1
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Desjardins G, Okon M, Graves BJ, McIntosh LP. Conformational Dynamics and the Binding of Specific and Nonspecific DNA by the Autoinhibited Transcription Factor Ets-1. Biochemistry 2016; 55:4105-18. [PMID: 27362745 PMCID: PMC5568661 DOI: 10.1021/acs.biochem.6b00460] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The affinity of the Ets-1 transcription factor for DNA is autoinhibited by an intrinsically disordered serine-rich region (SRR) and a helical inhibitory module (IM) appended to its winged helix-turn-helix ETS domain. Using NMR spectroscopy, we investigated how Ets-1 recognizes specific versus nonspecific DNA, with a focus on the roles of protein dynamics and autoinhibition in these processes. Upon binding either DNA, the two marginally stable N-terminal helices of the IM predominantly unfold, but still sample partially ordered conformations. Also, on the basis of amide chemical shift perturbation mapping, Ets-1 associates with both specific and nonspecific DNA through the same canonical ETS domain interface. These interactions are structurally independent of the SRR, and thus autoinhibition does not impart DNA-binding specificity. However, relative to the pronounced NMR spectroscopic changes in Ets-1 resulting from specific DNA binding, the spectra of the nonspecific DNA complexes showed conformational exchange broadening and lacked several diagnostic amide and indole signals attributable to hydrogen bonding interactions seen in reported X-ray crystallographic structures of this transcription factor with its cognate DNA sequences. Such differences are highlighted by the chemical shift and relaxation properties of several interfacial lysine and arginine side chains. Collectively, these data support a general model in which Ets-1 interacts with nonspecific DNA via dynamic electrostatic interactions, whereas hydrogen bonding drives the formation of well-ordered complexes with specific DNA.
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Affiliation(s)
- Geneviève Desjardins
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Barbara J. Graves
- Department of Oncological Sciences, University of Utah School of Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112-5550, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Lawrence P. McIntosh
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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2
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Shcherbinin DS, Gnedenko OV, Khmeleva SA, Usanov SA, Gilep AA, Yantsevich AV, Shkel TV, Yushkevich IV, Radko SP, Ivanov AS, Veselovsky AV, Archakov AI. Computer-aided design of aptamers for cytochrome p450. J Struct Biol 2015; 191:112-9. [PMID: 26166326 DOI: 10.1016/j.jsb.2015.07.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 06/25/2015] [Accepted: 07/09/2015] [Indexed: 10/23/2022]
Abstract
Aptamers are short single-stranded DNA or RNA oligonucleotides that can bind to their targets with high affinity and specificity. Usually, they are experimentally selected using the SELEX method. Here, we describe an approach toward the in silico selection of aptamers for proteins. This approach involves three steps: finding a potential binding site, designing the recognition and structural parts of the aptamers and evaluating the experimental affinity. Using this approach, a set of 15-mer aptamers for cytochrome P450 51A1 was designed using docking and molecular dynamics simulation. An experimental evaluation of the synthesized aptamers using SPR biosensor showed that these aptamers interact with cytochrome P450 51A1 with Kd values in the range of 10(-6)-10(-7) M.
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Affiliation(s)
- Dmitrii S Shcherbinin
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia.
| | - Oksana V Gnedenko
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | - Svetlana A Khmeleva
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | - Sergey A Usanov
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Andrei A Gilep
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Aliaksei V Yantsevich
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Tatsiana V Shkel
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Ivan V Yushkevich
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Sergey P Radko
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | - Alexis S Ivanov
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | | | - Alexander I Archakov
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
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3
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Abstract
Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their own structures and dynamics using as input seemingly random character strings of their sequence, following which they coalesce and perform integrated cellular functions. In large computational systems with finite interaction-codes, the appearance of conflicting goals is inevitable. Simple conflicting forces can lead to quite complex structures and behaviors, leading to the concept of frustration in condensed matter. We present here some basic ideas about frustration in biomolecules and how the frustration concept leads to a better appreciation of many aspects of the architecture of biomolecules, and especially how biomolecular structure connects to function by means of localized frustration. These ideas are simultaneously both seductively simple and perilously subtle to grasp completely. The energy landscape theory of protein folding provides a framework for quantifying frustration in large systems and has been implemented at many levels of description. We first review the notion of frustration from the areas of abstract logic and its uses in simple condensed matter systems. We discuss then how the frustration concept applies specifically to heteropolymers, testing folding landscape theory in computer simulations of protein models and in experimentally accessible systems. Studying the aspects of frustration averaged over many proteins provides ways to infer energy functions useful for reliable structure prediction. We discuss how frustration affects folding mechanisms. We review here how the biological functions of proteins are related to subtle local physical frustration effects and how frustration influences the appearance of metastable states, the nature of binding processes, catalysis and allosteric transitions. In this review, we also emphasize that frustration, far from being always a bad thing, is an essential feature of biomolecules that allows dynamics to be harnessed for function. In this way, we hope to illustrate how Frustration is a fundamental concept in molecular biology.
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4
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De S, Chan ACK, Coyne HJ, Bhachech N, Hermsdorf U, Okon M, Murphy MEP, Graves BJ, McIntosh LP. Steric mechanism of auto-inhibitory regulation of specific and non-specific DNA binding by the ETS transcriptional repressor ETV6. J Mol Biol 2014; 426:1390-406. [PMID: 24333486 PMCID: PMC4278593 DOI: 10.1016/j.jmb.2013.11.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/05/2013] [Accepted: 11/09/2013] [Indexed: 11/29/2022]
Abstract
DNA binding by the ETS transcriptional repressor ETV6 (or TEL) is auto-inhibited ~50-fold due to an α-helix that sterically blocks its ETS domain binding interface. Using NMR spectroscopy, we demonstrate that this marginally stable helix is unfolded, and not displaced to a non-inhibitory position, when ETV6 is bound to DNA containing a consensus (5')GGAA(3') recognition site. Although significantly lower in affinity, binding to non-specific DNA is auto-inhibited ~5-fold and is also accompanied by helix unfolding. Based on NMR chemical shift perturbations, both specific and non-specific DNA are bound via the same canonical ETS domain interface. However, spectral perturbations are smaller for the non-specific complex, suggesting weaker and less well-defined interactions than in the specific complex. In parallel, the crystal structure of ETV6 bound to a specific DNA duplex was determined. The structure of this complex reveals that a non-conserved histidine residue in the ETS domain recognition helix helps establish the specificity of ETV6 for DNA-binding sites containing (5')GGAA(3')versus(5')GGAT(3'). These studies provide a unified steric mechanism for attenuating ETV6 binding to both specific and non-specific DNA and expand the repertoire of characterized auto-inhibitory strategies utilized to regulate ETS factors.
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Affiliation(s)
- Soumya De
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Anson C K Chan
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - H Jerome Coyne
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Niraja Bhachech
- Department of Oncological Sciences, University of Utah School of Medicine, and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Ulrike Hermsdorf
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Michael E P Murphy
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Barbara J Graves
- Department of Oncological Sciences, University of Utah School of Medicine, and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3.
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5
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Parra RG, Espada R, Sánchez IE, Sippl MJ, Ferreiro DU. Detecting repetitions and periodicities in proteins by tiling the structural space. J Phys Chem B 2013; 117:12887-97. [PMID: 23758291 PMCID: PMC3807821 DOI: 10.1021/jp402105j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
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The
notion of energy landscapes provides conceptual tools for understanding
the complexities of protein folding and function. Energy landscape
theory indicates that it is much easier to find sequences that satisfy
the “Principle of Minimal Frustration” when the folded
structure is symmetric (Wolynes, P. G. Symmetry and the Energy Landscapes
of Biomolecules. Proc. Natl. Acad. Sci. U.S.A.1996, 93, 14249–14255). Similarly,
repeats and structural mosaics may be fundamentally related to landscapes
with multiple embedded funnels. Here we present analytical tools to
detect and compare structural repetitions in protein molecules. By
an exhaustive analysis of the distribution of structural repeats using
a robust metric, we define those portions of a protein molecule that
best describe the overall structure as a tessellation of basic units.
The patterns produced by such tessellations provide intuitive representations
of the repeating regions and their association toward higher order
arrangements. We find that some protein architectures can be described
as nearly periodic, while in others clear separations between repetitions
exist. Since the method is independent of amino acid sequence information,
we can identify structural units that can be encoded by a variety
of distinct amino acid sequences.
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Affiliation(s)
- R Gonzalo Parra
- Protein Physiology Lab, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN , Buenos Aires, Argentina
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6
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Marcovitz A, Levy Y. Weak frustration regulates sliding and binding kinetics on rugged protein-DNA landscapes. J Phys Chem B 2013; 117:13005-14. [PMID: 23668488 DOI: 10.1021/jp402296d] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A fundamental step in gene-regulatory activities, such as repression, transcription, and recombination, is the binding of regulatory DNA-binding proteins (DBPs) to specific targets in the genome. To rapidly localize their regulatory genomic sites, DBPs reduce the dimensionality of the search space by combining three-dimensional (3D) diffusion in solution with one-dimensional (1D) sliding along DNA. However, the requirement to form a thermodynamically stable protein-DNA complex at the cognate genomic target sequence imposes a challenge on the protein because, as it navigates one-dimensionally along the genome, it may come in close contact with sites that share partial or even complete sequence similarity with the functional DNA sequence. This puzzling issue creates a conflict between two basic requirements: finding the cognate site quickly and stably binding it. Here, we structurally assessed the interface adopted by a variety of DBPs to bind DNA specifically and nonspecifically, and found that many DBPs utilize one interface to specifically recognize a DNA sequence and another to assist in propagating along the DNA through nonspecific associations. While these two interfaces overlap each other in some proteins, they present partial overlap in others and frustrate the protein-DNA interface. Using coarse-grained molecular dynamics simulations, we demonstrate that the existence of frustration in DBPs is a compromise between rapid 1D diffusion along other regions in the genome (high frustration smoothens the landscape for sliding) and rapid formation of a stable and essentially active protein-DNA complex (low frustration reduces the free energy barrier for switching between the two binding modes).
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Affiliation(s)
- Amir Marcovitz
- Department of Structural Biology, Weizmann Institute of Science , Rehovot, 76100, Israel
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7
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Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation. Proc Natl Acad Sci U S A 2012; 109:17857-62. [PMID: 22988066 DOI: 10.1073/pnas.1201805109] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered proteins (IDP) are a broad class of proteins with relatively flat energy landscapes showing a high level of functional promiscuity, which are frequently regulated through posttranslational covalent modifications. Histone tails, which are the terminal segments of the histone proteins, are prominent IDPs that are implicated in a variety of signaling processes, which control chromatin organization and dynamics. Although a large body of work has been done on elucidating the roles of posttranslational modifications in functional regulation of IDPs, molecular mechanisms behind the observed behaviors are not fully understood. Using extensive atomistic molecular dynamics simulations, we found in this work that H4 tail mono-acetylation at LYS-16, which is a key covalent modification, induces a significant reorganization of the tail's conformational landscape, inducing partial ordering and enhancing the propensity for alpha-helical segments. Furthermore, our calculations of the potentials of mean force between the H4 tail and a DNA fragment indicate that contrary to the expectations based on simple electrostatic reasoning, the Lys-16 mono-acetylated H4 tail binds to DNA stronger than the unacetylated protein. Based on these results, we propose a molecular mechanism for the way Lys-16 acetylation might lead to experimentally observed disruption of compact chromatin fibers.
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8
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Oleksiak MF, Crawford DL. The relationship between phenotypic and environmental variation: do physiological responses reduce interindividual differences? Physiol Biochem Zool 2012; 85:572-84. [PMID: 23099455 DOI: 10.1086/666904] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
What is the effect of a variable environment on phenotypic variation? Does the physiological response to a new environment increase or decrease the differences among individuals? We provide a speculative hypothesis suggesting that the induction of a physiological response to environmental change minimizes phenotypic differences among individuals in outbred genetically variable populations. Although this suggestion runs counter to the general idea that environmental variation induces phenotypic variation, we provide evidence that this is not always the case. One explanation for this counterintuitive hypothesis is that in a variable environment, the physiological mechanism that maintains homeostasis changes the concentrations of active transcription factors (TFs). This change in TFs reduces the effectiveness of nucleotide polymorphisms in TF binding sites and thus reduces the variation among individuals in mRNA expression and in the phenotypes affected by these mRNA transcripts. Thus, there are fewer differences among individuals in a variable environment compared with the variation observed in a constant environment. Our conjecture is that the physiological mechanisms that maintain homeostasis in response to environmental variation canalize phenotypic variation. If our hypothesis is correct, then the physiological canalization of gene expression in a variable environment hides genetic variation and thereby reduces the evolutionary costs of polymorphism. This hypothesis provides a new perspective on the mechanisms by which high levels of genetic variation can persist in real-world populations.
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Affiliation(s)
- Marjorie F Oleksiak
- Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, Florida 33149, USA
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9
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Mapping the Transition State for DNA Bending by IHF. J Mol Biol 2012; 418:300-15. [DOI: 10.1016/j.jmb.2012.02.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 02/14/2012] [Accepted: 02/17/2012] [Indexed: 01/01/2023]
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10
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Sinha SK, Bandyopadhyay S. Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations. J Chem Phys 2012; 135:135101. [PMID: 21992339 DOI: 10.1063/1.3634004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Formation of protein-DNA complex is an important step in regulation of genes in living organisms. One important issue in this problem is the role played by water in mediating the protein-DNA interactions. In this work, we have carried out atomistic molecular dynamics simulations to explore the heterogeneous dynamics of water molecules present in different regions around a complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. It is demonstrated that such heterogeneous water motions around the complex are correlated with the relaxation time scales of hydrogen bonds formed by those water molecules with the protein and DNA. The calculations reveal the existence of a fraction of extraordinarily restricted water molecules forming a highly rigid thin layer in between the binding motifs of the protein and DNA. It is further proved that higher rigidity of water layers around the complex originates from more frequent reformations of broken water-water hydrogen bonds. Importantly, it is found that the formation of the complex affects the transverse and longitudinal degrees of freedom of surrounding water molecules in a nonuniform manner.
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Affiliation(s)
- Sudipta Kumar Sinha
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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11
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Frustration in protein-DNA binding influences conformational switching and target search kinetics. Proc Natl Acad Sci U S A 2011; 108:17957-62. [PMID: 22003125 DOI: 10.1073/pnas.1109594108] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Rapid recognition of DNA target sites involves facilitated diffusion through which alternative sites are searched on genomic DNA. A key mechanism facilitating the localization of the target by a DNA-binding protein (DBP) is one-dimensional diffusion (sliding) in which electrostatic forces attract the protein to the DNA. As the protein reaches its target DNA site, it switches from purely electrostatic binding to a specific set of interactions with the DNA bases that also involves hydrogen bonding and van der Waals forces. High overlap between the DBP patches used for nonspecific and specific interactions with DNA may enable an immediate transition between the two binding modes following target site localization. By contrast, an imperfect overlap may result in greater frustration between the two potentially competing binding modes and consequently slower switching between them. A structural analysis of 125 DBPs indicates frustration between the two binding modes that results in a large difference between the orientations of the protein to the DNA when it slides compared to when it specifically interacts with DNA. Coarse-grained molecular dynamics simulations of in silico designed peptides comprising the full range of frustrations between the two interfaces show slower transition from nonspecific to specific DNA binding as the overlap between the patches involved in the two binding modes decreases. The complex search kinetics may regulate the search by eliminating trapping of the protein in semispecific sites while sliding.
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12
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Phillips NB, Racca J, Chen YS, Singh R, Jancso-Radek A, Radek JT, Wickramasinghe NP, Haas E, Weiss MA. Mammalian testis-determining factor SRY and the enigma of inherited human sex reversal: frustrated induced fit in a bent protein-DNA complex. J Biol Chem 2011; 286:36787-807. [PMID: 21849498 DOI: 10.1074/jbc.m111.260091] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian testis-determining factor SRY contains a high mobility group box, a conserved eukaryotic motif of DNA bending. Mutations in SRY cause XY gonadal dysgenesis and somatic sex reversal. Although such mutations usually arise de novo in spermatogenesis, some are inherited and so specify male development in one genetic background (the father) but not another (the daughter). Here, we describe the biophysical properties of a representative inherited mutation, V60L, within the minor wing of the L-shaped domain (box position 5). Although the stability and DNA binding properties of the mutant domain are similar to those of wild type, studies of SRY-induced DNA bending by subnanosecond time-resolved fluorescence resonance energy transfer (FRET) revealed enhanced conformational fluctuations leading to long range variation in bend angle. (1)H NMR studies of the variant protein-DNA complex demonstrated only local perturbations near the mutation site. Because the minor wing of SRY folds on DNA binding, the inherited mutation presumably hinders induced fit. Stopped-flow FRET studies indicated that such frustrated packing leads to accelerated dissociation of the bent complex. Studies of SRY-directed transcriptional regulation in an embryonic gonadal cell line demonstrated partial activation of downstream target Sox9. Our results have demonstrated a nonlocal coupling between DNA-directed protein folding and protein-directed DNA bending. Perturbation of this coupling is associated with a genetic switch poised at the threshold of activity.
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Affiliation(s)
- Nelson B Phillips
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
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13
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Tafvizi A, Mirny LA, van Oijen AM. Dancing on DNA: kinetic aspects of search processes on DNA. Chemphyschem 2011; 12:1481-9. [PMID: 21560221 DOI: 10.1002/cphc.201100112] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Indexed: 11/12/2022]
Abstract
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the search for its target site, the DNA-associated protein is facing both thermodynamic and kinetic difficulties. The thermodynamic challenge lies in recognizing and tightly binding a cognate (specific) site among the billions of other (non-specific) sequences on the DNA. The kinetic difficulty lies in finding a cognate site in mere seconds amidst the crowded cellular environment that is filled with other DNA sequences and proteins. Herein, we discuss the history of the DNA search problem, the theoretical background and the various experimental methods used to study the kinetics of proteins searching for target sites on DNA.
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Affiliation(s)
- Anahita Tafvizi
- Dept. of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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14
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Intrinsically disordered proteins may escape unwanted interactions via functional misfolding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:693-712. [DOI: 10.1016/j.bbapap.2011.03.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 02/16/2011] [Accepted: 03/16/2011] [Indexed: 12/30/2022]
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15
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Torella R, Moroni E, Caselle M, Morra G, Colombo G. Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes. BMC STRUCTURAL BIOLOGY 2010; 10:42. [PMID: 21106075 PMCID: PMC3002361 DOI: 10.1186/1472-6807-10-42] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 11/24/2010] [Indexed: 01/08/2023]
Abstract
BACKGROUND Protein-DNA recognition underlies fundamental biological processes ranging from transcription to replication and modification. Herein, we present a computational study of the sequence modulation of internal dynamic properties and of intraprotein networks of aminoacid interactions that determine the stability and specificity of protein-DNA complexes. RESULTS To this aim, we apply novel theoretical approaches to analyze the dynamics and energetics of biological systems starting from MD trajectories. As model system, we chose different sequences of Zinc Fingers (ZF) of the Zif268 family bound with different sequences of DNA. The complexes differ for their experimental stability properties, but share the same overall 3 D structure and do not undergo structural modifications during the simulations. The results of our analysis suggest that the energy landscape for DNA binding may be populated by dynamically different states, even in the absence of major conformational changes. Energetic couplings between residues change in response to protein and/or DNA sequence variations thus modulating the selectivity of recognition and the relative importance of different regions for binding. CONCLUSIONS The results show differences in the organization of the intra-protein energy-networks responsible for the stabilization of the protein conformations recognizing and binding DNA. These, in turn, are reflected into different modulation of the ZF's internal dynamics. The results also show a correlation between energetic and dynamic properties of the different proteins and their specificity/selectivity for DNA sequences. Finally, a dynamic and energetic model for the recognition of DNA by Zinc Fingers is proposed.
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Affiliation(s)
- Rubben Torella
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
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16
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Dellarole M, Sánchez IE, de Prat Gay G. Thermodynamics of cooperative DNA recognition at a replication origin and transcription regulatory site. Biochemistry 2010; 49:10277-86. [PMID: 21047141 PMCID: PMC3091369 DOI: 10.1021/bi1014908] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
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Binding cooperativity guides the formation of protein−nucleic acid complexes, in particular those that are highly regulated such as replication origins and transcription sites. Using the DNA binding domain of the origin binding and transcriptional regulator protein E2 from human papillomavirus type 16 as model, and through isothermal titration calorimetry analysis, we determined a positive, entropy-driven cooperativity upon binding of the protein to its cognate tandem double E2 site. This cooperativity is associated with a change in DNA structure, where the overall B conformation is maintained. Two homologous E2 domains, those of HPV18 and HPV11, showed that the enthalpic−entropic components of the reaction and DNA deformation can diverge. Because the DNA binding helix is almost identical in the three domains, the differences must lie dispersed throughout this unique dimeric β-barrel fold. This is in surprising agreement with previous results for this domain, which revealed a strong coupling between global dynamics and DNA recognition.
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Affiliation(s)
- Mariano Dellarole
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-Conicet, Patricias Argentinas 435, Buenos Aires, Argentina
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17
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Huang Y, Liu Z. Nonnative interactions in coupled folding and binding processes of intrinsically disordered proteins. PLoS One 2010; 5:e15375. [PMID: 21079758 PMCID: PMC2973977 DOI: 10.1371/journal.pone.0015375] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 08/18/2010] [Indexed: 11/19/2022] Open
Abstract
Proteins function by interacting with other molecules, where both native and nonnative interactions play important roles. Native interactions contribute to the stability and specificity of a complex, whereas nonnative interactions mainly perturb the binding kinetics. For intrinsically disordered proteins (IDPs), which do not adopt rigid structures when being free in solution, the role of nonnative interactions may be more prominent in binding processes due to their high flexibilities. In this work, we investigated the effect of nonnative hydrophobic interactions on the coupled folding and binding processes of IDPs and its interplay with chain flexibility by conducting molecular dynamics simulations. Our results showed that the free-energy profiles became rugged, and intermediate states occurred when nonnative hydrophobic interactions were introduced. The binding rate was initially accelerated and subsequently dramatically decreased as the strength of the nonnative hydrophobic interactions increased. Both thermodynamic and kinetic analysis showed that disordered systems were more readily affected by nonnative interactions than ordered systems. Furthermore, it was demonstrated that the kinetic advantage of IDPs (“fly-casting” mechanism) was enhanced by nonnative hydrophobic interactions. The relationship between chain flexibility and protein aggregation is also discussed.
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Affiliation(s)
- Yongqi Huang
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Center for Theoretical Biology, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Zhirong Liu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Center for Theoretical Biology, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- * E-mail:
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Sánchez IE, Ferreiro DU, Gay GDP. Mutational analysis of kinetic partitioning in protein folding and protein-DNA binding. Protein Eng Des Sel 2010; 24:179-84. [PMID: 20876193 DOI: 10.1093/protein/gzq064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Kinetic partitioning between competing routes is present in many biological processes. Here, we propose a methodology to characterize kinetic partitioning through site-directed mutagenesis and apply it to parallel routes for unfolding of the TI I27 protein and for recognition of its target DNA by the human papillomavirus E2 protein. The balance between the two competing reaction routes can be quantified by the partitioning constant K(p). K(p) is easily modulated by point mutations, opening the way for the rational design of kinetic partitioning. Conserved wild-type residues strongly favor one of the two competing reactions, suggesting that in these systems there is an evolutionary pressure to shift partitioning towards a certain route. The mutations with the largest effects on partitioning cluster together in space, defining the protein regions most relevant for the modulation of partitioning. Such regions are neither fully coincident with nor strictly segregated from the regions that are important from each competing reaction. We dissected the mutational effects on partitioning into the contributions from each competing route using a new parameter called pi-value. The results suggest how the design of kinetic partitioning may be approached in each case.
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Affiliation(s)
- Ignacio E Sánchez
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina.
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