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Oct-1 POU domain-DNA interactions: cooperative binding of isolated subdomains and effects of covalent linkage.
Open accessAbstract
Structural and biochemical studies of Oct-1 POU domain-DNA interactions have raised important questions about cooperativity and the role of the linker connecting the POU-specific domain and the POU homeo domain. To analyze these interactions, we have studied binding of the isolated domains. Surprisingly, we find that two unlinked polypeptides corresponding to the POU-specific domain and the POU homeo domain bind cooperatively to the octamer site and have a coupling energy of 1.6 kcal/mole. We suggest that overlapping DNA contacts near the center of the octamer site may be the source of this cooperativity, as there are no protein-protein contacts between the domains in the crystal structure of the Oct-1 POU domain-DNA complex. These studies also have allowed us to describe the thermodynamic contribution of the linker (present in the intact POU domain) in terms of an effective concentration (3.6 mM). The broader implications for understanding cooperativity in protein-DNA recognition and gene regulation are discussed.
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“On lower affinity sites, however, the chelating effect provided by the linker may lower the overall entropic cost associated with binding, allowing PipPU to bind as efficiently as the wildtype proteins”
From Assembly requirements of PU.1–Pip (IRF‐4) activator complexes: inhibiting function in vivo using fused dimers (1999) · cites this paper as Klemm and Pabo, 1996
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Expanding the specificity of DNA targeting by harnessing cooperative assembly
Moretti, R., & Ansari, A. Z. (2008) · Biochimie · doi:10.1016/j.biochi.2008.02.014 · Cited by 25
Dong, B., & Zhao, F. (2006) · Biochemical Journal · doi:10.1042/bj20060570 · Cited by 25
“The central (A/T) pair (ATGCAAAT) is contacted by both POUS and POUH domains [ 29 ].”
The “Monkey‐Bar” Mechanism for Searching for the DNA Target Site: The Molecular Determinants
Vuzman, D., & Levy, Y. (2014) · Israel Journal of Chemistry · doi:10.1002/ijch.201400107 · Cited by 24
Wang, Z., Yang, X., Guo, S., Yang, Y., Su, X., Shen, Y., & Long, J. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.562314 · Cited by 24
“Such a cooperative binding mode also exists in DNA interaction of the POU domain of Oct-1 (40).”
BackgroundCooperative DNA binding by proteins through DNA shape complementarity
Hancock, S. P., Cascio, D., & Johnson, R. C. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz642 · Cited by 23
“For example, the POUspecific domain and the POU homeodomain bind cooperatively to the Oct-1 site even when the peptide segment that normally covalently links these DNA binding domains is removed (51).”
BackgroundShiina, M., Hamada, K., Inoue-Bungo, T., Shimamura, M., Uchiyama, A., Baba, S., Sato, K., Yamamoto, M., & Ogata, K. (2014) · Journal of Molecular Biology · doi:10.1016/j.jmb.2014.07.020 · Cited by 22
“Previous structural studies for TF-DNA complexes suggest that the allosteric nature of DNA plays a key role in the process of assembling TF-DNA complexes [43, 44].”
Analysis of Protein and DNA-Mediated Contributions to Cooperative Assembly of Protein–DNA Complexes
Senear, D. F., Ross, J. B. A., & Laue, T. M. (1998) · Methods · doi:10.1006/meth.1998.0641 · Cited by 22
Sequence and Positional Requirements for DNA Sites in a Mu Transpososome
Goldhaber-Gordon, I., Early, M. H., Gray, M. K., & Baker, T. A. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m110342200 · Cited by 21
Role of sequence encoded κB DNA geometry in gene regulation by Dorsal
Mrinal, N., Tomar, A., & Nagaraju, J. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr672 · Cited by 19
Modulation of DNA Binding by Gene-Specific Transcription Factors
Schleif, R. F. (2013) · Biochemistry · doi:10.1021/bi400968e · Cited by 19
Poon, G. M. K. (2007) · Biochemical Society Transactions · doi:10.1042/bst0351574 · Cited by 18
Functional interplay between the RK motif and linker segment dictates Oct4–DNA recognition
Kong, X., Liu, J., Li, L., Yue, L., Zhang, L., Jiang, H., Xie, X., & Luo, C. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv323 · Cited by 18
“The length of the linker may also regulate the configurational freedom of the two structured subdomains relative to the DNA sites, thereby influencing DNA site selection via a tethering mechanism (19).”
BackgroundResultStructure of human Brn-5 transcription factor in complex with CRH gene promoter
Pereira, J. H., & Kim, S. (2009) · Journal of Structural Biology · doi:10.1016/j.jsb.2009.05.003 · Cited by 15
Structural Aspects of Interaction of Homeodomains with DNA
Ledneva, R. K., Алексеевский, А. В., Васильев, С. А., Spirin, S., & Karyagina, A. S. (2001) · Molecular Biology · doi:10.1023/a:1012309917322 · Cited by 15
Contributions of distinct quaternary contacts to cooperative operator binding by Mnt repressor
Berggrun, A., & Sauer, R. T. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.041612198 · Cited by 15
Regulation of immune and tissue homeostasis by Drosophila POU factors
Tang, X., & Engström, Y. (2019) · Insect Biochemistry and Molecular Biology · doi:10.1016/j.ibmb.2019.04.003 · Cited by 13
Carlin, K. B., Cruz-Teran, C. A., Kumar, J. P., Gomes, C., & Rao, B. M. (2016) · ACS Synthetic Biology · doi:10.1021/acssynbio.6b00034 · Cited by 12
Thermodynamic model of gene regulation for the Or59b olfactory receptor in Drosophila
González, A., Jafari, S., Zenere, A., Alenius, M., & Altafini, C. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006709 · Cited by 12
Park, Y., Shin, J., Yang, J., Kim, H., Jung, Y., Oh, H., Kim, Y., Hwang, J., Park, M., Ban, C., et al. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2019.00444 · Cited by 12
“Although each domain does not have high binding affinity of each domain to target DNA binding sequences (BS, 5-ATGCAAAT-3) is not high enough, Oct-1 DBD can bind to BS with high affinity (KD = 9 × 10 −11 M) via cooperative binding of both domains (Klemm and Pabo, 1996).”
BackgroundFinger, L. D., Johansson, C. A., Rinaldi, B., Bouvet, P., & Feigon, J. F. (2004) · Biochemistry · doi:10.1021/bi049904d · Cited by 12
An engineered amino‐terminal domain of yeast phosphoglycerate kinase with native‐like structure
Sherman, M. A., Chen, Y., & Mas, M. T. (1997) · Protein Science · doi:10.1002/pro.5560060415 · Cited by 12
Metadata
- Authors
- Klemm, J. D., & Pabo, C. O.
- Affiliations
- Massachusetts Institute of Technology (US)
- ORCID
- Klemm, J D
- Venue
- Genes & Development
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 1996-01-01
- Volume
- 10
- Issue
- 1
- Pages
- 27-36
- ISSN
- 0890-9369 (ISSN-L)
- 1549-5477
- OpenAlex
- W2160488560
- Cited by
- 134
- References
- 20
- Citations by year
- 2024: 2 · 2022: 1 · 2021: 3 · 2020: 5 · 2019: 3 · 2018: 1 · 2017: 4 · 2016: 4 · 2015: 8 · 2014: 5 · 2013: 5 · 2012: 1
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genes & Development (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health (5r01gm031471-16, GM31471)
- National Institute of General Medical Sciences (GM-31471)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- Oct-1, POU domain, protein-DNA interactions, cooperative binding, binding thermodynamics, protein-DNA recognition, gene expression regulation
- MeSH terms
- Base Sequence, Binding Sites, Deoxyribonuclease I, DNA-Binding Proteins, Genes, Homeobox, Models, Molecular, Molecular Sequence Data, Mutation, Peptide Fragments, Thermodynamics, Transcription Factors, Homeodomain Proteins, DNA Footprinting, Octamer Transcription Factor-1, Host Cell Factor C1
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