Application of divergence entropy to characterize the structure of lipid-binding proteins
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Roksana Rosicka
Abstract
The lipid-binding protein present in the human brain is the object of this analysis. The expression of these proteins is especially important for nervous cell differentiation and their migration in the process of the development of the brain. The “fuzzy oil drop” model applied to the analysis of these proteins may suggest the mechanism of complex generation. It is shown that this type of complex may appear spontaneously in water environment. The presence of ligand does not imply any form of adaptation of the polypeptide chain to the ligand molecule. It can be speculated that ligand binding is of a static character without the necessity for mutual structural fitting. The structures of polypeptide in the apo- and complexed forms do not differ in respect to hydrophobic core formation. Such an interpretation is different than that observed in other ligand-binding proteins where the binding cavity needs to be specially fitted to the specific ligand. It can also be concluded that the lipid-binding process is of low specificity in this case.
Acknowledgments
The work was supported by Jagiellonian University – Medical College grant system (grant no. K/ZDS/001531).
Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.
Research funding: None declared.
Employment or leadership: None declared.
Honorarium: None declared.
Competing interests: The funding organization(s) played no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the report for publication.
References
1. Storch J, McDermott L. Structural and functional analysis of fatty acid-binding proteins. J Lipid Res 2009;50:S126–31.10.1194/jlr.R800084-JLR200Suche in Google Scholar
2. Feng L, Hatten ME, Heintz N. Brain lipid-binding protein (BLBP): a novel signaling system in the developing mammalian CNS. Neuron 1994;12:895–908.10.1016/0896-6273(94)90341-7Suche in Google Scholar
3. Frauenfelder H. The physics of proteins, tertiary structure of proteins biological and medical physics, biomedical engineering, 1st ed. New York: Springer-Verlag, 2010.10.1007/978-1-4419-1044-8_9Suche in Google Scholar
4. Alejster P, Banach M, Jurkowski W, Marchewka D, Roterman I. Comparative analysis of techniques oriented on the recognition of ligand binding area in proteins. In: Roterman-Konieczna, I, editor. Identification of ligand binding site and protein-protein interaction area. Dordrecht: Springer, 2013:55–86.10.1007/978-94-007-5285-6_4Suche in Google Scholar
5. Balendiran GK, Schnutgen F, Scapin G, Borchers T, Xhong N, Lim K, et al. Crystal structure and thermodynamic analysis of human brain fatty acid-binding protein. J Biol Chem 2000;275:27045–54.10.1016/S0021-9258(19)61478-XSuche in Google Scholar
6. Rademacher M, Zimmerman AW, Rüterjans H, Veerkamp JH, Lücke C. Solution structure of fatty acid-binding protein from human brain. Mol Cell Biochem 2002;239:61–8.10.1023/A:1020566909213Suche in Google Scholar
7. Kalinowska B, Banach M, Konieczny L, Roterman I. Application of divergence entropy to characterize the structure of the hydrophobic core in DNA interacting proteins. Entropy 2015;17: 1477–507.10.3390/e17031477Suche in Google Scholar
8. Levitt M. A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol 1976;104: 59–107.10.1016/0022-2836(76)90004-8Suche in Google Scholar
9. Kullbak S, Leibler RA. On information and sufficiency. Ann Math Stat 1951;22:79–86.10.1214/aoms/1177729694Suche in Google Scholar
10. Banach M, Konieczny L, Roterman I. The fuzzy oil drop model, based on hydrophobicity density distribution, generalizes the influence of water environment on protein structure and function. J Theor Biol 2014;359:6–17.10.1016/j.jtbi.2014.05.007Suche in Google Scholar PubMed
11. Kalinowska B, Banach M, Konieczny L, Marchewka D, Roterman I. Intrinsically disordered proteins-relation to general model expressing the active role of the water environment. Adv Protein Chem Struct Biol 2014;94:315–46.10.1016/B978-0-12-800168-4.00008-1Suche in Google Scholar PubMed
12. Roterman I, Konieczny L, Banach M, Marchewka D, Kalinowska B, Baster Z, et al. Simulation of the protein folding process. In: Adam L, editor. Computational methods to study the structure and dynamics of biomolecules and biomolecular processes. Berlin: Springer-Verlag, 2014:599–638.10.1007/978-3-642-28554-7_18Suche in Google Scholar
13. Klabunde T, Petrassi HM, Oza VB, Raman P, Kelly JW, Sacchettini JC. Rational design of potent human transthyretin amyloid disease inhibitors. Nat Struct Biol 2000;7:312–21.10.1038/74082Suche in Google Scholar
14. Innis SM, Sprecher H, Hachey D, Edmond D, Anderson RE. Neonatal polyunsaturated fatty acid metabolism. Lipids 1999;34:139–49.10.1007/s11745-999-0348-xSuche in Google Scholar
15. Lauritzen L, Hansen HS, Jorgensen MH, Michaelsen KF. The essentiality of long chain n-3 fatty acids in relation to development and function of the brain and retina. Prog Lipid Res 2001;40:1–94.10.1016/S0163-7827(00)00017-5Suche in Google Scholar
16. Voigt RG, Jensen CL, Fraley JK, Rozelle JC, Brown FR, Heird WC. Relationship between omega3 long-chain polyunsaturated fatty acid status during early infancy and neurodevelopmental status at 1 year of age. J Hum Nutr Diet 2002;15:111–20.10.1046/j.1365-277X.2002.00341.xSuche in Google Scholar
17. Innis SM. Dietary (n-3) fatty acids and brain development. J Nutr 2007;137:855–9.10.1093/jn/137.4.855Suche in Google Scholar PubMed
18. Swanson D, Block R, Mousa SA. Omega-3 fatty acids EPA and DHA: health benefits throughout life. Adv Nutr 2012;3:1–7.10.3945/an.111.000893Suche in Google Scholar PubMed PubMed Central
©2015 by De Gruyter
Artikel in diesem Heft
- Frontmatter
- Reviews
- From Hippocrates to statistics. A historical perspective
- Neural networks as a tool for modeling of biological systems
- Original Articles
- Phylogenetic aspects of the concept of intelligent life design
- A method of predicting the secondary protein structure based on dictionaries
- Application of divergence entropy to characterize the structure of lipid-binding proteins
- Hydrophobic core structure of macromomycin – the apoprotein of the antitumor antibiotic auromomycin – fuzzy oil drop model applied
- Interfaces for tetraplegic people – review of solutions supporting activities of daily living
- Erratum
- Erratum to: Building an audio/video-feedback system for simulation training in medical education
Artikel in diesem Heft
- Frontmatter
- Reviews
- From Hippocrates to statistics. A historical perspective
- Neural networks as a tool for modeling of biological systems
- Original Articles
- Phylogenetic aspects of the concept of intelligent life design
- A method of predicting the secondary protein structure based on dictionaries
- Application of divergence entropy to characterize the structure of lipid-binding proteins
- Hydrophobic core structure of macromomycin – the apoprotein of the antitumor antibiotic auromomycin – fuzzy oil drop model applied
- Interfaces for tetraplegic people – review of solutions supporting activities of daily living
- Erratum
- Erratum to: Building an audio/video-feedback system for simulation training in medical education
