Gustavo Elberto Epalza Sanchez/Sandbox 1

From Proteopedia

One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.

Molecular Playground banner: CRABP I, a model protein to study folding of β - sheet - rich proteins.

Molecular Playground banner: CRABP I, a carrier protein for retinoic acid, has an important role for vision.

Cellular Retinoic Acid Binding Proteins(CRABPs) are small cytosolic proteins (about 15.5 kDa and 136 residues) that belong to the family of intracellular lipid binding proteins (iLBP) which bind small hydrophobic ligands. It has been suggested that the two types of CRABPs, CRABP I and CRABP II are involved in retinoic acid metabolism or its transport into the nuclei controlling differentiation and proliferation processes by activation of retinoic acid receptors (RARs) and retinoid receptors X (RXSs) [1], [2]. High doses of retinoic acid induce malformations in embryo development, including facial defects and limb abnormalities; these retinoids have found use in a number of medical applications including the treatment of some cancers and skin disorders. [3] During embryonic development, the spatial and temporal expression of the CRABP gene appears to be strictly regulated [4]. Therefore, it has been suggested that CRABP could be involved in the formation of gradients of RA across various developing tissues. Although the structure of CRABP I is similar to the cellular retinol-binding proteins, it binds only retinoic acid at specific sites within the nucleus, which may contribute to vitamin A-directed differentiation in epithelial tissue.

Structure

Proteins in iLBP family have very high structural conservation despite having very low sequence identities [5], ranging from 18 to 80%, what suggests that CRABP I is very tolerant to mutations without changing the native structure and binding ability. [6] Similar to other members of the iLBP family, (PDBID: 1CBI) has two orthogonal five-stranded with a , known as the Schellman motif, [7] between the first and the second β-strands,showing α+β secondary domains. It contains a very large solvent accessible central cavity that binds (PDBID: 1CBS). This conserved is contained between strand 4 and 5 and has no inter-strand hydrogen bonds but is compensated by the presence of ordered water molecules. The helix-turn-helix motif between the first and second strands acts as a on the ligand binding pocket. Strands 7 and 8 are connected by the which has variable lengths within the family. There are 15 fully residues in CRABP I, seven are found in the helix I and II and 5 are in the β-barrel closure [8]. Besides, this protein has no disulfide bonds, cofactors or posttranslational modifications to make difficult the folding process. [9]It has been shown that the mutation , known as CRABP I wt*, gives more stability to the protein and it does not produce a significant conformational change relative to the .

The RA/CRABP interaction is predominantly hydrophobic, as the ligand forms ten contacts with non-polar side chains and only one salt bridge. The β-barrel contains a poorly accessible hydrophobic ligand-binding cavity. For Chain A, the residues in of CRABP I to RA correspond to PRO39,THR56, LEU120, ARG131, and TYR133. In case of Chain B, even though MET 27 is not one of the residues in chain B, it can be one of the the to RA which is bound to PRO39, THR56, LEU120, ARG131, and TYR133 in chain B of CRABP I. Comparison of the and the structure of the proteins in the iLBP family does not reveal a significant opening large enough to allow ligand entry and release [10]. Entry of RA into the cavity of CRABPs is proposed to occur via a region of the protein comprising determinants from the βC-D loop, the βE-F loop and the N-terminal region of helix II. This region of the protein referred to as the “portal” region of the protein has been extensively studied in other members of the iLBP family, in particular in the fatty acid binding protein, by X-ray crystallography, mutational analysis and multidimensional NMR [11].

See Also

• Cellular retinoic acid-binding protein 1 at Wikipedia

3D structure of Cellular retinoic acid-binding protein

CRABP I

2cbr - hCRABP I – human
1cbr - CRABP I + retinoic acid – mouse

CRABP II

2fs6, 2fs7 - hCRABP II
1blr - hCRABP II – NMR
3fek, 3fel, 3fen, 3fa7, 3fa8, 3fa9, 3i17, 3d95, 3d96, 3d97, 2frs - hCRABP II (mutant)
3f8a, 3f9d, 3fa6, 3cr6, 2g79, 2g7b – hCRABP II (mutant) + retinal analog
3cwk, 2g78, 4i9r, 4i9s, 4m6s, 4m7m – hCRABP II (mutant) + retinoic acid
2fr3, 2cbs, 3cbs, 1cbq, 1cbs – hCRABP II + retinoic acid
3fep - hCRABP II (mutant) + ligand

References

• [1] Venepally, P. et al. Biochemistry. 35, 9974-9982 (1996) PMID: 8756459 [PubMed - indexed for MEDLINE]
• [2] Wey, L. et. al. Molecular and cellular biochemistry, 200: 69-76 (1999) | doi: 10.1023/A:1006906415388
• [3] Kleywegt, G. et. al. Structure, Vol. 2, No. 12, 1994, 1241-1258 | doi:10.1016/S0969-2126(94)00125-1
• [4] Vaessen, et al. Differentiation. 40, 99-105 (1989). PMID: 2547683 [PubMed - indexed for MEDLINE]
• [5] Gunasekaran, K, "et al". PROTEINS: Structure, Function, and Bioinformatics. PMID: 14696180
• [6] Clark, P. et. al. Folding and design, 1998, 3, 401 – 412 | doi:10.1016/S1359-0278(98)00053-4
• [7] Rotondi, K. S. et. al. Biochemistry, 2003, 42, 7976 – 7985 | doi: 10.1021/bi034304k
• [8] Marcelino, A, "et al". PROTEINS: Structure, Function, and Bioinformatics. PMID: 16477649 [Pubmed- indexed for MEDLINE]
• [9] Clark, P. et. al. Protein science, 1996, 5, 1108 – 1117 | doi: 10.1002/pro.5560050613
• [10] Xiao, H. and I. A. Kaltashov,J Am Soc Mass Spectrom. 16(6),869-79 (2005). | doi:10.1016/j.jasms.2005.02.020
• [11] Krishnan, V. et al. Biochemistry 39(31), 9119-9129 (2000)PMID: 10924105 [PubMed - indexed for MEDLINE]
• [12] Sacchettini, J. et al. J Biol Chem. 267(33), 23534-23545 (1992)
• [13] Hodsdon, M.et al. Biochemistry. 36(6), 1450-60(1997)| doi:10.1021/bi961890r
• [14] Sjoelund, V. et al. Biochemistry.46, 13382–13390 (2007) | doi: 10.1021/bi700867c