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Addabbo RM, Hutchinson RB, Allaman HJ, Dalphin MD, Mecha MF, Liu Y, Staikos A, Cavagnero S. Critical Beginnings: Selective Tuning of Solubility and Structural Accuracy of Newly Synthesized Proteins by the Hsp70 Chaperone System. J Phys Chem B 2023; 127:3990-4014. [PMID: 37130318 PMCID: PMC10829761 DOI: 10.1021/acs.jpcb.2c08485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Proteins are particularly prone to aggregation immediately after release from the ribosome, and it is therefore important to elucidate the role of chaperones during these key steps of protein life. The Hsp70 and trigger factor (TF) chaperone systems interact with nascent proteins during biogenesis and immediately post-translationally. It is unclear, however, whether these chaperones can prevent formation of soluble and insoluble aggregates. Here, we address this question by monitoring the solubility and structural accuracy of globin proteins biosynthesized in an Escherichia coli cell-free system containing different concentrations of the bacterial Hsp70 and TF chaperones. We find that Hsp70 concentrations required to grant solubility to newly synthesized proteins are extremely sensitive to client-protein sequence. Importantly, Hsp70 concentrations yielding soluble client proteins are insufficient to prevent formation of soluble aggregates. In fact, for some aggregation-prone protein variants, avoidance of soluble-aggregate formation demands Hsp70 concentrations that exceed cellular levels in E. coli. In all, our data highlight the prominent role of soluble aggregates upon nascent-protein release from the ribosome and show the limitations of the Hsp70 chaperone system in the case of highly aggregation-prone proteins. These results demonstrate the need to devise better strategies to prevent soluble-aggregate formation upon release from the ribosome.
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Affiliation(s)
- Rayna M. Addabbo
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Rachel B. Hutchinson
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Heather J. Allaman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Matthew D. Dalphin
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Miranda F. Mecha
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Yue Liu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Alexios Staikos
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Silvia Cavagnero
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
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Haider MJ, Zhang HV, Sinha N, Fagan JA, Kiick KL, Saven JG, Pochan DJ. Self-assembly and soluble aggregate behavior of computationally designed coiled-coil peptide bundles. SOFT MATTER 2018; 14:5488-5496. [PMID: 29923575 PMCID: PMC6355460 DOI: 10.1039/c8sm00435h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Coiled-coil peptides have proven useful in a range of materials applications ranging from the formation of well-defined fibrils to responsive hydrogels. The ability to design from first principles their oligomerization and subsequent higher order assembly offers their expanded use in producing new materials. Toward these ends, homo-tetrameric, antiparallel, coiled-coil, peptide bundles have been designed computationally, synthesized via solid-phase methods, and their solution behavior characterized. Two different bundle-forming peptides were designed and examined. Within the targeted coiled coil structure, both bundles contained the same hydrophobic core residues. However, different exterior residues on the two different designs yielded sequences with different distributions of charged residues and two different expected isoelectric points of pI 4.4 and pI 10.5. Both coiled-coil bundles were extremely stable with respect to temperature (Tm > 80 C) and remained soluble in solution even at high (millimolar) peptide concentrations. The coiled-coil tetramer was confirmed to be the dominant species in solution by analytical sedimentation studies and by small-angle neutron scattering, where the scattering form factor is well represented by a cylinder model with the dimensions of the targeted coiled coil. At high concentrations (5-15 mM), evidence of interbundle structure was observed via neutron scattering. At these concentrations, the synthetic bundles form soluble aggregates, and interbundle distances can be determined via a structure factor fit to scattering data. The data support the successful design of robust coiled-coil bundles. Despite their different sequences, each sequence forms loosely associated but soluble aggregates of the bundles, suggesting similar dissociated states for each. The behavior of the dispersed bundles is similar to that observed for natural proteins.
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Affiliation(s)
- Michael J. Haider
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA. ,
| | - Huixi Violet Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Nairiti Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA. ,
| | - Jeffrey A. Fagan
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
| | - Kristi L. Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA. ,
| | - Jeffery G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Darrin J. Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA. ,
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Waudby CA, Launay H, Cabrita LD, Christodoulou J. Protein folding on the ribosome studied using NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 74:57-75. [PMID: 24083462 PMCID: PMC3991860 DOI: 10.1016/j.pnmrs.2013.07.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 07/17/2013] [Accepted: 07/17/2013] [Indexed: 05/11/2023]
Abstract
NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome-nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity.
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Lee JH, Cavagnero S. A novel tri-enzyme system in combination with laser-driven NMR enables efficient nuclear polarization of biomolecules in solution. J Phys Chem B 2013; 117:6069-81. [PMID: 23560683 DOI: 10.1021/jp4010168] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
NMR is an extremely powerful, yet insensitive technique. Many available nuclear polarization methods that address sensitivity are not directly applicable to low-concentration biomolecules in liquids and are often too invasive. Photochemically induced dynamic nuclear polarization (photo-CIDNP) is no exception. It needs high-power laser irradiation, which often leads to sample degradation, and photosensitizer reduction. Here, we introduce a novel tri-enzyme system that significantly overcomes the above challenges, rendering photo-CIDNP a practically applicable technique for NMR sensitivity enhancement in solution. The specificity of the nitrate reductase (NR) enzyme is exploited to selectively in situ reoxidize the reduced photo-CIDNP dye FMNH2. At the same time, the oxygen-scavenging ability of glucose oxidase (GO) and catalase (CAT) is synergistically employed to prevent sample photodegradation. The resulting tri-enzyme system (NR-GO-CAT) enables prolonged sensitivity-enhanced data collection in 1D and 2D heteronuclear NMR, leading to the highest photo-CIDNP sensitivity enhancement (48-fold relative to SE-HSQC) achieved to date for amino acids and polypeptides in solution. NR-GO-CAT extends the concentration limit of photo-CIDNP NMR down to the low micromolar range. In addition, sensitivity (relative to the reference SE-HSQC) is found to be inversely proportional to sample concentration, paving the way for the future analysis of even more diluted samples.
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Affiliation(s)
- Jung Ho Lee
- Department of Chemistry and Biophysics Program, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
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