Limitation of conformational space for proteins -- early stage folding simulation of human alpha and beta hemoglobin chains

• Autorzy: Bryliński M. , Jurkowski W. , Konieczny L. , Roterman I.
• Języki publikacji: EN

Abstrakty

EN

The starting structure of ab initio protein structure prediction methods is problematic as the energy minimization procedure stops searching for an optimal structure of the function's local minimum. The method presented in the paper helps to find the starting structure. Although it is based on the known native protein structure, it seems to deliver a key to the formation of a common universal starting structure. The limited conformational sub-space, defined on the basis of a geometrical model of the polypeptide backbone with the side chain-side chain interaction excluded, seems to deliver the original structure of the polypeptide, which is modified step by step as the role of the side chain interactions increases during the energy minimization procedure. Here, the method is applied to human hemoglobin chains alpha and ß to test the applicability of the method to proteins with a high content of helical forms and lacking disulphide bonds.

Słowa kluczowe

EN

early-stage folding; structure prediction; conformational space

• Wydawca: Politechnika Gdańska
• Czasopismo: TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk
• Rocznik: 2004
• Tom: Vol. 8, No 3
• Strony: 413--422
• Opis fizyczny: Bibliogr. 19 poz., rys.

Twórcy

autor

Bryliński M.

• Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Kopernika 17, 31-501 Cracow, Poland
• Institute of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland

autor

Jurkowski W.

• Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Kopernika 17, 31-501 Cracow, Poland
• Institute of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland

autor

Konieczny L.

• Institute of Medical Biochemistry, Collegium Medicum, Jagiellonian University, Kopernika 7, 31-034 Cracow, Poland

autor

Roterman I.

• Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Kopernika 17, 31-501 Cracow, Poland

Bibliografia

• [1] Dobson C M 2001 Phil. Trans. R. Soc. Lond. B 356 133
• [2] Chan H S and Dill K A 1998 Proteins Struc. Func. Gen. 30 2
• [3] Dill K A and Chan H S 1997 Nature Struct. Biol. 4 10
• [4] Alonso D O V and Daggett V 1998 Prot Sci. 7 860
• [5] Liwo A, Czaplewski C, Pillardy J and Scheraga H A 2001 J. Chem. Phys. 115 2323
• [6] Liwo A, Arfukowicz P, Czaplewski C, Ołdziej S, Pillardy J and Scheraga H A 2002 Proc. Natl. Acad. Sci. USA 99 1937
• [7] Fern`andez A, Kostov K and Berry R S 1999 Proc. Natl. Acad. Sci. USA 96 12991
• [8] Fern`andez A, Colubri A, Aqpigmanesi G and Burastero T 2001 Physica A 293 358
• [9] Sosnick T R, Berry R S, Colubri A and Fernandez A 2002 Proteins Struct. Func. Gen. 49 15
• [10] Roterman I 1995 J. Theoretical Biol. 177 283
• [11] Roterman I 1995 Biochimie 77 204
• [12] Jurkowski W, Bryliński M, Konieczny L, Wiśniowski Z and Roterman I 2004 Proteins Struct. Func. Bioinf. 55 115
• [13] Baldwin R L 2002 Science 295 1657
• [14] Scheraga H A 1992 Rev. Comput. Chem. 3 73
• [15] Gay D M 1983 ACM Trans. on Mathematical Software 9 503
• [16] Orengo C A, Bray J E, Hubbard T, LoConte L, Sillitoe I 1999 Proteins Struct. Func. Gen. Suppl. 3 149
• [17] Fersht A R and Daggett V 2002 Cell 108 573
• [18] Bryliński M, Jurkowski W, Konieczny L and Roterman I 2004 Bioinformatics 20 199
• [19] Bryliński M, Konieczny L and Roterman I 2004 Early Stage Folding in Proteins – Structure to Sequence Relation (submitted)