1
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Coñuecar R, Asela I, Rivera M, Galaz-Davison P, González-Higueras J, Hamilton GL, Engelberger F, Ramírez-Sarmiento CA, Babul J, Sanabria H, Medina E. DNA facilitates heterodimerization between human transcription factors FoxP1 and FoxP2 by increasing their conformational flexibility. iScience 2023; 26:107228. [PMID: 37485372 PMCID: PMC10362293 DOI: 10.1016/j.isci.2023.107228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 05/15/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Transcription factors regulate gene expression by binding to DNA. They have disordered regions and specific DNA-binding domains. Binding to DNA causes structural changes, including folding and interactions with other molecules. The FoxP subfamily of transcription factors in humans is unique because they can form heterotypic interactions without DNA. However, it is unclear how they form heterodimers and how DNA binding affects their function. We used computational and experimental methods to study the structural changes in FoxP1's DNA-binding domain when it forms a heterodimer with FoxP2. We found that FoxP1 has complex and diverse conformational dynamics, transitioning between compact and extended states. Surprisingly, DNA binding increases the flexibility of FoxP1, contrary to the typical folding-upon-binding mechanism. In addition, we observed a 3-fold increase in the rate of heterodimerization after FoxP1 binds to DNA. These findings emphasize the importance of structural flexibility in promoting heterodimerization to form transcriptional complexes.
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Affiliation(s)
- Ricardo Coñuecar
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Isabel Asela
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge González-Higueras
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - George L. Hamilton
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Felipe Engelberger
- Institute for Drug Discovery, Leipzig University Medical School, 04107 Leipzig, Germany
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Hugo Sanabria
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
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2
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Abstract
This mini-review represents a brief, disorder-centric consideration of the interplay between order and disorder in proteins. The goal here is to show that inside the cell, folding, non-folding, and misfolding of proteins are interlinked on multiple levels. This is evidenced by the highly heterogeneous spatio-temporal structural organization of a protein molecule, where one can find differently (dis)ordered components that can undergo local or global order-to-disorder and disorder-to-order transitions needed for functionality. This is further illustrated by the fact that at particular moments of their life, most notably during their synthesis and degradation, all proteins are at least partially disordered. In addition to these intrinsic forms of disorder, proteins are constantly facing extrinsic disorder, which is intrinsic disorder in their functional partners. All this comprises the multileveled protein disorder cycle.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
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3
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Hsu IS, Strome B, Lash E, Robbins N, Cowen LE, Moses AM. A functionally divergent intrinsically disordered region underlying the conservation of stochastic signaling. PLoS Genet 2021; 17:e1009629. [PMID: 34506483 PMCID: PMC8457507 DOI: 10.1371/journal.pgen.1009629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/22/2021] [Accepted: 08/06/2021] [Indexed: 12/18/2022] Open
Abstract
Stochastic signaling dynamics expand living cells' information processing capabilities. An increasing number of studies report that regulators encode information in their pulsatile dynamics. The evolutionary mechanisms that lead to complex signaling dynamics remain uncharacterized, perhaps because key interactions of signaling proteins are encoded in intrinsically disordered regions (IDRs), whose evolution is difficult to analyze. Here we focused on the IDR that controls the stochastic pulsing dynamics of Crz1, a transcription factor in fungi downstream of the widely conserved calcium signaling pathway. We find that Crz1 IDRs from anciently diverged fungi can all respond transiently to calcium stress; however, only Crz1 IDRs from the Saccharomyces clade support pulsatility, encode extra information, and rescue fitness in competition assays, while the Crz1 IDRs from distantly related fungi do none of the three. On the other hand, we find that Crz1 pulsing is conserved in the distantly related fungi, consistent with the evolutionary model of stabilizing selection on the signaling phenotype. Further, we show that a calcineurin docking site in a specific part of the IDRs appears to be sufficient for pulsing and show evidence for a beneficial increase in the relative calcineurin affinity of this docking site. We propose that evolutionary flexibility of functionally divergent IDRs underlies the conservation of stochastic signaling by stabilizing selection.
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Affiliation(s)
- Ian S. Hsu
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Bob Strome
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Emma Lash
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alan M. Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- * E-mail:
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4
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Price KL, Presler M, Uyehara CM, Shakes DC. The intrinsically disordered protein SPE-18 promotes localized assembly of MSP in Caenorhabditis elegans spermatocytes. Development 2021; 148:dev195875. [PMID: 33558389 PMCID: PMC7938801 DOI: 10.1242/dev.195875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/02/2021] [Indexed: 01/26/2023]
Abstract
Many specialized cells use unconventional strategies of cytoskeletal control. Nematode spermatocytes discard their actin and tubulin following meiosis, and instead employ the regulated assembly/disassembly of the Major Sperm Protein (MSP) to drive sperm motility. However, prior to the meiotic divisions, MSP is sequestered through its assembly into paracrystalline structures called fibrous bodies (FBs). The accessory proteins that direct this sequestration process have remained mysterious. This study reveals SPE-18 as an intrinsically disordered protein that is essential for MSP assembly within FBs. In spe-18 mutant spermatocytes, MSP forms disorganized cortical fibers, and the cells arrest in meiosis without forming haploid sperm. In wild-type spermatocytes, SPE-18 localizes to pre-FB complexes and functions with the kinase SPE-6 to localize MSP assembly. Changing patterns of SPE-18 localization uncover previously unappreciated complexities in FB maturation. Later, within newly individualized spermatids, SPE-18 is rapidly lost, yet SPE-18 loss alone is insufficient for MSP disassembly. Our findings reveal an alternative strategy for sequestering cytoskeletal elements, not as monomers but in localized, bundled polymers. Additionally, these studies provide an important example of disordered proteins promoting ordered cellular structures.
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Affiliation(s)
- Kari L Price
- Department of Biology, William & Mary, Williamsburg, VA 23187, USA
| | - Marc Presler
- Department of Biology, William & Mary, Williamsburg, VA 23187, USA
| | | | - Diane C Shakes
- Department of Biology, William & Mary, Williamsburg, VA 23187, USA
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5
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Shimoyama H, Yonezawa Y. Atomistic detailed free-energy landscape of intrinsically disordered protein studied by multi-scale divide-and-conquer molecular dynamics simulation. J Comput Chem 2021; 42:19-26. [PMID: 33030249 DOI: 10.1002/jcc.26429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/06/2020] [Accepted: 09/10/2020] [Indexed: 11/08/2022]
Abstract
Calcineurin (CaN) is a eukaryotic serine/threonine protein phosphatase activated by both Ca2+ and calmodulin (CaM), including intrinsically disordered region (IDR). The region undergoes folding into an α-helix form in the presence Ca2+ -loaded CaM. To sample the ordered structure of the IDR by conventional all atom model (AAM) molecular dynamics (MD) simulation, the IDR and Ca2+ -loaded CaM must be simultaneously treated. However, it is time-consuming task because the coupled folding and binding should include repeated binding and dissociation. Then, in this study, we propose novel multi-scale divide-and-conquer MD (MSDC-MD), which combines AAM-MD and coarse-grained model MD (CGM-MD). To speed up the conformation sampling, MSDC-MD simulation first treats the IDR by CGM to sample conformations from wide conformation space; then, multiple AAM-MD in a limited area is initiated using the resultant CGM conformation, which is reconstructed by homology modeling method. To investigate performance, we sampled the ordered conformation of the IDR using MSDC-MD; the root-mean-square distance (RMSD) with respect to the experimental structure was 2.23 Å.
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Affiliation(s)
| | - Yasushige Yonezawa
- High Pressure Protein Research Center, Institute of Advanced Technology, Kindai University, Wakayama, Japan
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6
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Abstract
The serine/threonine phosphatase calcineurin acts as a crucial connection between calcium signaling the phosphorylation states of numerous important substrates. These substrates include, but are not limited to, transcription factors, receptors and channels, proteins associated with mitochondria, and proteins associated with microtubules. Calcineurin is activated by increases in intracellular calcium concentrations, a process that requires the calcium sensing protein calmodulin binding to an intrinsically disordered regulatory domain in the phosphatase. Despite having been studied for around four decades, the activation of calcineurin is not fully understood. This review largely focuses on what is known about the activation process and highlights aspects that are currently not understood. Video abstract.
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Affiliation(s)
- Trevor P Creamer
- Center for Structural Biology, Department of Molecular & Cellular Biochemistry, 741 S. Limestone Street, Lexington, KY, 40536-0509, USA.
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7
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Cook EC, Creamer TP. Influence of electrostatic forces on the association kinetics and conformational ensemble of an intrinsically disordered protein. Proteins 2020; 88:1607-1619. [PMID: 32654182 DOI: 10.1002/prot.25979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/15/2020] [Accepted: 07/05/2020] [Indexed: 01/26/2023]
Abstract
Recent work has revealed that the association of a disordered region of a protein with a folded binding partner can occur as rapidly as association between two folded proteins. This is the case for the phosphatase calcineurin (CaN) and its association with its activator calmodulin. Calmodulin binds to the intrinsically disordered regulatory domain of CaN. Previous studies have shown that electrostatic steering can accelerate the binding of folded proteins with disordered ligands. Given that electrostatic forces are strong determinants of disordered protein ensembles, the relationship between electrostatics, conformational ensembles, and quaternary interactions is unclear. Here, we employ experimental approaches to explore the impact of electrostatic interactions on the association of calmodulin with the disordered regulatory region of CaN. We find that estimated association rate constants of calmodulin with our chosen calmodulin-substrates are within the diffusion-limited regime. The association rates are dependent on the ionic strength, indicating that favorable electrostatic forces increase the rate of association. Further, we show that charged amino acids outside the calmodulin-binding site modulate the binding rate. Conformational ensembles obtained from computer simulations suggest that electrostatic interactions within the regulatory domain might bias the conformational ensemble such that the calmodulin binding region is readily accessible. Given the prevalence of charged residues in disordered protein chains, our findings are likely relevant to many protein-protein interactions.
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Affiliation(s)
- Erik C Cook
- Center for Structural Biology and Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Trevor P Creamer
- Center for Structural Biology and Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
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8
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Uversky VN, Finkelstein AV. Life in Phases: Intra- and Inter- Molecular Phase Transitions in Protein Solutions. Biomolecules 2019; 9:E842. [PMID: 31817975 PMCID: PMC6995567 DOI: 10.3390/biom9120842] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Proteins, these evolutionarily-edited biological polymers, are able to undergo intramolecular and intermolecular phase transitions. Spontaneous intramolecular phase transitions define the folding of globular proteins, whereas binding-induced, intra- and inter- molecular phase transitions play a crucial role in the functionality of many intrinsically-disordered proteins. On the other hand, intermolecular phase transitions are the behind-the-scenes players in a diverse set of macrosystemic phenomena taking place in protein solutions, such as new phase nucleation in bulk, on the interface, and on the impurities, protein crystallization, protein aggregation, the formation of amyloid fibrils, and intermolecular liquid-liquid or liquid-gel phase transitions associated with the biogenesis of membraneless organelles in the cells. This review is dedicated to the systematic analysis of the phase behavior of protein molecules and their ensembles, and provides a description of the major physical principles governing intramolecular and intermolecular phase transitions in protein solutions.
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Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Moscow, Russia
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow, Russia
- Biology Department, Lomonosov Moscow State University, 119192 Moscow, Russia
- Bioltechnogy Department, Lomonosov Moscow State University, 142290 Pushchino, Moscow, Russia
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9
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Rydzanicz M, Wachowska M, Cook EC, Lisowski P, Kuźniewska B, Szymańska K, Diecke S, Prigione A, Szczałuba K, Szybińska A, Koppolu A, Murcia Pienkowski V, Kosińska J, Wiweger M, Kostrzewa G, Brzozowska M, Domańska-Pakieła D, Jurkiewicz E, Stawiński P, Gromadka A, Zielenkiewicz P, Demkow U, Dziembowska M, Kuźnicki J, Creamer TP, Płoski R. Novel calcineurin A (PPP3CA) variant associated with epilepsy, constitutive enzyme activation and downregulation of protein expression. Eur J Hum Genet 2018; 27:61-69. [PMID: 30254215 DOI: 10.1038/s41431-018-0254-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/22/2018] [Accepted: 08/09/2018] [Indexed: 12/17/2022] Open
Abstract
PPP3CA encodes calmodulin-binding catalytic subunit of calcineurin, a ubiquitously expressed calcium/calmodulin-regulated protein phosphatase. Recently de novo PPP3CA variants were reported as a cause of disease in 12 subjects presenting with epileptic encephalopathy and dysmorphic features. We describe a boy with similar phenotype and severe early onset epileptic encephalopathy in whom a novel de novo c.1324C>T (p.(Gln442Ter)) PPP3CA variant was found by whole exome sequencing. Western blot experiments in patient's cells (EBV transformed lymphocytes and neuronal cells derived through reprogramming) indicate that despite normal mRNA abundance the protein expression level is strongly reduced both for the mutated and wild-type protein. By in vitro studies with recombinant protein expressed in E. coli we show that c.1324C>T (p.(Gln442Ter)) results in constitutive activation of the enzyme. Our results confirm the role of PPP3CA defects in pathogenesis of a distinct neurodevelopmental disorder including severe epilepsy and dysmorphism and provide further functional clues regarding the pathogenic mechanism.
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Affiliation(s)
| | - Małgorzata Wachowska
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, Warsaw, Poland
| | - Erik C Cook
- Center for Structural Biology and Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, USA
| | - Paweł Lisowski
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland.,Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | | | - Krystyna Szymańska
- Department of Experimental and Clinical Neuropathology, Mossakowski Medical Research Center, Polish Academy of Sciences, Warsaw, Poland
| | - Sebastian Diecke
- Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Alessandro Prigione
- Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Agnieszka Koppolu
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Victor Murcia Pienkowski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Joanna Kosińska
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Małgorzata Wiweger
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Grażyna Kostrzewa
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Dorota Domańska-Pakieła
- Department of Child Neurology and Epileptology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Elżbieta Jurkiewicz
- Department of Diagnostic Imaging, The Children's Memorial Health Institute, Warsaw, Poland
| | - Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Gromadka
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Piotr Zielenkiewicz
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Urszula Demkow
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, Warsaw, Poland
| | | | - Jacek Kuźnicki
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Trevor P Creamer
- Center for Structural Biology and Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, USA
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.
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10
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Calcium-Binding Proteins with Disordered Structure and Their Role in Secretion, Storage, and Cellular Signaling. Biomolecules 2018; 8:biom8020042. [PMID: 29921816 PMCID: PMC6022996 DOI: 10.3390/biom8020042] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/12/2018] [Accepted: 06/14/2018] [Indexed: 12/19/2022] Open
Abstract
Calcium is one of the most important second messengers and its intracellular signaling regulates many aspects of cell physiology. Calcium ions, like phosphate ions, are highly charged and thus are able to alter protein conformation upon binding; thereby they constitute key factors in signal transduction. One of the most common calcium-binding structural motifs is the EF-hand, a well-defined helix-loop-helix structural domain, present in many calcium-binding proteins (CBPs). Nonetheless, some CBPs contain non-canonical, disordered motifs, which usually bind calcium with high capacity and low affinity, and which represent a subset of proteins with specific functions, but these functions rarely involve signaling. When compared with phosphorylation-mediated signal transduction, the role of intrinsic disorder in calcium signaling is significantly less prominent and not direct. The list of known examples of intrinsically disordered CBPs is relatively short and the disorder in these examples seems to be linked to secretion and storage. Calcium-sensitive phosphatase calcineurin is an exception, but it represents an example of transient disorder, which is, nevertheless, vital to the functioning of this protein. The underlying reason for the different role of disordered proteins in the two main cellular signaling systems appears to be linked to the gradient of calcium concentration, present in all living cells.
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11
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Abstract
![]()
Calcineurin
is a Ser/Thr phosphatase that is important for key
biological processes, including immune system activation. We previously
identified a region in the intrinsically disordered regulatory domain
of calcineurin that forms a critical amphipathic α-helix (the
“distal helix”) that is required for complete activation
of calcineurin. This distal helix was shown to have a Tm close to that of human body temperature. Because the Tm was determined in dilute buffer, we hypothesized
that other factors inherent to a cellular environment might modulate
the stability of the distal helix. One such factor that contributes
to stability in other proteins is macromolecular crowding. The cell
cytoplasm is comprised of up to 400 g/L protein, lipids, nucleic acids,
and other compounds. We hypothesize that the presence of such crowders
could increase the thermal stability of the distal helix and thus
lead to a more robust activation of calcineurin in vivo. Using biophysical and biochemical approaches, we show that the
distal helix of calcineurin is indeed stabilized when crowded by the
synthetic polymers dextran 70 and ficoll 70, and that this stabilization
of the distal helix increases the activity of calcineurin.
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Affiliation(s)
- Erik C Cook
- Center for Structural Biology, Department of Molecular and Cellular Biochemistry, University of Kentucky , 741 South Limestone Street, Lexington, Kentucky 40536-0509, United States
| | - Trevor P Creamer
- Center for Structural Biology, Department of Molecular and Cellular Biochemistry, University of Kentucky , 741 South Limestone Street, Lexington, Kentucky 40536-0509, United States
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12
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Uversky VN. Dancing Protein Clouds: The Strange Biology and Chaotic Physics of Intrinsically Disordered Proteins. J Biol Chem 2016; 291:6681-8. [PMID: 26851286 DOI: 10.1074/jbc.r115.685859] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Biologically active but floppy proteins represent a new reality of modern protein science. These intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered and intrinsically disordered protein regions (IDPRs) constitute a noticeable part of any given proteome. Functionally, they complement ordered proteins, and their conformational flexibility and structural plasticity allow them to perform impossible tricks and be engaged in biological activities that are inaccessible to well folded proteins with their unique structures. The major goals of this minireview are to show that, despite their simplified amino acid sequences, IDPs/IDPRs are complex entities often resembling chaotic systems, are structurally and functionally heterogeneous, and can be considered an important part of the structure-function continuum. Furthermore, IDPs/IDPRs are everywhere, and are ubiquitously engaged in various interactions characterized by a wide spectrum of binding scenarios and an even wider spectrum of structural and functional outputs.
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Affiliation(s)
- Vladimir N Uversky
- From the Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, the Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia, the Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia, and the Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russian Federation
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13
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Dunlap TB, Guo HF, Cook EC, Holbrook E, Rumi-Masante J, Lester TE, Colbert CL, Vander Kooi CW, Creamer TP. Stoichiometry of the calcineurin regulatory domain-calmodulin complex. Biochemistry 2014; 53:5779-90. [PMID: 25144868 DOI: 10.1021/bi5004734] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Calcineurin is an essential serine/threonine phosphatase that plays vital roles in neuronal development and function, heart growth, and immune system activation. Calcineurin is unique in that it is the only phosphatase known to be activated by calmodulin in response to increasing intracellular calcium concentrations. Calcium-loaded calmodulin binds to the regulatory domain of calcineurin, resulting in a conformational change that removes an autoinhibitory domain from the active site of the phosphatase. We have determined a 1.95 Å crystal structure of calmodulin bound to a peptide corresponding to its binding region from calcineurin. In contrast to previous structures of this complex, our structure has a stoichiometry of 1:1 and has the canonical collapsed, wraparound conformation observed for many calmodulin-substrate complexes. In addition, we have used size-exclusion chromatography and time-resolved fluorescence to probe the stoichiometry of binding of calmodulin to a construct corresponding to almost the entire regulatory domain from calcineurin, again finding a 1:1 complex. Taken in sum, our data strongly suggest that a single calmodulin protein is necessary and sufficient to bind to and activate each calcineurin enzyme.
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Affiliation(s)
- Tori B Dunlap
- Center for Structural Biology, Department of Molecular and Cellular Biochemistry, University of Kentucky , 741 South Limestone Street, Lexington, Kentucky 40536-0509, United States
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14
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Reddy KD, DeForte S, Uversky VN. Digested disorder: Quarterly intrinsic disorder digest (July-August-September, 2013). INTRINSICALLY DISORDERED PROTEINS 2014; 2:e27833. [PMID: 28232877 PMCID: PMC5314876 DOI: 10.4161/idp.27833] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 01/13/2014] [Indexed: 12/26/2022]
Abstract
The current literature on intrinsically disordered proteins grows fast. To keep interested readers up to speed with this literature, we continue a "Digested Disorder" project and represent a new issue of reader's digest of the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the third quarter of 2013; i.e., during the period of June, July, and September of 2013. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.
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Affiliation(s)
- Krishna D Reddy
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
| | - Shelly DeForte
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA; Department of Biological Sciences; Faculty of Science; King Abdulaziz University; Jeddah, Saudi Arabia; Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
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15
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Uversky VN. Disorder in the lifetime of a protein. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e26782. [PMID: 28516024 PMCID: PMC5424783 DOI: 10.4161/idp.26782] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/09/2013] [Accepted: 10/10/2013] [Indexed: 12/21/2022]
Abstract
Intrinsic disorder is everywhere and is inevitable. The non-folding propensity is inherent for numerous natural polypeptide chains, and many functional proteins and protein regions are intrinsically disordered. Furthermore, at particular moments in their life, most notably during their synthesis and degradation, all ordered proteins are at least partially unfolded (disordered). Also, there is a widely spread phenomenon of conditional (functional or transient) disorder, where functions of many ordered proteins require local or even global unfolding of their unique structures. Finally, extrinsic disorder (i.e., intrinsic disorder in functional partners of ordered proteins) should be taken into account too. Therefore, even if a protein is completely devoid of intrinsically disordered regions in its mature form (which is a rather exceptional situation), it faces different forms of disorder (intrinsic, extrinsic, or induced disorder) at all the stages of its functional life, from birth to death. The goal of this article is to briefly introduce this concept of disorder in the lifetime of a protein.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute; Morsani 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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