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Ghosh B, Boila LD, Choudhury S, Mondal P, Bhattacharjee S, Pal SK, Sengupta A, Roy S. A Potent Conformation-Constrained Synthetic Peptide Mimic of a Homeodomain Selectively Regulates Target Genes in Cells. ACS Chem Biol 2018; 13:2003-2009. [PMID: 29966078 DOI: 10.1021/acschembio.8b00488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA, as a target for therapeutic intervention, remains largely unexplored. DLX-4, a homeodomain containing transcription factor, and its spliced isoforms play crucial roles in many aspects of cellular biochemistry and important roles in many diseases. A smaller peptide mimicking the homeodomain of the transcription factor DLX-4 was designed and synthesized by suitable conjoining of its modified DNA-binding elements. The peptide binds to DLX-4 target sites on the regulatory region of the globin gene cluster with native-like affinity and specificity in vitro. When conjugated to cell penetrating and nuclear localization sequences, it upregulated some of the genes repressed by DLX-4 or its isoforms, such as β- and γ-globin genes in erythropoietin-induced differentiating CD34+ human hematopoietic stem/progenitor cells with high specificity by competing with the respective binding sites. Engineered peptides mimicking DNA-binding domains of transcription factors offer the potential for creating synthetic molecules for directly targeting DNA sites with high specificity.
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Affiliation(s)
- Basusree Ghosh
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Liberalis Debraj Boila
- Stem Cell & Leukemia Lab, Cancer Biology & Inflammatory Disorder Division, Translational Research Unit of Excellence (TRUE), Indian Institute of Chemical Biology, CN-6, Sector V, Salt Lake, Kolkata 700 091, India
| | - Susobhan Choudhury
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Priya Mondal
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Sayan Bhattacharjee
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Samir Kumar Pal
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Amitava Sengupta
- Stem Cell & Leukemia Lab, Cancer Biology & Inflammatory Disorder Division, Translational Research Unit of Excellence (TRUE), Indian Institute of Chemical Biology, CN-6, Sector V, Salt Lake, Kolkata 700 091, India
| | - Siddhartha Roy
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
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2
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Substrate-Induced Conformational Changes of the Tyrocidine Synthetase 1 Adenylation Domain Probed by Intrinsic Trp Fluorescence. Protein J 2017; 36:202-211. [DOI: 10.1007/s10930-017-9714-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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3
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Callis PR. Binding phenomena and fluorescence quenching. II: Photophysics of aromatic residues and dependence of fluorescence spectra on protein conformation. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.04.051] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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4
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Zhang H, Lee SJ, Richardson CC. The roles of tryptophans in primer synthesis by the DNA primase of bacteriophage T7. J Biol Chem 2012; 287:23644-56. [PMID: 22605336 DOI: 10.1074/jbc.m112.366096] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA primases catalyze the synthesis of oligoribonucleotides required for the initiation of lagging strand DNA synthesis. Prokaryotic primases consist of a zinc-binding domain (ZBD) necessary for recognition of a specific template sequence and a catalytic RNA polymerase domain. Interactions of both domains with the DNA template and ribonucleotides are required for primer synthesis. Five tryptophan residues are dispersed in the primase of bacteriophage T7: Trp-42 in the ZBD and Trp-69, -97, -147, and -255 in the RNA polymerase domain. Previous studies showed that replacement of Trp-42 with alanine in the ZBD decreases primer synthesis, whereas substitution of non-aromatic residues for Trp-69 impairs both primer synthesis and delivery. However, the roles of tryptophan at position 97, 147, or 255 remain elusive. To investigate the essential roles of these residues, we replaced each tryptophan with the structurally similar tyrosine and examined the effect of this subtle alteration on primer synthesis. The substitution at position 42, 97, or 147 reduced primer synthesis, whereas substitution at position 69 or 255 did not. The functions of the tryptophans were further examined at each step of primer synthesis. Alteration of residue 42 disturbed the conformation of the ZBD and resulted in partial loss of the zinc ion, impairing binding to the ssDNA template. Replacement of Trp-97 with tyrosine reduced the binding affinity to NTP and the catalysis step. The replacement of Trp-147 with tyrosine also impaired the catalytic step. Therefore, Trp-42 is important in maintaining the conformation of the ZBD for template binding; Trp-97 contributes to NTP binding and the catalysis step; and Trp-147 maintains the catalysis step.
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Affiliation(s)
- Huidong Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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5
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Doerdelmann T, Kojetin DJ, Baird-Titus JM, Solt LA, Burris TP, Rance M. Structural and biophysical insights into the ligand-free Pitx2 homeodomain and a ring dermoid of the cornea inducing homeodomain mutant. Biochemistry 2012; 51:665-76. [PMID: 22224469 PMCID: PMC3264736 DOI: 10.1021/bi201639x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The homeodomain-containing transcription factor Pitx2 (pituitary homeobox protein 2) is present in many developing embryonic tissues, including the heart. Its homeodomain is responsible for the recognition and binding to target DNA sequences and thus constitutes a major functional unit in the Pitx2 protein. Nuclear magnetic resonance techniques were employed to determine the solution structure of the native Pitx2 homeodomain and a R24H mutant that causes autosomal dominantly inherited ring dermoid of the cornea syndrome. The structures reveal that both isoforms possess the canonical homeodomain fold. However, the R24H mutation results in a 2-fold increase in DNA binding affinity and a 5 °C decrease in thermal stability, while changing the dynamic environment of the homeodomain only locally. When introduced into full-length Pitx2c, the mutation results in an only 25% loss of transactivation activity. Our data correlate well with clinical observations suggesting a milder deficiency for the R24H mutation compared to those of other Pitx2 homeodomain mutations.
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Affiliation(s)
- Thomas Doerdelmann
- University of Cincinnati, Department of Molecular Genetics, Biochemistry and Microbiology, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
| | - Douglas J. Kojetin
- University of Cincinnati, Department of Molecular Genetics, Biochemistry and Microbiology, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
- The Scripps Research Institute, Scripps Florida, Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Jamie M. Baird-Titus
- College of Mount St. Joseph, Department of Chemistry, 5701 Delhi Road, Cincinnati, OH 45233, USA
| | - Laura A. Solt
- The Scripps Research Institute, Scripps Florida, Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Thomas P. Burris
- The Scripps Research Institute, Scripps Florida, Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Mark Rance
- University of Cincinnati, Department of Molecular Genetics, Biochemistry and Microbiology, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
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6
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Li H, Greene LH. Sequence and structural analysis of the chitinase insertion domain reveals two conserved motifs involved in chitin-binding. PLoS One 2010; 5:e8654. [PMID: 20084296 PMCID: PMC2805709 DOI: 10.1371/journal.pone.0008654] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 12/05/2009] [Indexed: 01/01/2023] Open
Abstract
Background Chitinases are prevalent in life and are found in species including archaea, bacteria, fungi, plants, and animals. They break down chitin, which is the second most abundant carbohydrate in nature after cellulose. Hence, they are important for maintaining a balance between carbon and nitrogen trapped as insoluble chitin in biomass. Chitinases are classified into two families, 18 and 19 glycoside hydrolases. In addition to a catalytic domain, which is a triosephosphate isomerase barrel, many family 18 chitinases contain another module, i.e., chitinase insertion domain. While numerous studies focus on the biological role of the catalytic domain in chitinase activity, the function of the chitinase insertion domain is not completely understood. Bioinformatics offers an important avenue in which to facilitate understanding the role of residues within the chitinase insertion domain in chitinase function. Results Twenty-seven chitinase insertion domain sequences, which include four experimentally determined structures and span five kingdoms, were aligned and analyzed using a modified sequence entropy parameter. Thirty-two positions with conserved residues were identified. The role of these conserved residues was explored by conducting a structural analysis of a number of holo-enzymes. Hydrogen bonding and van der Waals calculations revealed a distinct subset of four conserved residues constituting two sequence motifs that interact with oligosaccharides. The other conserved residues may be key to the structure, folding, and stability of this domain. Conclusions Sequence and structural studies of the chitinase insertion domains conducted within the framework of evolution identified four conserved residues which clearly interact with the substrates. Furthermore, evolutionary studies propose a link between the appearance of the chitinase insertion domain and the function of family 18 chitinases in the subfamily A.
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Affiliation(s)
- Hai Li
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, United States of America
| | - Lesley H. Greene
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, United States of America
- * E-mail:
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Clavaguéra C, Piuzzi F, Dognon JP. Electronic Spectrum of Tryptophan-Phenylalanine. A Correlated Ab Initio and Time-Dependent Density Functional Theory Study. J Phys Chem B 2009; 113:16443-8. [DOI: 10.1021/jp906969n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Carine Clavaguéra
- Laboratoire des Mécanismes Réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France, Laboratoire Francis Perrin, CEA, IRAMIS, SPAM, F-91191 Gif-sur-Yvette, France, and Laboratoire Claude Fréjacques, CEA, IRAMIS, SIS2M, F-91191 Gif-sur-Yvette, France
| | - François Piuzzi
- Laboratoire des Mécanismes Réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France, Laboratoire Francis Perrin, CEA, IRAMIS, SPAM, F-91191 Gif-sur-Yvette, France, and Laboratoire Claude Fréjacques, CEA, IRAMIS, SIS2M, F-91191 Gif-sur-Yvette, France
| | - Jean-Pierre Dognon
- Laboratoire des Mécanismes Réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France, Laboratoire Francis Perrin, CEA, IRAMIS, SPAM, F-91191 Gif-sur-Yvette, France, and Laboratoire Claude Fréjacques, CEA, IRAMIS, SIS2M, F-91191 Gif-sur-Yvette, France
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8
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Callis PR. Exploring the Electrostatic Landscape of Proteins with Tryptophan Fluorescence. REVIEWS IN FLUORESCENCE 2009. [DOI: 10.1007/978-0-387-88722-7_10] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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9
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Hernández-Alcántara G, Rodríguez-Romero A, Reyes-Vivas H, Peon J, Cabrera N, Ortiz C, Enríquez-Flores S, De la Mora-De la Mora I, López-Velázquez G. Unraveling the mechanisms of tryptophan fluorescence quenching in the triosephosphate isomerase from Giardia lamblia. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1493-500. [PMID: 18620084 DOI: 10.1016/j.bbapap.2008.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2007] [Revised: 05/09/2008] [Accepted: 05/29/2008] [Indexed: 10/21/2022]
Abstract
In the native state several proteins exhibit a quenching of fluorescence of their tryptophans. We studied triosephosphate isomerase from Giardia lamblia (GlTIM) to dissect the mechanisms that account for the quenching of fluorescence of its Trp. GlTIM contains four Trp per monomer (Trp75, Trp162, Trp173, and Trp196) distributed throughout the 3D structure. The fluorescence of the denatured enzyme is 3-fold higher than that of native GlTIM. To ascertain the origin of this phenomenon, single and triple mutants of Trp per Phe were made. The intrinsic fluorescence was determined, and the data were interpreted on the basis of the crystal structure of the enzyme. Our data show that the fluorescence of all Trp residues is quenched through two different mechanisms. In one, fluorescence is quenched by aromatic-aromatic interactions due to the proximity and orientation of the indole groups of Trp196 and Trp162. The magnitude of the quenching of fluorescence in Trp162 is higher than in the other three Trp. Fluorescence quenching is also due to energy transfer to the charged residues that surround Trp 75, 173 and 196. Further analysis of the fluorescence of GlTIM showed that, among TIMs from other parasites, Trp at position 12 exhibits rather unique properties.
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10
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Fodor E, Ginsburg A. Specific DNA binding by the homeodomain Nkx2.5(C56S): detection of impaired DNA or unfolded protein by isothermal titration calorimetry. Proteins 2006; 64:13-8. [PMID: 16555308 DOI: 10.1002/prot.20960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Titrations of specific 18-bp duplex DNA with the cardiac-specific homeodomain Nkx2.5(C56S) have utilized an ultrasensitive isothermal titration calorimeter (ITC). As the free DNA nears depletion, we observe large apparent decreases in the binding enthalpy when the DNA is impaired or when the temperature is sufficiently high to produce some unfolding of the free protein. Either effect can be attributed to refolding of the biopolymer that occurs as a result of stabilization due to the large favorable change in free energy on the homeodomain binding to DNA (-49.4 kJ/mol at 298 K). In either case, thermodynamic parameters obtained in such ITC experiments are unreliable. By using a lower temperature (85 vs. 95 degrees C) during the annealing of complementary DNA strands, damage of the 18-bp duplex DNA (T(m) = 72 degrees C) is avoided, and titrations with the homeodomain are normal at temperatures from 10 to 40 degrees C when >95% of the protein is folded. Under the latter conditions, the heat capacity plot is linear with a DeltaC(p) value of -0.80 +/- 0.03 kJ K(-1) mol(-1), which is more negative than that calculated from the burial of solvent accessible surface areas (-0.64 +/- 0.05 kJ K(-1) mol(-1)), consistent with water structures being at the protein-DNA interfaces.
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Affiliation(s)
- Elfrieda Fodor
- Section on Protein Chemistry, Laboratory of Biochemistry, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-8012, USA
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11
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Glaaser IW, Bankston JR, Liu H, Tateyama M, Kass RS. A Carboxyl-terminal Hydrophobic Interface Is Critical to Sodium Channel Function. J Biol Chem 2006; 281:24015-23. [PMID: 16798729 DOI: 10.1074/jbc.m605473200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Perturbation of sodium channel inactivation, a finely tuned process that critically regulates the flow of sodium ions into excitable cells, is a common functional consequence of inherited mutations associated with epilepsy, skeletal muscle disease, autism, and cardiac arrhythmias. Understanding the structural basis of inactivation is key to understanding these disorders. Here we identify a novel role for a structural motif in the COOH terminus of the heart NaV1.5 sodium channel in determining channel inactivation. Structural modeling predicts an interhelical hydrophobic interface between paired EF hands in the proximal region of the NaV1.5 COOH terminus. The predicted interface is conserved among almost all EF hand-containing proteins and is the locus of a number of disease-associated mutations. Using the structural model as a guide, we provide biochemical and biophysical evidence that the structural integrity of this interface is necessary for proper Na+ channel inactivation gating. We thus demonstrate a novel role of the sodium channel COOH terminus structure in the control of channel inactivation and in pathologies caused by inherited mutations that disrupt it.
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Affiliation(s)
- Ian W Glaaser
- Department of Pharmacology, Columbia University, New York, New York 10032, USA
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12
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Lopes FJP, Vanario-Alonso CE, Bisch PM, Vieira FMC. A kinetic mechanism for Drosophila bicoid cooperative binding. J Theor Biol 2005; 235:185-98. [PMID: 15862588 DOI: 10.1016/j.jtbi.2005.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Revised: 12/21/2004] [Accepted: 01/05/2005] [Indexed: 10/25/2022]
Abstract
The Bicoid (Bcd) protein is a concentration-dependent transcriptional activator in the embryo of Drosophila melanogaster. Bcd regulates the expression of the maternal and zygotic gene hunchback (hb) that shows a step-like-function expression pattern, in the anterior half of the egg. The regulatory region of hb contains six major binding sites for the Bcd protein, named A1, A2, A3 (strong sites), and X1, X2, X3 (weak sites). Cooperativity between Bcd molecules binding to the hb enhancer element has been characterized as an important mechanism for the step-like shape of hb anterior expression domain. The objective of the present report is to analyse the mechanism of this cooperative binding based on a reaction network model. Using this method we have analysed experimental results from the literature describing how the Bcd protein binds to hb enhancer elements containing the A1 or X1 site alone or these two sites together at wild type distance. This approach allows us to estimate the kinetic constants of protein-protein and protein-DNA interactions. Moreover our results suggest that binding of a Bcd dimer to the hb enhancer element is more stable than binding of a monomer. We propose a cooperative kinetic mechanism for binding of Bcd to the hb enhancer element: First, a monomer binds to the site with a relatively low affinity; after that, another monomer binds to the first one with higher affinity, generating a dimer bound to the site. This yet unreported monomer-monomer cooperative mechanism takes place for occupancy of either one-site or two-site enhancer elements. In addition, we find cooperativity between neighbor sites, as previously reported in the literature.
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Affiliation(s)
- Francisco J P Lopes
- Instituto de Biofísica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21.949-900, Brazil.
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Abstract
The ARID (A–T Rich Interaction Domain) is a helix–turn–helix motif-based DNA-binding domain, conserved in all eukaryotes and diagnostic of a family that includes 15 distinct human proteins with important roles in development, tissue-specific gene expression and proliferation control. The 15 human ARID family proteins can be divided into seven subfamilies based on the degree of sequence identity between individual members. Most ARID family members have not been characterized with respect to their DNA-binding behavior, but it is already apparent that not all ARIDs conform to the pattern of binding AT-rich sequences. To understand better the divergent characteristics of the ARID proteins, we undertook a survey of DNA-binding properties across the entire ARID family. The results indicate that the majority of ARID subfamilies (i.e. five out of seven) bind DNA without obvious sequence preference. DNA-binding affinity also varies somewhat between subfamilies. Site-specific mutagenesis does not support suggestions made from structure analysis that specific amino acids in Loop 2 or Helix 5 are the main determinants of sequence specificity. Most probably, this is determined by multiple interacting differences across the entire ARID structure.
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Affiliation(s)
| | | | - Elizabeth Moran
- To whom correspondence should be addressed. Tel: +215 707 7313; Fax: +215 707 6989;
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14
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Stollar EJ, Gelpí JL, Velankar S, Golovin A, Orozco M, Luisi BF. Unconventional interactions between water and heterocyclic nitrogens in protein structures. Proteins 2004; 57:1-8. [PMID: 15326588 DOI: 10.1002/prot.20216] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We report an unusual interaction in which a water molecule approaches the heterocyclic nitrogen of tryptophan and histidine along an axis that is roughly perpendicular to the aromatic plane of the side chain. The interaction is distinct from the well-known conventional aromatic hydrogen-bond, and it occurs at roughly the same frequency in protein structures. Calculations indicate that the water-indole interaction is favorable energetically, and we find several cases in which such contacts are conserved among structural orthologs. The indole-water interaction links side chains and peptide backbone in turn regions, connects the side chains in beta-sheets, and bridges secondary elements from different domains. We suggest that the water-indole interaction can be indirectly responsible for the quenching of tryptophan fluorescence that is observed in the folding of homeodomains and, possibly, many other proteins. We also observe a similar interaction between water and the imidazole nitrogens of the histidine side chain. Taken together, these observations suggest that the unconventional water-indole and water-imidazole interactions provide a small but favorable contribution to protein structures.
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Affiliation(s)
- Elliott J Stollar
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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15
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Abdelkhalek HB, Beckers A, Schuster-Gossler K, Pavlova MN, Burkhardt H, Lickert H, Rossant J, Reinhardt R, Schalkwyk LC, Müller I, Herrmann BG, Ceolin M, Rivera-Pomar R, Gossler A. The mouse homeobox gene Not is required for caudal notochord development and affected by the truncate mutation. Genes Dev 2004; 18:1725-36. [PMID: 15231714 PMCID: PMC478193 DOI: 10.1101/gad.303504] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The floating head (flh) gene in zebrafish encodes a homeodomain protein, which is essential for notochord formation along the entire body axis. flh orthologs, termed Not genes, have been isolated from chick and Xenopus, but no mammalian ortholog has yet been identified. Truncate (tc) is an autosomal recessive mutation in mouse that specifically disrupts the development of the caudal notochord. Here, we demonstrate that truncate arose by a mutation in the mouse Not gene. The truncate allele (Nottc) contains a point mutation in the homeobox of Not that changes a conserved Phenylalanine residue in helix 1 to a Cysteine (F20C), and significantly destabilizes the homeodomain. Reversion of F20C in one allele of homozygous tc embryonic stem (ES) cells is sufficient to restore normal notochord formation in completely ES cell-derived embryos. We have generated a targeted mutation of Not by replacing most of the Not coding sequence, including the homeobox with the eGFP gene. The phenotype of NoteGFP/eGFP, NoteGFP/tc, and Nottc/tc embryos is very similar but slightly more severe in NoteGFP/eGFP than in Nottc/tc embryos. This confirms allelism of truncate and Not, and indicates that tc is not a complete null allele. Not expression is abolished in Foxa2 and T mutant embryos, suggesting that Not acts downstream of both genes during notochord development. This is in contrast to zebrafish embryos, in which flh interacts with ntl (zebrafish T) in a regulatory loop and is essential for development of the entire notochord, and suggests that different genetic control circuits act in different vertebrate species during notochord formation.
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Affiliation(s)
- Hanaa Ben Abdelkhalek
- Institute for Molecular Biology OE5250, Medizinische Hochschule Hannover, D-30625 Hannover, Germany
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16
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Lotte K, Plessow R, Brockhinke A. Static and time-resolved fluorescence investigations of tryptophan analogues--a solvent study. Photochem Photobiol Sci 2004; 3:348-59. [PMID: 15052363 DOI: 10.1039/b312436c] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The fluorescence properties of tryptophan, polytryptophan and seven of its analogues (7-azatryptophan, 5-hydroxytryptophan, 5-methoxytryptophan, 5-fluorotryptophan, 5-methyltryptophan, 5-bromotryptophan, and 6-fluorotryptophan) are studied using two novel fluorescence spectroscopic techniques for a wide range of solvent polarities. Two-dimensional mapping of all emission and all fluorescence spectra using excitation-emission spectroscopy (EES) has been used to determine quantum yields, positions of emission maxima, full widths at half maximum (FWHMs) as well as Stokes' shifts. Additionally, fluorescence lifetimes obtained from time-resolved experiments using a picosecond laser system are presented and compared with the data acquired from the static setup. This systematic study of the fluorescence characteristics is a prerequisite to assess the potential of these analogues to act as structure-conserving substitutes for tryptophan in protein fluorescence experiments. The potential of these analogues, to act as probes for the local environment, and allow estimation of the polarity in the vicinity of the fluorophore and its exposure to the solvent, is discussed.
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Affiliation(s)
- Kirsten Lotte
- Physikalische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany
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Stollar EJ, Mayor U, Lovell SC, Federici L, Freund SMV, Fersht AR, Luisi BF. Crystal structures of engrailed homeodomain mutants: implications for stability and dynamics. J Biol Chem 2003; 278:43699-708. [PMID: 12923178 DOI: 10.1074/jbc.m308029200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report the crystal structures and biophysical characterization of two stabilized mutants of the Drosophila Engrailed homeodomain that have been engineered to minimize electrostatic repulsion. Four independent copies of each mutant occupy the crystal lattice, and comparison of these structures illustrates variation that can be partly ascribed to networks of correlated conformational adjustments. Central to one network is leucine 26 (Leu26), which occupies alternatively two side chain rotameric conformations (-gauche and trans) and different positions within the hydrophobic core. Similar sets of conformational substates are observed in other Engrailed structures and in another homeodomain. The pattern of structural adjustments can account for NMR relaxation data and sequence co-variation networks in the wider homeodomain family. It may also explain the dysfunction associated with a P26L mutation in the human ARX homeodomain protein. Finally, we observe a novel dipolar interaction between a conserved tryptophan and a water molecule positioned along the normal to the indole ring. This interaction may explain the distinctive fluorescent properties of the homeodomain family.
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Affiliation(s)
- Elliott J Stollar
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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18
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Campanini B, Raboni S, Vaccari S, Zhang L, Cook PF, Hazlett TL, Mozzarelli A, Bettati S. Surface-exposed tryptophan residues are essential for O-acetylserine sulfhydrylase structure, function, and stability. J Biol Chem 2003; 278:37511-9. [PMID: 12813039 DOI: 10.1074/jbc.m305138200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
O-Acetylserine sulfhydrylase is a homodimeric enzyme catalyzing the last step of cysteine biosynthesis via a Bi Bi ping-pong mechanism. The subunit is composed of two domains, each containing one tryptophan residue, Trp50 in the N-terminal domain and Trp161 in the C-terminal domain. Only Trp161 is highly conserved in eucaryotes and bacteria. The coenzyme pyridoxal 5'-phosphate is bound in a cleft between the two domains. The enzyme undergoes an open to closed conformational transition upon substrate binding. The effect of single Trp to Tyr mutations on O-acetylserine sulfhydrylase structure, function, and stability was investigated with a variety of spectroscopic techniques. The mutations do not significantly alter the enzyme secondary structure but affect the catalysis, with a predominant influence on the second half reaction. The W50Y mutation strongly affects the unfolding pathway due to the destabilization of the intersubunit interface. The W161Y mutation, occurring in the C-terminal domain, produces a reduction of the accessibility of the active site to acrylamide and stabilizes thermodynamically the N-terminal domain, a result consistent with stronger interdomain interactions.
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Affiliation(s)
- Barbara Campanini
- Department of Biochemistry and Molecular Biology, University of Parma, Italy
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