Determinants of protein stability and folding: Comparative analysis of beta-lactoglobulins and liver basic fatty acid binding protein

Proteins: Structure, Function and Genetics

Volumn 61, Issue 2, 2005, Pages 366-376

  Ragona, Laura ^a   Colombo, Giorgio ^a,b   Catalano, Maddalena ^a   Molinari, Henriette ^c,d  

^a CNR   (Italy)

^b CNR   (Italy)

^c Dipto Scientifico e Tecnologico   (Italy)

^d UNIVERSITY OF VERONA   (Italy)

Author keywords

Beta lactoglobulins; Fatty acid binding proteins; Folding determinants; Lipocalins; Molecular dynamics simulations; Side chain side chain conservation

Indexed keywords

BETA LACTOGLOBULIN; FATTY ACID BINDING PROTEIN; LIPOCALIN; PROTEIN;

ARTICLE; LIVER; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; AMINO ACIDS; ANIMALS; CATTLE; COMPUTER SIMULATION; FATTY ACID-BINDING PROTEINS; HYDROPHOBICITY; LACTOGLOBULINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SEQUENCE ALIGNMENT; SWINE;

BOVINAE; SUIDAE;

EID: 26444556851     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20493     Document Type: Article

References (32)

1. Greene LH, Hamada D, Eyles SJ, Brew K. Conserved signature proposed for folding in the lipocalin superfamily. FEBS Lett 2003;553:39-44.
2. Ragona L, Fogolari F, Romagnoli S, Zetta L, Maubois JL, Molinari H. Unfolding and refolding of bovine beta-lactoglobulin monitored by hydrogen exchange measurements. J Mol Biol 1999;293:953-969.
3. Fogolari F, Ragona L, Licciardi S, Romagnoli S, Michelutti R, Ugolini R, Molinari H. Electrostatic properties of bovine beta-lactoglobulin. Proteins 2000;39:317-330.
4. Ugolini R, Ragona L, Silletti E, Fogolari F, Visschers RW, Alting AC, Molinari H. Dimerization, stability and electrostatic properties of porcine beta-lactoglobulin. Eur J Biochem 2001;268:4477-4488.
5. Ragona L, Fogolari F, Catalano M, Ugolini R, Zetta L, Molinari H. EF loop conformational change triggers ligand binding in beta-lactoglobulins. J Biol Chem 2003;278:38840-38846.
6. Vasile F, Ragona L, Catalano M, Zetta L, Perduca M, Monaco H, Molinari H. Solution structure of chicken liver basic fatty acid binding protein. J Biomol NMR 2003;25:157-160.
7. Tiana G, Simona F, De Mori GM, Broglia RA, Colombo G. Understanding the determinants of stability and folding of small globular proteins from their energetics. Protein Sci 2004;13:113-124.
8. Fogolari F, Ragona L, Zetta L, Romagnoli S, De Kruif KG, Molinari H. Monomeric bovine beta-lactoglobulin adopts a beta-barrel fold at pH 2. FEBS Lett 1998;436:149-154.
9. Brownlow S, Morais Cabral JH, Cooper R, Flower DR, Yewdall SJ, Polikarpov I, North AC, Sawyer L. Bovine beta-lactoglobulin at 1.8 Å resolution - still an enigmatic lipocalin. Structure 1997;5:481-495.
10. Kuwata K, Hoshino M, Forge V, Era S, Batt CA, Goto Y. Solution structure and dynamics of bovine beta-lactoglobulin A. Protein Sci 1999;8:2541-2545.
11. Berendsen H, Grigera J, Straatsma T. The missing term in effective pair potentials. J Phys Chem 1987;91:6269-6271.
12. Hess B, Bekker H, Fraaije JGEM, Berendsen HJC. A linear constraint solver for molecular simulations. J Comp Chem 1997;18: 1463-1472.
13. Miyamoto S, Kollman P. Settle: an analytical version of the shake and rattle algorithms for rigid water models. J Comp Chem 1992;13:952-962.
14. van Gunsteren WF, Berendsen HJ. Computer simulation as a tool for tracing the conformational differences between proteins in solution and in the crystalline state. J Mol Biol 1984;176:559-564.
15. van Gunsteren WF, Daura X, Mark AE. Encyclopedia of computational chemistry. Chichester, UK: Wiley; 1998. p 1211-1216.
16. Amadei A, Linssen AB, Berendsen HJ. Essential dynamics of proteins. Proteins 1993;17:412-425.
17. Gunasekaran K, Hagler AT, Gierasch LM. Sequence and structural analysis of cellular retinoic acid-binding proteins reveals a network of conserved hydrophobic interactions. Proteins 2004;54: 179-194.
18. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
19. Ragona L, Pusterla F, Zetta L, Monaco HL, Molinari H. Identification of a conserved hydrophobic cluster in partially folded bovine beta-lactoglobulin at pH 2. Fold Des 1997;2:281-290.
20. Kuznetsov IB, Rackovsky S. Class-specific correlations between protein folding rate, structure-derived, and sequence-derived descriptors. Proteins 2004;54:333-341.
21. Martinez JC, Pisabarro MT, Serrano L. Obligatory steps in protein folding and the conformational diversity of the transition state. Nat Struct Biol 1998;5:721-729.
22. Grantcharova VP, Riddle DS, Santiago JV, Baker D. Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nat Struct Biol 1998;5:714-720.
23. Riddle DS, Grantcharova VP, Santiago JV, Alm E, Ruczinski I, Baker D. Experiment and theory highlight role of native state topology in SH3 folding. Nat Struct Biol 1999;6:1016-1024.
24. McCallister EL, Aim E, Baker D. Critical role of beta-hairpin formation in protein G folding. Nat Struct Biol 2000;7:669-673.
25. Yagi M, Sakurai K, Kalidas C, Batt CA, Goto Y. Reversible unfolding of bovine beta-lactoglobulin mutants without a free thiol group. J Biol Chem 2003;278:47009-47015.
26. Forge V, Hoshino M, Kuwata K, Arai M, Kuwajima K, Batt CA, Goto Y. Is folding of beta-lactoglobulin non-hierarchic? Intermediate with native-like beta-sheet and non-native alpha-helix. J Mol Biol 2000;296:1039-1051.
27. Kuwata K, Shastry R, Cheng H, Hoshino M, Batt CA, Goto Y, Roder H. Structural and kinetic characterization of early folding events in beta-lactoglobulin. Nat Struct Biol 2001;8:151-155.
28. Greene LH, Chrysina ED, Irons LI, Papageorgiou AC, Acharya KR, Brew K. Role of conserved residues in structure and stability: tryptophans of human serum retinol-binding protein, a model for the lipocalin superfamily. Protein Sci 2001;10:2301-2316.
29. Ragona L, Catalano M, Zetta L, Longhi R, Fogolari F, Molinari H. Peptide models of folding initiation sites of bovine beta-lactoglobulin: identification of nativelike hydrophobic interactions involving G and H strands. Biochemistry 2002;41:2786-2796.
30. D'Alfonso L, Collini M, Ragona L, Ugolini R, Baldini G, Molinari H. Porcine beta-lactoglobulin chemical unfolding: Identification of a non-native alpha-helical intermediate. Proteins 2005;58:70-79.
31. Rotondi KS, Gierasch LM. Role of local sequence in the folding of cellular retinoic abinding protein I: structural propensities of reverse turns. Biochemistry 2003;42:7976-7985.
32. Rotondi KS, Gierasch LM. Local sequence information in cellular retinoic acid-binding protein I: specific residue roles in beta-turns. Biopolymers 2003;71:638-651.