine beta-trypsin, and P450cam (PDB entries 1AQB, 46 1G32, 47 3PTB, 48 and 2CPP 37 ). The ligand and all crystallographic waters were removed prior to surface calculations and a 1.5 Å probe radius was used along with a united atom model for the protein.…”

Section: Binding Site Hydrophobicitymentioning

confidence: 99%

Binding affinity prediction with different force fields: Examination of the linear interaction energy method

2004

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A systematic study of the linear interaction energy (LIE) method and the possible dependence of its parameterization on the force field and system (receptor binding site) is reported. We have calculated the binding free energy for nine different ligands in complex with P450cam using three different force fields (Amber95, Gromos87, and OPLS-AA). The results from these LIE calculations using our earlier parameterization give relative free energies of binding that agree remarkably well with the experimental data. However, the absolute energies are too positive for all three force fields, and it is clear that an additional constant term (gamma) is required in this case. Out of five examined LIE models, the same one emerges as the best for all three force fields, and this, in fact, corresponds to our earlier one apart from the addition of the constant gamma, which is almost identical for the three force fields. Thus, the present free energy calculations clearly indicate that the coefficients of the LIE method are independent of the force field used. Their relation to solvation free energies is also demonstrated. The only free parameter of the best model is gamma, which is found to depend on the hydrophobicity of the binding site. We also attempt to quantify the binding site hydrophobicity of four different proteins which shows that the ordering of gamma's for these sites reflects the fraction of hydrophobic surface area.

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“…Although members of this family display low sequence similarity (often lower than 20% of amino acid identities), all share a conserved folding pattern, an 8-stranded ␤-barrel flanked by an ␣-helix at the C-terminal end of the polypeptide chain. The lipocalin ␤-barrel often defines a central apolar cavity that serves for the binding and transport of small hydrophobic molecules such as retinol (retinol-binding protein (5,6)), odorant molecules (bovine odorant-binding protein (7,8)), or pheromones (mouse major urinary protein, mMUP 1 (9), and rat urinary ␣2-globulin (10)). Several lipocalins have been described as allergenic proteins, among which the mouse major urinary protein mMUP (11), rat urinary ␣2-globulin rat urinary ␣2-globulin (12), bovine ␤-lactoglobulin (13), cockroach allergen Bla g 4 (14), dog allergens Can f 1 and Can f 2 (15), and bovine allergen Bos d 2 (16).…”

mentioning

confidence: 99%

Crystal Structure of the Allergen Equ c 1

Lascombe¹,

Grégoire²,

Poncet³

et al. 2000

Journal of Biological Chemistry

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The three-dimensional structure of the major horse allergen Equ c 1 has been determined at 2.3 Å resolution by x-ray crystallography. Equ c 1 displays the typical fold of lipocalins, a ␤-barrel flanked by a C-terminal ␣-helix. The space between the two ␤-sheets of the barrel defines an internal cavity that could serve, as in other lipocalins, for the binding and transport of small hydrophobic ligands. Equ c 1 crystallizes in a novel dimeric form, which is distinct from that observed in other lipocalin dimers and corresponds to the functional form of the allergen. Binding studies of point mutants of the allergen with specific monoclonal antibodies raised in mouse and IgE serum from horse allergic patients allowed to identify putative B cell antigenic determinants. In addition, total inhibition of IgE serum recognition by a single specific monoclonal antibody revealed the restricted nature of the IgE binding target on the molecular surface of Equ c 1.The incidence of allergic diseases is increasing in developed countries resulting from growing exposure to allergens, altered stimulation of the immune system during development, and probably facilitating an adjuvant effect of the environment. Allergy to animals is distinguishable by its intensity and the possibility of sensitization by a limited contact with danders or hair. The animals responsible for allergy are obviously familiar domestic cats and dogs, but also the horse, which is often incriminated. Five main horse allergens have been isolated and purified (1, 2). Among these, the Equ c 1 protein (molecular mass 21.5 kDa, 187 amino acids, pI ϭ 4.5) has been defined as a major allergen, because it induces an IgE-mediated type I allergic reaction in a majority of the patients allergic to horses.Equ c 1 belongs to the lipocalin family (3, 4). Although members of this family display low sequence similarity (often lower than 20% of amino acid identities), all share a conserved folding pattern, an 8-stranded ␤-barrel flanked by an ␣-helix at the C-terminal end of the polypeptide chain. The lipocalin ␤-barrel often defines a central apolar cavity that serves for the binding and transport of small hydrophobic molecules such as retinol (retinol-binding protein (5, 6)), odorant molecules (bovine odorant-binding protein (7, 8)), or pheromones (mouse major urinary protein, mMUP 1 (9), and rat urinary ␣2-globulin (10)). Several lipocalins have been described as allergenic proteins, among which the mouse major urinary protein mMUP (11), rat urinary ␣2-globulin rat urinary ␣2-globulin (12), bovine ␤-lactoglobulin (13), cockroach allergen Bla g 4 (14), dog allergens Can f 1 and Can f 2 (15), and bovine allergen Bos d 2 (16).Whether a protein exhibits special structural characteristics that are responsible for its allergenic properties is an issue that remains poorly understood. Although the three-dimensional structures of some allergenic lipocalins are known (mMUP (9), rat urinary ␣2-globulin (10), bovine ␤-lactoglobulin (17, 18), and Bos d 2 (19)), little information is availa...

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Structure of pig plasma retinol-binding protein at 1.65 Å resolution

Cited by 27 publications

References 9 publications

Crystal structure of a truncated form of porcine odorant-binding protein

Crystal structure of a truncated form of porcine odorant-binding protein

Binding affinity prediction with different force fields: Examination of the linear interaction energy method

Crystal Structure of the Allergen Equ c 1

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