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Perera RP, Shaikhqasem A, Rostam N, Dickmanns A, Ficner R, Tittmann K, Dosch R. Bucky Ball Is a Novel Zebrafish Vasa ATPase Activator. Biomolecules 2021; 11:1507. [PMID: 34680140 PMCID: PMC8533965 DOI: 10.3390/biom11101507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 11/17/2022] Open
Abstract
Many multicellular organisms specify germ cells during early embryogenesis by the inheritance of ribonucleoprotein (RNP) granules known as germplasm. However, the role of complex interactions of RNP granules during germ cell specification remains elusive. This study characterizes the interaction of RNP granules, Buc, and zebrafish Vasa (zfVasa) during germ cell specification. We identify a novel zfVasa-binding motif (Buc-VBM) in Buc and a Buc-binding motif (zfVasa-BBM) in zfVasa. Moreover, we show that Buc and zfVasa directly bind in vitro and that this interaction is independent of the RNA. Our circular dichroism spectroscopy data reveal that the intrinsically disordered Buc-VBM peptide forms alpha-helices in the presence of the solvent trifluoroethanol. Intriguingly, we further demonstrate that Buc-VBM enhances zfVasa ATPase activity, thereby annotating the first biochemical function of Buc as a zfVasa ATPase activator. Collectively, these results propose a model in which the activity of zfVasa is a central regulator of primordial germ cell (PGC) formation and is tightly controlled by the germplasm organizer Buc.
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Affiliation(s)
| | - Alaa Shaikhqasem
- Department for Molecular Structural Biology, University of Goettingen, 37077 Goettingen, Germany; (A.S.); (A.D.); (R.F.)
| | - Nadia Rostam
- Institute for Human Genetics, University of Goettingen, 37073 Goettingen, Germany;
| | - Achim Dickmanns
- Department for Molecular Structural Biology, University of Goettingen, 37077 Goettingen, Germany; (A.S.); (A.D.); (R.F.)
| | - Ralf Ficner
- Department for Molecular Structural Biology, University of Goettingen, 37077 Goettingen, Germany; (A.S.); (A.D.); (R.F.)
- deCluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells” (MBExC), University of Goettingen, 37073 Goettingen, Germany
| | - Kai Tittmann
- Department of Molecular Enzymology, University of Goettingen, 37077 Goettingen, Germany;
| | - Roland Dosch
- Department of Developmental Biochemistry, University of Goettingen, 37077 Goettingen, Germany;
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Vincenzi M, Mercurio FA, Leone M. About TFE: Old and New Findings. Curr Protein Pept Sci 2019; 20:425-451. [PMID: 30767740 DOI: 10.2174/1389203720666190214152439] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 01/28/2023]
Abstract
The fluorinated alcohol 2,2,2-Trifluoroethanol (TFE) has been implemented for many decades now in conformational studies of proteins and peptides. In peptides, which are often disordered in aqueous solutions, TFE acts as secondary structure stabilizer and primarily induces an α -helical conformation. The exact mechanism through which TFE plays its stabilizing roles is still debated and direct and indirect routes, relying either on straight interaction between TFE and molecules or indirect pathways based on perturbation of solvation sphere, have been proposed. Another still unanswered question is the capacity of TFE to favor in peptides a bioactive or a native-like conformation rather than simply stimulate the raise of secondary structure elements that reflect only the inherent propensity of a specific amino-acid sequence. In protein studies, TFE destroys unique protein tertiary structure and often leads to the formation of non-native secondary structure elements, but, interestingly, gives some hints about early folding intermediates. In this review, we will summarize proposed mechanisms of TFE actions. We will also describe several examples, in which TFE has been successfully used to reveal structural properties of different molecular systems, including antimicrobial and aggregation-prone peptides, as well as globular folded and intrinsically disordered proteins.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia A Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
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3
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Lou YC, Chou CC, Yeh HH, Chien CY, Sadotra S, Hsu CH, Chen C. Structural basis for -35 element recognition by σ 4 chimera proteins and their interactions with PmrA response regulator. Proteins 2019; 88:69-81. [PMID: 31293000 DOI: 10.1002/prot.25768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 06/03/2019] [Accepted: 07/06/2019] [Indexed: 11/06/2022]
Abstract
In class II transcription activation, the transcription factor normally binds to the promoter near the -35 position and contacts the domain 4 of σ factors (σ4 ) to activate transcription. However, σ4 of σ70 appears to be poorly folded on its own. Here, by fusing σ4 with the RNA polymerase β-flap-tip-helix, we constructed two σ4 chimera proteins, one from σ70 σ 4 70 c and another from σS σ 4 S c of Klebsiella pneumoniae. The two chimera proteins well folded into a monomeric form with strong binding affinities for -35 element DNA. Determining the crystal structure of σ 4 S c in complex with -35 element DNA revealed that σ 4 S c adopts a similar structure as σ4 in the Escherichia coli RNA polymerase σS holoenzyme and recognizes -35 element DNA specifically by several conserved residues from the helix-turn-helix motif. By using nuclear magnetic resonance (NMR), σ 4 70 c was demonstrated to recognize -35 element DNA similar to σ 4 S c . Carr-Purcell-Meiboom-Gill relaxation dispersion analyses showed that the N-terminal helix and the β-flap-tip-helix of σ 4 70 c have a concurrent transient α-helical structure and DNA binding reduced the slow dynamics on σ 4 70 c . Finally, only σ 4 70 c was shown to interact with the response regulator PmrA and its promoter DNA. The chimera proteins are capable of -35 element DNA recognition and can be used for study with transcription factors or other factors that interact with domain 4 of σ factors.
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Affiliation(s)
- Yuan-Chao Lou
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
| | - Chun-Chi Chou
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
| | - Hsin-Hong Yeh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
| | - Chia-Yu Chien
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan, ROC
| | - Sushant Sadotra
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC.,Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, ROC.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan, ROC
| | - Chun-Hua Hsu
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan, ROC.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan, ROC
| | - Chinpan Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
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4
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Liu Y, Yang M, Cheng H, Sun N, Liu S, Li S, Wang Y, Zheng Y, Uversky VN. The effect of phosphorylation on the salt-tolerance-related functions of the soybean protein PM18, a member of the group-3 LEA protein family. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2017; 1865:1291-1303. [PMID: 28867216 DOI: 10.1016/j.bbapap.2017.08.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 08/08/2017] [Accepted: 08/27/2017] [Indexed: 12/29/2022]
Abstract
Enzymatically driven post-translated modifications (PTMs) usually happen within the intrinsically disordered regions of a target protein and can modulate variety of protein functions. Late embryogenesis abundant (LEA) proteins are a family of the plant intrinsically disordered proteins (IDPs). Despite their important roles in plant stress response, there is currently limited knowledge on the presence and functional and structural effects of phosphorylation on LEA proteins. In this study, we identified three phosphorylation sites (Ser90, Tyr136, and Thr266) in the soybean PM18 protein that belongs to the group-3 LEA proteins. In yeast expression system, PM18 protein increased the salt tolerance of yeast, and the phosphorylation of this protein further enhanced its protective function. Further analysis revealed that Ser90 and Tyr136 are more important than Thr266, and these two sites might work cooperatively in regulating the salt resistance function of PM18. The circular dichroism analysis showed that PM18 protein was disordered in aqueous media, and phosphorylation did not affect the disordered status of this protein. However, phosphorylation promoted formation of more helical structure in the presence of sodium dodecyl sulfate (SDS) or trifluoroethanol (TFE). Furthermore, in dedicated in vitro experiments, phosphorylated PM18 protein was able to better protect lactate dehydrogenase (LDH) from the inactivation induced by the freeze-thaw cycles than its un- or dephosphorylated forms. All these data indicate that phosphorylation may have regulatory effects on the stress-tolerance-related function of LEA proteins. Therefore, further studies are needed to shed more light on functional and structural roles of phosphorylation in LEA proteins.
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Affiliation(s)
- Yun Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong 518060, China.
| | - Meiyan Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Hua Cheng
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Nan Sun
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Simu Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Shuiming Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Yong Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Yizhi Zheng
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong 518060, China.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL, USA; Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region 142290, Russia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia.
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5
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Tiffany H, Sonkar K, Gage MJ. The insertion sequence of the N2A region of titin exists in an extended structure with helical characteristics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:1-10. [PMID: 27742555 DOI: 10.1016/j.bbapap.2016.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 12/15/2022]
Abstract
The giant sarcomere protein titin is the third filament in muscle and is integral to maintaining sarcomere integrity as well as contributing to both active and passive tension. Titin is a multi-domain protein that contains regions of repeated structural elements. The N2A region sits at the boundary between the proximal Ig region of titin that is extended under low force and the PEVK region that is extended under high force. Multiple binding interactions have been associated with the N2A region and it has been proposed that this region acts as a mechanical stretch sensor. The focus of this work is a 117 amino acid portion of the N2A region (N2A-IS), which resides between the proximal Ig domains and the PEVK region. Our work has shown that the N2A-IS region is predicted to contain helical structure in the center while both termini are predicted to be disordered. Recombinantly expressed N2A-IS protein contains 13% α-helical structure, as measured via circular dichroism. Additional α-helical structure can be induced with 2,2,2-trifluoroethanol, suggesting that there is transient helical structure that might be stabilized in the context of the entire N2A region. The N2A-IS region does not exhibit any cooperativity in either thermal or chemical denaturation studies while size exclusion chromatography and Fluorescence Resonance Energy Transfer demonstrates that the N2A-IS region has an extended structure. Combined, these results lead to a model of the N2A-IS region having a helical core with extended N- and C-termini.
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Affiliation(s)
- Holly Tiffany
- Department of Biology, Northern Arizona University, Flagstaff, AZ, United States
| | - Kanchan Sonkar
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ, United States
| | - Matthew J Gage
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ, United States; Center for Bioengineering Innovation, Northern Arizona University, Flagstaff, AZ, United States; Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, United States.
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6
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Jaremko Ł, Jaremko M, Nowakowski M, Ejchart A. The Quest for Simplicity: Remarks on the Free-Approach Models. J Phys Chem B 2015; 119:11978-87. [PMID: 26301699 DOI: 10.1021/acs.jpcb.5b07181] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nuclear magnetic relaxation provides a powerful method giving insight into molecular motions at atomic resolution on a broad time scale. Dynamics of biological macromolecules has been widely exploited by measuring (15)N and (13)C relaxation data. Interpretation of these data relies almost exclusively on the use of the model-free approach (MFA) and its extended version (EMFA) which requires no particular physical model of motion and a small number of parameters. It is shown that EMFA is often unable to cope with three different time scales and fails to describe slow internal motions properly. In contrast to EMFA, genuine MFA with two time scales can reproduce internal motions slower than the overall tumbling. It is also shown that MFA and simplified EMFA are equivalent with respect to the values of the N-H bond length and chemical shift anisotropy. Therefore, the vast majority of (15)N relaxation data for proteins can be satisfactorily interpreted solely with MFA.
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Affiliation(s)
- Łukasz Jaremko
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) , Am Fassberg 11, 37077 Göttingen, Germany
| | - Mariusz Jaremko
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Michał Nowakowski
- Centre of New Technologies, University of Warsaw , Banacha 2C, 02-097 Warsaw, Poland
| | - Andrzej Ejchart
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Pawinskiego 5A, 02-106 Warsaw, Poland
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Brain expressed and X-linked (Bex) proteins are intrinsically disordered proteins (IDPs) and form new signaling hubs. PLoS One 2015; 10:e0117206. [PMID: 25612294 PMCID: PMC4303428 DOI: 10.1371/journal.pone.0117206] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/20/2014] [Indexed: 11/19/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are abundant in complex organisms. Due to their promiscuous nature and their ability to adopt several conformations IDPs constitute important points of network regulation. The family of Brain Expressed and X-linked (Bex) proteins consists of 5 members in humans (Bex1-5). Recent reports have implicated Bex proteins in transcriptional regulation and signaling pathways involved in neurodegeneration, cancer, cell cycle and tumor growth. However, structural and biophysical data for this protein family is almost non-existent. We used bioinformatics analyses to show that Bex proteins contain long regions of intrinsic disorder which are conserved across all members. Moreover, we confirmed the intrinsic disorder by circular dichroism spectroscopy of Bex1 after expression and purification in E. coli. These observations strongly suggest that Bex proteins constitute a new group of IDPs. Based on these findings, together with the demonstrated promiscuity of Bex proteins and their involvement in different signaling pathways, we propose that Bex family members play important roles in the formation of protein network hubs.
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Adrover M, Sanchis P, Vilanova B, Pauwels K, Martorell G, Pérez JJ. Conformational ensembles of neuromedin C reveal a progressive coil-helix transition within a binding-induced folding mechanism. RSC Adv 2015. [DOI: 10.1039/c5ra12753j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
NMR has been used to elucidate the folding pathway of neuromedin C and to characterize the architecture of the NMC–SDS micelle complex. Its C-terminal region is more prone to acquire an α-helical fold than the N-terminus, and it also binds to micelles.
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Affiliation(s)
- Miquel Adrover
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears (UIB)
- Palma de Mallorca
- Spain
| | - Pilar Sanchis
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears (UIB)
- Palma de Mallorca
- Spain
| | - Bartolomé Vilanova
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears (UIB)
- Palma de Mallorca
- Spain
| | - Kris Pauwels
- Structural Biology Brussels
- Vrije Universiteit Brussels (VUB)
- 1050 Brussels
- Belgium
- Structural Biology Research Centre
| | - Gabriel Martorell
- Serveis Científico-Tècnics
- Universitat de les Illes Balears (UIB)
- Palma de Mallorca
- Spain
| | - Juan Jesús Pérez
- Departament d'Enginyeria Química
- Universitat Politecnica de Catalunya (UPC)
- ETSEIB
- Barcelona
- Spain
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