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.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
On lower-affinity sites, the linker's chelating effect may lower entropic cost, allowing PipPU to bind as efficiently as wild-type proteins.
“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
The “Contribution of the linker to cooperative binding” section (page unavailable) says the linker produces a chelate effect and reduces the entropic cost of complex formation. The paper studies Oct-1 POU-domain binding; it does not establish that PipPU binds lower-affinity sites as efficiently as wild-type proteins. (LLM, conf=0.87)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
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 · see citing works
Self-citationGuan, K., & Dixon, J. (1991) · Analytical Biochemistry · doi:10.1016/0003-2697(91)90534-z · Cited by 1,735 · see citing works
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 · see citing works
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 · see citing works
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 1,047 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
Self-citationHerr, W., & Cleary, M. A. (1995) · Genes & Development · doi:10.1101/gad.9.14.1679 · Cited by 388 · see citing works
Proteins : structures and molecular principles
Creighton, T. E. (1983) · W.H. Freeman eBooks · Cited by 358 · see citing works
Fairall, L., Schwabe, J. W. R., Chapman, L., Finch, J. T., & Rhodes, D. (1993) · Nature · doi:10.1038/366483a0 · Cited by 355 · see citing works
Refined 1.8 Å crystal structure of the λ repressor-operator complex
Beamer, L. J., & Pabo, C. O. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90690-l · Cited by 301 · see citing works
Self-citationMetal-dependent folding of a single zinc finger from transcription factor IIIA.
Frankel, A. D., Berg, J. M., & Pabo, C. O. (1987) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.84.14.4841 · Cited by 298 · see citing works
Self-citationThe DNA binding specificity of the bipartite POU domain and its subdomains.
Verrijzer, C. P., Alkema, M. J., van Weperen, W. W., van Leeuwen, H. C., Strating, M., & van der Vliet, P. C. (1992) · The EMBO Journal · doi:10.1002/j.1460-2075.1992.tb05606.x · Cited by 266 · see citing works
Li, P., He, X., Gerrero, M. R., Mok, M., Aggarwal, A. K., & Rosenfeld, M. G. (1993) · Genes & Development · doi:10.1101/gad.7.12b.2483 · Cited by 161 · see citing works
Regulation of the mec‐3 gene by the C.elegans homeoproteins UNC‐86 and MEC‐3.
Xue, D., Finney, M., Ruvkun, G., & Chalfie, M. (1992) · The EMBO Journal · doi:10.1002/j.1460-2075.1992.tb05604.x · Cited by 124 · see citing works
Nekludova, L., & Pabo, C. O. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.15.6948 · Cited by 103 · see citing works
Self-citationSegments of the POU domain influence one another's DNA-binding specificity.
Aurora, R., & Herr, W. (1992) · Molecular and Cellular Biology · doi:10.1128/mcb.12.2.455 · Cited by 97 · see citing works
DNA conformation and configuration in protein-DNA complexes
TRAVERS, A. A. (1992) · Current Opinion in Structural Biology · doi:10.1016/0959-440x(92)90180-f · Cited by 39 · see citing works
Quantitative DNase I Footprinting
Brenowitz, M. D., Senear, D. F., Jamison, E., & Dalma‐Weiszhausz, D. D. (1993) · Elsevier eBooks · doi:10.1016/b978-0-12-586500-5.50008-4 · Cited by 15 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
DNA Recognition by Cys<sub>2</sub>His<sub>2</sub> 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 · see citing works
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 · see citing works
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 555 · see citing works
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 482 · see citing works
The transcriptional foundation of pluripotency
Chambers, I., & Tomlinson, S. R. (2009) · Development · doi:10.1242/dev.024398 · Cited by 454 · see citing works
The origin of protein interactions and allostery in colocalization
Kuriyan, J., & Eisenberg, D. S. (2007) · Nature · doi:10.1038/nature06524 · Cited by 380 · see citing works
Structure of a HoxB1–Pbx1 Heterodimer Bound to DNA
Piper, D. E., Batchelor, A. H., Chang, C., Cleary, M. L., & Wolberger, C. (1999) · Cell · doi:10.1016/s0092-8674(00)80662-5 · Cited by 328 · see citing works
Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding
Gajiwala, K. S., Chen, H., Cornille, F., Roques, B. P., Reith, W., Mach, B., & Burley, S. K. (2000) · Nature · doi:10.1038/35002634 · Cited by 317 · see citing works
Botquin, V., Hess, H., Fuhrmann, G., Anastassiadis, K., Gross, M. K., Vriend, G., & Schöler, H. R. (1998) · Genes & Development · doi:10.1101/gad.12.13.2073 · Cited by 314 · see citing works
Structure of a DNA-bound Ultrabithorax–Extradenticle homeodomain complex
Passner, J. M., Ryoo, H. D., Shen, L., Mann, R. S., & Aggarwal, A. K. (1999) · Nature · doi:10.1038/17833 · Cited by 312 · see citing works
Structural perspective of cooperative transcription factor binding
Morgunova, E. Y., & Taipale, J. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.03.006 · Cited by 242 · see citing works
D, B. A. M., & Rosenfeld, M. G. (2001) · Endocrine Reviews · doi:10.1210/edrv.22.1.0421 · Cited by 240 · see citing works
The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation
Bottomley (2001) · Nature Structural Biology · doi:10.1038/89675 · Cited by 224 · see citing works
The virtuoso of versatility: POU proteins that flex to fit 1 1Edited by P. Wright
Phillips, K. L., & Luisi, B. F. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4107 · Cited by 229 · see citing works
Kim, J., & Pabo, C. O. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.6.2812 · Cited by 221 · see citing works
Self-citationStructure of the RXR–RAR DNA‐binding complex on the retinoic acid response element DR1
Rastinejad, F., Wagner, T., Zhao, Q., & Khorasanizadeh, S. (2000) · The EMBO Journal · doi:10.1093/emboj/19.5.1045 · Cited by 217 · see citing works
Brass, A. L., Zhu, A. Q., & Singh, H. (1999) · The EMBO Journal · doi:10.1093/emboj/18.4.977 · Cited by 207 · see citing works
Intrinsically disordered regions as affinity tuners in protein–DNA interactions
Vuzman, D., & Levy, Y. (2011) · Molecular BioSystems · doi:10.1039/c1mb05273j · Cited by 199 · see citing works
Retinoid X receptor and its partners in the nuclear receptor family
Rastinejad, F. (2001) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(00)00165-2 · Cited by 175 · see citing works
The role of HMG I(Y) in the assembly and function of the IFN‐β enhanceosome
Yie, J., Merika, M., Munshi, N., Chen, G., & Thanos, D. (1999) · The EMBO Journal · doi:10.1093/emboj/18.11.3074 · Cited by 175 · see citing works
Crystal structure of ATF‐2/c‐Jun and IRF‐3 bound to the interferon‐β enhancer
Panne, D., Maniatis, T., & Harrison, S. (2004) · EMBO Journal · doi:10.1038/sj.emboj.7600453 · Cited by 182 · see citing works
Williams, D. C., Cai, M., & Clore, G. M. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m309790200 · Cited by 164 · see citing works
OCT4: Dynamic DNA binding pioneers stem cell pluripotency
Jerabek, S., Merino, F., Schöler, H. R., & Cojocaru, V. (2013) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2013.10.001 · Cited by 155 · see citing works
Crystal structure of PU. 1/IRF-4/DNA ternary complex
Escalante, C. R., Brass, A. L., Pongubala, J. M. R., Shatova, E., Shen, L., Singh, H., & Aggarwal, A. K. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00703-7 · Cited by 154 · see citing works
Polymer Models of Protein Stability, Folding, and Interactions
Zhou, H. (2004) · Biochemistry · doi:10.1021/bi036269n · Cited by 156 · see citing works
A unique Oct4 interface is crucial for reprogramming to pluripotency
Esch, D., Vahokoski, J., Groves, M. R., Pogenberg, V., Cojocaru, V., Bruch, H. V., Han, D., Drexler, H. C. A., Araúzo-Bravo, M. J., Ng, C. K. L., et al. (2013) · Nature Cell Biology · doi:10.1038/ncb2680 · Cited by 156 · see citing works
DNA-binding-domain fusions enhance the targeting range and precision of Cas9
Bolukbasi, M. F., Gupta, A., Oikemus, S., Derr, A. G., Garber, M. G., Brodsky, M. H., Zhu, L. J., & Wolfe, S. A. (2015) · Nature Methods · doi:10.1038/nmeth.3624 · Cited by 114 · see citing works
E2F-7: a distinctive E2F family member with an unusual organization of DNA-binding domains
Logan, N., Delavaine, L., Graham, A., Reilly, C., Wilson, J. R., Brummelkamp, T. R., Hijmans, E. M., Bernards, R., & Thangue, N. B. L. (2004) · Oncogene · doi:10.1038/sj.onc.1207649 · Cited by 111 · see citing works
Structure of IRF-3 Bound to the PRDIII-I Regulatory Element of the Human Interferon-β Enhancer
Escalante, C. R., Nistal‐Villán, E., Shen, L., García‐Sastre, A., & Aggarwal, A. K. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.04.022 · Cited by 108 · see citing works
Lannoy, V. J., Bürglin, T. R., Rousseau, G. G., & Lemaigre, F. P. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.22.13552 · Cited by 107 · see citing works
Eukaryotic transcription factors
Tan, S., & Richmond, T. J. (1998) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(98)80008-0 · Cited by 104 · see citing works
The transcriptional code of human IFN-β gene expression
Ford, E., & Thanos, D. (2010) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2010.01.010 · Cited by 102 · see citing works
Linker length and composition influence the flexibility of Oct‐1 DNA binding
van Leeuwen, H. C., Strating, M., Rensen, M., de Laat, W. L., & van der Vliet, P. C. (1997) · The EMBO Journal · doi:10.1093/emboj/16.8.2043 · Cited by 100 · see citing works
Thermodynamics of specific and non-specific DNA binding by the c-myb DNA-binding domain
Oda, M., Furukawa, K., Ogata, K., Sarai, A., & Nakamura, H. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1564 · Cited by 100 · see citing works
Doucleff, M., & Clore, G. M. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0805050105 · Cited by 99 · see citing works
The Affinity-Enhancing Roles of Flexible Linkers in Two-Domain DNA-Binding Proteins
Zhou, H. (2001) · Biochemistry · doi:10.1021/bi015795g · Cited by 97 · see citing works
Ubiquitin-mediated proteolysis of vertebrate G1- and S-phase regulators
Yew, P. R. (2001) · Journal of Cellular Physiology · doi:10.1002/1097-4652(2001)9999:9999 · Cited by 103 · see citing works
Ackerman, M. E., Levary, D. A., Tobon, G., Hackel, B. J., Orcutt, K. D., & Wittrup, K. D. (2009) · Biotechnology Progress · doi:10.1002/btpr.174 · Cited by 93 · see citing works
Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development
Kazemian, M., Pham, H. N., Wolfe, S. A., Brodsky, M. H., & Sinha, S. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt598 · Cited by 85 · see citing works
Sequence-specific DNA binding of the B-cell-specific coactivator OCA-B.Preprint
Cepek, K. L., Chasman, D. I., & Sharp, P. A. (1996) · Genes & Development · doi:10.1101/gad.10.16.2079 · Cited by 88 · see citing works
Structure of the heterodimeric ecdysone receptor DNA‐binding complex
Devarakonda, S., Harp, J. M., Kim, Y., Ożyhar, A., & Rastinejad, F. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg569 · Cited by 87 · see citing works
Nucleosome allostery in pioneer transcription factor binding
Tan, C., & Takada, S. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2005500117 · Cited by 82 · see citing works
Zhou, H. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00372-3 · Cited by 81 · see citing works
Gruber, C. A., Rhee, J. M., Gleiberman, A. S., & Turner, E. E. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.5.2391 · Cited by 81 · see citing works
Facilitated DNA Search by Multidomain Transcription Factors: Cross Talk via a Flexible Linker
Vuzman, D., Polonsky, M., & Levy, Y. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2010.06.007 · Cited by 76 · see citing works
Phelan, M. L., & Featherstone, M. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.13.8635 · Cited by 66 · see citing works
POU Domain Factors in Neural Development
Schonemann, M. D., Ryan, A. K., Erkman, L., McEvilly, R. J., Bermingham, J. R., & Rosenfeld, M. G. (1998) · Advances in experimental medicine and biology · doi:10.1007/978-1-4615-4871-3_4 · Cited by 59 · see citing works
Kobi, D., Steunou, A., Dembélé, D., Gras, S. L., Larue, L., Nieto, L., & Davidson, I. (2010) · Pigment Cell & Melanoma Research · doi:10.1111/j.1755-148x.2010.00697.x · Cited by 58 · see citing works
Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells
Mistri, T. K., Devasia, A. G., Chu, L. T., Ng, W. P., Halbritter, F., Colby, D., Martynoga, B., Tomlinson, S. R., Chambers, I., Robson, P., et al. (2015) · EMBO Reports · doi:10.15252/embr.201540467 · Cited by 58 · see citing works
POU domain transcription factors in embryonic development
Veenstra, G. J. C., van der Vliet, P. C., & Destrée, O. (1997) · Molecular Biology Reports · doi:10.1023/a:1006855632268 · Cited by 56 · see citing works
Equilibrium Stability and Sub-Millisecond Refolding of a Designed Single-Chain Arc Repressor
Robinson, C. R., & Sauer, R. T. (1996) · Biochemistry · doi:10.1021/bi961375t · Cited by 54 · see citing works
Cao, Y., Knöchel, S., Donow, C., Miethe, J., Kaufmann, E., & Knöchel, W. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m407544200 · Cited by 52 · see citing works
Thermodynamics of a Designed Protein Catenane
Blankenship, J. W., & Dawson, P. E. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00115-3 · Cited by 52 · see citing works
Highly Cooperative Homodimerization Is a Conserved Property of Neural POU Proteins
Rhee, J. M., Gruber, C. A., Brodie, T. B., Trieu, M., & Turner, E. E. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.51.34196 · Cited by 52 · see citing works
Analysis on multi-domain cooperation for predicting protein-protein interactions
Wang, R., Wang, Y., Wu, L., Zhang, X.-S., & Chen, L. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-391 · Cited by 50 · see citing works
Targeted Chemical Wedges Reveal the Role of Allosteric DNA Modulation in Protein−DNA Assembly
Moretti, R., Donato, L. J., Brezinski, M. L., Stafford, R., Hoff, H., Thorson, J. S., Dervan, P. B., & Ansari, A. Z. (2008) · ACS Chemical Biology · doi:10.1021/cb700258r · Cited by 50 · see citing works
Christoffels, V. M., Sassi, H., Ruijter, J. M., Moorman, A. F. M., Grange, T., & Lamers, W. H. (1999) · Hepatology · doi:10.1002/hep.510290413 · Cited by 44 · see citing works
Takayama, Y., & Clore, G. M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1100050108 · Cited by 43 · see citing works
Kang, H., Gan, J., Zhao, J., Kong, W., Zhang, J., Zhu, M., Li, F., Song, Y., Qin, J., & Liang, H. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw954 · Cited by 41 · see citing works
Zhou, H. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.090258 · Cited by 40 · see citing works
Dimerization of zinc fingers mediated by peptides evolved in vitro from random sequences
Wang, B., & Pabo, C. O. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.17.9568 · Cited by 38 · see citing works
Self-citationOct‐4: more than just a POUerful marker of the mammalian germline?
Brehm, A., Ovitt, C. E., & Schöler, H. R. (1998) · Apmis · doi:10.1111/j.1699-0463.1998.tb01326.x · Cited by 36 · see citing works
Piece by piece: Building a ribozyme
Gray, M. W., & Gopalan, V. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.rev119.009929 · Cited by 33 · see citing works
Li, M., Cao, H., Lai, L., & Liu, Z. (2018) · Protein Science · doi:10.1002/pro.3475 · Cited by 34 · see citing works
Structural Basis for Induced Fit Mechanisms in DNA Recognition by the Pdx1 Homeodomain,
Longo, A., Guanga, G. P., & Rose, R. B. (2007) · Biochemistry · doi:10.1021/bi060969l · Cited by 34 · see citing works
Characterization of Sequence-Specific DNA Binding by the Transcription Factor Oct-1
Lundbäck, T., Chang, J.-F., Phillips, K. L., Luisi, B. F., & Ladbury, J. E. (2000) · Biochemistry · doi:10.1021/bi000377h · Cited by 32 · see citing works
Structural determinants of the IRF4/DNA homodimeric complex
Sundararaj, S., Seneviratne, S., Williams, S. J., Enders, A., & Casarotto, M. G. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1287 · Cited by 31 · see citing works
Biochemical and Physiological Properties of the DNA Binding Domain of AraC Protein
Timmes, A. G., Rodgers, M. E., & Schleif, R. F. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.05.018 · Cited by 31 · see citing works
A Brn2–Zic1 axis specifies the neuronal fate of retinoic-acid-treated embryonic stem cells
Urban, S., Kobi, D., Ennen, M., Langer, D., Gras, S. L., Ye, T., & Davidson, I. (2015) · Journal of Cell Science · doi:10.1242/jcs.168849 · Cited by 30 · see citing works
Linkage between Operator Binding and Dimer to Octamer Self-Assembly of Bacteriophage λ cI Repressor
Rusinova, E. V., Ross, J. B. A., Laue, T. M., Sowers, L. C., & Senear, D. F. (1997) · Biochemistry · doi:10.1021/bi971368k · Cited by 30 · see citing works
Jafari, S., & Alenius, M. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005051 · Cited by 28 · see citing works
Transcription Factor Oct-1: Plasticity and Multiplicity of Functions
Sytina, E. V., & Pankratova, E. V. (2003) · Molecular Biology · doi:10.1023/a:1026068506793 · Cited by 29 · see citing works
Poon, G. M. K., Brokx, R. D., Sung, M., & Gariépy, J. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.10.051 · Cited by 28 · see citing works
Structural basis of Hox specificity.
Wilson, D. S., & Desplan, C. (1999) · Nature Structural Biology · doi:10.1038/7524 · Cited by 28 · see citing works
Long-range electrostatic interactions influence the orientation of Fos-Jun binding at AP-1 sites.
Ramirez-Carrozzi, V. R., & Kerppola, T. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4286 · Cited by 27 · see citing works
Subekti, D. R. G., Murata, A., Itoh, Y., Fukuchi, S., Takahashi, H., Kanbayashi, S., Takahashi, S., & Kamagata, K. (2017) · Biochemistry · doi:10.1021/acs.biochem.7b00292 · Cited by 27 · see citing works
Kjærgaard, M., Glavina, J., & Chemes, L. B. (2020) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2020.09.012 · Cited by 27 · see citing works
Merino, F., Bouvier, B., & Cojocaru, V. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004287 · Cited by 27 · see citing works
Murphy, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.11.2068 · Cited by 27 · see citing works
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 · see citing works
Dong, B., & Zhao, F. (2006) · Biochemical Journal · doi:10.1042/bj20060570 · Cited by 25 · see citing works
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 · see citing works
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 · see citing works
Cooperative 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 · see citing works
Shiina, 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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
Modulation of DNA Binding by Gene-Specific Transcription Factors
Schleif, R. F. (2013) · Biochemistry · doi:10.1021/bi400968e · Cited by 19 · see citing works
Poon, G. M. K. (2007) · Biochemical Society Transactions · doi:10.1042/bst0351574 · Cited by 18 · see citing works
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 · see citing works
Structure 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 16 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
Finger, L. D., Johansson, C. A., Rinaldi, B., Bouvet, P., & Feigon, J. F. (2004) · Biochemistry · doi:10.1021/bi049904d · Cited by 12 · see citing works
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 · see citing works
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
