Crystal structure of rat intestinal fatty-acid-binding protein

Sacchettini, James C.; Gordon, Jeffrey I.; Banaszak, Leonard J.

doi:10.1016/0022-2836(89)90392-6

Cited by 347 publications

(205 citation statements)

References 34 publications

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“…The secondary structure elements determined in this work by use of homonuclear two-dimensional NMR spectroscopy largely correspond with those of the crystal structures of related proteins (Sacchettini et al, 1989a;Muller-Fahrnow et al, 1991;Scapin et al, 1992). Two short a-helices and ten antiparallel strands with P-sheet structure were traced, with narrow turns between most strands and a gap in the P-sheet between strands D and E.…”

Section: Secondary Structuressupporting

confidence: 64%

Sequence‐specific ¹H‐NMR assignment and determination of the secondary structure of bovine heart fatty‐acid‐binding protein

Lücke

Lassen

Kreienkamp

et al. 1992

European Journal of Biochemistry

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The nearly complete sequence‐specific 1H resonance assignment of the pI = 4.9 isoform of cytosolic 15‐kDa fatty‐acid‐binding protein from bovine heart (H‐FABPc) by homonuclear two‐dimensional NMR spectroscopy is presented. Regular secondary structure elements were identified from NOE spectra and the sequence locations of slowly exchanging backbone amide protons. The molecular structure of the protein was found to consist mainly of ten antiparallel β‐strands and two short α‐helices. The data presented here for the first time for a hydrophobic molecule transporter of the fatty‐acid‐binding protein type is the basis for a complete tertiary structure determination currently in progress.

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Section: Secondary Structuressupporting

confidence: 64%

Sequence‐specific ¹H‐NMR assignment and determination of the secondary structure of bovine heart fatty‐acid‐binding protein

Lücke

Lassen

Kreienkamp

et al. 1992

European Journal of Biochemistry

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“…This paper reports a study showing that streptavidin, and by inference other avidins, is also a member of the calycin superfa- The structures of a representative lipocalin, retinolbinding protein (RBP) [4], and a representative FABP, rat intestinal fatty acid-binding protein (I-FABP) [6], were superimposed manually onto that of streptavidin [5], using interactive computer graphics, in order to facilitate their quantitative structural comparison. From this the equivalent parts of their structures were established allowing a 'common core' characteristic of the underlying fold to be determined.…”

Section: Resultsmentioning

confidence: 99%

“…Coordinates for the structures of human retinol binding protein (databank code IRBP) [4], rat intestinal fatty acid binding protein (code ZIFB) [6] and streptavidin (code ISTP) [2] were obtained from the Brookhaven Protein Databank [7]. Structures were compared manually by the interactive manipulation of C, coordinates using the molecular graphics program WHAT-IF [8].…”

Section: Methodsmentioning

confidence: 99%

Structural relationship of streptavidin to the calycin protein superfamily

Flower

1993

FEBS Letters

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Streptavidin is a binding protein, from the bacteria Streptomyces av~dznu, with remarkable affinity for the vitamin biotin. The lipocalins and the fatty acid-binding proteins (FABPs), are two other protein families which also act by binding small hydrophobic molecules. Within a similar overall folding pattern (a p-barrel with a repeated +l topology), large parts of the lipocalin, FABP, and streptavidin molecules can be structurally equivalenced. The first structurally conserved region within the three-dimensional alignment, or common core, characteristic of the three groups corresponds to an unusual structural feature (a short 3,,, helix leading into a B-strand, the first of the barrel), conserved in both its conformation and its location within their folds, which also displays characteristic sequence conservation. These similarities of structure and sequence suggest that all three families form part of a larger group: the calycin structural superfamily.

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“…However, the mechanism and energetics of ligand binding differ widely among the calycins. For example, rat intestinal fatty acid binding protein (I-FABP), an abundant cytoplasmic calycin, binds palmitate (in an extended conformation, as in BLG) in a Ϸ500 Å 3 globular cavity of mixed polarity and occupied by 20-30 water molecules (31,36). This contrasts sharply with the completely nonpolar, empty binding cavity in BLG that seems to be poised for receiving an acyl chain or other nonpolar ligand.…”

Section: Discussionmentioning

confidence: 99%

A dry ligand-binding cavity in a solvated protein

Qvist

Davidovic

Hamelberg

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

129

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Ligands usually bind to proteins by displacing water from the binding site. The affinity and kinetics of binding therefore depend on the hydration characteristics of the site. Here, we show that the extreme case of a completely dehydrated free binding site is realized for the large nonpolar binding cavity in bovine ␤-lactoglobulin. Because spatially delocalized water molecules may escape detection by x-ray diffraction, we use water 17 O and 2 H magnetic relaxation dispersion (MRD), 13 C NMR spectroscopy, molecular dynamics simulations, and free energy calculations to establish the absence of water from the binding cavity. Whereas carbon nanotubes of the same diameter are filled by a hydrogenbonded water chain, the MRD data show that the binding pore in the apo protein is either empty or contains water molecules with subnanosecond residence times. However, the latter possibility is ruled out by the computed hydration free energies, so we conclude that the 315 Å 3 binding pore is completely empty. The apo protein is thus poised for efficient binding of fatty acids and other nonpolar ligands. The qualitatively different hydration of the ␤-lactoglobulin pore and carbon nanotubes is caused by subtle differences in water-wall interactions and water entropy.␤-lactoglobulin ͉ free energy simulation ͉ hydrophobic hydration ͉ magnetic relaxation dispersion G lobular proteins are stabilized by dense atomic packing and by water exclusion from the nonpolar core region. However, the packing density is not uniform and a typical protein contains approximately four cavities per 100 residues of sufficient size to accommodate at least one water molecule (1). Small nonpolar cavities are usually empty and can be regarded as packing defects, whereas small polar cavities tend to be occupied by structural water molecules that stabilize the folded protein by H-bonding to otherwise unsatisfied peptide partners (2). Large cavities are frequently linked to protein functions, such as ligand binding and transport, membrane translocation, and enzyme catalysis. Some of these large cavities are lined exclusively or predominantly by nonpolar sidechains. The question whether such large nonpolar cavities are empty or contain water molecules is of fundamental biological importance (3-8).The principal tool of structural biology, x-ray crystallography, cannot easily resolve this issue. There are three potential problems. (i) Because water molecules interact only weakly with the nonpolar cavity walls, they tend to be positionally disordered. As a result of such delocalization, the electron density of the water molecules may fall below the detection limit. (ii) At a typical resolution limit of Ϸ2 Å, a contaminating nonpolar ligand may be misinterpreted as a water cluster (9, 10). (iii) For structures determined at cryogenic temperatures, the hydration status of the cavity may be altered by re-equilibration during the flash cooling process (11).In favorable cases, water molecules in nonpolar protein cavities can be inferred from intermolecular nuclear O...

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Crystal structure of rat intestinal fatty-acid-binding protein

Cited by 347 publications

References 34 publications

Sequence‐specific ¹H‐NMR assignment and determination of the secondary structure of bovine heart fatty‐acid‐binding protein

Sequence‐specific ¹H‐NMR assignment and determination of the secondary structure of bovine heart fatty‐acid‐binding protein

Structural relationship of streptavidin to the calycin protein superfamily

A dry ligand-binding cavity in a solvated protein

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Crystal structure of rat intestinal fatty-acid-binding protein

Cited by 347 publications

References 34 publications

Sequence‐specific 1H‐NMR assignment and determination of the secondary structure of bovine heart fatty‐acid‐binding protein

Sequence‐specific 1H‐NMR assignment and determination of the secondary structure of bovine heart fatty‐acid‐binding protein

Structural relationship of streptavidin to the calycin protein superfamily

A dry ligand-binding cavity in a solvated protein

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Sequence‐specific ¹H‐NMR assignment and determination of the secondary structure of bovine heart fatty‐acid‐binding protein

Sequence‐specific ¹H‐NMR assignment and determination of the secondary structure of bovine heart fatty‐acid‐binding protein