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Pal S, Banerjee S, Prabhakaran EN. α-Helices propagating from stable nucleators exhibit unconventional thermal folding. FEBS Lett 2021; 595:2942-2949. [PMID: 34716991 DOI: 10.1002/1873-3468.14216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/07/2022]
Abstract
Although the effect of thermal perturbations on protein structure has long been modeled in helical peptides, several details, such as the relation between the thermal stabilities of the propagating and nucleating segments of helices, remain elusive. We had earlier reported on the helix-nucleating propensities of covalent H-bond surrogate-constrained α-turns. Here, we analyze the thermal stabilities of helices that propagate along peptides appended to these α-helix nucleators using their NMR and far-UV CD spectra. Unconventional thermal folding of these helix models reveals that the helical fold in propagating backbones resists thermal perturbations as long as their nucleating template is intact. The threshold temperature of such resistance is also influenced by the extent of similarity between the natures of helical folds in the nucleating and propagating segments. Correlations between helicities and rigidities of helix-nucleating and helix-propagating segments reveal subtle interdependence, which explains cooperativity and residual helix formation during protein folding.
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Affiliation(s)
- Sunit Pal
- Department of Chemistry, Indian Institute of Science, Bangalore, India
| | - Shreya Banerjee
- Department of Chemistry, Indian Institute of Science, Bangalore, India
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2
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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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Lan YJ, Yeh PS, Kao TY, Lo YC, Sue SC, Chen YW, Hwang DW, Chiang YW. Anti-apoptotic BCL-2 regulation by changes in dynamics of its long unstructured loop. Commun Biol 2020; 3:668. [PMID: 33184407 PMCID: PMC7665024 DOI: 10.1038/s42003-020-01390-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
BCL-2, a key protein in inhibiting apoptosis, has a 65-residue-long highly flexible loop domain (FLD) located on the opposite side of its ligand-binding groove. In vivo phosphorylation of the FLD enhances the affinity of BCL-2 for pro-apoptotic ligands, and consequently anti-apoptotic activity. However, it remains unknown as to how the faraway, unstructured FLD modulates the affinity. Here we investigate the protein-ligand interactions by fluorescence techniques and monitor protein dynamics by DEER and NMR spectroscopy tools. We show that phosphomimetic mutations on the FLD lead to a reduction in structural flexibility, hence promoting ligand access to the groove. The bound pro-apoptotic ligands can be displaced by the BCL-2-selective inhibitor ABT-199 efficiently, and thus released to trigger apoptosis. We show that changes in structural flexibility on an unstructured loop can activate an allosteric protein that is otherwise structurally inactive.
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Affiliation(s)
- Yu-Jing Lan
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Pei-Shan Yeh
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Te-Yu Kao
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Yuan-Chao Lo
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yu-Wen Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Dennis W Hwang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan.
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4
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PEGylation-based strategy to identify pathways involved in the activation of apoptotic BAX protein. Biochim Biophys Acta Gen Subj 2020; 1864:129541. [PMID: 31987956 DOI: 10.1016/j.bbagen.2020.129541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 10/25/2022]
Abstract
BACKGROUND BAX activation is a crucial step for commitment to apoptosis. Several activators, such as BimBH3-based therapeutic peptides and cleaved Bid (cBid) protein, can trigger BAX-mediated apoptosis, but it is unclear whether they proceed through the same pathway. METHODS Here we utilize PEGylation-based approach, which is shown to efficiently shield individual binding grooves in BAX from activators, to investigate and reveal that the activators take different routes to induce BAX-mediated apoptosis. Various spectroscopic/biochemical tools, including electron spin resonance, circular dichroism, fluorescence recovery after photobleaching, and label-transfer assay, were employed to reveal details in the processes. RESULTS We observe a key mutant BAX 164-PEG that acts differently in response to cBid and BimBH3 stimuli. While BimBH3 directly interacts with the trigger groove (TG) to induce the conformational changes in BAX that includes the release of α9 from the canonical groove (CG) and oligomerization, cBid engages with CG and works with mitochondrial lipids to fully activate BAX. CONCLUSION PEGylation-based approach is proven useful to shield individual binding grooves of BAX from apoptotic stimuli. Groove engagement in CG of BAX is required for a full cBid-induced BAX activation. This study has identified differences in the pathways involved during the initiation of BAX activation by full-length cBid protein versus synthetic BimBH3-based peptides. GENERAL SIGNIFICANCE Our finding is potentially valuable for therapeutic application as the pore-forming activity of 164-PEG is independent from the cBid-mediated apoptotic pathways, but can be administrated by the synthetic short peptides.
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Lai YC, Li CC, Sung TC, Chang CW, Lan YJ, Chiang YW. The role of cardiolipin in promoting the membrane pore-forming activity of BAX oligomers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1861:268-280. [PMID: 29958826 DOI: 10.1016/j.bbamem.2018.06.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/17/2018] [Accepted: 06/22/2018] [Indexed: 01/31/2023]
Abstract
BCL-2-associated X (BAX) protein acts as a gatekeeper in regulating mitochondria-dependent apoptosis. Under cellular stress, BAX becomes activated and transforms into a lethal oligomer that causes mitochondrial outer membrane permeabilization (MOMP). Previous studies have identified several structural features of the membrane-associated BAX oligomer; they include the formation of the BH3-in-groove dimer, the collapse of the helical hairpin α5-α6, and the membrane insertion of α9 helix. However, it remains unclear as to the role of lipid environment in determining the conformation and the pore-forming activity of the BAX oligomers. Here we study molecular details of the membrane-associated BAX in various lipid environments using fluorescence and ESR techniques. We identify the inactive versus active forms of membrane-associated BAX, only the latter of which can induce stable and large membrane pores that are sufficient in size to pass apoptogenic factors. We reveal that the presence of CL is crucial to promoting the association between BAX dimers, hence the active oligomers. Without the presence of CL, BAX dimers assemble into an inactive oligomer that lacks the ability to form stable pores in the membrane. This study suggests an important role of CL in determining the formation of active BAX oligomers.
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Affiliation(s)
- Yei-Chen Lai
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chieh-Chin Li
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Tai-Ching Sung
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chia-Wei Chang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yu-Jing Lan
- 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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6
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Kuo YH, Chiang YW. Slow Dynamics around a Protein and Its Coupling to Solvent. ACS CENTRAL SCIENCE 2018; 4:645-655. [PMID: 29806012 PMCID: PMC5968437 DOI: 10.1021/acscentsci.8b00139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Indexed: 05/25/2023]
Abstract
Solvent is essential for protein dynamics and function, but its role in regulating the dynamics remains debated. Here, we employ saturation transfer electron spin resonance (ST-ESR) to explore the issue and characterize the dynamics on a longer (from μs to s) time scale than has been extensively studied. We first demonstrate the reliability of ST-ESR by showing that the dynamical changeovers revealed in the spectra agree to liquid-liquid transition (LLT) in the state diagram of the glycerol/water system. Then, we utilize ST-ESR with four different probes to systematically map out the variation in local (site-specific) dynamics around a protein surface at subfreezing temperatures (180-240 K) in 10 mol % glycerol/water mixtures. At highly exposed sites, protein and solvent dynamics are coupled, whereas they deviate from each other when temperature is greater than LLT temperature (∼190 K) of the solvent. At less exposed sites, protein however exhibits a dynamic, which is distinct from the bulk solvent, throughout the temperature range studied. Dominant dynamic components are thus revealed, showing that (from low to high temperatures) the overall structural fluctuation, rotamer dynamics, and internal side-chain dynamics, in turn, dominate the temperature dependence of spin-label motions. The structural fluctuation component is relatively slow, collective, and independent of protein structural segments, which is thus inferred to a fundamental dynamic component intrinsic to protein. This study corroborates that bulk solvent plasticizes protein and facilitates rather than slaves protein dynamics.
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Hung CL, Lin YY, Chang HH, Chiang YW. Accessing local structural disruption of Bid protein during thermal denaturation by absorption-mode ESR spectroscopy. RSC Adv 2018; 8:34656-34669. [PMID: 35548640 PMCID: PMC9087001 DOI: 10.1039/c8ra06740f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 10/04/2018] [Indexed: 01/19/2023] Open
Abstract
The apoptotic function of Bid does not depend on its native structure.
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Affiliation(s)
- Chien-Lun Hung
- Department of Chemistry
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Yu-Ying Lin
- Department of Chemistry
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Hsin-Ho Chang
- 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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8
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Chang KJ, Kuo YH, Chiang YW. Study of Protein Dynamics under Nanoconfinement by Spin-Label ESR: A Case of T4 Lysozyme Protein. J Phys Chem B 2017; 121:4355-4363. [DOI: 10.1021/acs.jpcb.7b00014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kuo-Jung Chang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yun-Hsuan Kuo
- 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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Sung TC, Li CY, Lai YC, Hung CL, Shih O, Yeh YQ, Jeng US, Chiang YW. Solution Structure of Apoptotic BAX Oligomer: Oligomerization Likely Precedes Membrane Insertion. Structure 2015; 23:1878-1888. [PMID: 26299946 DOI: 10.1016/j.str.2015.07.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/06/2015] [Accepted: 07/28/2015] [Indexed: 12/23/2022]
Abstract
Proapoptotic BAX protein is largely cytosolic in healthy cells, but it oligomerizes and translocates to mitochondria upon receiving apoptotic stimuli. A long-standing challenge has been the inability to capture any structural information beyond the onset of activation. Here, we present solution structures of an activated BAX oligomer by means of spectroscopic and scattering methods, providing details about the monomer-monomer interfaces in the oligomer and how the oligomer is assembled from homodimers. We show that this soluble oligomer undergoes a direct conversion into membrane-inserted oligomer, which has the ability of inducing apoptosis and structurally resembles a membrane-embedded oligomer formed from BAX monomers in lipid environment. Structural differences between the soluble and the membrane-inserted oligomers are manifested in the C-terminal helices. Our data suggest an alternative pathway of apoptosis in which BAX oligomer formation occurs prior to membrane insertion.
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Affiliation(s)
- Tai-Ching Sung
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Ching-Yu Li
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yei-Chen Lai
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chien-Lun Hung
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.
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