Limits...
The complex of cytochrome f and plastocyanin from Nostoc sp. PCC 7119 is highly dynamic.

Scanu S, Förster J, Finiguerra MG, Shabestari MH, Huber M, Ubbink M - Chembiochem (2012)

Bottom Line: The complex from Nostoc sp.Chemical-shift-perturbation analysis showed that the presence of spin labels on the surface of Cyt f does not significantly affect the binding of Pc.The paramagnetic relaxation enhancement results are not consistent with a single orientation of Pc, thus indicating that multiple orientations must occur and suggesting that an encounter state represents a large fraction of the complex.

View Article: PubMed Central - PubMed

Affiliation: Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.

Show MeSH

Related in: MedlinePlus

A)–C) Observed and predicted PRE values for amide protons in Pcbound to MTSL-conjugated Cyt f variants. The observedPREs were extrapolated to represent the 100 % bound state of Pc(green dots). PREs at 400 s−1 represent lower limits.The PREs calculated from the NMR solution structure based on PCS (PDBID: 1TU2, model 1[16]) are shownas blue symbols. The PREs calculated from the NMR solution structurebased on PREs are shown as red symbols. D)–F) Experimental andback-calculated distances between Pc amide protons and MTSL-conjugatedCyt f variants. The white circles and black linerepresent the distances calculated from the experimental PREs (whichwere extrapolated to 100 % bound Pc); gray area: error margins.The distances derived from the NMR solution structure based on PREs areshown as a red line. The distances derived from the NMR solutionstructure based on PCS (PDB ID: 1TU2, model 1[16]) are shown as a blue line.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3569876&req=5

fig04: A)–C) Observed and predicted PRE values for amide protons in Pcbound to MTSL-conjugated Cyt f variants. The observedPREs were extrapolated to represent the 100 % bound state of Pc(green dots). PREs at 400 s−1 represent lower limits.The PREs calculated from the NMR solution structure based on PCS (PDBID: 1TU2, model 1[16]) are shownas blue symbols. The PREs calculated from the NMR solution structurebased on PREs are shown as red symbols. D)–F) Experimental andback-calculated distances between Pc amide protons and MTSL-conjugatedCyt f variants. The white circles and black linerepresent the distances calculated from the experimental PREs (whichwere extrapolated to 100 % bound Pc); gray area: error margins.The distances derived from the NMR solution structure based on PREs areshown as a red line. The distances derived from the NMR solutionstructure based on PCS (PDB ID: 1TU2, model 1[16]) are shown as a blue line.

Mentions: The fraction of free Pc (f1) is 0.76, and that ofbound Pc (f2+f3)is 0.24. By dividing the observed PRE by 0.24, the PRE for 100 % bound Pcis obtained. These extrapolated PREs are plotted in Figure 4 (green symbols) against the Pc residue number.Strikingly, the patterns are qualitatively similar for the three spin labelpositions, thus indicating that the same patches of Pc are strongly affected.When the fraction of AB* is neglected(f2≈0), the PRE can be predicted from themodel of the final complex. By using model 1 from PDB ID: 1TU2, thePREAB values were predicted for each amide in Pc (Figure 4, blue symbols). Clearly, themodel alone cannot account for the observed PREs. Also, docking calculationswere performed with distances derived from the PREs as restraints. Apart from avan der Waals repulsion function (to avoid steric collisions) no otherinteractions were included. The ensemble of the ten best structures is shown inFigure 5 and compared with the modelbased on PCS. In both cases, Pc is bound in the region close to the haem, butthe orientation differs. However, also the PRE-based model alone cannot accountfor the observed PREs and the back calculated distances (Figure 4, red symbols in the left panel, red line in theright panel).


The complex of cytochrome f and plastocyanin from Nostoc sp. PCC 7119 is highly dynamic.

Scanu S, Förster J, Finiguerra MG, Shabestari MH, Huber M, Ubbink M - Chembiochem (2012)

A)–C) Observed and predicted PRE values for amide protons in Pcbound to MTSL-conjugated Cyt f variants. The observedPREs were extrapolated to represent the 100 % bound state of Pc(green dots). PREs at 400 s−1 represent lower limits.The PREs calculated from the NMR solution structure based on PCS (PDBID: 1TU2, model 1[16]) are shownas blue symbols. The PREs calculated from the NMR solution structurebased on PREs are shown as red symbols. D)–F) Experimental andback-calculated distances between Pc amide protons and MTSL-conjugatedCyt f variants. The white circles and black linerepresent the distances calculated from the experimental PREs (whichwere extrapolated to 100 % bound Pc); gray area: error margins.The distances derived from the NMR solution structure based on PREs areshown as a red line. The distances derived from the NMR solutionstructure based on PCS (PDB ID: 1TU2, model 1[16]) are shown as a blue line.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3569876&req=5

fig04: A)–C) Observed and predicted PRE values for amide protons in Pcbound to MTSL-conjugated Cyt f variants. The observedPREs were extrapolated to represent the 100 % bound state of Pc(green dots). PREs at 400 s−1 represent lower limits.The PREs calculated from the NMR solution structure based on PCS (PDBID: 1TU2, model 1[16]) are shownas blue symbols. The PREs calculated from the NMR solution structurebased on PREs are shown as red symbols. D)–F) Experimental andback-calculated distances between Pc amide protons and MTSL-conjugatedCyt f variants. The white circles and black linerepresent the distances calculated from the experimental PREs (whichwere extrapolated to 100 % bound Pc); gray area: error margins.The distances derived from the NMR solution structure based on PREs areshown as a red line. The distances derived from the NMR solutionstructure based on PCS (PDB ID: 1TU2, model 1[16]) are shown as a blue line.
Mentions: The fraction of free Pc (f1) is 0.76, and that ofbound Pc (f2+f3)is 0.24. By dividing the observed PRE by 0.24, the PRE for 100 % bound Pcis obtained. These extrapolated PREs are plotted in Figure 4 (green symbols) against the Pc residue number.Strikingly, the patterns are qualitatively similar for the three spin labelpositions, thus indicating that the same patches of Pc are strongly affected.When the fraction of AB* is neglected(f2≈0), the PRE can be predicted from themodel of the final complex. By using model 1 from PDB ID: 1TU2, thePREAB values were predicted for each amide in Pc (Figure 4, blue symbols). Clearly, themodel alone cannot account for the observed PREs. Also, docking calculationswere performed with distances derived from the PREs as restraints. Apart from avan der Waals repulsion function (to avoid steric collisions) no otherinteractions were included. The ensemble of the ten best structures is shown inFigure 5 and compared with the modelbased on PCS. In both cases, Pc is bound in the region close to the haem, butthe orientation differs. However, also the PRE-based model alone cannot accountfor the observed PREs and the back calculated distances (Figure 4, red symbols in the left panel, red line in theright panel).

Bottom Line: The complex from Nostoc sp.Chemical-shift-perturbation analysis showed that the presence of spin labels on the surface of Cyt f does not significantly affect the binding of Pc.The paramagnetic relaxation enhancement results are not consistent with a single orientation of Pc, thus indicating that multiple orientations must occur and suggesting that an encounter state represents a large fraction of the complex.

View Article: PubMed Central - PubMed

Affiliation: Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.

Show MeSH
Related in: MedlinePlus