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Hjalte J, Diehl C, Leung AE, Poon JF, Porcar L, Dalgliesh R, Sjögren H, Wahlgren M, Sanchez-Fernandez A. Modulating protein unfolding and refolding via the synergistic association of an anionic and a nonionic surfactant. J Colloid Interface Sci 2024; 672:244-255. [PMID: 38838632 DOI: 10.1016/j.jcis.2024.05.157] [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: 04/02/2024] [Revised: 05/03/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024]
Abstract
HYPOTHESIS Nonionic surfactants can counter the deleterious effect that anionic surfactants have on proteins, where the folded states are retrieved from a previously unfolded state. However, further studies are required to refine our understanding of the underlying mechanism of the refolding process. While interactions between nonionic surfactants and tightly folded proteins are not anticipated, we hypothesized that intermediate stages of surfactant-induced unfolding could define new interaction mechanisms by which nonionic surfactants can further alter protein conformation. EXPERIMENTS In this work, the behavior of three model proteins (human growth hormone, bovine serum albumin, and β-lactoglobulin) was investigated in the presence of the anionic surfactant sodium dodecylsulfate, the nonionic surfactant β-dodecylmaltoside, and mixtures of both surfactants. The transitions occurring to the proteins were determined using intrinsic fluorescence spectroscopy and far-UV circular dichroism. Based on these results, we developed a detailed interaction model for human growth hormone. Using nuclear magnetic resonance and contrast-variation small-angle neutron scattering, we studied the amino acid environment and the conformational state of the protein. FINDINGS The results demonstrate the key role of surfactant cooperation in defining the conformational state of the proteins, which can shift away or toward the folded state depending on the nonionic-to-ionic surfactant ratio. Dodecylmaltoside, initially a non-interacting surfactant, can unexpectedly associate with sodium dodecylsulfate-unfolded proteins to further impact their conformation at low nonionic-to-ionic surfactant ratio. When this ratio increases, the protein begins to retrieve the folded state. However, the native conformation cannot be fully recovered due to remnant surfactant molecules still adsorbed to the protein. This study demonstrates that the conformational landscape of the protein depends on a delicate interplay between the surfactants, ultimately controlled by the ratio between them, resulting in unpredictable changes in the protein conformation.
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Affiliation(s)
- Johanna Hjalte
- Food Technology, Engineering and Nutrition, Lund University, Box 124, 221 00 Lund, Sweden
| | - Carl Diehl
- SARomics Biostructures AB, Medicon Village, Scheelevägen 2, 223 81 Lund, Sweden
| | - Anna E Leung
- European Spallation Source, Box 176, 221 00 Lund, Sweden
| | - Jia-Fei Poon
- Food Technology, Engineering and Nutrition, Lund University, Box 124, 221 00 Lund, Sweden; European Spallation Source, Box 176, 221 00 Lund, Sweden
| | - Lionel Porcar
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Rob Dalgliesh
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK
| | - Helen Sjögren
- Ferring Pharmaceuticals A/S, Amager Strandvej 405, 2770 Kastrup, Denmark
| | - Marie Wahlgren
- Food Technology, Engineering and Nutrition, Lund University, Box 124, 221 00 Lund, Sweden
| | - Adrian Sanchez-Fernandez
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), Department of Chemical Engineering, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain.
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2
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Zeng Y, Tang X, Chen J, Kang X, Bai D. Optimizing total RNA extraction method for human and mice samples. PeerJ 2024; 12:e18072. [PMID: 39346072 PMCID: PMC11439393 DOI: 10.7717/peerj.18072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 08/19/2024] [Indexed: 10/01/2024] Open
Abstract
Background Extracting high-quality total RNA is pivotal for advanced RNA molecular studies, such as Next-generation sequencing and expression microarrays where RNA is hybridized. Despite the development of numerous extraction methods in recent decades, like the cetyl-trimethyl ammonium bromide (CTAB) and the traditional TRIzol reagent methods, their complexity and high costs often impede their application in small-scale laboratories. Therefore, a practical and economical method for RNA extraction that maintains high standards of efficiency and quality needs to be provided to optimize RNA extraction from human and mice tissues. Method This study proposes enhancements to the TRIzol method by incorporating guanidine isothiocyanate (GITC-T method) and sodium dodecyl sulfate (SDS-T method). We evaluated the effectiveness of these modified methods compared to the TRIzol method using a micro-volume UV-visible spectrophotometer, electrophoresis, q-PCR, RNA-Seq, and whole transcriptome sequencing. Result The micro-volume UV-visible spectrophotometer, electrophoresis, and RNA-Seq demonstrated that the GITC-T method yielded RNA with higher yields, integrity, and purity, while the consistency in RNA quality between the two methods was confirmed. Taking mouse cerebral cortex tissue as a sample, the yield of total RNA extracted by the GITC-T method was 1,959.06 ± 49.68 ng/mg, while the yield of total RNA extracted by the TRIzol method was 1,673.08 ± 86.39 ng/mg. At the same time, the OD260/280 of the total RNA samples extracted by the GITC-T method was 2.03 ± 0.012, and the OD260/230 was 2.17 ± 0.031, while the OD260/280 of the total RNA samples extracted by the TRIzol method was 2.013 ± 0.041 and the OD260/230 was 2.11 ± 0.062. Furthermore, q-PCR indicated that the GITC-T method achieved higher yields, purity, and greater transcript abundance of total RNA from the same types of animal samples than the TRIzol method. Conclusion The GITC-T method not only yields higher purity and quantity of RNA but also reduces reagent consumption and overall costs, thereby presenting a more feasible option for small-scale laboratory settings.
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Affiliation(s)
- Yumei Zeng
- Department of Neurology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xiaoxue Tang
- Institute of Neurological Diseases, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Jinwen Chen
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Xi Kang
- Department of Neurology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Dazhang Bai
- Department of Neurology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Institute of Neurological Diseases, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
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3
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Recoulat Angelini AA, Roman EA, González Flecha FL. The Structural Stability of Membrane Proteins Revisited: Combined Thermodynamic and Spectral Phasor Analysis of SDS-induced Denaturation of a Thermophilic Cu(I)-transport ATPase. J Mol Biol 2024; 436:168689. [PMID: 38936696 DOI: 10.1016/j.jmb.2024.168689] [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: 02/09/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
Assessing membrane protein stability is among the major challenges in protein science due to their inherent complexity, which complicates the application of conventional biophysical tools. In this work, sodium dodecyl sulfate-induced denaturation of AfCopA, a Cu(I)-transport ATPase from Archaeoglobus fulgidus, was explored using a combined model-free spectral phasor analysis and a model-dependent thermodynamic analysis. Decrease in tryptophan and 1-anilino-naphthalene-8-sulfonate fluorescence intensity, displacements in the spectral phasor space, and the loss of ATPase activity were reversibly induced by this detergent. Refolding from the SDS-induced denatured state yields an active enzyme that is functionally and spectroscopically indistinguishable from the native state of the protein. Phasor analysis of Trp spectra allowed us to identify two intermediate states in the SDS-induced denaturation of AfCopA, a result further supported by principal component analysis. In contrast, traditional thermodynamic analysis detected only one intermediate state, and including the second one led to overparameterization. Additionally, ANS fluorescence spectral analysis detected one more intermediate and a gradual change at the level of the hydrophobic transmembrane surface of the protein. Based on this evidence, a model for acquiring the native structure of AfCopA in a membrane-like environment is proposed.
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Affiliation(s)
- Alvaro A Recoulat Angelini
- Universidad de Buenos Aires - CONICET, Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Junín 956, Buenos Aires, Argentina
| | - Ernesto A Roman
- Universidad de Buenos Aires - CONICET, Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Junín 956, Buenos Aires, Argentina
| | - F Luis González Flecha
- Universidad de Buenos Aires - CONICET, Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Junín 956, Buenos Aires, Argentina.
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4
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Kumar S, Aswal VK. Evolution of the structure and interaction in the surfactant-dependent heat-induced gelation of protein. SOFT MATTER 2024; 20:5553-5563. [PMID: 38957095 DOI: 10.1039/d4sm00284a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
The addition of a surfactant and/or an increase in temperature disrupt the native structure of proteins, where high temperature further results in protein gelation. However, in a mixed protein-surfactant system, surfactant concentration and temperature have been observed to exhibit both mutually associative and counter-balancing effects towards heat-induced gelation of protein-surfactant dispersion. This study is conducted on globular bovine serum albumin (BSA) protein and cationic surfactant dodecyl trimethyl ammonium bromide (DTAB), which interact strongly owing to their oppositely charged nature. The findings reveal that the BSA-DTAB suspension undergoes gelation with increasing temperature but only at lower concentrations of DTAB, where the presence of the surfactant facilitates gelation (associative effect). Conversely, as the surfactant concentration increases beyond a critical value, temperature-driven gelation of the BSA-DTAB system is completely inhibited, despite surfactant-induced protein denaturation (counter-balancing effect). To conceptualize these results, we compared them with observations made in a system comprising protein and a similarly charged surfactant, sodium dodecyl sulfate (SDS). It has been further demonstrated that the anionic surfactant (SDS) can restrict protein gelation at much lower concentration compared to the cationic surfactant (DTAB). The evolution of the structure and interaction during gel formation/inhibition has been examined to understand the underlying mechanism guiding these sol-gel transitions. We present a comprehensive phase diagram, encompassing the solution/gel states of the protein-surfactant dispersion, with respect to the dispersion temperature, surfactant concentration, and ionic behavior (anionic or cationic) of the surfactants.
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Affiliation(s)
- Sugam Kumar
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.
- Homi Bhabha National Institute, Mumbai 400 094, India
| | - Vinod K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.
- Homi Bhabha National Institute, Mumbai 400 094, India
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5
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Nakahara Y, Kawaguchi T, Matsuda Y, Endo Y, Date M, Takahashi K, Kato K, Okasora T, Ejima D, Nagaki A. Spatiotemporal Control of Protein Refolding through Flash-Change Reaction Conditions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:8483-8492. [PMID: 38618876 DOI: 10.1021/acs.langmuir.4c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Recombinant protein production is an essential aspect of biopharmaceutical manufacturing, with Escherichia coli serving as a primary host organism. Protein refolding is vital for protein production; however, conventional refolding methods face challenges such as scale-up limitations and difficulties in controlling protein conformational changes on a millisecond scale. In this study, we demonstrate the novel application of flow microreactors (FMR) in controlling protein conformational changes on a millisecond scale, enabling efficient refolding processes and opening up new avenues in the science of FMR technology. FMR technology has been primarily employed for small-molecule synthesis, but our novel approach successfully expands its application to protein refolding, offering precise control of the buffer pH and solvent content. Using interleukin-6 as a model, the system yielded an impressive 96% pure refolded protein and allowed for gram-scale production. This FMR system allows flash changes in the reaction conditions, effectively circumventing protein aggregation during refolding. To the best of our knowledge, this is the first study to use FMR for protein refolding, which offers a more efficient and scalable method for protein production. The study results highlight the utility of the FMR as a high-throughput screening tool for streamlined scale-up and emphasize the importance of understanding and controlling intermediates in the refolding process. The FMR technique offers a promising approach for enhancing protein refolding efficiency and has demonstrated its potential in streamlining the process from laboratory-scale research to industrial-scale production, making it a game-changing technology in the field.
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Affiliation(s)
- Yuichi Nakahara
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
- Department of Chemistry, Graduate School of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Hokkaido, Japan
| | - Tomoko Kawaguchi
- Department of Chemistry, Graduate School of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Hokkaido, Japan
| | - Yutaka Matsuda
- Ajinomoto Bio-Pharma Services, 11040 Roselle Street, San Diego, California 92121, United States
| | - Yuta Endo
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Masayo Date
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Kazutoshi Takahashi
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Keisuke Kato
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Takahiro Okasora
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Daisuke Ejima
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Aiichiro Nagaki
- Department of Chemistry, Graduate School of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Hokkaido, Japan
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6
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Arasakumar N, Loganathan V, Natesh R, Ponnuraj K. HrpY protein of Ralstonia solanacearum exhibits spontaneous formation of pilus like assembly: analysis of its stability. J Biomol Struct Dyn 2024:1-12. [PMID: 38230438 DOI: 10.1080/07391102.2024.2304678] [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: 08/02/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024]
Abstract
Type 3 secretory system (T3SS), a complex protein machinery has a unique virulence mechanism that involves injecting effector proteins directly into host cells. The T3SS effector proteins are transported through an extracellular long hollow needle made up of multiple copies of a small protein. In T3SS of the plant pathogen Ralstonia solanacearum, the 8.6 kDa HrpY protein assembles into a large needle like apparatus (pilus) for transporting effector proteins. To study structural details of HrpY, we recombinantly expressed and purified HrpY in E. coli. The dynamic light scattering (DLS) analysis showed that rHrpY has spontaneously formed oligomers of large order (>100 nm). Transmission electron microscopy of rHrpY samples revealed that the large structures are tube like assembly having dimensions 86.3-166.6 nm and 5.8-6.8 nm in length and width respectively. Different molecular sizes of the purified rHrpY hindered the crystallization of the protein. The stability of oligomer assembly was studied with denaturants and surfactants. Denaturants like urea and guanidine HCl could not break them apart; however, detergents like SDS, sarkosyl, Octyl-β-Glucoside, CHAPS, Tween 20, Tween 80 and Triton X-100 showed disassembly of the oligomer. rHrpY assembly was found to withstand up to 50 °C and the circular dichroism analysis revealed that there is no significant change in the secondary structural composition with increase in temperature. However, change in the secondary structure was observed with the addition of SDS.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Naveen Arasakumar
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, India
| | - Vikraam Loganathan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, India
| | - Ramanathan Natesh
- Indian Institute of Science Education and Research Thiruvananthapuram (IISER-TVM), Vithura, Trivandrum, India
| | - Karthe Ponnuraj
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, India
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7
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Krishnan S, Sasi S, Kodakkattumannil P, Al Senaani S, Lekshmi G, Kottackal M, Amiri KMA. Cationic and anionic detergent buffers in sequence yield high-quality genomic DNA from diverse plant species. Anal Biochem 2024; 684:115372. [PMID: 37940013 DOI: 10.1016/j.ab.2023.115372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/15/2023] [Accepted: 10/26/2023] [Indexed: 11/10/2023]
Abstract
Because of the heterogeneity among seedlings of outbreeding species, the use of seedling tissues as a source of DNA is unsuitable for the genomic characterization of elite germplasms. High-quality DNA, free of RNA, proteins, polysaccharides, secondary metabolites, and shearing, is mandatory for downstream molecular biology applications, especially for next-generation genome sequencing and pangenome analysis aiming to capture the complete genetic diversity within a species. The study aimed to accomplish an efficient protocol for the extraction of high-quality DNA suitable for diverse plant species/tissues. We describe a reliable, and consistent protocol suitable for the extraction of DNA from 42 difficult-to-extract plant species belonging to 33 angiosperm (monocot and dicot) families, including tissues such as seeds, roots, endosperm, and flower/fruit tissues. The protocol was first optimized for the outbreeding recalcitrant trees viz., Prosopis cineraria, Conocarpus erectus, and Phoenix dactylifera, which are rich in proteins, polysaccharides, and secondary metabolites, and the quality of the extracted DNA was confirmed by downstream applications. Nine procedures were attempted to extract high-quality, impurities-free DNA from these three plant species. Extraction of the ethanol-precipitated DNA from cetyltrimethylammonium bromide (CTAB) protocol using sodium dodecyl sulfate (SDS) buffer, i.e., the extraction using a cationic (CTAB) detergent followed by an anionic (SDS) detergent was the key for high yield and high purity (1.75-1.85 against A260/280 and an A260/230 ratio of >2) DNA. A vice versa extraction procedure, i.e., SDS buffer followed by CTAB buffer, and also CTAB buffer followed by CTAB, did not yield good-quality DNA. PCR (using different primers) and restriction endonuclease digestion of the DNA extracted from these three plants validated the protocol. The accomplishment of the genome of P. cineraria using the DNA extracted using the modified protocol confirmed its applicability to genomic studies. The optimized protocol successful in extracting high-quality DNA from diverse plant species/tissues extends its applicability and is useful for accomplishing genome sequences of elite germplasm of recalcitrant plant species with quality reads.
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Affiliation(s)
- Saranya Krishnan
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates
| | - Shina Sasi
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates
| | - Preshobha Kodakkattumannil
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates
| | - Salima Al Senaani
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates
| | - Geetha Lekshmi
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates
| | - Martin Kottackal
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates.
| | - Khaled M A Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates; Department of Biology, College of Science, United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates.
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8
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Stachurska K, Marcisz U, Długosz M, Antosiewicz JM. Kinetics of Structural Transitions Induced by Sodium Dodecyl Sulfate in α-Chymotrypsin. ACS OMEGA 2023; 8:49137-49149. [PMID: 38162786 PMCID: PMC10753550 DOI: 10.1021/acsomega.3c07256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 01/03/2024]
Abstract
The temporal changes in circular dichroism at 222 and 260 nm were recorded by using stopped-flow spectroscopy after mixing α-chymotrypsin solutions with sodium dodecyl sulfate solutions. Simultaneously with the circular dichroism signal, the fluorescence emission was recorded. Changes in the secondary and tertiary structures of chymotrypsin induced by sodium dodecyl sulfate are characterized by either three or four one-way reactions with relaxation amplitudes and times precisely determined by an advanced numerical procedure of Kuzmič. Quantitatively, transitions within the secondary and tertiary structures of the protein are significantly different. Moreover, changes in the tertiary structure depend on the type of recorded signal (either circular dichroism or fluorescence) and the wavelength of the incident radiation. The latter observation is particularly interesting as it indicates that the contributions of protein's different tryptophans to the total recorded fluorescence depend on the excitation wavelength. We present several results justifying this hypothesis.
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Affiliation(s)
- Karolina Stachurska
- Biophysics Division, Institute of Experimental
Physics, Faculty of Physics, University
of Warsaw, Pasteura 5 Street, 02-093 Warsaw, Poland
| | - Urszula Marcisz
- Biophysics Division, Institute of Experimental
Physics, Faculty of Physics, University
of Warsaw, Pasteura 5 Street, 02-093 Warsaw, Poland
| | - Maciej Długosz
- Biophysics Division, Institute of Experimental
Physics, Faculty of Physics, University
of Warsaw, Pasteura 5 Street, 02-093 Warsaw, Poland
| | - Jan M. Antosiewicz
- Biophysics Division, Institute of Experimental
Physics, Faculty of Physics, University
of Warsaw, Pasteura 5 Street, 02-093 Warsaw, Poland
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9
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Chen R, Song Y, Wang Z, Ji H, Du Z, Ma Q, Yang Y, Liu X, Li N, Sun Y. Developments in small-angle X-ray scattering (SAXS) for characterizing the structure of surfactant-macromolecule interactions and their complex. Int J Biol Macromol 2023; 251:126288. [PMID: 37582436 DOI: 10.1016/j.ijbiomac.2023.126288] [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: 04/19/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/17/2023]
Abstract
The surfactant-macromolecule interactions (SMI) are one of the most critical topics for scientific research and industrial application. Small-angle X-ray scattering (SAXS) is a powerful tool for comprehensively studying the structural and conformational features of macromolecules at a size ranging from Angstroms to hundreds of nanometers with a time-resolve in milliseconds scale. The SAXS integrative techniques have emerged for comprehensively analyzing the SMI and the structure of their complex in solution. Here, the various types of emerging interactions of surfactant with macromolecules, such as protein, lipid, nuclear acid, polysaccharide and virus, etc. have been systematically reviewed. Additionally, the principle of SAXS and theoretical models of SAXS for describing the structure of SMI as well as their complex has been summarized. Moreover, the recent developments in the applications of SAXS for charactering the structure of SMI have been also highlighted. Prospectively, the capacity to complement artificial intelligence (AI) in the structure prediction of biological macromolecules and the high-throughput bioinformatics sequencing data make SAXS integrative structural techniques expected to be the primary methodology for illuminating the self-assembling dynamics and nanoscale structure of SMI. As advances in the field continue, we look forward to proliferating uses of SAXS based upon its abilities to robustly produce mechanistic insights for biology and medicine.
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Affiliation(s)
- Ruixin Chen
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Yang Song
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Zhichun Wang
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Hang Ji
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Zhongyao Du
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Qingwen Ma
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Ying Yang
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Xingxun Liu
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, Jiangsu, China
| | - Na Li
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, CAS, Shanghai, China.
| | - Yang Sun
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China.
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10
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Raw J, Franco LR, de C. Rodrigues LF, Barbosa LRS. Unveiling the Three-Step Model for the Interaction of Imidazolium-Based Ionic Liquids on Albumin. ACS OMEGA 2023; 8:38101-38110. [PMID: 37867681 PMCID: PMC10586182 DOI: 10.1021/acsomega.3c04188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/08/2023] [Indexed: 10/24/2023]
Abstract
The effect of the ionic liquids (ILs) 1-methyl-3-tetradecylimidazolium chloride ([C14MIM][Cl]), 1-dodecyl-3-methylimidazolium chloride ([C12MIM][Cl]), and 1-decyl-methylimidazolium chloride ([C10MIM][Cl]) on the structure of bovine serum albumin (BSA) was investigated by fluorescence spectroscopy, ultraviolet-visible (UV-vis) spectroscopy, small-angle X-ray scattering (SAXS), and molecular dynamics (MD) simulations. Concerning the fluorescence measurements, we observed a blue shift and a fluorescence quenching as the IL concentration increased in the solution. Such behavior was observed for all three studied imidazolium-based ILs, being larger as the number of methylene groups in the alkyl chain increased. UV-vis absorbance measurements indicate that even at relatively small IL/protein ratios, like 1:1 or 1:2, ([C14MIM][Cl]) is able to change, at least partially, the sample turbidity. SAXS results agree with the spectroscopic techniques and suggest that the proteins underwent partial unfolding, evidenced by an increase in the radius of gyration (Rg) of the scattering particle. In the absence and presence of ([C14MIM][Cl]) = 3 mM BSA Rg increases from 29.1 to 45.1 Å, respectively. Together, these results indicate that the interaction of BSA with ILs is divided into three stages: the first stage is characterized by the protein in its native form. It takes place for protein/IL ≤ 1:2, and the interaction is predominantly due to the electrostatic forces provided by the negative charges on the surface of BSA and the cationic polar head of the ILs. In the second stage, higher IL concentrations induce the unfolding of the protein, most likely inducing the unfolding of domains I and III, in such a way that the protein's secondary structure is kept almost unaltered. In the last stage, IL micelles start to form, and therefore, the interaction with protein reaches a saturation point and free micelles may be formed. We believe that this work provides new information about the interaction of ILs with BSA.
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Affiliation(s)
- Juliana Raw
- Department
of General Physics, University of São
Paulo, Institute of Physics, São Paulo 05508-000, SP, Brazil
| | - Leandro R. Franco
- Department
of Engineering and Physics, Karlstad University, Karlstad 65188, Sweden
| | - Luiz Fernando de C. Rodrigues
- Department
of General Physics, University of São
Paulo, Institute of Physics, São Paulo 05508-000, SP, Brazil
- Brazilian
Synchrotron Light Laboratory (LNLS), Brazilian
Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, SP Brazil
| | - Leandro R. S. Barbosa
- Department
of General Physics, University of São
Paulo, Institute of Physics, São Paulo 05508-000, SP, Brazil
- Brazilian
Synchrotron Light Laboratory (LNLS), Brazilian
Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, SP Brazil
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11
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Mo L, Chen J, Cai C, Guo Y, Zeng LH, Li S, Tan J. The Amphiphilic Property and Structure of β-Amyloid Peptide Contribute to Its Impacts on the Activities of Horseradish Peroxidase and Alkaline Phosphatase. ACS Chem Neurosci 2023; 14:3019-3024. [PMID: 37607046 DOI: 10.1021/acschemneuro.3c00391] [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: 08/24/2023] Open
Abstract
Recent studies have found that β-amyloid (Aβ) oligomers may play much more important roles than amyloid plaques in the pathogenesis of Alzheimer's disease (AD). However, due to the complexity of Aβ, studying the structural basis of Aβ oligomer toxicity is challenging. Here, we assessed the amphiphilic property and β-hairpin structure of Aβ monomer. The potential impacts of Aβ oligomers and three sequence-modifying peptides on the enzyme activities of horseradish peroxidase (HRP) and alkaline phosphatase (ALP) were further evaluated. We demonstrated that Aβ oligomer possesses the ability to alter the activity of two enzymes. Moreover, modifications on the hydrophobic region and β-turn structure of Aβ monomer significantly alter its impacts on the enzyme activities. In addition, these modifications also change the bonding modes of Aβ monomers or oligomers binding to HRP, as assessed by molecular docking. All of these findings provide direct experimental evidence to reveal the critical roles of the amphiphilic property and β-sheet structure of Aβ monomer in its impacts on protein activity.
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Affiliation(s)
- Ling Mo
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Key Laboratory of Molecular Biology of Guizhou Medical University, Guiyang 550004, China
| | - Jiang Chen
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Key Laboratory of Molecular Biology of Guizhou Medical University, Guiyang 550004, China
| | - Chuanbin Cai
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Key Laboratory of Molecular Biology of Guizhou Medical University, Guiyang 550004, China
| | - Yi Guo
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Key Laboratory of Molecular Biology of Guizhou Medical University, Guiyang 550004, China
| | - Ling-Hui Zeng
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou 310015, China
| | - Song Li
- The First Affiliated Hospital of Dalian Medical University, Dalian 116021, China
| | - Jun Tan
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Key Laboratory of Molecular Biology of Guizhou Medical University, Guiyang 550004, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou 310015, China
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12
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Recoulat Angelini AA, Incicco JJ, Melian NA, González-Flecha FL. Susceptibility of Cu(I) transport ATPases to sodium dodecyl sulfate. Relevance of the composition of the micellar phase. Arch Biochem Biophys 2023; 745:109704. [PMID: 37527700 DOI: 10.1016/j.abb.2023.109704] [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: 05/26/2023] [Revised: 07/11/2023] [Accepted: 07/28/2023] [Indexed: 08/03/2023]
Abstract
Sodium dodecyl sulfate (SDS) is a well-known protein denaturing agent. A less known property of this detergent is that it can activate or inactivate some enzymes at sub-denaturing concentrations. In this work we explore the effect of SDS on the ATPase activity of a hyper-thermophilic and a mesophilic Cu(I) ATPases reconstituted in mixed micelles of phospholipids and a non-denaturing detergent. An iterative procedure was used to evaluate the partition of SDS between the aqueous and the micellar phases, allowing to determine the composition of micelles prepared from phospholipid/detergent mixtures. The incubation of enzymes with SDS in the presence of different amounts of phospholipids reveals that higher SDS concentrations are required to obtain the same degree of inactivation when the initial concentration of phospholipids is increased. Remarkably, we found that, if represented as a function of the mole fraction of SDS in the micelle, the degree of inactivation obtained at different amounts of amphiphiles converges to a single inactivation curve. To interpret this result, we propose a simple model involving active and inactive enzyme molecules in equilibrium. This model allowed us to estimate the Gibbs free energy change for the inactivation process and its derivative with respect to the mole fraction of SDS in the micellar phase, the latter being a measure of the susceptibility of the enzyme to SDS. Our results showed that the inactivation free energy changes are similar for both proteins. Conversely, susceptibility to SDS is significantly lower for the hyperthermophilic ATPase, suggesting an inverse relation between thermophilicity and susceptibility to SDS.
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Affiliation(s)
- Alvaro A Recoulat Angelini
- Universidad de Buenos Aires - CONICET, Laboratorio de Biofísica Molecular. Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina
| | - J Jeremías Incicco
- Universidad de Buenos Aires - CONICET, Laboratorio de Biofísica Molecular. Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina
| | - Noelia A Melian
- Universidad de Buenos Aires - CONICET, Laboratorio de Biofísica Molecular. Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina
| | - F Luis González-Flecha
- Universidad de Buenos Aires - CONICET, Laboratorio de Biofísica Molecular. Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina.
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13
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Wright BL, Masuda MY, Ortiz DR, Dao A, Civello B, Pyon GC, Schulze AR, Yiannas JA, Rank MA, Kita H, Doyle AD. Allergies Come Clean: The Role of Detergents in Epithelial Barrier Dysfunction. Curr Allergy Asthma Rep 2023; 23:443-451. [PMID: 37233851 PMCID: PMC10527525 DOI: 10.1007/s11882-023-01094-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
PURPOSE OF REVIEW The prevalence and incidence of allergic disease have been rising in Westernized countries since the twentieth century. Increasingly, evidence suggests that damage to the epithelium initiates and shapes innate and adaptive immune responses to external antigens. The objective of this review is to examine the role of detergents as a potential risk factor for developing allergic disease. RECENT FINDINGS Herein, we identify key sources of human detergent exposure. We summarize the evidence suggesting a possible role for detergents and related chemicals in initiating epithelial barrier dysfunction and allergic inflammation. We primarily focus on experimental models of atopic dermatitis, asthma, and eosinophilic esophagitis, which show compelling associations between allergic disease and detergent exposure. Mechanistic studies suggest that detergents disrupt epithelial barrier integrity through their effects on tight junction or adhesion molecules and promote inflammation through epithelial alarmin release. Environmental exposures that disrupt or damage the epithelium may account for the increasing rates of allergic disease in genetically susceptible individuals. Detergents and related chemical compounds represent possible modifiable risk factors for the development or exacerbation of atopy.
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Affiliation(s)
- Benjamin L Wright
- Division of Allergy, Asthma, and Clinical Immunology, Department of Medicine, Mayo Clinic Arizona, Scottsdale, AZ, USA.
- Section of Allergy and Immunology, Division of Pulmonology, Phoenix Children's Hospital, Phoenix, AZ, USA.
| | - Mia Y Masuda
- Division of Allergy, Asthma, and Clinical Immunology, Department of Medicine, Mayo Clinic Arizona, Scottsdale, AZ, USA
- Department of Immunology, Mayo Clinic, Mayo Clinic Arizona, Rochester, Scottsdale, Minnesota, AZ, USA
| | - Danna R Ortiz
- Division of Allergy, Asthma, and Clinical Immunology, Department of Medicine, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Adelyn Dao
- Division of Allergy, Asthma, and Clinical Immunology, Department of Medicine, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Blake Civello
- University of Arizona College of Medicine - Phoenix, Phoenix, AZ, USA
| | - Grace C Pyon
- Division of Allergy, Asthma, and Clinical Immunology, Department of Medicine, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Aliviya R Schulze
- Division of Allergy, Asthma, and Clinical Immunology, Department of Medicine, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - James A Yiannas
- Department of Dermatology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Matthew A Rank
- Division of Allergy, Asthma, and Clinical Immunology, Department of Medicine, Mayo Clinic Arizona, Scottsdale, AZ, USA
- Section of Allergy and Immunology, Division of Pulmonology, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Hirohito Kita
- Division of Allergy, Asthma, and Clinical Immunology, Department of Medicine, Mayo Clinic Arizona, Scottsdale, AZ, USA
- Section of Allergy and Immunology, Division of Pulmonology, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Alfred D Doyle
- Division of Allergy, Asthma, and Clinical Immunology, Department of Medicine, Mayo Clinic Arizona, Scottsdale, AZ, USA
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14
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Klausser R, Kopp J, Prada Brichtova E, Gisperg F, Elshazly M, Spadiut O. State-of-the-art and novel approaches to mild solubilization of inclusion bodies. Front Bioeng Biotechnol 2023; 11:1249196. [PMID: 37545893 PMCID: PMC10399460 DOI: 10.3389/fbioe.2023.1249196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 07/12/2023] [Indexed: 08/08/2023] Open
Abstract
Throughout the twenty-first century, the view on inclusion bodies (IBs) has shifted from undesired by-products towards a targeted production strategy for recombinant proteins. Inclusion bodies can easily be separated from the crude extract after cell lysis and contain the product in high purity. However, additional solubilization and refolding steps are required in the processing of IBs to recover the native protein. These unit operations remain a highly empirical field of research in which processes are developed on a case-by-case basis using elaborate screening strategies. It has been shown that a reduction in denaturant concentration during protein solubilization can increase the subsequent refolding yield due to the preservation of correctly folded protein structures. Therefore, many novel solubilization techniques have been developed in the pursuit of mild solubilization conditions that avoid total protein denaturation. In this respect, ionic liquids have been investigated as promising agents, being able to solubilize amyloid-like aggregates and stabilize correctly folded protein structures at the same time. This review briefly summarizes the state-of-the-art of mild solubilization of IBs and highlights some challenges that prevent these novel techniques from being yet adopted in industry. We suggest mechanistic models based on the thermodynamics of protein unfolding with the aid of molecular dynamics simulations as a possible approach to solve these challenges in the future.
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Affiliation(s)
- Robert Klausser
- Research Division Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience, Vienna, Austria
- Christian Doppler Laboratory IB Processing 4.0, Technische Universität Wien, Vienna, Austria
| | - Julian Kopp
- Research Division Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience, Vienna, Austria
- Christian Doppler Laboratory IB Processing 4.0, Technische Universität Wien, Vienna, Austria
| | - Eva Prada Brichtova
- Research Division Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience, Vienna, Austria
- Christian Doppler Laboratory IB Processing 4.0, Technische Universität Wien, Vienna, Austria
| | - Florian Gisperg
- Research Division Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience, Vienna, Austria
- Christian Doppler Laboratory IB Processing 4.0, Technische Universität Wien, Vienna, Austria
| | - Mohamed Elshazly
- Research Division Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience, Vienna, Austria
- Christian Doppler Laboratory IB Processing 4.0, Technische Universität Wien, Vienna, Austria
| | - Oliver Spadiut
- Research Division Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience, Vienna, Austria
- Christian Doppler Laboratory IB Processing 4.0, Technische Universität Wien, Vienna, Austria
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15
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Functional amyloid in a lipid-like environment: a merry dance of many steps. Essays Biochem 2022; 66:1035-1046. [PMID: 36205438 DOI: 10.1042/ebc20220062] [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: 08/08/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022]
Abstract
Functional amyloid, which unlike its pathological counterpart serves a biological purpose, is produced in a carefully orchestrated sequence of events. In bacteria, the major amyloid component is transported over the periplasm and through the outer membrane to assemble on the bacterial cell surface. During its life time, the amyloid protein may be exposed to both membrane lipids and extracellular surfactant, making it relevant to study its interactions with these components in vitro. Particularly for charged surfactants, the interaction is quite complex and highly dependent on the surfactant:protein molar ratio. Low ratios typically promote aggregation, likely by binding the proteins to micelles and thus increasing the local concentration of proteins, while higher concentrations see an inhibition of the same process as the protein is diluted out and immobilized on individual micelles. This is particularly pronounced for strongly anionic surfactants like SDS; the naturally occurring biosurfactant rhamnolipid interacts more weakly with the protein, which still not only allows aggregation but also leads to less detrimental effects at higher ratios. Similarly, anionic vesicle-forming lipids largely stimulate aggregation likely because of weaker interactions. Anionic lysolipids, thanks to their micelle-forming properties, resemble SDS in their impact on fibrillation. There are also examples of systems where membrane binding sequesters an otherwise amyloidogenic sequence and prevents fibrillation or-quite the opposite- liberates another part of the protein to engage in self-assembly. Thus, membranes and surfactants have very varied roles to play in the biogenesis and function of bacterial amyloid.
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