Protein backbone dynamics revealed by quasi spectral density function analysis of amide N-15 nuclei.
Spectral density functions J(0), J(omega N), and J(omega H + omega N) of individual amide N-15 nuclei in proteins were approximated by a quasi spectral density function (QSDF). Using this function, the backbone dynamics were analyzed for seven protein systems on which data have been published. We defined J(0; omega N) as the difference between the J(0) and the J(omega N) values, which describes motions slower than 50 (or 60) MHz, and J(omega N; omega H+N) as the difference between the J(omega N) and the J(omega H + omega N) values, which describes motions slower than 450 (or 540) MHz. The QSDF analysis can easily extract the J(0; omega N) of protein backbones, which have often some relation to biologically relevant reactions. Flexible N-terminal regions in eglin c and glucose permease IIA and a loop region in eglin c showed smaller values of both the J(0; omega N) and the J(omega N; omega H+N) as compared with the other regions, indicating increases in motions faster than nanosecond. The values of the J(0; omega N) for the backbone of the FK506 binding protein showed a large variation in the apoprotein but fell in a very narrow range after the binding of FK506. Characteristic increase or decrease in the values of J(0) and J(omega N) was observed in two or three residues located between secondary structures.
Ishima
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Nagayama Protein Array Project, ERATO, JRDC, Tsukuba Research Consortium, Japan.
Nagayama
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K
D002147:Calmodulin / Q000737:chemistry; D002352:Carrier Proteins / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry; D006360:Heat-Shock Proteins / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D015394:Molecular Structure; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D016283:Proto-Oncogene Proteins p21(ras) / Q000737:chemistry; D015843:Serpins / Q000737:chemistry; D013057:Spectrum Analysis / Q000379:methods; D022021:Tacrolimus Binding Proteins; D013816:Thermodynamics; D013879:Thioredoxins / Q000737:chemistry
D002147:Calmodulin; D002352:Carrier Proteins; D004268:DNA-Binding Proteins; D006360:Heat-Shock Proteins; D011506:Proteins; D015843:Serpins; C028656:eglin proteinase inhibitors; D013879:Thioredoxins; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System; C031629:phosphoenolpyruvate-glucose phosphotransferase; D016283:Proto-Oncogene Proteins p21(ras); D022021:Tacrolimus Binding Proteins