The DOI matches its Crossref record; 20 of the 20 references it cites were found in a registry or an index.
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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Citations
Cites
Zinc Finger-DNA Recognition: Crystal Structure of a Zif268-DNA Complex at 2.1 Å
Pavletich, N. P., & Pabo, C. O. (1991) · Science · doi:10.1126/science.2028256 · Cited by 2,081
Self-citationGuan, K., & Dixon, J. (1991) · Analytical Biochemistry · doi:10.1016/0003-2697(91)90534-z · Cited by 1,735
Crystal Structure of a CAP-DNA Complex: the DNA Is Bent by 90°
Schultz, S. C., Shields, G. C., & Steitz, T. A. (1991) · Science · doi:10.1126/science.1653449 · Cited by 1,116
Crystal structure of a yeast TBP/TATA-box complex
Kim, Y., Geiger, J. H., Hahn, S., & Sigler, P. B. (1993) · Nature · doi:10.1038/365512a0 · Cited by 1,085
Co-crystal structure of TBP recognizing the minor groove of a TATA element
Kim, J. L., Nikolov, D. B., & Burley, S. K. (1993) · Nature · doi:10.1038/365520a0 · Cited by 1,065
Crystal Structure of a Five-Finger GLI-DNA Complex: New Perspectives on Zinc Fingers
Pavletich, N. P., & Pabo, C. O. (1993) · Science · doi:10.1126/science.8378770 · Cited by 669
Self-citationKlemm, J. D., Rould, M. A., Aurora, R., Herr, W., & Pabo, C. O. (1994) · Cell · doi:10.1016/0092-8674(94)90231-3 · Cited by 506
Self-citationStructure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions
Jordan, & Pabo, C. (1988) · Science · doi:10.1126/science.3187530 · Cited by 407
Self-citationHerr, W., & Cleary, M. A. (1995) · Genes & Development · doi:10.1101/gad.9.14.1679 · Cited by 388
Proteins : structures and molecular principles
Creighton, T. E. (1983) · W.H. Freeman eBooks · Cited by 358
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DNA Recognition by Cys2His2 Zinc Finger Proteins
Wolfe, S. A., Nekludova, L., & Pabo, C. O. (2000) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.29.1.183 · Cited by 1,053
Self-citationAn Atomic Model of the Interferon-β Enhanceosome
Panne, D., Maniatis, T., & Harrison, S. C. (2007) · Cell · doi:10.1016/j.cell.2007.05.019 · Cited by 625
“What interactions can give rise to cooperativity of transcription-factor association with the IFN-b enhancer in the absence of strong contacts between adjacent proteins? In principle, cooperative binding can arise through nucleotide sequence-dependent structural changes in the DNA that allow formation of complementary…”
DNA-dependent formation of transcription factor pairs alters their binding specificity
Jolma, A., Yin, Y., Nitta, K. R., Dave, K., Popov, A. N., Taipale, M., Enge, M., Kivioja, T., Morgunova, E. Y., & Taipale, J. (2015) · Nature · doi:10.1038/nature15518 · Cited by 577
POU domain family values: flexibility, partnerships, and developmental codes.Preprint
Ryan, A. K., & Rosenfeld, M. G. (1997) · Genes & Development · doi:10.1101/gad.11.10.1207 · Cited by 483
The transcriptional foundation of pluripotency
Chambers, I., & Tomlinson, S. R. (2009) · Development · doi:10.1242/dev.024398 · Cited by 470
“Subsequent analyses have demonstrated that reduction in the level of Nanog increases the REVIEW Development 136 (14) Oct4 352 aa C-TADPOUSN-TAD POUHD Sox2 319 aa HMG TAD Nanog 305 aa WR CD2CD1HDNDA B C Fig.”
BackgroundInfluential
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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