1
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Saha R, Chakraborty S, Sinha K, Pyne P, Pal S, Barman A, Chakrabarty S, Mitra RK. Ion-Pairing Propensity in Guanidinium Salts Dictates Their Protein (De)stabilization Behavior. J Phys Chem Lett 2024:10341-10348. [PMID: 39373553 DOI: 10.1021/acs.jpclett.4c01646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Since the proposition of the Hofmeister series, guanidinium (Gdm) salts hold a special mention in protein science owing to their contrasting effect on protein(s) depending on the counteranion(s). For example, while GdmCl is known to act as a potential protein denaturant, Gdm2SO4 offers minimal effect on protein structure. Despite the fact that theoretical studies reckon the formation of ion-pairing to be responsible for such behavior, experimental validation of this hypothesis is still in sparse. In this study, we combine electrochemical impedance spectroscopy (EIS) and THz spectroscopy to underline the effect of GdmCl and Gdm2SO4 on a model amide molecule N-methylacetamide (NMA). Molecular dynamics (MD) simulation studies predict that Gdm2SO4 forms heteroion pairing in water, which inhibits Gdm+ ions to approach NMA molecules, while in case of GdmCl, Gdm+ ions directly interact with NMA. The experimental findings on ion hydration, specifically the detailed analysis of the ion-water rattling mode, which appears in the THz frequency domain, unambiguously endorse this hypothesis. Our study establishes the fact that the propensity of ion-pairing in Gdm salts dictates their (de)stabilization effect on proteins.
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Affiliation(s)
- Ria Saha
- Department of Chemical and Biological Sciences, S.N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Subhadip Chakraborty
- Department of Chemical and Biological Sciences, S.N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Krishnendu Sinha
- Department of Chemical and Biological Sciences, S.N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Partha Pyne
- Department of Chemical and Biological Sciences, S.N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Sreya Pal
- Department of Condensed Matter and Materials Physics, S.N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Anjan Barman
- Department of Condensed Matter and Materials Physics, S.N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Suman Chakrabarty
- Department of Chemical and Biological Sciences, S.N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Rajib Kumar Mitra
- Department of Chemical and Biological Sciences, S.N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
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2
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Lim LZ, Song J. NMR Dynamic View of the Destabilization of WW4 Domain by Chaotropic GdmCl and NaSCN. Int J Mol Sci 2024; 25:7344. [PMID: 39000450 PMCID: PMC11242413 DOI: 10.3390/ijms25137344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
GdmCl and NaSCN are two strong chaotropic salts commonly used in protein folding and stability studies, but their microscopic mechanisms remain enigmatic. Here, by CD and NMR, we investigated their effects on conformations, stability, binding and backbone dynamics on ps-ns and µs-ms time scales of a 39-residue but well-folded WW4 domain at salt concentrations ≤200 mM. Up to 200 mM, both denaturants did not alter the tertiary packing of WW4, but GdmCl exerted more severe destabilization than NaSCN. Intriguingly, GdmCl had only weak binding to amide protons, while NaSCN showed extensive binding to both hydrophobic side chains and amide protons. Neither denaturant significantly affected the overall ps-ns backbone dynamics, but they distinctively altered µs-ms backbone dynamics. This study unveils that GdmCl and NaSCN destabilize a protein before the global unfolding occurs with differential binding properties and µs-ms backbone dynamics, implying the absence of a simple correlation between thermodynamic stability and backbone dynamics of WW4 at both ps-ns and µs-ms time scales.
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Affiliation(s)
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore
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3
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Jonsson O, Lundell A, Rosell J, You S, Ahlgren K, Swenson J. Comparison of Sucrose and Trehalose for Protein Stabilization Using Differential Scanning Calorimetry. J Phys Chem B 2024; 128:4922-4930. [PMID: 38733344 PMCID: PMC11129304 DOI: 10.1021/acs.jpcb.4c00022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
The disaccharide trehalose is generally acknowledged as a superior stabilizer of proteins and other biomolecules in aqueous environments. Despite many theories aiming to explain this, the stabilization mechanism is still far from being fully understood. This study compares the stabilizing properties of trehalose with those of the structurally similar disaccharide sucrose. The stability has been evaluated for the two proteins, lysozyme and myoglobin, at both low and high temperatures by determining the glass transition temperature, Tg, and the denaturation temperature, Tden. The results show that the sucrose-containing samples exhibit higher Tden than the corresponding trehalose-containing samples, particularly at low water contents. The better stabilizing effect of sucrose at high temperatures may be explained by the fact that sucrose, to a greater extent, binds directly to the protein surface compared to trehalose. Both sugars show Tden elevation with an increasing sugar-to-protein ratio, which allows for a more complete sugar shell around the protein molecules. Finally, no synergistic effects were found by combining trehalose and sucrose. Conclusively, the exact mechanism of protein stabilization may vary with the temperature, as influenced by temperature-dependent interactions between the protein, sugar, and water. This variability can make trehalose to a superior stabilizer under some conditions and sucrose under others.
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Affiliation(s)
| | | | | | | | - Kajsa Ahlgren
- Department of Physics, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Jan Swenson
- Department of Physics, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
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4
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Zhu T, Sun J, Pang H, Wu B. Computational Enzyme Redesign Enhances Tolerance to Denaturants for Peptide C-Terminal Amidation. JACS AU 2024; 4:788-797. [PMID: 38425901 PMCID: PMC10900485 DOI: 10.1021/jacsau.3c00792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
The escalating demand for biocatalysts in pharmaceutical and biochemical applications underscores the critical imperative to enhance enzyme activity and durability under high denaturant concentrations. Nevertheless, the development of a practical computational redesign protocol for improving enzyme tolerance to denaturants is challenging due to the limitations of relying solely on model-driven approaches to adequately capture denaturant-enzyme interactions. In this study, we introduce an enzyme redesign strategy termed GRAPE_DA, which integrates multiple data-driven and model-driven computational methods to mitigate the sampling biases inherent in a single approach and comprehensively predict beneficial mutations on both the protein surface and backbone. To illustrate the methodology's effectiveness, we applied it to engineer a peptidylamidoglycolate lyase, resulting in a variant exhibiting up to a 24-fold increase in peptide C-terminal amidation activity under 2.5 M guanidine hydrochloride. We anticipate that this integrated engineering strategy will facilitate the development of enzymatic peptide synthesis and functionalization under denaturing conditions and highlight the role of engineering surface residues in governing protein stability.
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Affiliation(s)
- Tong Zhu
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinyuan Sun
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Pang
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bian Wu
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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5
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Sun H, Le S, Guo Z, Chen H. Exploring the free energy landscape of proteins using magnetic tweezers. Methods Enzymol 2024; 694:237-261. [PMID: 38492953 DOI: 10.1016/bs.mie.2023.12.008] [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: 03/18/2024]
Abstract
Proteins fold to their native states by searching through the free energy landscapes. As single-domain proteins are the basic building block of multiple-domain proteins or protein complexes composed of subunits, the free energy landscapes of single-domain proteins are of critical importance to understand the folding and unfolding processes of proteins. To explore the free energy landscapes of proteins over large conformational space, the stability of native structure is perturbed by biochemical or mechanical means, and the conformational transition process is measured. In single molecular manipulation experiments, stretching force is applied to proteins, and the folding and unfolding transitions are recorded by the extension time course. Due to the broad force range and long-time stability of magnetic tweezers, the free energy landscape over large conformational space can be obtained. In this article, we describe the magnetic tweezers instrument design, protein construct design and preparation, fluid chamber preparation, common-used measuring protocols including force-ramp and force-jump measurements, and data analysis methods to construct the free energy landscape. Single-domain cold shock protein is introduced as an example to build its free energy landscape by magnetic tweezers measurements.
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Affiliation(s)
- Hao Sun
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, P.R. China
| | - Shimin Le
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, P.R. China
| | - Zilong Guo
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, P.R. China.
| | - Hu Chen
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, P.R. China; Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, P.R. China.
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6
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Valenzuela-Gómez F, Arechaga I, Cabezón E. Nanopore sensing reveals a preferential pathway for the co-translocational unfolding of a conjugative relaxase-DNA complex. Nucleic Acids Res 2023; 51:6857-6869. [PMID: 37264907 PMCID: PMC10359608 DOI: 10.1093/nar/gkad492] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/05/2023] [Accepted: 05/26/2023] [Indexed: 06/03/2023] Open
Abstract
Bacterial conjugation is the main mechanism for the dissemination of antibiotic resistance genes. A single DNA strand of the conjugative plasmid is transferred across bacterial membranes covalently bound to a large multi-domain protein, named relaxase, which must be unfolded to traverse the secretion channel. Two tyrosine residues of the relaxase (Y18 and Y26 in relaxase TrwC) play an important role in the processing of conjugative DNA. We have used nanopore technology to uncover the unfolding states that take place during translocation of the relaxase-DNA complex. We observed that the relaxase unfolding pathway depends on the tyrosine residue involved in conjugative DNA binding. Transfer of the nucleoprotein complex is faster when DNA is bound to residue Y18. This is the first time in which a protein-DNA complex that is naturally translocated through bacterial membranes has been analyzed by nanopore sensing, opening new horizons to apply this technology to study protein secretion.
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Affiliation(s)
- Fernando Valenzuela-Gómez
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria- CSIC, 39011 Santander, Spain
| | - Ignacio Arechaga
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria- CSIC, 39011 Santander, Spain
| | - Elena Cabezón
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria- CSIC, 39011 Santander, Spain
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7
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Shen X, Zheng H, Han M, Xu X, Li B, Guo Q. Intermolecular forces regulate in-vitro digestion of whey protein emulsion gels: Towards controlled lipid release. J Colloid Interface Sci 2023; 649:245-254. [PMID: 37348344 DOI: 10.1016/j.jcis.2023.06.023] [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: 03/22/2023] [Revised: 05/12/2023] [Accepted: 06/05/2023] [Indexed: 06/24/2023]
Abstract
HYPOTHESIS The utilization of emulsion-filled protein hydrogels for controlled lipid release in the gastrointestinal tract (GIT) displays great potential in drug delivery and obesity treatment. However, how intermolecular interactions among protein molecules influence lipid digestion of the gels is still understudied. EXPERIMENTS Differently structured whey protein emulsion gels were fabricated by heating emulsions with blocking of disulfide bonds (the "noncovalent" gel), noncovalent interactions (the "disulfide" gel), or neither of these (the "control" gel). The intermolecular interactions-gel structure-lipid digestion relationship was investigated by characterizing structural/mechanical properties of the gels and monitoring their dynamic breakdown in a simulated GIT. FINDINGS Although the disulfide-crosslinked protein network formed thick interfacial layers around oil droplets and resisted intestinal proteolysis, the "disulfide" gel had the fastest lipolysis rate, indicating that it could not inhibit the access of lipases to oil droplets. In contrast, the "noncovalent" gel was more susceptible to in-vitro digestion than the "control" gel because of lower gel strength, resulting in a faster lipolysis rate. This demonstrated that intermolecular disulfide bonds and noncovalent interactions played distinctive roles in the digestion of the gels; they represented the structural backbone and the infill in the gel structure, respectively.
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Affiliation(s)
- Xingxing Shen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Engineering Research Center for Fruits and Vegetables Processing, China Agricultural University, Beijing 100083, China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing, China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, China; Maanshan Safety Inspection Center for Food and Drug, Maanshan Administration for Market Regulation, Maanshan 243000, China
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Engineering Research Center for Fruits and Vegetables Processing, China Agricultural University, Beijing 100083, China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing, China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, China
| | - Menghan Han
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Engineering Research Center for Fruits and Vegetables Processing, China Agricultural University, Beijing 100083, China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing, China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, China
| | - Xiyu Xu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Engineering Research Center for Fruits and Vegetables Processing, China Agricultural University, Beijing 100083, China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing, China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, China
| | - Bingyi Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Engineering Research Center for Fruits and Vegetables Processing, China Agricultural University, Beijing 100083, China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing, China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, China
| | - Qing Guo
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Engineering Research Center for Fruits and Vegetables Processing, China Agricultural University, Beijing 100083, China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing, China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, China.
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8
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Sun H, Yao C, You K, Chen C, Liu S, Xu Z. Nanopore single-molecule biosensor in protein denaturation analysis. Anal Chim Acta 2023; 1243:340830. [PMID: 36697181 DOI: 10.1016/j.aca.2023.340830] [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: 11/10/2022] [Revised: 01/02/2023] [Accepted: 01/11/2023] [Indexed: 01/13/2023]
Abstract
Unclear issues in protein studies include but not limited to the stability and denaturation mechanism in the presence of denaturants. Herein, we report a dynamic monitoring approach based on nanopore single-molecule biosensor, which can detect the protein's folding and unfolding transitions by recording a nanopore ionic current. When gradually increasing the concentration of denaturant guanidine hydrochloride (GdmCl), sensitive responses were observed with lysozyme unfolding. The emergence of the featured biphasic-pulse demonstrated the existence of a stable intermediate. It was the first time to experimentally confirm the dynamic equilibrium between the intermediate and the native states at single molecule level, therefore consolidating the standpoint of lysozyme denaturation process following the three-state model. Additionally, we got more insights into the conformation about the intermediate as globular-like structure, larger gyration radius, and enhanced positive charge density. We considered that the manner of denaturant toward lysozyme adopts the "direct" model based on stronger electrostatic and van der Waals forces. Nanopore biosensor exhibited excellent sensitivity with a low detection concentration of 280 pM and reproducibility in analysing the folding intermediate of lysozyme.
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Affiliation(s)
- Hong Sun
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China.
| | - Chuan Yao
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
| | - Kaibo You
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
| | - Can Chen
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
| | - Shuoshuo Liu
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
| | - Zhihong Xu
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
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9
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Giri P, Verma D. Dual crosslinked injectable protein-based hydrogels with cell anti-adhesive properties. Biomed Mater 2023; 18. [PMID: 36716499 DOI: 10.1088/1748-605x/acb74e] [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: 09/05/2022] [Accepted: 01/30/2023] [Indexed: 02/01/2023]
Abstract
Currently, one of the most severe clinical concerns is post-surgical tissue adhesions. Using films or hydrogel to separate the injured tissue from surrounding tissues has proven the most effective method for minimizing adhesions. Therefore, by combining dual crosslinking with calcium ions (Ca2+) and tetrakis(hydroxymethyl) phosphonium chloride, we were able to create a novel, stable, robust, and injectable dual crosslinking hydrogel using albumin (BSA). This dual crosslinking has preserved the microstructure of the hydrogel network during the degradation process, which contributes to the hydrogel's mechanical strength and stability in a physiological situation. At 60% strain, compressive stress was 48.81 kPa obtained. It also demonstrated excellent self-healing characteristics (within 25 min), tissue adhesion, excellent cytocompatibility, and a quick gelling time of 27 ± 6 s. Based on these features, the dual crosslinked injectable hydrogels might find exciting applications in biomedicine, particularly for preventing post-surgical adhesions.
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Affiliation(s)
- Pijush Giri
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Odisha 769008, India
| | - Devendra Verma
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Odisha 769008, India
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10
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Gupta MN, Uversky VN. Pre-Molten, Wet, and Dry Molten Globules en Route to the Functional State of Proteins. Int J Mol Sci 2023; 24:ijms24032424. [PMID: 36768742 PMCID: PMC9916686 DOI: 10.3390/ijms24032424] [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: 12/31/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Transitions between the unfolded and native states of the ordered globular proteins are accompanied by the accumulation of several intermediates, such as pre-molten globules, wet molten globules, and dry molten globules. Structurally equivalent conformations can serve as native functional states of intrinsically disordered proteins. This overview captures the characteristics and importance of these molten globules in both structured and intrinsically disordered proteins. It also discusses examples of engineered molten globules. The formation of these intermediates under conditions of macromolecular crowding and their interactions with nanomaterials are also reviewed.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence: ; Tel.: +1-813-494-5816
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11
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Hu X, Zhao J, Zhao Y, Zhang H, Wang Q, Ge B, Wang X, He H, Nau WM, Wang X, Huang F. Direct Observation and Real-Time Tracking of an Extraordinarily Stable Folding Intermediate in Mitotic Arrest Deficient Protein 2 Folding by Single-Molecule Fluorescence Resonance Energy Transfer. J Phys Chem Lett 2023; 14:763-769. [PMID: 36651986 DOI: 10.1021/acs.jpclett.2c03181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Although ensemble experiments have suggested that mitotic arrest deficient protein 2 (Mad2), a metamorphic protein, has folding intermediates, direct evidence and characterization are not available. It remains an outstanding challenge to capture the folding intermediates in real time, which is crucial to elucidate the folding mechanism, but the folding intermediates are normally unstable and only exist transiently. By combining confocal-microscopy-based and total internal reflection fluorescence (TIRF)-microscopy-based single-molecule Förster resonance energy transfer (sm-FRET) techniques, we have investigated the folding/unfolding process of Mad2 and captured its folding intermediate at the single-molecule level. This provides direct evidence for the existence of an intermediate along the folding pathway of Mad2. The folding intermediate proved to be extraordinarily stable, with an extremely long average dwell time of 2.3 s under the conditions of 3 M GdmCl at ambient temperature. The folding trajectories obtained from TIRF experiments further suggest that the intermediate is on-pathway to native Mad2.
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Affiliation(s)
- Xiang Hu
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China
- Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Jincheng Zhao
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China
- Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Yuanyuan Zhao
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China
- Department of Chronic and Non-communicable Disease Control and Prevention, Qingdao Center for Disease Control and Prevention, Qingdao 266033, China
| | - Huiting Zhang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China
- Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Qian Wang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an 710065, China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China
- Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiaoqiang Wang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China
- Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Hua He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China
- Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Werner M Nau
- School of Science, Constructor University, 28759 Bremen, Germany
| | - Xiaojuan Wang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China
- Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China
- Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
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12
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Dutta P, Roy P, Sengupta N. Effects of External Perturbations on Protein Systems: A Microscopic View. ACS OMEGA 2022; 7:44556-44572. [PMID: 36530249 PMCID: PMC9753117 DOI: 10.1021/acsomega.2c06199] [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: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.
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Affiliation(s)
- Pallab Dutta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
| | - Priti Roy
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma74078, United States
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
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13
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Ajayi S, Asakereh I, Rezasoltani H, Davidson D, Khajehpour M. Does Urea Preferentially Interact with Amide Moieties or Nonpolar Sidechains? A Question Answered Through a Judicious Selection of Model Systems. Chemphyschem 2022; 24:e202200731. [PMID: 36478636 DOI: 10.1002/cphc.202200731] [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: 10/04/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
The transfer model suggests that urea unfolds proteins mainly by increasing the solubility of the amide backbone, probably through urea-induced increase in hydrogen bonding. Other studies suggest that urea addition increases the magnitude of solvent-solute van der Waals interactions, which increases the solubility of nonpolar sidechains. More recent analyses hypothesize that urea has a similar effect in increasing the solubility of backbone and sidechain groups. In this work, we compare the effects of urea addition on the solvation of amides and alkyl groups. At first, we study the effects of urea addition upon solvent hydrogen bonding acidity and basicity through the perturbation in the fluorescence spectrum of probes 1-AN and 1-DMAN. Our results demonstrate that the solvent's hydrogen bonding properties are minimally affected by urea addition. Subsequently, we show that urea addition does not perturb the intra-molecular hydrogen bonding in salicylic acid significantly. Finally, we investigate how urea preferentially interacts with amide and alkyl groups moieties in water by comparing the effects of urea addition upon the solubility of acetaminophen and 4-tertbutylphenol. We show that urea affects amide and t-butyl solubility (lowers the transfer free energy of both amide (backbone) and alkyl (sidechain) groups) in a similar fashion. In other words, preferential interaction of urea with both moieties contributes to protein denaturation.
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Affiliation(s)
- Simisola Ajayi
- Department of Chemistry, the, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Iman Asakereh
- Department of Chemistry, the, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Hanieh Rezasoltani
- Department of Chemistry, the, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - David Davidson
- Department of Chemistry, the, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Mazdak Khajehpour
- Department of Chemistry, the, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
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14
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Acharya N, Jha SK. Dry Molten Globule-Like Intermediates in Protein Folding, Function, and Disease. J Phys Chem B 2022; 126:8614-8622. [PMID: 36286394 DOI: 10.1021/acs.jpcb.2c04991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The performance of a protein depends on its correct folding to the final functional native form. Hence, understanding the process of protein folding has remained an important field of research for the scientific community for the past five decades. Two important intermediate states, namely, wet molten globule (WMG) and dry molten globule (DMG), have emerged as critical milestones during protein folding-unfolding reactions. While much has been discussed about WMGs as a common unfolding intermediate, the evidence for DMGs has remained elusive owing to their near-native features, which makes them difficult to probe using global structural probes. This Review puts together the available literature and new evidence on DMGs to give a broader perspective on the universality of DMGs and discuss their significance in protein folding, function, and disease.
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Affiliation(s)
- Nirbhik Acharya
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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15
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Rico-Pasto M, Zaltron A, Davis SJ, Frutos S, Ritort F. Molten globule-like transition state of protein barnase measured with calorimetric force spectroscopy. Proc Natl Acad Sci U S A 2022; 119:e2112382119. [PMID: 35271392 PMCID: PMC8931224 DOI: 10.1073/pnas.2112382119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 01/31/2022] [Indexed: 01/11/2023] Open
Abstract
SignificanceUnderstanding the molecular forces driving the unfolded polypeptide chain to self-assemble into a functional native structure remains an open question. However, identifying the states visited during protein folding (e.g., the transition state between the unfolded and native states) is tricky due to their transient nature. Here, we introduce calorimetric force spectroscopy in a temperature jump optical trap to determine the enthalpy, entropy, and heat capacity of the transition state of protein barnase. We find that the transition state has the properties of a dry molten globule, that is, high free energy and low configurational entropy, being structurally similar to the native state. This experimental single-molecule study characterizes the thermodynamic properties of the transition state in funneled energy landscapes.
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Affiliation(s)
- Marc Rico-Pasto
- Small Biosystems Lab, Condensed Matter Physics Department, University of Barcelona, 08028 Barcelona, Spain
| | - Annamaria Zaltron
- Physics and Astronomy Department, University of Padova, 35131 Padova, Italy
| | - Sebastian J. Davis
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | | | - Felix Ritort
- Small Biosystems Lab, Condensed Matter Physics Department, University of Barcelona, 08028 Barcelona, Spain
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16
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Abstract
Proteins have dynamic structures that undergo chain motions on time scales spanning from picoseconds to seconds. Resolving the resultant conformational heterogeneity is essential for gaining accurate insight into fundamental mechanistic aspects of the protein folding reaction. The use of high-resolution structural probes, sensitive to population distributions, has begun to enable the resolution of site-specific conformational heterogeneity at different stages of the folding reaction. Different states populated during protein folding, including the unfolded state, collapsed intermediate states, and even the native state, are found to possess significant conformational heterogeneity. Heterogeneity in protein folding and unfolding reactions originates from the reduced cooperativity of various kinds of physicochemical interactions between various structural elements of a protein, and between a protein and solvent. Heterogeneity may arise because of functional or evolutionary constraints. Conformational substates within the unfolded state and the collapsed intermediates that exchange at rates slower than the subsequent folding steps give rise to heterogeneity on the protein folding pathways. Multiple folding pathways are likely to represent distinct sequences of structure formation. Insight into the nature of the energy barriers separating different conformational states populated during (un)folding can also be obtained by resolving heterogeneity.
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Affiliation(s)
- Sandhya Bhatia
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.,Indian Institute of Science Education and Research, Pune 411008, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.,Indian Institute of Science Education and Research, Pune 411008, India
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17
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Lai Z, Bai S, Li A, Feng X, He Q. Trimacrocyclic hexasubstituted benzenes for recognition of guanidinium and their anti-cancer and antimicrobial activities. Org Chem Front 2022. [DOI: 10.1039/d2qo00619g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We report the facile synthesis of two trimacrocyclic hexasubstituted benzenes for selective guanidinium recognition and extraction, along with their anti-cancer and antimicrobial activities.
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Affiliation(s)
- Zhenzhen Lai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Silei Bai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Aimin Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Xinxin Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Qing He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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18
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Chemically stable fluorescent proteins for advanced microscopy. Nat Methods 2022; 19:1612-1621. [PMID: 36344833 PMCID: PMC9718679 DOI: 10.1038/s41592-022-01660-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 09/26/2022] [Indexed: 11/09/2022]
Abstract
We report the rational engineering of a remarkably stable yellow fluorescent protein (YFP), 'hyperfolder YFP' (hfYFP), that withstands chaotropic conditions that denature most biological structures within seconds, including superfolder green fluorescent protein (GFP). hfYFP contains no cysteines, is chloride insensitive and tolerates aldehyde and osmium tetroxide fixation better than common fluorescent proteins, enabling its use in expansion and electron microscopies. We solved crystal structures of hfYFP (to 1.7-Å resolution), a monomeric variant, monomeric hyperfolder YFP (1.6 Å) and an mGreenLantern mutant (1.2 Å), and then rationally engineered highly stable 405-nm-excitable GFPs, large Stokes shift (LSS) monomeric GFP (LSSmGFP) and LSSA12 from these structures. Lastly, we directly exploited the chemical stability of hfYFP and LSSmGFP by devising a fluorescence-assisted protein purification strategy enabling all steps of denaturing affinity chromatography to be visualized using ultraviolet or blue light. hfYFP and LSSmGFP represent a new generation of robustly stable fluorescent proteins developed for advanced biotechnological applications.
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19
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The native state conformational heterogeneity in the energy landscape of protein folding. Biophys Chem 2022; 283:106761. [DOI: 10.1016/j.bpc.2022.106761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 11/18/2022]
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20
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Otzen DE, Pedersen JN, Somavarapu AK, Clement A, Ji M, Petersen EH, Pedersen JS, Urban S, Schafer NP. Cys-labeling kinetics of membrane protein GlpG: a role for specific SDS binding and micelle changes? Biophys J 2021; 120:4115-4128. [PMID: 34370995 DOI: 10.1016/j.bpj.2021.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/20/2021] [Accepted: 08/03/2021] [Indexed: 01/01/2023] Open
Abstract
Empirically, α-helical membrane protein folding stability in surfactant micelles can be tuned by varying the mole fraction MFSDS of anionic (sodium dodecyl sulfate (SDS)) relative to nonionic (e.g., dodecyl maltoside (DDM)) surfactant, but we lack a satisfying physical explanation of this phenomenon. Cysteine labeling (CL) has thus far only been used to study the topology of membrane proteins, not their stability or folding behavior. Here, we use CL to investigate membrane protein folding in mixed DDM-SDS micelles. Labeling kinetics of the intramembrane protease GlpG are consistent with simple two-state unfolding-and-exchange rates for seven single-Cys GlpG variants over most of the explored MFSDS range, along with exchange from the native state at low MFSDS (which inconveniently precludes measurement of unfolding kinetics under native conditions). However, for two mutants, labeling rates decline with MFSDS at 0-0.2 MFSDS (i.e., native conditions). Thus, an increase in MFSDS seems to be a protective factor for these two positions, but not for the five others. We propose different scenarios to explain this and find the most plausible ones to involve preferential binding of SDS monomers to the site of CL (based on computational simulations) along with changes in size and shape of the mixed micelle with changing MFSDS (based on SAXS studies). These nonlinear impacts on protein stability highlights a multifaceted role for SDS in membrane protein denaturation, involving both direct interactions of monomeric SDS and changes in micelle size and shape along with the general effects on protein stability of changes in micelle composition.
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Affiliation(s)
- Daniel E Otzen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark.
| | - Jannik Nedergaard Pedersen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Arun Kumar Somavarapu
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Anders Clement
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Ming Ji
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Emil Hartvig Petersen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark; Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Sinisa Urban
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nicholas P Schafer
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
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21
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Hung CL, Kuo YH, Lee SW, Chiang YW. Protein Stability Depends Critically on the Surface Hydrogen-Bonding Network: A Case Study of Bid Protein. J Phys Chem B 2021; 125:8373-8382. [PMID: 34314184 DOI: 10.1021/acs.jpcb.1c03245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding how proteins retain structural stability is not only of fundamental importance in biophysics but also critical to industrial production of antibodies and vaccines. Protein stability is known to depend mainly on two effects: internal hydrophobicity and H-bonding between the protein surface and solvent. A challenging task is to identify their individual contributions to a protein. Here, we investigate the structural stability of the apoptotic Bid protein in solutions containing various concentrations of guanidinium hydrochloride and urea using a combination of recently developed methods including the QTY (glutamine, threonine, and tyrosine) code and electron spin resonance-based peak-height analysis. We show that when the internal hydrophobicity of Bid is broken down using the QTY code, the surface H-bonding alone is sufficient to retain the structural stability intact. When the surface H-bonding is disrupted, Bid becomes sensitive to the temperature-dependent internal hydrophobicity such that it exhibits a reversible cold unfolding above water's freezing point. Using the combined approach, we show that the free-energy contributions of the two effects can be more reliably obtained. The surface H bonds are more important than the other effect in determining the structural stability of Bid protein.
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Affiliation(s)
- Chien-Lun Hung
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yun-Hsuan Kuo
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Su Wei Lee
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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22
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Bender AT, Sullivan BP, Lillis L, Posner JD. Enzymatic and Chemical-Based Methods to Inactivate Endogenous Blood Ribonucleases for Nucleic Acid Diagnostics. J Mol Diagn 2020; 22:1030-1040. [PMID: 32450280 DOI: 10.1016/j.jmoldx.2020.04.211] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/20/2020] [Accepted: 04/28/2020] [Indexed: 01/28/2023] Open
Abstract
There are ongoing research efforts into simple and low-cost point-of-care nucleic acid amplification tests (NATs) addressing widespread diagnostic needs in resource-limited clinical settings. Nucleic acid testing for RNA targets in blood specimens typically requires sample preparation that inactivates robust blood ribonucleases (RNases) that can rapidly degrade exogenous RNA. Most NATs rely on decades-old methods that lyse pathogens and inactivate RNases with high concentrations of guanidinium salts. Herein, we investigate alternatives to standard guanidinium-based methods for RNase inactivation using an activity assay with an RNA substrate that fluoresces when cleaved. The effects of proteinase K, nonionic surfactants, SDS, dithiothreitol, and other additives on RNase activity in human serum are reported. Although proteinase K has been widely used in protocols for nuclease inactivation, it was found that high concentrations of proteinase K are unable to eliminate RNase activity in serum, unless used in concert with denaturing concentrations of SDS. It was observed that SDS must be combined with proteinase K, dithiothreitol, or both for irreversible and complete RNase inactivation in serum. This work provides an alternative chemistry for inactivating endogenous RNases for use in simple, low-cost point-of-care NATs for blood-borne pathogens.
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Affiliation(s)
- Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | | | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Seattle, Washington; Department of Chemical Engineering, University of Washington, Seattle, Washington; Department of Family Medicine, University of Washington, Seattle, Washington.
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23
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Sarkar S, Singh PC. Alteration of the groove width of DNA induced by the multimodal hydrogen bonding of denaturants with DNA bases in its grooves affects their stability. Biochim Biophys Acta Gen Subj 2020; 1864:129498. [DOI: 10.1016/j.bbagen.2019.129498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 02/08/2023]
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24
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Abstract
Surprisingly, the densities of proteins in solution, which are important fundamental biophysical quantities, have not been accurately measured. The lack of such data can limit meaningful interpretation of physical and chemical features of proteins and enzymes. Here, we demonstrate a new technique using superparamagnetic iron oxide nanoparticles (SPIONs) for magnetic levitation (MagLev), which promises to more precisely measure the density of proteins in solution. As a test of our new technique, we have levitated human plasma proteins using MagLev. By using standard density glass beads for calibration, MagLev showed that the levitated plasma proteins have a measured density in solution of 1.03 ± 0.02 g/cm3, which is much lower than those reported or assumed in the past literature (i.e., ∼1.35 g/cm3). Our findings suggest that MagLev may provide useful insights into the measurement of densities for better understanding the solution properties of proteins and their interactions both with other proteins in solution and with solvating water molecules.
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Affiliation(s)
- Ali Akbar Ashkarran
- Precision Health Program , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Kenneth S Suslick
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Morteza Mahmoudi
- Precision Health Program , Michigan State University , East Lansing , Michigan 48824 , United States
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25
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Nandi T, Desai A, Ainavarapu SRK. The unfolding transition state of ubiquitin with charged residues has higher energy than that with hydrophobic residues. Phys Chem Chem Phys 2020; 22:23158-23168. [DOI: 10.1039/d0cp03876h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The native-state structure and folding pathways of a protein are encoded in its amino acid sequence.
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Affiliation(s)
- Tathagata Nandi
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400005
- India
| | - Amogh Desai
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400005
- India
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26
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Ganguly P, Shea JE. Distinct and Nonadditive Effects of Urea and Guanidinium Chloride on Peptide Solvation. J Phys Chem Lett 2019; 10:7406-7413. [PMID: 31721587 DOI: 10.1021/acs.jpclett.9b03004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Using enhanced-sampling replica exchange fully atomistic molecular dynamics simulations, we show that, individually, urea and guanidinium chloride (GdmCl) denature the Trpcage protein, but remarkably, the helical segment 1NLYIQWL7 of the protein is stabilized in mixed denaturant solutions. GdmCl induces protein denaturation via a combination of direct and indirect effects involving dehydration of the protein and destabilization of stabilizing salt bridges. In contrast, urea denatures the protein through favorable protein-urea preferential interactions, with peptide-specific indirect effects of urea on the water structure around the protein. In the case of the helical segment of Trpcage, urea "oversolvates" the peptide backbone by reorganizing water molecules from the peptide side chains to the peptide backbone. An intricate nonadditive thermodynamic balance between GdmCl-induced dehydration of the peptide and the urea-induced changes in solvation structure triggers partial counteraction to urea denaturation and stabilization of the helix.
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Affiliation(s)
- Pritam Ganguly
- Department of Chemistry and Biochemistry , University of California at Santa Barbara , Santa Barbara , California 93106 , United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry , University of California at Santa Barbara , Santa Barbara , California 93106 , United States
- Department of Physics , University of California at Santa Barbara , Santa Barbara , California 93106 , United States
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27
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Molecular level insight into the counteraction of trehalose on the activity as well as denaturation of lysozyme induced by guanidinium chloride. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2019.110489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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28
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Wu K, Stull F, Lee C, Bardwell JCA. Protein folding while chaperone bound is dependent on weak interactions. Nat Commun 2019; 10:4833. [PMID: 31645566 PMCID: PMC6811625 DOI: 10.1038/s41467-019-12774-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/23/2019] [Indexed: 12/31/2022] Open
Abstract
It is generally assumed that protein clients fold following their release from chaperones instead of folding while remaining chaperone-bound, in part because binding is assumed to constrain the mobility of bound clients. Previously, we made the surprising observation that the ATP-independent chaperone Spy allows its client protein Im7 to fold into the native state while continuously bound to the chaperone. Spy apparently permits sufficient client mobility to allow folding to occur while chaperone bound. Here, we show that strengthening the interaction between Spy and a recently discovered client SH3 strongly inhibits the ability of the client to fold while chaperone bound. The more tightly Spy binds to its client, the more it slows the folding rate of the bound client. Efficient chaperone-mediated folding while bound appears to represent an evolutionary balance between interactions of sufficient strength to mediate folding and interactions that are too tight, which tend to inhibit folding. Spy is an ATP independent chaperone that allows folding of its client protein Im7 while continuously bound to Spy. Here the authors employ kinetics measurements to study the folding of another Spy client protein SH3 and find that Spy’s ability to allow a client to fold while bound is inversely related to how strongly it interacts with that client.
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Affiliation(s)
- Kevin Wu
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109-1085, USA.,Department of Biophysics, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Frederick Stull
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109-1085, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA.,Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008-5413, USA
| | - Changhan Lee
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109-1085, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109-1085, USA. .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA.
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29
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Nandi T, Yadav A, Ainavarapu SRK. Experimental comparison of energy landscape features of ubiquitin family proteins. Proteins 2019; 88:449-461. [DOI: 10.1002/prot.25822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/05/2019] [Accepted: 09/18/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Tathagata Nandi
- Department of Chemical SciencesTata Institute of Fundamental Research Mumbai India
| | - Anju Yadav
- Department of Chemical SciencesTata Institute of Fundamental Research Mumbai India
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30
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Muttathukattil AN, Srinivasan S, Halder A, Reddy G. Role of Guanidinium-Carboxylate Ion Interaction in Enzyme Inhibition with Implications for Drug Design. J Phys Chem B 2019; 123:9302-9311. [DOI: 10.1021/acs.jpcb.9b06130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Aswathy N. Muttathukattil
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sriraksha Srinivasan
- Department of Chemistry, St. Joseph’s College, Bangalore, Karnataka 560027, India
| | - Antarip Halder
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
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31
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The Effect of Dimethyl Sulfoxide on the Lysozyme Unfolding Kinetics, Thermodynamics, and Mechanism. Biomolecules 2019; 9:biom9100547. [PMID: 31569484 PMCID: PMC6843525 DOI: 10.3390/biom9100547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 02/07/2023] Open
Abstract
The thermal stability of proteins in the presence of organic solvents and the search for ways to increase this stability are important topics in industrial biocatalysis and protein engineering. The denaturation of hen egg-white lysozyme in mixtures of water with dimethyl sulfoxide (DMSO) with a broad range of compositions was studied using a combination of differential scanning calorimetry (DSC), circular dichroism (CD), and spectrofluorimetry techniques. In this study, for the first time, the kinetics of unfolding of lysozyme in DMSO–water mixtures was characterized. In the presence of DMSO, a sharp decrease in near-UV CD and an increase in the fluorescence signal were observed at lower temperatures than the DSC denaturation peak. It was found that differences in the temperatures of the CD and DSC signal changes increase as the content of DMSO increases. Changes in CD and fluorescence are triggered by a break of the tertiary contacts, leading to an intermediate state, while the DSC peak corresponds to a subsequent complete loss of the native structure. In this way, the commonly used two-state model was proven to be unsuitable to describe the unfolding of lysozyme in the presence of DMSO. In kinetic studies, it was found that even high concentrations of DMSO do not drastically change the activation energy of the initial stage of unfolding associated with a disruption of the tertiary structure, while the enthalpy of denaturation shows a significant dependence on DMSO content. This observation suggests that the structure of the transition state upon unfolding remains similar to the structure of the native state.
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32
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Nshogozabahizi J, Aubrey K, Ross J, Thakor N. Applications and limitations of regulatory
RNA
elements in synthetic biology and biotechnology. J Appl Microbiol 2019; 127:968-984. [DOI: 10.1111/jam.14270] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/09/2019] [Accepted: 03/21/2019] [Indexed: 12/13/2022]
Affiliation(s)
- J.C. Nshogozabahizi
- Department of Chemistry and Biochemistry Alberta RNA Research and Training Institute (ARRTI) University of Lethbridge Lethbridge AB Canada
| | - K.L. Aubrey
- Department of Chemistry and Biochemistry Alberta RNA Research and Training Institute (ARRTI) University of Lethbridge Lethbridge AB Canada
| | - J.A. Ross
- Department of Chemistry and Biochemistry Alberta RNA Research and Training Institute (ARRTI) University of Lethbridge Lethbridge AB Canada
| | - N. Thakor
- Department of Chemistry and Biochemistry Alberta RNA Research and Training Institute (ARRTI) University of Lethbridge Lethbridge AB Canada
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33
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Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein. Proc Natl Acad Sci U S A 2019; 116:6806-6811. [PMID: 30877249 DOI: 10.1073/pnas.1818744116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The successful de novo design of proteins can provide insights into the physical chemical basis of stability, the role of evolution in constraining amino acid sequences, and the production of customizable platforms for engineering applications. Previous guanidine hydrochloride (GdnHCl; an ionic denaturant) experiments of a designed, naturally occurring βα fold, Di-III_14, revealed a cooperative, two-state unfolding transition and a modest stability. Continuous-flow mixing experiments in our laboratory revealed a simple two-state reaction in the microsecond to millisecond time range and consistent with the thermodynamic results. In striking contrast, the protein remains folded up to 9.25 M in urea, a neutral denaturant, and hydrogen exchange (HDX) NMR analysis in water revealed the presence of numerous high-energy states that interconvert on a time scale greater than seconds. The complex protection pattern for HDX corresponds closely with a pair of electrostatic networks on the surface and an extensive network of hydrophobic side chains in the interior of the protein. Mutational analysis showed that electrostatic and hydrophobic networks contribute to the resistance to urea denaturation for the WT protein; remarkably, single charge reversals on the protein surface restore the expected urea sensitivity. The roughness of the energy surface reflects the densely packed hydrophobic core; the removal of only two methyl groups eliminates the high-energy states and creates a smooth surface. The design of a very stable βα fold containing electrostatic and hydrophobic networks has created a complex energy surface rarely observed in natural proteins.
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34
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Luzuriaga MA, Welch RP, Dharmarwardana M, Benjamin CE, Li S, Shahrivarkevishahi A, Popal S, Tuong LH, Creswell CT, Gassensmith JJ. Enhanced Stability and Controlled Delivery of MOF-Encapsulated Vaccines and Their Immunogenic Response In Vivo. ACS APPLIED MATERIALS & INTERFACES 2019; 11:9740-9746. [PMID: 30776885 DOI: 10.1021/acsami.8b20504] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Vaccines have an innate tendency to lose their structural conformation upon environmental and chemical stressors. A loss in conformation reduces the therapeutic ability to prevent the spread of a pathogen. Herein, we report an in-depth study of zeolitic imidazolate framework-8 and its ability to provide protection for a model viral vector against denaturing conditions. The immunoassay and spectroscopy analysis together demonstrate enhanced thermal and chemical stability to the conformational structure of the encapsulated viral nanoparticle. The long-term biological activity of this virus-ZIF composite was investigated in animal models to further elucidate the integrity of the encapsulated virus, the biosafety, and immunogenicity of the overall composite. Additionally, histological analysis found no observable tissue damage in the skin or vital organs in mice, following multiple subcutaneous administrations. This study shows that ZIF-based protein composites are strong candidates for improved preservation of proteinaceous drugs, are biocompatible, and are capable of controlling the release and adsorption of drugs in vivo.
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35
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Baliga C, Selmke B, Worobiew I, Borbat P, Sarma SP, Trommer WE, Varadarajan R, Aghera N. CcdB at pH 4 Forms a Partially Unfolded State with a Dry Core. Biophys J 2019; 116:807-817. [PMID: 30777307 DOI: 10.1016/j.bpj.2019.01.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 01/18/2019] [Accepted: 01/23/2019] [Indexed: 12/14/2022] Open
Abstract
pH is an important factor that affects the protein structure, stability, and activity. Here, we probe the nature of the low-pH structural form of the homodimeric CcdB (controller of cell death B) protein. Characterization of CcdB protein at pH 4 and 300 K using circular dichroism spectroscopy, 8-anilino-1-naphthalene-sulphonate binding, and Trp solvation studies suggests that it forms a partially unfolded state with a dry core at equilibrium under these conditions. CcdB remains dimeric at pH 4 as shown by multiple techniques, such as size-exclusion chromatography coupled to multiangle light scattering, analytical ultracentrifugation, and electron paramagnetic resonance. Comparative analysis using two-dimensional 15N-1H heteronuclear single-quantum coherence NMR spectra of CcdB at pH 4 and 7 suggests that the pH 4 and native state have similar but nonidentical structures. Hydrogen-exchange-mass-spectrometry studies demonstrate that the pH 4 state has substantial but anisotropic changes in local stability with core regions close to the dimer interface showing lower protection but some other regions showing higher protection relative to pH 7.
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Affiliation(s)
- Chetana Baliga
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Benjamin Selmke
- Department of Chemistry, TU Kaiserslautern, Kaiserslautern, Germany
| | - Irina Worobiew
- Department of Chemistry, TU Kaiserslautern, Kaiserslautern, Germany
| | - Peter Borbat
- Department of Chemistry and Chemical Biology, ACERT National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York
| | - Siddhartha P Sarma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
| | - Nilesh Aghera
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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36
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Mishra P, Jha SK. Slow Motion Protein Dance Visualized Using Red-Edge Excitation Shift of a Buried Fluorophore. J Phys Chem B 2019; 123:1256-1264. [PMID: 30640479 DOI: 10.1021/acs.jpcb.8b11151] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It has been extremely challenging to detect protein structures with a dynamic core, such as dry molten globules, that remain in equilibrium with the tightly packed native (N) state and that are important for a myriad of entropy-driven protein functions. Here, we detect the higher entropy conformations of a human serum protein, using red-edge excitation shift experiments. We covalently introduced a fluorophore inside the protein core and observed that in a subset of native population, the side chains of the polar and buried residues have different spatial arrangements than the mean population and that they solvate the fluorophore on a timescale much slower than the nanosecond timescale of fluorescence. Our results provide direct evidence for the dense fluidity of protein core and show that alternate side-chain packing arrangements exist in the core that might be important for multiple binding functions of this protein.
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Affiliation(s)
- Prajna Mishra
- Physical and Materials Chemistry Division, Academy of Scientific and Innovative Research (AcSIR) , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road , Pune 411008 , Maharashtra , India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, Academy of Scientific and Innovative Research (AcSIR) , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road , Pune 411008 , Maharashtra , India
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37
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Usuki S, Yamatoya K, Kawamura Y, Yamaguchi Y, Suzuki N, Katsumata KI, Terashima C, Fujishima A, Kudo A, Nakata K. Denaturation of Lysozyme with Visible-light-responsive Photocatalysts of Ground Rhodium-doped and Ground Rhodium-antimony-co-doped Strontium Titanate. J Oleo Sci 2018; 67:1521-1533. [PMID: 30504623 DOI: 10.5650/jos.ess18155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Protein denaturants play an important role in medical and biological research, and development of new denaturants is widely explored to study aging and various diseases. In this research, we treated lysozyme, a model protein, with photocatalysts of ground Rh-doped SrTiO3 (g-STO:Rh) and ground Rh-Sb-co-doped SrTiO3 (g-STO:Rh/Sb) under visible light irradiation to explore the potential of those photocatalysts as denaturants. SDS-PAGE showed that photocatalysis with g-STO:Rh induced the fragmentation of lysozyme into unidentifiable decomposition products. BCA and Bradford protein assays indicated that the peptide bonds and basic, aromatic and N-terminal amino acid residues in lysozyme were denaturated by g-STO:Rh photocatalysis. The denaturation of those amino acids, as quantified by the decreased solubility of lysozyme, was estimated to be more severe by Bradford protein assay than by BCA protein assay. Circular dichroism (CD) spectra of lysozyme revealed that the secondary structure was denatured by g-STO:Rh photocatalysis, indicating that g-STO:Rh photocatalysis is especially effective against the amino acid residues that form the secondary structure via hydrogen bonds. Furthermore, the lytic activity of lysozyme was reduced by g-STO:Rh photocatalysis, owing to denaturation of the enzyme. The visible-light-responsive photocatalyst of g-STO:Rh/Sb accelerates the oxidation reaction and has stronger oxidizing power than g-STO:Rh. Lysozyme was denatured more quickly by g-STO:Rh/Sb photocatalysis than by g-STO:Rh according to analysis by SDS-PAGE, CD spectroscopy, BCA and Bradford protein assays, and lytic activity. These results suggest that higher photocatalytic activity induces more significant denaturation of lysozyme, implying that the main factor of photocatalytic denaturation of lysozyme is oxidation. It should be noted that, as far as we know, this is the first report for denaturation of protein using visible-light-responsive photocatalyst.
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Affiliation(s)
- Sho Usuki
- Photocatalysis International Research Center, Research Institute for Science and Technology, Tokyo University of Science.,Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
| | - Kenji Yamatoya
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
| | - Yuki Kawamura
- Photocatalysis International Research Center, Research Institute for Science and Technology, Tokyo University of Science.,Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
| | - Yuichi Yamaguchi
- Photocatalysis International Research Center, Research Institute for Science and Technology, Tokyo University of Science.,Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
| | - Norihiro Suzuki
- Photocatalysis International Research Center, Research Institute for Science and Technology, Tokyo University of Science
| | - Ken-Ichi Katsumata
- Photocatalysis International Research Center, Research Institute for Science and Technology, Tokyo University of Science
| | - Chiaki Terashima
- Photocatalysis International Research Center, Research Institute for Science and Technology, Tokyo University of Science
| | - Akira Fujishima
- Photocatalysis International Research Center, Research Institute for Science and Technology, Tokyo University of Science
| | - Akihiko Kudo
- Photocatalysis International Research Center, Research Institute for Science and Technology, Tokyo University of Science.,Department of Applied Chemistry, Faculty of Science, Tokyo University of Science
| | - Kazuya Nakata
- Photocatalysis International Research Center, Research Institute for Science and Technology, Tokyo University of Science.,Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
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38
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Kohn EM, Lee JY, Calabro A, Vaden TD, Caputo GA. Heme Dissociation from Myoglobin in the Presence of the Zwitterionic Detergent N, N-Dimethyl- N-Dodecylglycine Betaine: Effects of Ionic Liquids. Biomolecules 2018; 8:biom8040126. [PMID: 30380655 PMCID: PMC6315634 DOI: 10.3390/biom8040126] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 01/24/2023] Open
Abstract
We have investigated myoglobin protein denaturation using the zwitterionic detergent Empigen BB (EBB, N,N-Dimethyl-N-dodecylglycine betaine). A combination of absorbance, fluorescence, and circular dichroism spectroscopic measurements elucidated the protein denaturation and heme dissociation from myoglobin. The results indicated that Empigen BB was not able to fully denature the myoglobin structure, but apparently can induce the dissociation of the heme group from the protein. This provides a way to estimate the heme binding free energy, ΔGdissociation. As ionic liquids (ILs) have been shown to perturb the myoglobin protein, we have investigated the effects of the ILs 1-butyl-3-methylimidazolium chloride (BMICl), 1-ethyl-3-methylimidazolium acetate (EMIAc), and 1-butyl-3-methylimidazolium tetrafluoroborate (BMIBF4) in aqueous solution on the ΔGdissociation values. Absorbance experiments show the ILs had minimal effect on ΔGdissociation values when compared to controls. Fluorescence and circular dichroism data confirm the ILs have no effect on heme dissociation, demonstrating that low concentrations ILs do not impact the heme dissociation from the protein and do not significantly denature myoglobin on their own or in combination with EBB. These results provide important data for future studies of the mechanism of IL-mediated protein stabilization/destabilization and biocompatibility studies.
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Affiliation(s)
- Eric M Kohn
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA.
- Bantivoglio Honors College, Rowan University, Glassboro, NJ 08028, USA.
| | - Joshua Y Lee
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA.
- Bantivoglio Honors College, Rowan University, Glassboro, NJ 08028, USA.
| | - Anthony Calabro
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA.
| | - Timothy D Vaden
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA.
| | - Gregory A Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA.
- Department of Molecular & Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA.
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39
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Pedrote MM, de Oliveira GAP, Felix AL, Mota MF, Marques MDA, Soares IN, Iqbal A, Norberto DR, Gomes AMO, Gratton E, Cino EA, Silva JL. Aggregation-primed molten globule conformers of the p53 core domain provide potential tools for studying p53C aggregation in cancer. J Biol Chem 2018; 293:11374-11387. [PMID: 29853637 PMCID: PMC6065177 DOI: 10.1074/jbc.ra118.003285] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/10/2018] [Indexed: 12/16/2022] Open
Abstract
The functionality of the tumor suppressor p53 is altered in more than 50% of human cancers, and many individuals with cancer exhibit amyloid-like buildups of aggregated p53. An understanding of what triggers the pathogenic amyloid conversion of p53 is required for the further development of cancer therapies. Here, perturbation of the p53 core domain (p53C) with subdenaturing concentrations of guanidine hydrochloride and high hydrostatic pressure revealed native-like molten globule (MG) states, a subset of which were highly prone to amyloidogenic aggregation. We found that MG conformers of p53C, probably representing population-weighted averages of multiple states, have different volumetric properties, as determined by pressure perturbation and size-exclusion chromatography. We also found that they bind the fluorescent dye 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) and have a native-like tertiary structure that occludes the single Trp residue in p53. Fluorescence experiments revealed conformational changes of the single Trp and Tyr residues before p53 unfolding and the presence of MG conformers, some of which were highly prone to aggregation. p53C exhibited marginal unfolding cooperativity, which could be modulated from unfolding to aggregation pathways with chemical or physical forces. We conclude that trapping amyloid precursor states in solution is a promising approach for understanding p53 aggregation in cancer. Our findings support the use of single-Trp fluorescence as a probe for evaluating p53 stability, effects of mutations, and the efficacy of therapeutics designed to stabilize p53.
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Affiliation(s)
- Murilo M Pedrote
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil
| | - Guilherme A P de Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908.
| | - Adriani L Felix
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil
| | - Michelle F Mota
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil
| | - Mayra de A Marques
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil
| | - Iaci N Soares
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil
| | - Anwar Iqbal
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil
| | - Douglas R Norberto
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil
| | - Andre M O Gomes
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Biomedical Engineering Department, University of California, Irvine, California 92697-2717
| | - Elio A Cino
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Jerson L Silva
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil.
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40
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Holehouse AS, Pappu RV. Collapse Transitions of Proteins and the Interplay Among Backbone, Sidechain, and Solvent Interactions. Annu Rev Biophys 2018; 47:19-39. [PMID: 29345991 PMCID: PMC10740066 DOI: 10.1146/annurev-biophys-070317-032838] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Proteins can collapse into compact globules or form expanded, solvent-accessible, coil-like conformations. Additionally, they can fold into well-defined three-dimensional structures or remain partially or entirely disordered. Recent discoveries have shown that the tendency for proteins to collapse or remain expanded is not intrinsically coupled to their ability to fold. These observations suggest that proteins do not have to form compact globules in aqueous solutions. They can be intrinsically disordered, collapsed, or expanded, and even form well-folded, elongated structures. This ability to decouple collapse from folding is determined by the sequence details of proteins. In this review, we highlight insights gleaned from studies over the past decade. Using a polymer physics framework, we explain how the interplay among sidechains, backbone units, and solvent determines the driving forces for collapsed versus expanded states in aqueous solvents.
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Affiliation(s)
- Alex S Holehouse
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in Saint Louis, Saint Louis, Missouri 63130, USA; ,
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in Saint Louis, Saint Louis, Missouri 63130, USA; ,
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41
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Oprzeska-Zingrebe EA, Smiatek J. Aqueous ionic liquids in comparison with standard co-solutes : Differences and common principles in their interaction with protein and DNA structures. Biophys Rev 2018; 10:809-824. [PMID: 29611033 DOI: 10.1007/s12551-018-0414-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/12/2018] [Indexed: 12/29/2022] Open
Abstract
Ionic liquids (ILs) are versatile solvents for a broad range of biotechnological applications. Recent experimental and simulation results highlight the potential benefits of dilute ILs in aqueous solution (aqueous ILs) in order to modify protein and DNA structures systematically. In contrast to a limited number of standard co-solutes like urea, ectoine, trimethylamine-N-oxide (TMAO), or guanidinium chloride, the large amount of possible cation and anion combinations in aqueous ILs can be used to develop tailor-made stabilizers or destabilizers for specific purposes. In this review article, we highlight common principles and differences between aqueous ILs and standard co-solutes with a specific focus on their underlying macromolecular stabilization or destabilization behavior. In combination with statistical thermodynamics theories, we present an efficient framework, which is used to classify structure modification effects consistently. The crucial importance of enthalpic and entropic contributions to the free energy change upon IL-assisted macromolecular unfolding in combination with a complex destabilization mechanism is described in detail. A special focus is also set on aqueous IL-DNA interactions, for which experimental and simulation outcomes are summarized and discussed in the context of previous findings.
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Affiliation(s)
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569, Stuttgart, Germany. .,Helmholtz Institute Münster: Ionics in Energy Storage (HI MS - IEK 12), Forschungszentrum Jülich GmbH, Corrensstrasse 46, 48149, Münster, Germany.
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42
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Yue Z, Shen J. pH-Dependent cooperativity and existence of a dry molten globule in the folding of a miniprotein BBL. Phys Chem Chem Phys 2018; 20:3523-3530. [PMID: 29336449 DOI: 10.1039/c7cp08296g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Solution pH plays an important role in protein dynamics, stability, and folding; however, detailed mechanisms remain poorly understood. Here we use continuous constant pH molecular dynamics in explicit solvent with pH replica exchange to describe the pH profile of the folding cooperativity of a miniprotein BBL, which has drawn intense debate in the past. Our data reconciled the two opposing hypotheses (downhill vs. two-state) and uncovered a sparsely populated unfolding intermediate. As pH is lowered from 7 to 5, the folding barrier vanishes. As pH continues to decrease, the unfolding barrier lowers and denaturation is triggered by the protonation of Asp162, consistent with experimental evidence. Interestingly, unfolding proceeded via an intermediate, with intact secondary structure and a compact, unlocked hydrophobic core shielded from solvent, lending support to the recent hypothesis of a universal dry molten globule in protein folding. Our work demonstrates that constant pH molecular dynamics is a unique tool for testing this and other hypotheses to advance the knowledge in protein dynamics, stability, and folding.
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Affiliation(s)
- Zhi Yue
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201-1075, USA.
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43
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de Oliveira GA, Silva JL. The push-and-pull hypothesis in protein unfolding, misfolding and aggregation. Biophys Chem 2017; 231:20-26. [DOI: 10.1016/j.bpc.2017.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 03/25/2017] [Accepted: 03/27/2017] [Indexed: 01/17/2023]
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44
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Singh MI, Jain V. Identification and Characterization of an Inside-Out Folding Intermediate of T4 Phage Sliding Clamp. Biophys J 2017; 113:1738-1749. [PMID: 29045868 DOI: 10.1016/j.bpj.2017.08.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/15/2017] [Accepted: 08/28/2017] [Indexed: 10/18/2022] Open
Abstract
Protein folding process involves formation of transiently occurring intermediates that are difficult to isolate and characterize. It is both necessary and interesting to characterize the structural conformations adopted by these intermediates, also called molten globules (MG), to understand protein folding. Here, we investigated the equilibrium (un)folding intermediate state of T4 phage gene product 45 (gp45, also known as DNA polymerase processivity factor or sliding clamp) obtained during chemical denaturation. We show that gp45 undergoes substantial conformational rearrangement during unfolding and forms an expanded dry-MG. By monitoring the fluorescence of tryptophans that were strategically introduced at various sites, we demonstrate that the urea-treated molecule has its surface residues flip inside the core, and closely placed residues move farther. We were also able to isolate and purify the MG form of gp45 in native condition (i.e., nondenaturing buffer, at physiological pH and temperature); characteristics of this purified molecule substantially match with urea-treated wild-type gp45. To the best of our knowledge, this is one of the few reports that demonstrate the isolation and purification of a protein folding intermediate in native condition. We believe that our work not only allows us to dissect the process of protein folding, but will also help in the designing of folding inhibitors against sliding clamps to treat a wide variety of diseases from bacterial infection to cancer, due to the vast presence of clamps in all the domains of life.
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Affiliation(s)
- Manika Indrajit Singh
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India.
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45
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Mishra P, Jha SK. An Alternatively Packed Dry Molten Globule-like Intermediate in the Native State Ensemble of a Multidomain Protein. J Phys Chem B 2017; 121:9336-9347. [DOI: 10.1021/acs.jpcb.7b07032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Prajna Mishra
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra 411008, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra 411008, India
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46
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Sen S, Goluguri RR, Udgaonkar JB. A Dry Transition State More Compact Than the Native State Is Stabilized by Non-Native Interactions during the Unfolding of a Small Protein. Biochemistry 2017; 56:3699-3703. [DOI: 10.1021/acs.biochem.7b00388] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Sreemantee Sen
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Rama Reddy Goluguri
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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47
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Bolognesi MM, Manzoni M, Scalia CR, Zannella S, Bosisio FM, Faretta M, Cattoretti G. Multiplex Staining by Sequential Immunostaining and Antibody Removal on Routine Tissue Sections. J Histochem Cytochem 2017; 65:431-444. [PMID: 28692376 PMCID: PMC5533273 DOI: 10.1369/0022155417719419] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Multiplexing, labeling for multiple immunostains in the very same cell or tissue section in situ, has raised considerable interest. The methods proposed include the use of labeled primary antibodies, spectral separation of fluorochromes, bleaching of the fluorophores or chromogens, blocking of previous antibody layers, all in various combinations. The major obstacles to the diffusion of this technique are high costs in custom antibodies and instruments, low throughput, and scarcity of specialized skills or facilities. We have validated a method based on common primary and secondary antibodies and diffusely available fluorescent image scanners. It entails rounds of four-color indirect immunofluorescence, image acquisition, and removal (stripping) of the antibodies, before another stain is applied. The images are digitally registered and the autofluorescence is subtracted. Removal of antibodies is accomplished by disulfide cleavage and a detergent or by a chaotropic salt treatment, this latter followed by antigen refolding. More than 30 different antibody stains can be applied to one single section from routinely fixed and embedded tissue. This method requires a modest investment in hardware and materials and uses freeware image analysis software. Multiplexing on routine tissue sections is a high throughput tool for in situ characterization of neoplastic, reactive, inflammatory, and normal cells.
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Affiliation(s)
- Maddalena Maria Bolognesi
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (MMB, MM, CRS, SZ, FMB, GC)
| | - Marco Manzoni
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (MMB, MM, CRS, SZ, FMB, GC)
| | - Carla Rossana Scalia
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (MMB, MM, CRS, SZ, FMB, GC)
| | - Stefano Zannella
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (MMB, MM, CRS, SZ, FMB, GC)
| | - Francesca Maria Bosisio
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (MMB, MM, CRS, SZ, FMB, GC).,Laboratory of Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium (FMB)
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (MF)
| | - Giorgio Cattoretti
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (MMB, MM, CRS, SZ, FMB, GC).,Department of Pathology, Azienda Socio-Sanitaria Territoriale Monza, Monza, Italy (GC)
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48
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Winardhi RS, Tang Q, Chen J, Yao M, Yan J. Probing Small Molecule Binding to Unfolded Polyprotein Based on its Elasticity and Refolding. Biophys J 2017; 111:2349-2357. [PMID: 27926836 DOI: 10.1016/j.bpj.2016.10.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 09/21/2016] [Accepted: 10/24/2016] [Indexed: 10/20/2022] Open
Abstract
Unfolded protein, a disordered structure found before folding of newly synthesized protein or after protein denaturation, is a substrate for binding by many cellular factors such as heat-stable proteins, chaperones, and many small molecules. However, it is challenging to directly probe such interactions in physiological solution conditions because proteins are largely in their folded state. In this work we probed small molecule binding to mechanically unfolded polyprotein using sodium dodecyl sulfate (SDS) as an example. The effect of binding is quantified based on changes in the elasticity and refolding of the unfolded polyprotein in the presence of SDS. We show that this single-molecule mechanical detection of binding to unfolded polyprotein can serve, to our knowledge, as a novel label-free assay with a great potential to study many factors that interact with unfolded protein domains, which underlie many important biological processes.
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Affiliation(s)
- Ricksen S Winardhi
- Department of Physics, National University of Singapore, Singapore, Singapore; Mechanobiology Institute, National University of Singapore, Singapore, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | - Qingnan Tang
- Department of Physics, National University of Singapore, Singapore, Singapore; Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Jin Chen
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Mingxi Yao
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Jie Yan
- Department of Physics, National University of Singapore, Singapore, Singapore; Mechanobiology Institute, National University of Singapore, Singapore, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore.
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49
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Yeh YQ, Liao KF, Shih O, Shiu YJ, Wu WR, Su CJ, Lin PC, Jeng US. Probing the Acid-Induced Packing Structure Changes of the Molten Globule Domains of a Protein near Equilibrium Unfolding. J Phys Chem Lett 2017; 8:470-477. [PMID: 28067527 DOI: 10.1021/acs.jpclett.6b02722] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Using simultaneously scanning small-angle X-ray scattering (SAXS) and UV-vis absorption with integrated online size exclusion chromatography, supplemental with molecular dynamics simulations, we unveil the long-postulated global structure evolution of a model multidomain protein bovine serum albumin (BSA) during acid-induced unfolding. Our results differentiate three global packing structures of the three molten globule domains of BSA, forming three intermediates I1, I2, and E along the unfolding pathway. The I1-I2 transition, overlooked in all previous studies, involves mainly coordinated reorientations across interconnected molten globule subdomains, and the transition activates a critical pivot domain opening of the protein for entering into the E form, with an unexpectedly large unfolding free energy change of -9.5 kcal mol-1, extracted based on the observed packing structural changes. The revealed local packing flexibility and rigidity of the molten globule domains in the E form elucidate how collective motions of the molten globule domains profoundly influence the folding-unfolding pathway of a multidomain protein.
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Affiliation(s)
- Yi-Qi Yeh
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Kuei-Fen Liao
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Ying-Jen Shiu
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Wei-Ru Wu
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Chun-Jen Su
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Po-Chang Lin
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
- Department of Chemical Engineering, National Tsing Hua University , Hsinchu 30013, Taiwan
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50
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Heyda J, Okur HI, Hladílková J, Rembert KB, Hunn W, Yang T, Dzubiella J, Jungwirth P, Cremer PS. Guanidinium can both Cause and Prevent the Hydrophobic Collapse of Biomacromolecules. J Am Chem Soc 2017; 139:863-870. [PMID: 28054487 PMCID: PMC5499822 DOI: 10.1021/jacs.6b11082] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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A combination of Fourier transform
infrared and phase transition
measurements as well as molecular computer simulations, and thermodynamic
modeling were performed to probe the mechanisms by which guanidinium
(Gnd+) salts influence the stability of the collapsed versus
uncollapsed state of an elastin-like polypeptide (ELP), an uncharged
thermoresponsive polymer. We found that the cation’s action
was highly dependent upon the counteranion with which it was paired.
Specifically, Gnd+ was depleted from the ELP/water interface
and was found to stabilize the collapsed state of the macromolecule
when paired with well-hydrated anions such as SO42–. Stabilization in this case occurred via an excluded volume (or
depletion) effect, whereby SO42– was
strongly partitioned away from the ELP/water interface. Intriguingly,
at low salt concentrations, Gnd+ was also found to stabilize
the collapsed state of the ELP when paired with SCN–, which is a strong binder for the ELP. In this case, the anion and
cation were both found to be enriched in the collapsed state of the
polymer. The collapsed state was favored because the Gnd+ cross-linked the polymer chains together. Moreover, the anion helped
partition Gnd+ to the polymer surface. At higher salt concentrations
(>1.5 M), GndSCN switched to stabilizing the uncollapsed state
because
a sufficient amount of Gnd+ and SCN– partitioned
to the polymer surface to prevent cross-linking from occurring. Finally,
in a third case, it was found that salts which interacted in an intermediate
fashion with the polymer (e.g., GndCl) favored the uncollapsed conformation
at all salt concentrations. These results provide a detailed, molecular-level,
mechanistic picture of how Gnd+ influences the stability
of polypeptides in three distinct physical regimes by varying the
anion. It also helps explain the circumstances under which guanidinium
salts can act as powerful and versatile protein denaturants.
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Affiliation(s)
- Jan Heyda
- Institut für Weiche Materie und Funktionale Materialien, Helmholtz-Zentrum Berlin für Materialien und Energie , Hahn-Meitner Platz 1, 14109 Berlin, Germany.,Physical Chemistry Department, University of Chemistry and Technology, Prague , Technicka 5, 16628 Prague 6, Czech Republic
| | | | - Jana Hladílková
- Division of Theoretical Chemistry, Lund University , POB 124, 22 100 Lund, Sweden.,Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | | | - William Hunn
- Chemistry Department, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
| | | | - Joachim Dzubiella
- Institut für Weiche Materie und Funktionale Materialien, Helmholtz-Zentrum Berlin für Materialien und Energie , Hahn-Meitner Platz 1, 14109 Berlin, Germany.,Institut für Physik, Humboldt-Universität zu Berlin , Newtonstr. 15, 12489 Berlin, Germany
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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