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Vang J, Pustovalova Y, Korzhnev DM, Gorbatyuk O, Keeler C, Hodsdon ME, Hoch JC. Architecture of the Two Metal Binding Sites in Prolactin. Biophys J 2022; 121:1312-1321. [PMID: 35192840 PMCID: PMC9034190 DOI: 10.1016/j.bpj.2022.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/14/2021] [Accepted: 02/15/2022] [Indexed: 11/29/2022] Open
Abstract
Metal binding by members of the growth hormone (GH) family of hematopoietic cytokines has been a subject of considerable interest. However, beyond appreciation of its role in reversible packing of GH proteins in secretory granules, the molecular mechanisms of metal binding and granule formation remain poorly understood. Here, we investigate metal binding by a GH family member prolactin (PRL) using paramagnetic metal titration and chelation experiments. Cu2+-mediated paramagnetic relaxation enhancement measurements identified two partial metal-binding sites on the opposite faces of PRL composed of residues H30/H180 and E93/H97, respectively. Coordination of metal ions by these two sites causes formation of inter-molecular bridges between the PRL protomers and enables formation of reversible higher aggregates. These findings in vitro suggest a model for reversible packaging of PRL in secretory granules. The proposed mechanism of metal-promoted PRL aggregation lends insight and support to the previously suggested role of metal coordination in secretory granule formation by GH proteins.
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Affiliation(s)
- Janus Vang
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut
| | - Yulia Pustovalova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut
| | - Oksana Gorbatyuk
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut
| | - Camille Keeler
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut
| | - Michael E Hodsdon
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut
| | - Jeffrey C Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut.
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Improvement of PR8-Derived Recombinant Clade 2.3.4.4c H5N6 Vaccine Strains by Optimization of Internal Genes and H103Y Mutation of Hemagglutinin. Vaccines (Basel) 2020; 8:vaccines8040781. [PMID: 33419331 PMCID: PMC7766170 DOI: 10.3390/vaccines8040781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 12/04/2022] Open
Abstract
Clade 2.3.4.4c H5N6 avian influenza A viruses (AIVs) may have originally adapted to infect chickens and have caused highly pathogenic avian influenza (HPAI) in poultry and human fatalities. Although A/Puerto Rico/8/1934 (H1N1) (PR8)-derived recombinant clade 2.3.4.4c H5N6 vaccine strains have been effective in embryonated chicken eggs-based vaccine production system, they need to be improved in terms of immunogenicity and potential mammalian pathogenicity. We replaced the PB2 gene alone or the PB2 (polymerase basic protein 2), NP (nucleoprotein), M (matrix protein) and NS (non-structural protein) genes together in the PR8 strain with corresponding genes from AIVs with low pathogenicity to remove mammalian pathogenicity and to match CD8+ T cell epitopes with contemporary HPAI viruses, respectively, without loss of viral fitness. Additionally, we tested the effect of the H103Y mutation of hemagglutinin (HA) on antigen productivity, mammalian pathogenicity and heat/acid stability. The replacement of PB2 genes and the H103Y mutation reduced the mammalian pathogenicity but increased the antigen productivity of the recombinant vaccine strains. The H103Y mutation increased heat stability but unexpectedly decreased acid stability, probably resulting in increased activation pH for HA. Interestingly, vaccination with inactivated recombinant virus with replaced NP, M and NS genes halted challenge virus shedding earlier than the recombinant vaccine without internal genes replacement. In conclusion, we successfully generated recombinant clade 2.3.4.4c H5N6 vaccine strains that were less pathogenic to mammals and more productive and heat stable than conventional PR8-derived recombinant strains by optimization of internal genes and the H103Y mutation of HA.
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Montanucci L, Martelli PL, Ben-Tal N, Fariselli P. A natural upper bound to the accuracy of predicting protein stability changes upon mutations. Bioinformatics 2018; 35:1513-1517. [DOI: 10.1093/bioinformatics/bty880] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 09/07/2018] [Accepted: 10/16/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ludovica Montanucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Pier Luigi Martelli
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Piero Fariselli
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
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Narayan A, Naganathan AN. Switching Protein Conformational Substates by Protonation and Mutation. J Phys Chem B 2018; 122:11039-11047. [PMID: 30048131 DOI: 10.1021/acs.jpcb.8b05108] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein modules that regulate the availability and conformational status of transcription factors determine the rapidity, duration, and magnitude of cellular response to changing conditions. One such system is the single-gene product Cnu, a four-helix bundle transcription co-repressor, which acts as a molecular thermosensor regulating the expression of virulence genes in enterobacteriaceae through modulation of its native conformational ensemble. Cnu and related genes have also been implicated in pH-dependent expression of virulence genes. We hypothesize that protonation of a conserved buried histidine (H45) in Cnu promotes large electrostatic frustration, thus disturbing the H-NS, a transcription factor, binding face. Spectroscopic and calorimetric methods reveal that H45 exhibits a suppressed p Ka of ∼5.1, the protonation of which switches the conformation to an alternate native ensemble in which the fourth helix is disordered. The population redistribution can also be achieved through a mutation H45V, which does not display any switching behavior at pH values greater than 4. The Wako-Saitô-Muñoz-Eaton (WSME) statistical mechanical model predicts specific differences in the conformations and fluctuations of the fourth and first helices of Cnu determining the observed pH response. We validate these predictions through fluorescence lifetime measurements of a sole tryptophan, highlighting the presence of both native and non-native interactions in the regions adjoining the binding face of Cnu. Our combined experimental-computational study thus shows that Cnu acts both as a thermo- and pH-sensor orchestrated via a subtle but quantifiable balance between the weak packing of a structural element and protonation of a buried histidine that promotes electrostatic frustration.
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Affiliation(s)
- Abhishek Narayan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
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Contini A, Tiana G. A many-body term improves the accuracy of effective potentials based on protein coevolutionary data. J Chem Phys 2016; 143:025103. [PMID: 26178131 DOI: 10.1063/1.4926665] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The study of correlated mutations in alignments of homologous proteins proved to be successful not only in the prediction of their native conformation but also in the development of a two-body effective potential between pairs of amino acids. In the present work, we extend the effective potential, introducing a many-body term based on the same theoretical framework, making use of a principle of maximum entropy. The extended potential performs better than the two-body one in predicting the energetic effect of 308 mutations in 14 proteins (including membrane proteins). The average value of the parameters of the many-body term correlates with the degree of hydrophobicity of the corresponding residues, suggesting that this term partly reflects the effect of the solvent.
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Affiliation(s)
- A Contini
- Department of Physics, Università degli Studi di Milano, via Celoria 16, 20133 Milano, Italy
| | - G Tiana
- Department of Physics, Università degli Studi di Milano, and INFN, via Celoria 16, 20133 Milano, Italy
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Premzl M. Third party data gene data set of eutherian growth hormone genes. GENOMICS DATA 2015; 6:166-9. [PMID: 26697363 PMCID: PMC4664738 DOI: 10.1016/j.gdata.2015.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 09/06/2015] [Accepted: 09/07/2015] [Indexed: 10/31/2022]
Abstract
Among 146 potential coding sequences, the most comprehensive eutherian growth hormone gene data set annotated 100 complete coding sequences. The eutherian comparative genomic analysis protocol first described 5 major gene clusters of eutherian growth hormone genes. The present updated gene classification and nomenclature of eutherian growth hormone genes integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis into new framework of future experiments. The curated third party data gene data set of eutherian growth hormone genes was deposited in European Nucleotide Archive under accession numbers LM644135-LM644234.
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Affiliation(s)
- Marko Premzl
- Laboratory of Genomics, Centre of Animal Reproduction, 55 Heinzel St, Zagreb, Croatia
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Blane A, Fanucchi S. Effect of pH on the Structure and DNA Binding of the FOXP2 Forkhead Domain. Biochemistry 2015; 54:4001-7. [DOI: 10.1021/acs.biochem.5b00155] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Ashleigh Blane
- Protein Structure-Function
Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Sylvia Fanucchi
- Protein Structure-Function
Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050, South Africa
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Yang N, Liu C, Peck AR, Girondo MA, Yanac AF, Tran TH, Utama FE, Tanaka T, Freydin B, Chervoneva I, Hyslop T, Kovatich AJ, Hooke JA, Shriver CD, Rui H. Prolactin-Stat5 signaling in breast cancer is potently disrupted by acidosis within the tumor microenvironment. Breast Cancer Res 2014; 15:R73. [PMID: 24004716 PMCID: PMC3978581 DOI: 10.1186/bcr3467] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 07/12/2013] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION Emerging evidence in estrogen receptor-positive breast cancer supports the notion that prolactin-Stat5 signaling promotes survival and maintenance of differentiated luminal cells, and loss of nuclear tyrosine phosphorylated Stat5 (Nuc-pYStat5) in clinical breast cancer is associated with increased risk of antiestrogen therapy failure. However, the molecular mechanisms underlying loss of Nuc-pYStat5 in breast cancer remain poorly defined. METHODS We investigated whether moderate extracellular acidosis of pH 6.5 to 6.9 frequently observed in breast cancer inhibits prolactin-Stat5 signaling, using in vitro and in vivo experimental approaches combined with quantitative immunofluorescence protein analyses to interrogate archival breast cancer specimens. RESULTS Moderate acidosis at pH 6.8 potently disrupted signaling by receptors for prolactin but not epidermal growth factor, oncostatin M, IGF1, FGF or growth hormone. In breast cancer specimens there was mutually exclusive expression of Nuc-pYStat5 and GLUT1, a glucose transporter upregulated in glycolysis-dependent carcinoma cells and an indirect marker of lactacidosis. Mutually exclusive expression of GLUT1 and Nuc-pYStat5 occurred globally or regionally within tumors, consistent with global or regional acidosis. All prolactin-induced signals and transcripts were suppressed by acidosis, and the acidosis effect was rapid and immediately reversible, supporting a mechanism of acidosis disruption of prolactin binding to receptor. T47D breast cancer xenotransplants in mice displayed variable acidosis (pH 6.5 to 6.9) and tumor regions with elevated GLUT1 displayed resistance to exogenous prolactin despite unaltered levels of prolactin receptors and Stat5. CONCLUSIONS Moderate extracellular acidosis effectively blocks prolactin signaling in breast cancer. We propose that acidosis-induced prolactin resistance represents a previously unrecognized mechanism by which breast cancer cells may escape homeostatic control.
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Nilsson L, Ådén J, Niemiec MS, Nam K, Wittung-Stafshede P. Small pH and Salt Variations Radically Alter the Thermal Stability of Metal-Binding Domains in the Copper Transporter, Wilson Disease Protein. J Phys Chem B 2013; 117:13038-50. [DOI: 10.1021/jp402415y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lina Nilsson
- Chemistry
Department and ‡Computational Life Science Center (CLiC), Umeå University, 90187 Umeå, Sweden
| | - Jörgen Ådén
- Chemistry
Department and ‡Computational Life Science Center (CLiC), Umeå University, 90187 Umeå, Sweden
| | - Moritz S. Niemiec
- Chemistry
Department and ‡Computational Life Science Center (CLiC), Umeå University, 90187 Umeå, Sweden
| | - Kwangho Nam
- Chemistry
Department and ‡Computational Life Science Center (CLiC), Umeå University, 90187 Umeå, Sweden
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Achilonu I, Fanucchi S, Cross M, Fernandes M, Dirr HW. Role of individual histidines in the pH-dependent global stability of human chloride intracellular channel 1. Biochemistry 2012; 51:995-1004. [PMID: 22242893 DOI: 10.1021/bi201541w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chloride intracellular channel proteins exist in both a soluble cytosolic form and a membrane-bound form. The mechanism of conversion between the two forms is not properly understood, although one of the contributing factors is believed to be the variation in pH between the cytosol (~7.4) and the membrane (~5.5). We systematically mutated each of the three histidine residues in CLIC1 to an alanine at position 74 and a phenylalanine at positions 185 and 207. We examined the effect of the histidine-mediated pH dependence on the structure and global stability of CLIC1. None of the mutations were found to alter the global structure of the protein. However, the stability of H74A-CLIC1 and H185F-CLIC1, as calculated from the equilibrium unfolding data, is no longer dependent on pH because similar trends are observed at pH 7.0 and 5.5. The crystal structures show that the mutations result in changes in the local hydrogen bond coordination. Because the mutant total free energy change upon unfolding is not different from that of the wild type at pH 7.0, despite the presence of intermediates that are not seen in the wild type, we propose that it may be the stability of the intermediate state rather than the native state that is dependent on pH. On the basis of the lower stability of the intermediate in the H74A and H185F mutants compared to that of the wild type, we conclude that both His74 and His185 are involved in triggering the pH changes to the conformational stability of wild-type CLIC1 via their protonation, which stabilizes the intermediate state.
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Affiliation(s)
- Ikechukwu Achilonu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050, South Africa
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12
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Abstract
Human prolactin (hPRL) binds two human prolactin receptor molecules, creating active heterotrimeric complexes. Receptors bind dissimilar hormone surfaces termed site 1 and site 2 in an obligate ordered process. We sought to map the functional epitopes in site 1 of hPRL. Extensive alanine mutagenesis (102 of the 199 residues) showed approximately 40% of these mutant hPRLs changed the ΔG for site 1 receptor binding. Six of these residues are within 3.5 Å of the receptor and form the site 1 functional epitopes. We identified a set of noncovalent interactions between these six residues and the receptor. We identified a second group of site 1 residues that are between 3.5 and 5 Å from the receptor where alanine mutations reduced the affinity. This second group has noncovalent interactions with other hormone residues and stabilized the topology of the functional epitopes by linking these to the body of the protein. Finally, we identified a third group of residues that are outside site 1 (>5 Å) and extend to site 2 and whose mutation to alanine significantly weakened receptor binding at site 1 of prolactin. These three groups of residues form a contiguous structural motif between sites 1 and 2 of human prolactin and may constitute structural features that functionally couple sites 1 and 2. This work identifies the residues that form the functional epitopes for site 1 of human prolactin and also identifies a set of residues that support the concept that sites 1 and 2 are functionally coupled by an allosteric mechanism.
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Affiliation(s)
- Geeta Vittal Rao
- Ohio State Biophysics Program, Ohio State University, 1925 Coffey Road, Columbus, OH 43210, USA
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Kulkarni MV, Tettamanzi MC, Murphy JW, Keeler C, Myszka DG, Chayen NE, Lolis EJ, Hodsdon ME. Two independent histidines, one in human prolactin and one in its receptor, are critical for pH-dependent receptor recognition and activation. J Biol Chem 2010; 285:38524-33. [PMID: 20889499 DOI: 10.1074/jbc.m110.172072] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human prolactin (hPRL), a member of the family of hematopoietic cytokines, functions as both an endocrine hormone and autocrine/paracrine growth factor. We have previously demonstrated that recognition of the hPRL·receptor depends strongly on solution acidity over the physiologic range from pH 6 to pH 8. The hPRL·receptor binding interface contains four histidines whose protonation is hypothesized to regulate pH-dependent receptor recognition. Here, we systematically dissect its molecular origin by characterizing the consequences of His to Ala mutations on pH-dependent receptor binding kinetics, site-specific histidine protonation, and high resolution structures of the intermolecular interface. Thermodynamic modeling of the pH dependence to receptor binding affinity reveals large changes in site-specific protonation constants for a majority of interface histidines upon complexation. Removal of individual His imidazoles reduces these perturbations in protonation constants, which is most likely explained by the introduction of solvent-filled, buried cavities in the crystallographic structures without inducing significant conformational rearrangements.
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Affiliation(s)
- Mandar V Kulkarni
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut 06520, USA
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Hansen MJK, Olsen JG, Bernichtein S, O'Shea C, Sigurskjold BW, Goffin V, Kragelund BB. Development of prolactin receptor antagonists with reduced pH-dependence of receptor binding. J Mol Recognit 2010; 24:533-47. [PMID: 20842635 DOI: 10.1002/jmr.1064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 05/26/2010] [Accepted: 05/26/2010] [Indexed: 01/03/2023]
Abstract
The cytokine hormone prolactin has a vast number of diverse functions. Unfortunately, it also exhibits tumor growth promoting properties, which makes the development of prolactin receptor antagonists a priority. Prolactin binds to its cognate receptor with much lower affinity at low pH than at physiological pH and since the extracellular environment around solid tumors often is acidic, it is desirable to develop antagonists that have improved binding affinity at low pH. The pK(a) value of a histidine side chain is ∼6.8 making histidine residues obvious candidates for examination. From evaluation of known molecular structures of human prolactin, of the prolactin receptor and of different complexes of the two, three histidine residues in the hormone-receptor binding site 1 were selected for mutational studies. We analyzed 10 variants by circular dichroism spectroscopy, affinity and thermodynamic characterization of receptor binding by isothermal titration calorimetry combined with in vitro bioactivity in living cells. Histidine residue 27 was recognized as a central hot spot for pH sensitivity and conservative substitutions at this site resulted in strong receptor binding at low pH. Pure antagonists were developed earlier and the histidine mutations were introduced within such background. The antagonistic properties were maintained and the high affinity at low pH conserved. The implications of these findings may open new areas of research in the field of prolactin cancer biology.
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Affiliation(s)
- Mathilde J Kaas Hansen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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