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Target-binding behavior of IDPs via pre-structured motifs. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:187-247. [PMID: 34656329 DOI: 10.1016/bs.pmbts.2021.07.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Pre-Structured Motifs (PreSMos) are transient secondary structures observed in many intrinsically disordered proteins (IDPs) and serve as protein target-binding hot spots. The prefix "pre" highlights that PreSMos exist a priori in the target-unbound state of IDPs as the active pockets of globular proteins pre-exist before target binding. Therefore, a PreSMo is an "active site" of an IDP; it is not a spatial pocket, but rather a secondary structural motif. The classical and perhaps the most effective approach to understand the function of a protein has been to determine and investigate its structure. Ironically or by definition IDPs do not possess structure (here structure refers to tertiary structure only). Are IDPs then entirely structureless? The PreSMos provide us with an atomic-resolution answer to this question. For target binding, IDPs do not rely on the spatial pockets afforded by tertiary or higher structures. Instead, they utilize the PreSMos possessing particular conformations that highly presage the target-bound conformations. PreSMos are recognized or captured by targets via conformational selection (CS) before their conformations eventually become stabilized via structural induction into more ordered bound structures. Using PreSMos, a number of, if not all, IDPs can bind targets following a sequential pathway of CS followed by an induced fit (IF). This chapter presents several important PreSMos implicated in cancers, neurodegenerative diseases, and other diseases along with discussions on their conformational details that mediate target binding, a structural rationale for unstructured proteins.
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Salient Features of Monomeric Alpha-Synuclein Revealed by NMR Spectroscopy. Biomolecules 2020; 10:biom10030428. [PMID: 32164323 PMCID: PMC7175124 DOI: 10.3390/biom10030428] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/09/2020] [Accepted: 03/04/2020] [Indexed: 12/17/2022] Open
Abstract
Elucidating the structural details of proteins is highly valuable and important for the proper understanding of protein function. In the case of intrinsically disordered proteins (IDPs), however, obtaining the structural details is quite challenging, as the traditional structural biology tools have only limited use. Nuclear magnetic resonance (NMR) is a unique experimental tool that provides ensemble conformations of IDPs at atomic resolution, and when studying IDPs, a slightly different experimental strategy needs to be employed than the one used for globular proteins. We address this point by reviewing many NMR investigations carried out on the α-synuclein protein, the aggregation of which is strongly correlated with Parkinson’s disease.
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Transient Secondary Structures as General Target-Binding Motifs in Intrinsically Disordered Proteins. Int J Mol Sci 2018; 19:ijms19113614. [PMID: 30445805 PMCID: PMC6275026 DOI: 10.3390/ijms19113614] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 12/21/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are unorthodox proteins that do not form three-dimensional structures under non-denaturing conditions, but perform important biological functions. In addition, IDPs are associated with many critical diseases including cancers, neurodegenerative diseases, and viral diseases. Due to the generic name of “unstructured” proteins used for IDPs in the early days, the notion that IDPs would be completely unstructured down to the level of secondary structures has prevailed for a long time. During the last two decades, ample evidence has been accumulated showing that IDPs in their target-free state are pre-populated with transient secondary structures critical for target binding. Nevertheless, such a message did not seem to have reached with sufficient clarity to the IDP or protein science community largely because similar but different expressions were used to denote the fundamentally same phenomenon of presence of such transient secondary structures, which is not surprising for a quickly evolving field. Here, we summarize the critical roles that these transient secondary structures play for diverse functions of IDPs by describing how various expressions referring to transient secondary structures have been used in different contexts.
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Kim DH, Han KH. PreSMo Target-Binding Signatures in Intrinsically Disordered Proteins. Mol Cells 2018; 41:889-899. [PMID: 30352491 PMCID: PMC6199570 DOI: 10.14348/molcells.2018.0192] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 08/07/2018] [Accepted: 08/22/2018] [Indexed: 12/26/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are highly unorthodox proteins that do not form three-dimensional structures under physiological conditions. The discovery of IDPs has destroyed the classical structure-function paradigm in protein science, 3-D structure = function, because IDPs even without well-folded 3-D structures are still capable of performing important biological functions and furthermore are associated with fatal diseases such as cancers, neurodegenerative diseases and viral pandemics. Pre-structured motifs (PreSMos) refer to transient local secondary structural elements present in the target-unbound state of IDPs. During the last two decades PreSMos have been steadily acknowledged as the critical determinants for target binding in dozens of IDPs. To date, the PreSMo concept provides the most convincing structural rationale explaining the IDP-target binding behavior at an atomic resolution. Here we present a brief developmental history of PreSMos and describe their common characteristics. We also provide a list of newly discovered PreSMos along with their functional relevance.
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Affiliation(s)
- Do-Hyoung Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141,
Korea
| | - Kyou-Hoon Han
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141,
Korea
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5
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Kim DH, Wright A, Han KH. An NMR study on the intrinsically disordered core transactivation domain of human glucocorticoid receptor. BMB Rep 2018; 50:522-527. [PMID: 28946939 PMCID: PMC5683822 DOI: 10.5483/bmbrep.2017.50.10.152] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Indexed: 01/30/2023] Open
Abstract
A large number of transcriptional activation domains (TADs) are intrinsically unstructured, meaning they are devoid of a three-dimensional structure. The fact that these TADs are transcriptionally active without forming a 3-D structure raises the question of what features in these domains enable them to function. One of two TADs in human glucocorticoid receptor (hGR) is located at its N-terminus and is responsible for ~70% of the transcriptional activity of hGR. This 58-residue intrinsically-disordered TAD, named tau1c in an earlier study, was shown to form three helices under trifluoroethanol, which might be important for its activity. We carried out heteronuclear multi-dimensional NMR experiments on hGR tau1c in a more physiological aqueous buffer solution and found that it forms three helices that are ~30% pre-populated. Since pre-populated helices in several TADs were shown to be key elements for transcriptional activity, the three pre-formed helices in hGR tau1c delineated in this study should be critical determinants of the transcriptional activity of hGR. The presence of pre-structured helices in hGR tau1c strongly suggests that the existence of pre-structured motifs in target-unbound TADs is a very broad phenomenon.
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Affiliation(s)
- Do-Hyoung Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Anthony Wright
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kyou-Hoon Han
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; Department of Nano and Bioinformatics, University of Science and Technology, Daejeon 34113, Korea
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6
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Kim D, Lee C, Lee S, Kim K, Han JJ, Cha E, Lim J, Cho Y, Hong S, Han K. The Mechanism of p53 Rescue by SUSP4. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201607819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Do‐Hyoung Kim
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Chewook Lee
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Si‐Hyung Lee
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Kyung‐Tae Kim
- Molecular Epidemology Branch Research Institute National Cancer Center 323 Ilsandong-gu, Goyang-si Gyeonggi-do 10408 Korea
| | - Joan J. Han
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- College of Human Medicine Michigan State University East Lansing MI 48824 USA
| | - Eun‐Ji Cha
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Ji‐Eun Lim
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Ye‐Jin Cho
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- Department of Bioinformatics University of Science and Technology 217, Gajeong-ro, Yuseong-gu Daejoen 34113 Korea
| | - Seung‐Hee Hong
- Division of Food Science and Culinary Art, Food and Nutrition Major Shinhan University 95 Hoam-ro, Uijeongbu-si Gyeonggi-do 11644 Korea
| | - Kyou‐Hoon Han
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- Department of Bioinformatics University of Science and Technology 217, Gajeong-ro, Yuseong-gu Daejoen 34113 Korea
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7
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Kim D, Lee C, Lee S, Kim K, Han JJ, Cha E, Lim J, Cho Y, Hong S, Han K. The Mechanism of p53 Rescue by SUSP4. Angew Chem Int Ed Engl 2016; 56:1278-1282. [DOI: 10.1002/anie.201607819] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/25/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Do‐Hyoung Kim
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Chewook Lee
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Si‐Hyung Lee
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Kyung‐Tae Kim
- Molecular Epidemology Branch Research Institute National Cancer Center 323 Ilsandong-gu, Goyang-si Gyeonggi-do 10408 Korea
| | - Joan J. Han
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- College of Human Medicine Michigan State University East Lansing MI 48824 USA
| | - Eun‐Ji Cha
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Ji‐Eun Lim
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Ye‐Jin Cho
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- Department of Bioinformatics University of Science and Technology 217, Gajeong-ro, Yuseong-gu Daejoen 34113 Korea
| | - Seung‐Hee Hong
- Division of Food Science and Culinary Art, Food and Nutrition Major Shinhan University 95 Hoam-ro, Uijeongbu-si Gyeonggi-do 11644 Korea
| | - Kyou‐Hoon Han
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- Department of Bioinformatics University of Science and Technology 217, Gajeong-ro, Yuseong-gu Daejoen 34113 Korea
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8
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Jo KS, Jo HR, Kim CG, Kim CG, Won HS. Intrinsically disordered fold of a PIAS1-binding domain of CP2b. JOURNAL OF THE KOREAN MAGNETIC RESONANCE SOCIETY 2014. [DOI: 10.6564/jkmrs.2014.18.1.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Contribution of proline to the pre-structuring tendency of transient helical secondary structure elements in intrinsically disordered proteins. Biochim Biophys Acta Gen Subj 2014; 1840:993-1003. [DOI: 10.1016/j.bbagen.2013.10.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 10/25/2013] [Accepted: 10/28/2013] [Indexed: 01/23/2023]
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10
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Theillet FX, Kalmar L, Tompa P, Han KH, Selenko P, Dunker AK, Daughdrill GW, Uversky VN. The alphabet of intrinsic disorder: I. Act like a Pro: On the abundance and roles of proline residues in intrinsically disordered proteins. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e24360. [PMID: 28516008 PMCID: PMC5424786 DOI: 10.4161/idp.24360] [Citation(s) in RCA: 184] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 03/17/2013] [Indexed: 11/19/2022]
Abstract
A significant fraction of every proteome is occupied by biologically active proteins that do not form unique three-dimensional structures. These intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) have essential biological functions and are characterized by extensive structural plasticity. Such structural and functional behavior is encoded in the amino acid sequences of IDPs/IDPRs, which are enriched in disorder-promoting residues and depleted in order-promoting residues. In fact, amino acid residues can be arranged according to their disorder-promoting tendency to form an alphabet of intrinsic disorder that defines the structural complexity and diversity of IDPs/IDPRs. This review is the first in a series of publications dedicated to the roles that different amino acid residues play in defining the phenomenon of protein intrinsic disorder. We start with proline because data suggests that of the 20 common amino acid residues, this one is the most disorder-promoting.
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Affiliation(s)
- Francois-Xavier Theillet
- In-cell NMR Spectroscopy; Leibniz Institute of Molecular Pharmacology (FMP Berlin); Berlin, Germany
| | - Lajos Kalmar
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels, Belgium
| | - Peter Tompa
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels, Belgium.,Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest, Hungary
| | - Kyou-Hoon Han
- Department of Bioinformatics; University of Science and Technology; Daejeon, Yuseong-gu, Korea.,Biomedical Translational Research Center; Division of Convergent Biomedical Research; Korea Research Institute of Bioscience and Biotechnology; Daejeon, Yuseong-gu, Korea
| | - Philipp Selenko
- In-cell NMR Spectroscopy; Leibniz Institute of Molecular Pharmacology (FMP Berlin); Berlin, Germany
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics; Department of Biochemistry and Molecular Biology; Indiana University School of Medicine; Indianapolis, IN USA
| | - Gary W Daughdrill
- Center for Drug Discovery and Innovation; Department of Cell Biology, Microbiology and Molecular Biology; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow Region, Russia
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11
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Lee WK, Lee SY, Na JH, Jang SW, Park CR, Kim SY, Lee SH, Han KH, Yu YG. Mitoxantrone Binds to Nopp140, an Intrinsically Unstructured Protein, and Modulate its Interaction with Protein Kinase CK2. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.6.2005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Zaborowska J, Taylor A, Roeder RG, Murphy S. A novel TBP-TAF complex on RNA polymerase II-transcribed snRNA genes. Transcription 2012; 3:92-104. [PMID: 22441827 PMCID: PMC3337830 DOI: 10.4161/trns.19783] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Initiation of transcription of most human genes transcribed by RNA polymerase II (RNAP II) requires the formation of a preinitiation complex comprising TFIIA, B, D, E, F, H and RNAP II. The general transcription factor TFIID is composed of the TATA-binding protein and up to 13 TBP-associated factors. During transcription of snRNA genes, RNAP II does not appear to make the transition to long-range productive elongation, as happens during transcription of protein-coding genes. In addition, recognition of the snRNA gene-type specific 3' box RNA processing element requires initiation from an snRNA gene promoter. These characteristics may, at least in part, be driven by factors recruited to the promoter. For example, differences in the complement of TAFs might result in differential recruitment of elongation and RNA processing factors. As precedent, it already has been shown that the promoters of some protein-coding genes do not recruit all the TAFs found in TFIID. Although TAF5 has been shown to be associated with RNAP II-transcribed snRNA genes, the full complement of TAFs associated with these genes has remained unclear. Here we show, using a ChIP and siRNA-mediated approach, that the TBP/TAF complex on snRNA genes differs from that found on protein-coding genes. Interestingly, the largest TAF, TAF1, and the core TAFs, TAF10 and TAF4, are not detected on snRNA genes. We propose that this snRNA gene-specific TAF subset plays a key role in gene type-specific control of expression.
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Affiliation(s)
| | - Alice Taylor
- Sir William Dunn School of Pathology; University of Oxford; Oxford, UK
| | - Robert G. Roeder
- Laboratory of Biochemistry and Molecular Biology; The Rockefeller University; New York, NY USA
| | - Shona Murphy
- Sir William Dunn School of Pathology; University of Oxford; Oxford, UK
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13
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Abstract
Proteins provide much of the scaffolding for life, as well as undertaking a variety of essential catalytic reactions. These characteristic functions have led us to presuppose that proteins are in general functional only when well structured and correctly folded. As we begin to explore the repertoire of possible protein sequences inherent in the human and other genomes, two stark facts that belie this supposition become clear: firstly, the number of apparent open reading frames in the human genome is significantly smaller than appears to be necessary to code for all of the diverse proteins in higher organisms, and secondly that a significant proportion of the protein sequences that would be coded by the genome would not be expected to form stable three-dimensional (3D) structures. Clearly the genome must include coding for a multitude of alternative forms of proteins, some of which may be partly or fully disordered or incompletely structured in their functional states. At the same time as this likelihood was recognized, experimental studies also began to uncover examples of important protein molecules and domains that were incompletely structured or completely disordered in solution, yet remained perfectly functional. In the ensuing years, we have seen an explosion of experimental and genome-annotation studies that have mapped the extent of the intrinsic disorder phenomenon and explored the possible biological rationales for its widespread occurrence. Answers to the question 'why would a particular domain need to be unstructured?' are as varied as the systems where such domains are found. This review provides a survey of recent new directions in this field, and includes an evaluation of the role not only of intrinsically disordered proteins but also of partially structured and highly dynamic members of the disorder-order continuum.
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Vojnic E, Mourão A, Seizl M, Simon B, Wenzeck L, Larivière L, Baumli S, Baumgart K, Meisterernst M, Sattler M, Cramer P. Structure and VP16 binding of the Mediator Med25 activator interaction domain. Nat Struct Mol Biol 2011; 18:404-9. [PMID: 21378965 DOI: 10.1038/nsmb.1997] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 12/03/2010] [Indexed: 12/22/2022]
Abstract
Eukaryotic transcription is regulated by interactions between gene-specific activators and the coactivator complex Mediator. Here we report the NMR structure of the Mediator subunit Med25 (also called Arc92) activator interaction domain (ACID) and analyze the structural and functional interaction of ACID with the archetypical acidic transcription activator VP16. Unlike other known activator targets, ACID forms a seven-stranded β-barrel framed by three helices. The VP16 subdomains H1 and H2 bind to opposite faces of ACID and cooperate during promoter-dependent activated transcription in a in vitro system. The activator-binding ACID faces are functionally required and conserved among higher eukaryotes. Comparison with published activator structures reveals that the VP16 activation domain uses distinct interaction modes to adapt to unrelated target surfaces and folds that evolved for activator binding.
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Affiliation(s)
- Erika Vojnic
- Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany
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15
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Wands AM, Wang N, Lum JK, Hsieh J, Fierke CA, Mapp AK. Transient-state kinetic analysis of transcriptional activator·DNA complexes interacting with a key coactivator. J Biol Chem 2011; 286:16238-45. [PMID: 21317429 DOI: 10.1074/jbc.m110.207589] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Several lines of evidence suggest that the prototypical amphipathic transcriptional activators Gal4, Gcn4, and VP16 interact with the key coactivator Med15 (Gal11) during transcription initiation despite little sequence homology. Recent cross-linking data further reveal that at least two of the activators utilize the same binding surface within Med15 for transcriptional activation. To determine whether these three activators use a shared binding mechanism for Med15 recruitment, we characterized the thermodynamics and kinetics of Med15·activator·DNA complex formation by fluorescence titration and stopped-flow techniques. Combination of each activator·DNA complex with Med15 produced biphasic time courses. This is consistent with a minimum two-step binding mechanism composed of a bimolecular association step limited by diffusion, followed by a conformational change in the Med15·activator·DNA complex. Furthermore, the equilibrium constant for the conformational change (K(2)) correlates with the ability of an activator to stimulate transcription. VP16, the most potent of the activators, has the largest K(2) value, whereas Gcn4, the least potent, has the smallest value. This correlation is consistent with a model in which transcriptional activation is regulated at least in part by the rearrangement of the Med15·activator·DNA ternary complex. These results are the first detailed kinetic characterization of the transcriptional activation machinery and provide a framework for the future design of potent transcriptional activators.
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Affiliation(s)
- Amberlyn M Wands
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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16
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Du JX, McConnell BB, Yang VW. A small ubiquitin-related modifier-interacting motif functions as the transcriptional activation domain of Krüppel-like factor 4. J Biol Chem 2010; 285:28298-308. [PMID: 20584900 DOI: 10.1074/jbc.m110.101717] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The zinc finger transcription factor, Krüppel-like factor 4 (KLF4), regulates numerous biological processes, including proliferation, differentiation, and embryonic stem cell self-renewal. Although the DNA sequence to which KLF4 binds is established, the mechanism by which KLF4 controls transcription is not well defined. Small ubiquitin-related modifier (SUMO) is an important regulator of transcription. Here we show that KLF4 is both SUMOylated at a single lysine residue and physically interacts with SUMO-1 in a region that matches an acidic and hydrophobic residue-rich SUMO-interacting motif (SIM) consensus. The SIM in KLF4 is required for transactivation of target promoters in a SUMO-1-dependent manner. Mutation of either the acidic or hydrophobic residues in the SIM significantly impairs the ability of KLF4 to interact with SUMO-1, activate transcription, and inhibit cell proliferation. Our study provides direct evidence that SIM in KLF4 functions as a transcriptional activation domain. A survey of transcription factor sequences reveals that established transactivation domains of many transcription factors contain sequences highly related to SIM. These results, therefore, illustrate a novel mechanism by which SUMO interaction modulates the activity of transcription factors.
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Affiliation(s)
- James X Du
- Division of Digestive Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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