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Rodríguez CS, Laurents DV. Architectonic principles of polyproline II helix bundle protein domains. Arch Biochem Biophys 2024; 756:109981. [PMID: 38593862 DOI: 10.1016/j.abb.2024.109981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/18/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024]
Abstract
Glycine rich polyproline II helix assemblies are an emerging class of natural domains found in several proteins with different functions and diverse origins. The distinct properties of these domains relative to those composed of α-helices and β-sheets could make glycine-rich polyproline II helix assemblies a useful building block for protein design. Whereas the high population of polyproline II conformers in disordered state ensembles could facilitate glycine-rich polyproline II helix folding, the architectonic bases of these structures are not well known. Here, we compare and analyze their structures to uncover common features. These protein domains are found to be highly tolerant of distinct flanking sequences. This speaks to the robustness of this fold and strongly suggests that glycine rich polyproline II assemblies could be grafted with other protein domains to engineer new structures and functions. These domains are also well packed with few or no cavities. Moreover, a significant trend towards antiparallel helix configuration is observed in all these domains and could provide stabilizing interactions among macrodipoles. Finally, extensive networks of Cα-H···OC hydrogen bonds are detected in these domains. Despite their diverse evolutionary origins and activities, glycine-rich polyproline II helix assemblies share architectonic features which could help design novel proteins.
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Affiliation(s)
| | - Douglas V Laurents
- Instituto de Química Física "Blas Cabrera" CSIC, Serrano 119 Madrid, Spain.
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2
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Simmons JR, Gasmi-Seabrook G, Rainey JK. Structural features, intrinsic disorder, and modularity of a pyriform spidroin 1 core repetitive domain. Biochem Cell Biol 2023; 101:271-283. [PMID: 36802452 DOI: 10.1139/bcb-2022-0338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Orb-weaving spiders produce up to seven silk types, each with distinct biological roles, protein compositions, and mechanics. Pyriform (or piriform) silk is composed of pyriform spidroin 1 (PySp1) and is the fibrillar component of attachment discs that attach webs to substrates and to each other. Here, we characterize the 234-residue repeat unit (the "Py unit") from the core repetitive domain of Argiope argentata PySp1. Solution-state nuclear magnetic resonance (NMR) spectroscopy-based backbone chemical shift and dynamics analysis demonstrate a structured core flanked by disordered tails, structuring that is maintained in a tandem protein of two connected Py units, indicative of structural modularity of the Py unit in the context of the repetitive domain. Notably, AlphaFold2 predicts the Py unit structure with low confidence, echoing low confidence and poor agreement to the NMR-derived structure for the Argiope trifasciata aciniform spidroin (AcSp1) repeat unit. Rational truncation, validated through NMR spectroscopy, provided a 144-residue construct retaining the Py unit core fold, enabling near-complete backbone and side chain 1H, 13C, and 15N resonance assignment. A six α-helix globular core is inferred, flanked by regions of intrinsic disorder that would link helical bundles in tandem repeat proteins in a beads-on-a-string architecture.
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Affiliation(s)
- Jeffrey R Simmons
- Department of Biochemistry& Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | | | - Jan K Rainey
- Department of Biochemistry& Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, Halifax, NS B3H 4R2, Canada
- School of Biomedical Engineering, Dalhousie University, Halifax, NS B3H 4R2, Canada
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Scholl CL, Holmstrup M, Graham LA, Davies PL. Polyproline type II helical antifreeze proteins are widespread in Collembola and likely originated over 400 million years ago in the Ordovician Period. Sci Rep 2023; 13:8880. [PMID: 37264058 DOI: 10.1038/s41598-023-35983-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/26/2023] [Indexed: 06/03/2023] Open
Abstract
Antifreeze proteins (AFPs) bind to ice crystals to prevent organisms from freezing. A diversity of AFP folds has been found in fish and insects, including alpha helices, globular proteins, and several different beta solenoids. But the variety of AFPs in flightless arthropods, like Collembola, has not yet been adequately assessed. Here, antifreeze activity was shown to be present in 18 of the 22 species of Collembola from cold or temperate zones. Several methods were used to characterize these AFPs, including isolation by ice affinity purification, MALDI mass spectrometry, amino acid composition analysis, tandem mass spectrometry sequencing, transcriptome sequencing, and bioinformatic investigations of sequence databases. All of these AFPs had a high glycine content and were predicted to have the same polyproline type II helical bundle fold, a fold unique to Collembola. These Hexapods arose in the Ordovician Period with the two orders known to produce AFPs diverging around 400 million years ago during the Andean-Saharan Ice Age. Therefore, it is likely that the AFP arose then and persisted in many lineages through the following two ice ages and intervening warm periods, unlike the AFPs of fish which arose independently during the Cenozoic Ice Age beginning ~ 30 million years ago.
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Affiliation(s)
- Connor L Scholl
- Department of Biomedical and Molecular Sciences, Queen's University, 18 Stuart Street, Kingston, ON, K7L3N6, Canada
| | - Martin Holmstrup
- Section of Terrestrial Ecology, Department of Ecoscience, Aarhus University, C.F. Møllers Allé 4, 8000, Aarhus C, Denmark
- Arctic Research Center, Aarhus University, Ny Munkegade 114, 8000, Aarhus C, Denmark
| | - Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, 18 Stuart Street, Kingston, ON, K7L3N6, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, 18 Stuart Street, Kingston, ON, K7L3N6, Canada.
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Stengel D, Saric M, Johnson HR, Schiller T, Diehl J, Chalek K, Onofrei D, Scheibel T, Holland GP. Tyrosine's Unique Role in the Hierarchical Assembly of Recombinant Spider Silk Proteins: From Spinning Dope to Fibers. Biomacromolecules 2023; 24:1463-1474. [PMID: 36791420 DOI: 10.1021/acs.biomac.2c01467] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Producing recombinant spider silk fibers that exhibit mechanical properties approaching native spider silk is highly dependent on the constitution of the spinning dope. Previously published work has shown that recombinant spider silk fibers spun from dopes with phosphate-induced pre-assembly (biomimetic dopes) display a toughness approaching native spider silks far exceeding the mechanical properties of fibers spun from dopes without pre-assembly (classical dopes). Dynamic light scattering experiments comparing the two dopes reveal that biomimetic dope displays a systematic increase in assembly size over time, while light microscopy indicates liquid-liquid-phase separation (LLPS) as evidenced by the formation of micron-scale liquid droplets. Solution nuclear magnetic resonance (NMR) shows that the structural state in classical and biomimetic dopes displays a general random coil conformation in both cases; however, some subtle but distinct differences are observed, including a more ordered state for the biomimetic dope and small chemical shift perturbations indicating differences in hydrogen bonding of the protein in the different dopes with notable changes occurring for Tyr residues. Solid-state NMR demonstrates that the final wet-spun fibers from the two dopes display no structural differences of the poly(Ala) stretches, but biomimetic fibers display a significant difference in Tyr ring packing in non-β-sheet, disordered helical domains that can be traced back to differences in dope preparations. It is concluded that phosphate pre-orders the recombinant silk protein in biomimetic dopes resulting in LLPS and fibers that exhibit vastly improved toughness that could be due to aromatic ring packing differences in non-β-sheet domains that contain Tyr.
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Affiliation(s)
- Dillan Stengel
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Dr, San Diego, California 92182-1030, United States
| | - Merisa Saric
- Lehrstuhl Biomaterialien, Fakultät für Ingenieurwissenschaften, Universität Bayreuth, Prof.-Rüdiger-Bormann-Street 1, Bayreuth 95447, Germany
| | - Hannah R Johnson
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Dr, San Diego, California 92182-1030, United States
| | - Tim Schiller
- Lehrstuhl Biomaterialien, Fakultät für Ingenieurwissenschaften, Universität Bayreuth, Prof.-Rüdiger-Bormann-Street 1, Bayreuth 95447, Germany
| | - Johannes Diehl
- Lehrstuhl Biomaterialien, Fakultät für Ingenieurwissenschaften, Universität Bayreuth, Prof.-Rüdiger-Bormann-Street 1, Bayreuth 95447, Germany
| | - Kevin Chalek
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Dr, San Diego, California 92182-1030, United States
| | - David Onofrei
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Dr, San Diego, California 92182-1030, United States
| | - Thomas Scheibel
- Lehrstuhl Biomaterialien, Fakultät für Ingenieurwissenschaften, Universität Bayreuth, Prof.-Rüdiger-Bormann-Street 1, Bayreuth 95447, Germany
| | - Gregory P Holland
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Dr, San Diego, California 92182-1030, United States
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Chen X, Wu J, Yang F, Zhou M, Wang R, Huang J, Rong Y, Liu J, Wang S. New insight into the mechanism by which antifreeze peptides regulate the physiological function of Streptococcus thermophilus subjected to freezing stress. J Adv Res 2023; 45:127-140. [PMID: 35599106 PMCID: PMC10006524 DOI: 10.1016/j.jare.2022.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 04/14/2022] [Accepted: 05/03/2022] [Indexed: 11/20/2022] Open
Abstract
INTRODUCTION Antifreeze peptides regulate the physiological functions of frozen cells and even their apoptosis; however, the mechanisms by which antifreeze peptides regulate these processes remain unclear, although the interactions between cell membranes and ice are well known to be important in this process. OBJECTIVES Our study aims to investigate how antifreeze peptides regulate cell physiological functions during the freezing process. METHODS We investigated the cryoprotective effect of rsfAFP on the physiological functions of S. thermophilus under freezing stress by measuring cellular metabolism activity, intracellular enzyme activity, cell membrane characterization, and cell apoptosis. The mechanism by which rsfAFP impacts S. thermophilus physiological functions under freezing stress was investigated using multispectral techniques and cryo-TEM. RESULTS We show that a recombinant antifreeze peptide (rsfAFP) interacts with the extracellular capsular polysaccharides and peptidoglycan of Streptococcus thermophilus and ice to cover the outer layer of the membrane, forming a dense protective layer that regulates the molecular structure of extracellular ice crystals, which results in reduced extracellular membrane damage, depressed apoptosis and increased intracellular metabolic activity. This interaction mechanism was indicated by the fact that S. thermophilus better maintained its permeability barrier, membrane fluidity, membrane structural integrity, and cytoplasmic membrane potential during freezing stress with rsfAFP treatment. CONCLUSION These results provide new insights into the mechanism by which rsfAFP regulates frozen cellphysiological functionsand apoptosis under freezing stress.
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Affiliation(s)
- Xu Chen
- School of Mechanical Science & Engineering, Huazhong University of Science and Technology, Wuhan 430074, China; College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Jinhong Wu
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fujia Yang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Mi Zhou
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ruibin Wang
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianlian Huang
- Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing of Ministry of Agriculture and Rural Affairs, Xiamen 361022, China
| | - Yuzhi Rong
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Jianhua Liu
- International Faculty of Applied Technology, Yibin University, Yibin, Sichuan 644000, China
| | - Shaoyun Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, China.
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Daniecki NJ, Bhatt MR, Yap GPA, Zondlo NJ. Proline C-H Bonds as Loci for Proline Assembly via C-H/O Interactions. Chembiochem 2022; 23:e202200409. [PMID: 36129371 DOI: 10.1002/cbic.202200409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/20/2022] [Indexed: 01/25/2023]
Abstract
Proline residues within proteins lack a traditional hydrogen bond donor. However, the hydrogens of the proline ring are all sterically accessible, with polarized C-H bonds at Hα and Hδ that exhibit greater partial positive character and can be utilized as alternative sites for molecular recognition. C-H/O interactions, between proline C-H bonds and oxygen lone pairs, have been previously identified as modes of recognition within protein structures and for higher-order assembly of protein structures. In order to better understand intermolecular recognition of proline residues, a series of proline derivatives was synthesized, including 4R-hydroxyproline nitrobenzoate methyl ester, acylated on the proline nitrogen with bromoacetyl and glycolyl groups, and Boc-4S-(4-iodophenyl)hydroxyproline methyl amide. All three derivatives exhibited multiple close intermolecular C-H/O interactions in the crystallographic state, with H⋅⋅⋅O distances as close as 2.3 Å. These observed distances are well below the 2.72 Å sum of the van der Waals radii of H and O, and suggest that these interactions are particularly favorable. In order to generalize these results, we further analyzed the role of C-H/O interactions in all previously crystallized derivatives of these amino acids, and found that all 26 structures exhibited close intermolecular C-H/O interactions. Finally, we analyzed all proline residues in the Cambridge Structural Database of small-molecule crystal structures. We found that the majority of these structures exhibited intermolecular C-H/O interactions at proline C-H bonds, suggesting that C-H/O interactions are an inherent and important mode for recognition of and higher-order assembly at proline residues. Due to steric accessibility and multiple polarized C-H bonds, proline residues are uniquely positioned as sites for binding and recognition via C-H/O interactions.
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Affiliation(s)
- Noah J Daniecki
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Megh R Bhatt
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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Treviño MÁ, López-Sánchez R, Moya MR, Pantoja-Uceda D, Mompeán M, Laurents DV. Insight into polyproline II helical bundle stability in an antifreeze protein denatured state. Biophys J 2022; 121:4560-4568. [PMID: 36815707 PMCID: PMC9748357 DOI: 10.1016/j.bpj.2022.10.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 10/06/2022] [Accepted: 10/24/2022] [Indexed: 11/02/2022] Open
Abstract
The use of polyproline II (PPII) helices in protein design is currently hindered by limitations in our understanding of their conformational stability and folding. Recent studies of the snow flea antifreeze protein (sfAFP), a useful model system composed of six PPII helices, suggested that a low denatured state entropy contributes to folding thermodynamics. Here, circular dichroism spectroscopy revealed minor populations of PPII like conformers at low temperature. To get atomic level information on the conformational ensemble and entropy of the reduced, denatured state of sfAFP, we have analyzed its chemical shifts and {1H}-15N relaxation parameters by NMR spectroscopy at four experimental conditions. No significant populations of stable secondary structure were detected. The stiffening of certain N-terminal residues at neutral versus acidic pH and shifted pKa values leads us to suggest that favorable charge-charge interactions could bias the conformational ensemble to favor the formation the C1-C28 disulfide bond during nascent folding, although no evidence for preferred contacts between these positions was detected by paramagnetic relaxation enhancement under denaturing conditions. Despite a high content of flexible glycine residues, the mobility of the sfAFP denatured ensemble is similar for denatured α/β proteins both on fast ps/ns as well as slower μs/ms timescales. These results are in line with a conformational entropy in the denatured ensemble resembling that of typical proteins and suggest that new structures based on PPII helical bundles should be amenable to protein design.
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Ramírez de Mingo D, Pantoja-Uceda D, Hervás R, Carrión-Vázquez M, Laurents DV. Conformational dynamics in the disordered region of human CPEB3 linked to memory consolidation. BMC Biol 2022; 20:129. [PMID: 35658951 PMCID: PMC9166367 DOI: 10.1186/s12915-022-01310-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 04/25/2022] [Indexed: 11/10/2022] Open
Abstract
Background Current understanding of the molecular basis of memory consolidation points to an important function of amyloid formation by neuronal-specific isoforms of the cytoplasmic polyadenylation element binding (CPEB) protein family. In particular, CPEB is thought to promote memory persistence through formation of self-sustaining prion-like amyloid assemblies at synapses, mediated by its intrinsically disordered region (IDR) and leading to permanent physical alterations at the basis of memory persistence. Although the molecular mechanisms by which amyloid formation takes place in CPEB have been described in invertebrates, the way amyloid formation occurs in the human homolog CPEB3 (hCPEB3) remains unclear. Here, we characterize by NMR spectroscopy the atomic level conformation and ps-ms dynamics of the 426-residue IDR of hCPEB3, which has been associated with episodic memory in humans. Results We show that the 426-residue N-terminal region of hCPEB3 is a dynamic, intrinsically disordered region (IDR) which lacks stable folded structures. The first 29 residues, M1QDDLLMDKSKTQPQPQQQQRQQQQPQP29, adopt a helical + disordered motif, and residues 86–93: P83QQPPPP93, and 166–175: P166PPPAPAPQP175 form polyproline II (PPII) helices. The (VG)5 repeat motif is completely disordered, and residues 200–250 adopt three partially populated α-helices. Residues 345–355, which comprise the nuclear localization signal (NLS), form a modestly populated α-helix which may mediate STAT5B binding. These findings allow us to suggest a model for nascent hCPEB3 structural transitions at single residue resolution, advancing that amyloid breaker residues, like proline, are a key difference between functional versus pathological amyloids. Conclusion Our NMR spectroscopic analysis of hCPEB3 provides insights into the first structural transitions involved in protein–protein and protein-mRNA interactions. The atomic level understanding of these structural transitions involved in hCPEB3 aggregation is a key first step toward understanding memory persistence in humans, as well as sequence features that differentiate beneficial amyloids from pathological ones. Areas Biophysics, Structural Biology, Biochemistry & Neurosciences. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01310-6.
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Becht DC, Leavens MJ, Zeng B, Rothfuss MT, Briknarová K, Bowler BE. Residual Structure in the Denatured State of the Fast-Folding UBA(1) Domain from the Human DNA Excision Repair Protein HHR23A. Biochemistry 2022; 61:767-784. [PMID: 35430812 PMCID: PMC9150713 DOI: 10.1021/acs.biochem.2c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure of the first ubiquitin-associated domain from HHR23A, UBA(1), was determined by X-ray crystallography at a 1.60 Å resolution, and its stability, folding kinetics, and residual structure under denaturing conditions have been investigated. The concentration dependence of thermal denaturation and size-exclusion chromatography indicate that UBA(1) is monomeric. Guanidine hydrochloride (GdnHCl) denaturation experiments reveal that the unfolding free energy, ΔGu°'(H2O), of UBA(1) is 2.4 kcal mol-1. Stopped-flow folding kinetics indicates sub-millisecond folding with only proline isomerization phases detectable at 25 °C. The full folding kinetics are observable at 4 °C, yielding a folding rate constant, kf, in the absence of a denaturant of 13,000 s-1 and a Tanford β-value of 0.80, consistent with a compact transition state. Evaluation of the secondary structure via circular dichroism shows that the residual helical structure in the denatured state is replaced by polyproline II structure as the GdnHCl concentration increases. Analysis of NMR secondary chemical shifts for backbone 15NH, 13CO, and 13Cα atoms between 4 and 7 M GdnHCl shows three islands of residual helical secondary structure that align in sequence with the three native-state helices. Extrapolation of the NMR data to 0 M GdnHCl demonstrates that helical structure would populate to 17-33% in the denatured state under folding conditions. Comparison with NMR data for a peptide corresponding to helix 1 indicates that this helix is stabilized by transient tertiary interactions in the denatured state of UBA(1). The high helical content in the denatured state, which is enhanced by transient tertiary interactions, suggests a diffusion-collision folding mechanism.
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Affiliation(s)
- Dustin C. Becht
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Moses J. Leavens
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Baisen Zeng
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Michael T. Rothfuss
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Klára Briknarová
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
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Chen X, Wu J, Li X, Yang F, Huang D, Huang J, Wang S, Guyonnet V. Snow flea antifreeze peptide for cryopreservation of lactic acid bacteria. NPJ Sci Food 2022; 6:10. [PMID: 35115563 PMCID: PMC8813996 DOI: 10.1038/s41538-022-00128-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/10/2022] [Indexed: 01/10/2023] Open
Abstract
Cryogenic machining is one of the most commonly used techniques for processing and preserving in food industry, and traditional antifreeze agents cannot regulate the mechanical stress damage caused by ice crystals formed during recrystallization or thawing. In this study, we successfully developed an express system of a novel recombinant snow flea antifreeze peptide (rsfAFP), which has significant ice recrystallization inhibition ability, thermal hysteresis activity and alters ice nucleation, thus regulating extracellular ice crystal morphology and recrystallization. We showed that rsfAFP improved the survival rate, acid-producing ability, freezing stability, and cellular metabolism activity of Streptococcus thermophilus. We further showed that rsfAFP interacts with the membrane and ice crystals to cover the outer layer of cells, forming a dense protective layer that maintains the physiological functions of S. thermophilus under freezing stress. These findings provide the scientific basis for using rsfAFP as an effective antifreeze agent for lactic acid bacteria cryopreservation or other frozen food.
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Affiliation(s)
- Xu Chen
- College of Biological Science and Engineering, Fuzhou University, 350108, Fuzhou, Fujian, China.,College of Chemical Engineering, Fuzhou University, 350108, Fuzhou, Fujian, China
| | - Jinhong Wu
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Xiaozhen Li
- College of Biological Science and Engineering, Fuzhou University, 350108, Fuzhou, Fujian, China
| | - Fujia Yang
- College of Biological Science and Engineering, Fuzhou University, 350108, Fuzhou, Fujian, China.,College of Chemical Engineering, Fuzhou University, 350108, Fuzhou, Fujian, China
| | - Dan Huang
- Fujian Provincial Key Laboratory of Frozen Processed Aquatic Products, 361022, Xiamen, China.,Fujian Anjoy Food Co. Ltd, 361022, Xiamen, China
| | - Jianlian Huang
- Fujian Provincial Key Laboratory of Frozen Processed Aquatic Products, 361022, Xiamen, China.,Fujian Anjoy Food Co. Ltd, 361022, Xiamen, China
| | - Shaoyun Wang
- College of Biological Science and Engineering, Fuzhou University, 350108, Fuzhou, Fujian, China.
| | - Vincent Guyonnet
- FFI Consulting Ltd, 2488 Lyn Road, Brockville, ON, K6V 5T3, Canada
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Mompeán M, Treviño MÁ, Laurents DV. Partial structure, dampened mobility, and modest impact of a His tag in the SARS-CoV-2 Nsp2 C-terminal region. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:1129-1137. [PMID: 34633480 PMCID: PMC8503394 DOI: 10.1007/s00249-021-01575-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/10/2021] [Accepted: 10/03/2021] [Indexed: 11/30/2022]
Abstract
Intrinsically disordered proteins (IDPs) play essential roles in regulating physiological processes in eukaryotic cells. Many viruses use their own IDPs to "hack" these processes to deactivate host defenses and promote viral growth. Thus, viral IDPs are attractive drug targets. While IDPs are hard to study by X-ray crystallography or cryo-EM, atomic level information on their conformational preferences and dynamics can be obtained using NMR spectroscopy. SARS-CoV-2 Nsp2, whose C-terminal region (CtR) is predicted to be disordered, interacts with human proteins that regulate translation initiation and endosome vesicle sorting. Molecules that block these interactions could be valuable leads for drug development. The 13Cβ and backbone 13CO, 1HN, 13Cα, and 15N nuclei of Nsp2's 45-residue CtR were assigned and used to characterize its structure and dynamics in three contexts; namely: (1) retaining an N-terminal His tag, (2) without the His tag and with an adventitious internal cleavage, and (3) lacking both the His tag and the internal cleavage. Two five-residue segments adopting a minor extended population were identified. Overall, the dynamic behavior is midway between a completely rigid and a fully flexible chain. Whereas the presence of an N-terminal His tag and internal cleavage stiffen and loosen, respectively, neighboring residues, they do not affect the tendency of two regions to populate extended conformations.
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Affiliation(s)
- Miguel Mompeán
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain
| | - Miguel Á Treviño
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain
| | - Douglas V Laurents
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain.
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Mompeán M, Oroz J, Laurents DV. Do polyproline II helix associations modulate biomolecular condensates? FEBS Open Bio 2021; 11:2390-2399. [PMID: 33934561 PMCID: PMC8409303 DOI: 10.1002/2211-5463.13163] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 03/29/2021] [Accepted: 04/09/2021] [Indexed: 12/22/2022] Open
Abstract
Biomolecular condensates are microdroplets that form inside cells and serve to selectively concentrate proteins, RNAs and other molecules for a variety of physiological functions, but can contribute to cancer, neurodegenerative diseases and viral infections. The formation of these condensates is driven by weak, transient interactions between molecules. These weak associations can operate at the level of whole protein domains, elements of secondary structure or even moieties composed of just a few atoms. Different types of condensates do not generally combine to form larger microdroplets, suggesting that each uses a distinct class of attractive interactions. Here, we address whether polyproline II (PPII) helices mediate condensate formation. By combining with PPII-binding elements such as GYF, WW, profilin, SH3 or OCRE domains, PPII helices help form lipid rafts, nuclear speckles, P-body-like neuronal granules, enhancer complexes and other condensates. The number of PPII helical tracts or tandem PPII-binding domains can strongly influence condensate stability. Many PPII helices have a low content of proline residues, which hinders their identification. Recently, we characterized the NMR spectral properties of a Gly-rich, Pro-poor protein composed of six PPII helices. Based on those results, we predicted that many Gly-rich segments may form PPII helices and interact with PPII-binding domains. This prediction is being tested and could join the palette of verified interactions contributing to biomolecular condensate formation.
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Affiliation(s)
- Miguel Mompeán
- Departamento de Química Física BiológicaInstituto de Química Física RocasolanoCSICMadridEspaña
| | - Javier Oroz
- Departamento de Química Física BiológicaInstituto de Química Física RocasolanoCSICMadridEspaña
| | - Douglas V. Laurents
- Departamento de Química Física BiológicaInstituto de Química Física RocasolanoCSICMadridEspaña
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14
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Ruidiaz SF, Dreier JE, Hartmann-Petersen R, Kragelund BB. The disordered PCI-binding human proteins CSNAP and DSS1 have diverged in structure and function. Protein Sci 2021; 30:2069-2082. [PMID: 34272906 PMCID: PMC8442969 DOI: 10.1002/pro.4159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 12/30/2022]
Abstract
Intrinsically disordered proteins (IDPs) regularly constitute components of larger protein assemblies contributing to architectural stability. Two small, highly acidic IDPs have been linked to the so-called PCI complexes carrying PCI-domain subunits, including the proteasome lid and the COP9 signalosome. These two IDPs, DSS1 and CSNAP, have been proposed to have similar structural propensities and functions, but they display differences in their interactions and interactome sizes. Here we characterized the structural properties of human DSS1 and CSNAP at the residue level using NMR spectroscopy and probed their propensities to bind ubiquitin. We find that distinct structural features present in DSS1 are completely absent in CSNAP, and vice versa, with lack of relevant ubiquitin binding to CSNAP, suggesting the two proteins to have diverged in both structure and function. Our work additionally highlights that different local features of seemingly similar IDPs, even subtle sequence variance, may endow them with different functional traits. Such traits may underlie their potential to engage in multiple interactions thereby impacting their interactome sizes.
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Affiliation(s)
- Sarah F Ruidiaz
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,REPIN, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Jesper E Dreier
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,REPIN, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Rasmus Hartmann-Petersen
- REPIN, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,REPIN, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
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15
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Zhu S, Yu J, Chen X, Zhang Q, Cai X, Ding Y, Zhou X, Wang S. Dual cryoprotective strategies for ice-binding and stabilizing of frozen seafood: A review. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.02.069] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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16
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Glycine rich segments adopt polyproline II helices: Implications for biomolecular condensate formation. Arch Biochem Biophys 2021; 704:108867. [PMID: 33794191 DOI: 10.1016/j.abb.2021.108867] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 11/22/2022]
Abstract
Many intrinsically disordered proteins contain Gly-rich regions which are generally assumed to be disordered. Such regions often form biomolecular condensates which play essential roles in organizing cellular processes. However, the bases of their formation and stability are still not completely understood. Based on NMR studies of the Gly-rich H. harveyi "snow flea" antifreeze protein, we recently proposed that Gly-rich sequences, such as the third "RGG" region of Fused in Sarcoma (FUS) protein, may adopt polyproline II helices whose association might stabilize condensates. Here, this hypothesis is tested with a polypeptide corresponding to the third RGG region of FUS. NMR spectroscopy and molecular dynamics simulations suggest that significant populations of polyproline II helix are present. These findings are corroborated in a model peptide Ac-RGGYGGRGGWGGRGGY-NH2, where a peak characteristic of polyproline II helix is observed using CD spectroscopy. Its intensity suggests a polyproline II population of 40%. This result is supported by data from FTIR and NMR spectroscopies. In the latter, NOE correlations are observed between the Tyr and Arg, and Arg and Trp side chain hydrogens, confirming that side chains spaced three residues apart are close in space. Taken together, the data are consistent with a polyproline II helix, which is bent to optimize interactions between guanidinium and aromatic moieties, in equilibrium with a statistical coil ensemble. These results lend credence to the hypothesis that Gly-rich segments of disordered proteins may form polyproline II helices which help stabilize biomolecular condensates.
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17
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Scholl CL, Tsuda S, Graham LA, Davies PL. Crystal waters on the nine polyproline type II helical bundle springtail antifreeze protein from Granisotoma rainieri match the ice lattice. FEBS J 2021; 288:4332-4347. [PMID: 33460499 DOI: 10.1111/febs.15717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/18/2020] [Accepted: 01/11/2021] [Indexed: 01/03/2023]
Abstract
A springtail (Collembola) identified as Granisotoma rainieri was collected from snow in Hokkaido, Japan, in late winter when nighttime temperatures were below zero. Extracts of these arthropods showed antifreeze activity by shaping ice crystals and stopping their growth. The glycine-rich proteins responsible for this freezing point depression were isolated by ice-affinity purification and had principal masses of ~ 6.9 and 9.6 kDa. We identified a transcript for a 9.6-kDa component and produced it as a His-tagged recombinant protein for structural analysis. Its crystal structure was solved to a resolution of 1.21 Å and revealed a polyproline type II helical bundle, similar to the six-helix Hypogastrura harveyi AFP, but with nine helices organized into two layers held together by an extensive network of hydrogen bonds. One of the layers is flat, regular, and hydrophobic and likely serves as the ice-binding side. Although this surface makes close protein-protein contacts with its symmetry mate in the crystal, it has bound chains of waters present that resemble those on the basal and primary prism planes of ice. Molecular dynamic simulations indicate most of these crystal waters would preferentially occupy these sites if exposed to bulk solvent in the absence of the symmetry mate. These prepositioned waters lend further support to the ice-binding mechanism in which AFPs organize ice-like waters on one surface to adsorb to ice. DATABASES: Structural data are available in the Protein Data Bank under the accession number 7JJV. Transcript data are available in GenBank under accession numbers MT780727, MT780728, MT780729, MT780730, MT780731 and MT985982.
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Affiliation(s)
- Connor L Scholl
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Sakae Tsuda
- Bioproduction Research Institute, National Institute of Advanced Science and Technology (AIST), Sapporo, Japan
| | - Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
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18
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Oroz J, Félix SS, Cabrita EJ, Laurents DV. Structural transitions in Orb2 prion-like domain relevant for functional aggregation in memory consolidation. J Biol Chem 2020; 295:18122-18133. [PMID: 33093173 PMCID: PMC7939463 DOI: 10.1074/jbc.ra120.015211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
The recent structural elucidation of ex vivo Drosophila Orb2 fibrils revealed a novel amyloid formed by interdigitated Gln and His residue side chains belonging to the prion-like domain. However, atomic-level details on the conformational transitions associated with memory consolidation remain unknown. Here, we have characterized the nascent conformation and dynamics of the prion-like domain (PLD) of Orb2A using a nonconventional liquid-state NMR spectroscopy strategy based on 13C detection to afford an essentially complete set of 13Cα, 13Cβ, 1Hα, and backbone 13CO and 15N assignments. At pH 4, where His residues are protonated, the PLD is disordered and flexible, except for a partially populated α-helix spanning residues 55-60, and binds RNA oligos, but not divalent cations. At pH 7, in contrast, His residues are predominantly neutral, and the Q/H segments adopt minor populations of helical structure, show decreased mobility and start to self-associate. At pH 7, the His residues do not bind RNA or Ca2+, but do bind Zn2+, which promotes further association. These findings represent a remarkable case of structural plasticity, based on which an updated model for Orb2A functional amyloidogenesis is suggested.
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Affiliation(s)
- Javier Oroz
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Madrid, Spain
| | - Sara S Félix
- Departamento de Química Faculdade de Ciências e Tecnologia, UCIBIO, Universidade Nova de Lisboa, Caparica, Portugal
| | - Eurico J Cabrita
- Departamento de Química Faculdade de Ciências e Tecnologia, UCIBIO, Universidade Nova de Lisboa, Caparica, Portugal
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19
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Abrogation of prenucleation, transient oligomerization of the Huntingtin exon 1 protein by human profilin I. Proc Natl Acad Sci U S A 2020; 117:5844-5852. [PMID: 32127471 DOI: 10.1073/pnas.1922264117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human profilin I reduces aggregation and concomitant toxicity of the polyglutamine-containing N-terminal region of the huntingtin protein encoded by exon 1 (httex1) and responsible for Huntington's disease. Here, we investigate the interaction of profilin with httex1 using NMR techniques designed to quantitatively analyze the kinetics and equilibria of chemical exchange at atomic resolution, including relaxation dispersion, exchange-induced shifts, and lifetime line broadening. We first show that the presence of two polyproline tracts in httex1, absent from a shorter huntingtin variant studied previously, modulates the kinetics of the transient branched oligomerization pathway that precedes nucleation, resulting in an increase in the populations of the on-pathway helical coiled-coil dimeric and tetrameric species (τex ≤ 50 to 70 μs), while leaving the population of the off-pathway (nonproductive) dimeric species largely unaffected (τex ∼750 μs). Next, we show that the affinity of a single molecule of profilin to the polyproline tracts is in the micromolar range (K diss ∼ 17 and ∼ 31 μM), but binding of a second molecule of profilin is negatively cooperative, with the affinity reduced ∼11-fold. The lifetime of a 1:1 complex of httex1 with profilin, determined using a shorter huntingtin variant containing only a single polyproline tract, is shown to be on the submillisecond timescale (τ ex ∼ 600 μs and K diss ∼ 50 μM). Finally, we demonstrate that, in stable profilin-httex1 complexes, the productive oligomerization pathway, leading to the formation of helical coiled-coil httex1 tetramers, is completely abolished, and only the pathway resulting in "nonproductive" dimers remains active, thereby providing a mechanistic basis for how profilin reduces aggregation and toxicity of httex1.
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20
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Pantoja-Uceda D, Oroz J, Fernández C, de Alba E, Giraldo R, Laurents DV. Conformational Priming of RepA-WH1 for Functional Amyloid Conversion Detected by NMR Spectroscopy. Structure 2020; 28:336-347.e4. [PMID: 31918960 DOI: 10.1016/j.str.2019.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 10/03/2019] [Accepted: 12/16/2019] [Indexed: 12/21/2022]
Abstract
How proteins with a stable globular fold acquire the amyloid state is still largely unknown. RepA, a versatile plasmidic DNA binding protein from Pseudomonas savastanoi, is functional as a transcriptional repressor or as an initiator or inhibitor of DNA replication, the latter via assembly of an amyloidogenic oligomer. Its N-terminal domain (WH1) is responsible for discrimination between these functional abilities by undergoing insufficiently understood structural changes. RepA-WH1 is a stable dimer whose conformational dynamics had not been explored. Here, we have studied it through NMR {1H}-15N relaxation and H/D exchange kinetics measurements. The N- and the C-terminal α-helices, and the internal amyloidogenic loop, are partially unfolded in solution. S4-indigo, a small inhibitor of RepA-WH1 amyloidogenesis, binds to and tethers the N-terminal α-helix to a β-hairpin that is involved in dimerization, thus providing evidence for a priming role of fraying ends and dimerization switches in the amyloidogenesis of folded proteins.
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Affiliation(s)
- David Pantoja-Uceda
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, c/ Serrano 119, Madrid 28006, Spain
| | - Javier Oroz
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, c/ Serrano 119, Madrid 28006, Spain
| | - Cristina Fernández
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, c/ Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Eva de Alba
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, c/ Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Rafael Giraldo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, c/ Ramiro de Maeztu 9, Madrid 28040, Spain.
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, c/ Serrano 119, Madrid 28006, Spain.
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21
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Kubyshkin V, Budisa N. Anticipating alien cells with alternative genetic codes: away from the alanine world! Curr Opin Biotechnol 2019; 60:242-249. [DOI: 10.1016/j.copbio.2019.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 05/07/2019] [Indexed: 12/24/2022]
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22
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Oroz J, Laurents DV. RNA binding proteins: Diversity from microsurgeons to cowboys. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194398. [PMID: 31271896 DOI: 10.1016/j.bbagrm.2019.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/03/2019] [Accepted: 06/13/2019] [Indexed: 01/21/2023]
Abstract
The conformation and mechanism of proteins that degrade and bind RNA, which has provided key insights into post-transcriptional gene regulation, is explored here. During the twentieth century's last decades, the characterization of ribonucleases and RNA binding domains revealed the diversity of their reaction mechanisms and modes of RNA recognition, and the bases of protein folding, substrate specificity and binding affinity. More recent research showed how these domains combine through oligomerization or genetic recombination to create larger proteins with highly specific and readily programmable ribonucleolytic activity. In the last 15 years, the study of the capacity of proteins, usually disordered, to pool RNAs into discrete, non-aqueous microdroplets to facilitate their transport, modification and degradation - analogous to cowboys herding cattle - has advanced our comprehension of gene expression. Finally, the current uses of RNA binding proteins and the future applications of protein/RNA microdroplets are highlighted.
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Affiliation(s)
- Javier Oroz
- "Rocasolano" Institute of Physical Chemistry, Spanish National Research Council, Serrano 119, Madrid 28006, Spain
| | - Douglas V Laurents
- "Rocasolano" Institute of Physical Chemistry, Spanish National Research Council, Serrano 119, Madrid 28006, Spain.
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23
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Kubyshkin V, Budisa N. Promotion of the collagen triple helix in a hydrophobic environment. Org Biomol Chem 2019; 17:2502-2507. [DOI: 10.1039/c9ob00070d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The collagen triple helix is better suited for octanol than for water.
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Affiliation(s)
| | - Nediljko Budisa
- Institute of Chemistry
- Technical University of Berlin
- Berlin
- Germany
- University of Manitoba
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