Summary
To speed up the structure-based analysis of protein function, we have developed the concept of Experimentally Validated 3D Models (EVAMs), i.e., structural models that can be generated relatively fast by a combination of bioinformatics and experiments. Here, we test the suitability of EVAMs for functional studies by applying the concept to two small proteins, saposin B and saposin C. We find that EVAMs are well able to explain some of the functional properties of these proteins, such as their pH-dependent association with lipid bilayers, that are known from independent biophysical experiments.
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References
Bashford D, Case DA, Dalvitt C, Tennant L, Wright PE (1993) Electrostatic calculations of side-chain pKavalues in myoglobin and comparison with NMR data for histidines. Biochemistry 32, 8045–8056
Bashford D, Karplus M (1990) pka ’s of ionizable groups in proteins: Atomic detail from a continuum electrostatic model. Biochemistry 29, 10219–10225
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculation. J Comp Chem 4, 187–217
Hoffmann D, Kramer B, Washio T, Steinmetzer T, Rarey M, Lengauer T (1999) Two-stage method for protein-ligand docking. J Med Chem 42, 4422–4433
Hoffmann D, Schnaible V, Wefing S, Albrecht M, Hanisch D, Zimmer R (2002) A new method for the fast solution of protein-3D-structures, combining experiments and bioinformatics. In: Coupling of Biological and Electronic SystemsProceedings of the 2nd caesarium K-H Hoffmann (ed.) Springer, Berlin, 59–78
Hoffmann D, Zimmer R (1999) Chemical activation mediated by the transfer of fluorescent energy for elucidating the 3D-structure of biological macromolecules. German Patent Office PCT WO 99/41607
Kolter T, Sandhoff K (1999) Sphingolipids — Their metabolic pathways and the pathobiochemistry of neurodegenerative diseases. Angew Chem Int Ed 38, 1532–1568
Laaksonen L (2001) gOpenMol. http://www.csc.fi/~laaksone/gopenmol/
Liepinsh E, Andersson M, Ruysschaert JM, Otting G (1997) Saposin fold revealed by the NMR structure of NK-lysin. Nat Struct Biol 4, 793–795
Linke T, Wilkening G, Lansmann S, Moczall H, Bartelsen O, Weisgerber J, Sandhoff K (2001) Stimulation of acid sphingomyelinase activity by lysosomal lipids and sphingolipid activator proteins. Biol Chem 382, 283–290
Mevissen H, Thiele R, Zimmer R, Lengauer T (1994) The ToPLign software environment — Toolbox for protein alignment. InBioinformatik ‘84 . IMB, Jena, Germany
Vaccaro AM, Ciaffoni F, Tatti M, Savioli R, Barca A, Tognozzi D, Scerch C (1995) pH-dependent conformational properties of saposins and their interactions with phospholipid membranes. J Biol Chem 270, 30576–30580
Vaccaro AM, Salvioli R, Barca A, Tatti M, Ciaffoni F, Maras B, Siciliano R, Zappacosta F, Amoresano A, Pucci P (1995) structural analysis of saposin B and C. JBiol Chem 270, 9953–9960
Vaccaro AM, Salvioli R, Tatti M, Ciaffoni F (1999) Saposins and their interaction with lipids. Neurochem Res 24, 307–314
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Hoffmann, D. (2003). A Functional Study on Saposin B and C Using Experimentally Validated Models. In: Alt, W., Chaplain, M., Griebel, M., Lenz, J. (eds) Polymer and Cell Dynamics. Mathematics and Biosciences in Interaction. Birkhäuser, Basel. https://doi.org/10.1007/978-3-0348-8043-5_3
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DOI: https://doi.org/10.1007/978-3-0348-8043-5_3
Publisher Name: Birkhäuser, Basel
Print ISBN: 978-3-0348-9417-3
Online ISBN: 978-3-0348-8043-5
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