apply in the run where you examine the interaction in order to
rule out that oligomerization of A is taking place in the concentration range used.
19. In SEDPHAT, the decadic logarithm of the association constant K A is varied. Since from Eq. 2.
K A ¼
1
K D
ð7Þ
just calculate the decadic logarithm of the inverse of your
estimated value for K D to get a starting value for the fit. A good
starting value for s AB would be a value somewhat higher than
the highest value measured for s rb .
20. In “Fitting Options” in the “Options” menu, you can choose
between the simplex, Marquardt-Levenberg, and simulatedannealing algorithms for the nonlinear least-square
fitting [29].
Acknowledgments
We gratefully thank Lidia Litz for excellent technical assistance,
Dr. Dietmar J. Manstein for scientific and financial support,
Dr. Natalie Naue for valuable discussions, and Dr. Hidde
L. Ploegh and Dr. Joachim Orth for providing the SrtA expressing
plasmid. This project was supported by a grant from the Deutsche
Forschungsgemeinschaft (CU 35/1-1 to U.C.).
References
1. Cole JL (ed) (2015) Analytical ultracentrifugation, Methods in enzymology, vol 562. Academic Press, New York
2. Uchiyama S, Arisaka F, Stafford WF, Laue TM
(eds) (2016) Analytical ultracentrifugation:
instrumentation, software, and applications.
Springer, Tokyo
3. Schuck P, Zhao H (2018) Sedimentation
velocity analytical ultracentrifugation: interacting systems. CRC Press, Boca Raton
4. Schuck P, Zhao H, Brautigam CA, Ghirlando
R (2016) Basic principles of analytical ultracentrifugation. CRC Press, Boca Raton
5. Kelman Z, Yuzhakov A, Andjelkovic J, O’Donnell M (1998) Devoted to the lagging strandthe χ subunit of DNA polymerase III holoenzyme contacts SSB to promote processive elongation and sliding clamp assembly. EMBO J
17:2436–2449
6. Naue N, Fedorov R, Pich A et al (2011) Sitedirected mutagenesis of the χ subunit of DNA
polymerase III and single-stranded DNA-binding protein of E. coli reveals key residues for
their interaction. Nucleic Acids Res
39:1398–1407
7. Witte G, Urbanke C, Curth U (2003) DNA
polymerase III chi subunit ties single-stranded
DNA binding protein to the bacterial replication
machinery.
Nucleic
Acids
Res
31:4434–4440
8. MacGregor IK, Anderson AL, Laue TM
(2004) Fluorescence detection for the XLI
analytical ultracentrifuge. Biophys Chem
108:165–185
9. Nelson TG, Ramsay GD, Laue TM (2016)
Fluorescence
detection
system.
In:
Uchiyama S, Arisaka F, Stafford WF, Lau T
(eds) Analytical ultracentrifugation: instrumentation, software, and applications, 1st
edn. Springer, Tokyo, pp 39–61
10. Gu Q, Kenny JE (2009) Improvement of inner
filter effect correction based on determination
420
Andrea Bogutzki and Ute Curth
rule out that oligomerization of A is taking place in the concentration range used.
19. In SEDPHAT, the decadic logarithm of the association constant K A is varied. Since from Eq. 2.
K A ¼
1
K D
ð7Þ
just calculate the decadic logarithm of the inverse of your
estimated value for K D to get a starting value for the fit. A good
starting value for s AB would be a value somewhat higher than
the highest value measured for s rb .
20. In “Fitting Options” in the “Options” menu, you can choose
between the simplex, Marquardt-Levenberg, and simulatedannealing algorithms for the nonlinear least-square
fitting [29].
Acknowledgments
We gratefully thank Lidia Litz for excellent technical assistance,
Dr. Dietmar J. Manstein for scientific and financial support,
Dr. Natalie Naue for valuable discussions, and Dr. Hidde
L. Ploegh and Dr. Joachim Orth for providing the SrtA expressing
plasmid. This project was supported by a grant from the Deutsche
Forschungsgemeinschaft (CU 35/1-1 to U.C.).
References
1. Cole JL (ed) (2015) Analytical ultracentrifugation, Methods in enzymology, vol 562. Academic Press, New York
2. Uchiyama S, Arisaka F, Stafford WF, Laue TM
(eds) (2016) Analytical ultracentrifugation:
instrumentation, software, and applications.
Springer, Tokyo
3. Schuck P, Zhao H (2018) Sedimentation
velocity analytical ultracentrifugation: interacting systems. CRC Press, Boca Raton
4. Schuck P, Zhao H, Brautigam CA, Ghirlando
R (2016) Basic principles of analytical ultracentrifugation. CRC Press, Boca Raton
5. Kelman Z, Yuzhakov A, Andjelkovic J, O’Donnell M (1998) Devoted to the lagging strandthe χ subunit of DNA polymerase III holoenzyme contacts SSB to promote processive elongation and sliding clamp assembly. EMBO J
17:2436–2449
6. Naue N, Fedorov R, Pich A et al (2011) Sitedirected mutagenesis of the χ subunit of DNA
polymerase III and single-stranded DNA-binding protein of E. coli reveals key residues for
their interaction. Nucleic Acids Res
39:1398–1407
7. Witte G, Urbanke C, Curth U (2003) DNA
polymerase III chi subunit ties single-stranded
DNA binding protein to the bacterial replication
machinery.
Nucleic
Acids
Res
31:4434–4440
8. MacGregor IK, Anderson AL, Laue TM
(2004) Fluorescence detection for the XLI
analytical ultracentrifuge. Biophys Chem
108:165–185
9. Nelson TG, Ramsay GD, Laue TM (2016)
Fluorescence
detection
system.
In:
Uchiyama S, Arisaka F, Stafford WF, Lau T
(eds) Analytical ultracentrifugation: instrumentation, software, and applications, 1st
edn. Springer, Tokyo, pp 39–61
10. Gu Q, Kenny JE (2009) Improvement of inner
filter effect correction based on determination
420
Andrea Bogutzki and Ute Curth