1
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Roeselová A, Maslen SL, Shivakumaraswamy S, Pellowe GA, Howell S, Joshi D, Redmond J, Kjær S, Skehel JM, Balchin D. Mechanism of chaperone coordination during cotranslational protein folding in bacteria. Mol Cell 2024; 84:2455-2471.e8. [PMID: 38908370 DOI: 10.1016/j.molcel.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/12/2024] [Accepted: 06/01/2024] [Indexed: 06/24/2024]
Abstract
Protein folding is assisted by molecular chaperones that bind nascent polypeptides during mRNA translation. Several structurally distinct classes of chaperones promote de novo folding, suggesting that their activities are coordinated at the ribosome. We used biochemical reconstitution and structural proteomics to explore the molecular basis for cotranslational chaperone action in bacteria. We found that chaperone binding is disfavored close to the ribosome, allowing folding to precede chaperone recruitment. Trigger factor recognizes compact folding intermediates that expose an extensive unfolded surface, and dictates DnaJ access to nascent chains. DnaJ uses a large surface to bind structurally diverse intermediates and recruits DnaK to sequence-diverse solvent-accessible sites. Neither Trigger factor, DnaJ, nor DnaK destabilize cotranslational folding intermediates. Instead, the chaperones collaborate to protect incipient structure in the nascent polypeptide well beyond the ribosome exit tunnel. Our findings show how the chaperone network selects and modulates cotranslational folding intermediates.
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Affiliation(s)
- Alžběta Roeselová
- Protein Biogenesis Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Sarah L Maslen
- Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | | | - Grant A Pellowe
- Protein Biogenesis Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Steven Howell
- Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Dhira Joshi
- Chemical Biology Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Joanna Redmond
- Chemical Biology Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - J Mark Skehel
- Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - David Balchin
- Protein Biogenesis Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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2
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Koh M, Lim H, Jin H, Kim M, Hong Y, Hwang YK, Woo Y, Kim ES, Kim SY, Kim KM, Lim HK, Jung J, Kang S, Park B, Lee HB, Han W, Lee MS, Moon A. ANXA2 (annexin A2) is crucial to ATG7-mediated autophagy, leading to tumor aggressiveness in triple-negative breast cancer cells. Autophagy 2024; 20:659-674. [PMID: 38290972 PMCID: PMC10936647 DOI: 10.1080/15548627.2024.2305063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 12/29/2023] [Indexed: 02/01/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is associated with a poor prognosis and metastatic growth. TNBC cells frequently undergo macroautophagy/autophagy, contributing to tumor progression and chemotherapeutic resistance. ANXA2 (annexin A2), a potential therapeutic target for TNBC, has been reported to stimulate autophagy. In this study, we investigated the role of ANXA2 in autophagic processes in TNBC cells. TNBC patients exhibited high levels of ANXA2, which correlated with poor outcomes. ANXA2 increased LC3B-II levels following bafilomycin A1 treatment and enhanced autophagic flux in TNBC cells. Notably, ANXA2 upregulated the phosphorylation of HSF1 (heat shock transcription factor 1), resulting in the transcriptional activation of ATG7 (autophagy related 7). The mechanistic target of rapamycin kinase complex 2 (MTORC2) played an important role in ANXA2-mediated ATG7 transcription by HSF1. MTORC2 did not affect the mRNA level of ANXA2, but it was involved in the protein stability of ANXA2. HSPA (heat shock protein family A (Hsp70)) was a potential interacting protein with ANXA2, which may protect ANXA2 from lysosomal proteolysis. ANXA2 knockdown significantly increased sensitivity to doxorubicin, the first-line chemotherapeutic regimen for TNBC treatment, suggesting that the inhibition of autophagy by ANXA2 knockdown may overcome doxorubicin resistance. In a TNBC xenograft mouse model, we demonstrated that ANXA2 knockdown combined with doxorubicin administration significantly inhibited tumor growth compared to doxorubicin treatment alone, offering a promising avenue to enhance the effectiveness of chemotherapy. In summary, our study elucidated the molecular mechanism by which ANXA2 modulates autophagy, suggesting a potential therapeutic approach for TNBC treatment.Abbreviation: ATG: autophagy related; ChIP: chromatin-immunoprecipitation; HBSS: Hanks' balanced salt solution; HSF1: heat shock transcription factor 1; MTOR: mechanistic target of rapamycin kinase; TNBC: triple-negative breast cancer; TFEB: transcription factor EB; TFE3: transcription factor binding to IGHM enhancer 3.
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Affiliation(s)
- Minsoo Koh
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Hyesol Lim
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Hao Jin
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Minjoo Kim
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Yeji Hong
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Young Keun Hwang
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Yunjung Woo
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Eun-Sook Kim
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Sun Young Kim
- Department of Chemistry, College of Science and Technology, Duksung Women’s University, Seoul, Korea
| | - Kyung Mee Kim
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Hyun Kyung Lim
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Joohee Jung
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Sujin Kang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Boyoun Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Han-Byoel Lee
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Wonshik Han
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Myung-Shik Lee
- Avison Biomedical Research Center, Yonsei University College of Medicine, Seoul, Korea
| | - Aree Moon
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
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3
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Gracia B, Montes P, Gutierrez AM, Arun B, Karras GI. Protein-folding chaperones predict structure-function relationships and cancer risk in BRCA1 mutation carriers. Cell Rep 2024; 43:113803. [PMID: 38368609 PMCID: PMC10941025 DOI: 10.1016/j.celrep.2024.113803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/28/2023] [Accepted: 02/01/2024] [Indexed: 02/20/2024] Open
Abstract
Predicting the risk of cancer mutations is critical for early detection and prevention, but differences in allelic severity of human carriers confound risk predictions. Here, we elucidate protein folding as a cellular mechanism driving differences in mutation severity of tumor suppressor BRCA1. Using a high-throughput protein-protein interaction assay, we show that protein-folding chaperone binding patterns predict the pathogenicity of variants in the BRCA1 C-terminal (BRCT) domain. HSP70 selectively binds 94% of pathogenic BRCA1-BRCT variants, most of which engage HSP70 more than HSP90. Remarkably, the magnitude of HSP70 binding linearly correlates with loss of folding and function. We identify a prevalent class of human hypomorphic BRCA1 variants that bind moderately to chaperones and retain partial folding and function. Furthermore, chaperone binding signifies greater mutation penetrance and earlier cancer onset in the clinic. Our findings demonstrate the utility of chaperones as quantitative cellular biosensors of variant folding, phenotypic severity, and cancer risk.
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Affiliation(s)
- Brant Gracia
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patricia Montes
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Angelica Maria Gutierrez
- Department of Breast Medical Oncology and Clinical Cancer Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Banu Arun
- Department of Breast Medical Oncology and Clinical Cancer Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Georgios Ioannis Karras
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA.
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4
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Ambrose AJ, Zerio CJ, Sivinski J, Zhu X, Godek J, Sanchez JL, Khanna M, Khanna R, Lairson L, Zhang DD, Chapman E. Human Hsp70 Substrate-Binding Domains Recognize Distinct Client Proteins. Biochemistry 2024; 63:251-263. [PMID: 38243804 DOI: 10.1021/acs.biochem.3c00531] [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: 01/22/2024]
Abstract
The 13 Hsp70 proteins in humans act on unique sets of substrates with diversity often being attributed to J-domain-containing protein (Hsp40 or JDP) cofactors. We were therefore surprised to find drastically different binding affinities for Hsp70-peptide substrates, leading us to probe substrate specificity among the 8 canonical Hsp70s from humans. We used peptide arrays to characterize Hsp70 binding and then mined these data using machine learning to develop an algorithm for isoform-specific prediction of Hsp70 binding sequences. The results of this algorithm revealed recognition patterns not predicted based on local sequence alignments. We then showed that none of the human isoforms can complement heat-shocked DnaK knockout Escherichia coli cells. However, chimeric Hsp70s consisting of the human nucleotide-binding domain and the substrate-binding domain of DnaK complement during heat shock, providing further evidence in vivo of the divergent function of the Hsp70 substrate-binding domains. We also demonstrated that the differences in heat shock complementation among the chimeras are not due to loss of DnaJ binding. Although we do not exclude JDPs as additional specificity factors, our data demonstrate substrate specificity among the Hsp70s, which has important implications for inhibitor development in cancer and neurodegeneration.
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Affiliation(s)
- Andrew J Ambrose
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Christopher J Zerio
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jared Sivinski
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Xiaoyi Zhu
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jack Godek
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jonathan L Sanchez
- Department of Pharmacology, College of Medicine, The University of Arizona Health Sciences, Tucson, Arizona 85424, United States
| | - May Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York 10010, United States
| | - Rajesh Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York 10010, United States
| | - Luke Lairson
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Donna D Zhang
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Eli Chapman
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
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5
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Apostolidou D, Zhang P, Pandya D, Bock K, Liu Q, Yang W, Marszalek PE. Tandem repeats of highly bioluminescent NanoLuc are refolded noncanonically by the Hsp70 machinery. Protein Sci 2024; 33:e4895. [PMID: 38284490 PMCID: PMC10804678 DOI: 10.1002/pro.4895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024]
Abstract
Chaperones are a large family of proteins crucial for maintaining cellular protein homeostasis. One such chaperone is the 70 kDa heat shock protein (Hsp70), which plays a crucial role in protein (re)folding, stability, functionality, and translocation. While the key events in the Hsp70 chaperone cycle are well established, a relatively small number of distinct substrates were repetitively investigated. This is despite Hsp70 engaging with a plethora of cellular proteins of various structural properties and folding pathways. Here we analyzed novel Hsp70 substrates, based on tandem repeats of NanoLuc (Nluc), a small and highly bioluminescent protein with unique structural characteristics. In previous mechanical unfolding and refolding studies, we have identified interesting misfolding propensities of these Nluc-based tandem repeats. In this study, we further investigate these properties through in vitro bulk experiments. Similar to monomeric Nluc, engineered Nluc dyads and triads proved to be highly bioluminescent. Using the bioluminescence signal as the proxy for their structural integrity, we determined that heat-denatured Nluc dyads and triads can be efficiently refolded by the E. coli Hsp70 chaperone system, which comprises DnaK, DnaJ, and GrpE. In contrast to previous studies with other substrates, we observed that Nluc repeats can be efficiently refolded by DnaK and DnaJ, even in the absence of GrpE co-chaperone. Taken together, our study offers a new powerful substrate for chaperone research and raises intriguing questions about the Hsp70 mechanisms, particularly in the context of structurally diverse proteins.
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Affiliation(s)
- Dimitra Apostolidou
- Department of Mechanical Engineering and Materials ScienceDuke UniversityDurhamNorth CarolinaUnited States
| | - Pan Zhang
- Department of ChemistryDuke UniversityDurhamNorth CarolinaUnited States
| | - Devanshi Pandya
- Department of Electrical and Computer EngineeringDuke UniversityDurhamNorth CarolinaUnited States
| | - Kaden Bock
- Department of Biomedical EngineeringDuke UniversityDurhamNorth CarolinaUnited States
| | - Qinglian Liu
- Department of Physiology and Biophysics, School of MedicineVirginia Commonwealth UniversityRichmondVirginiaUnited States
| | - Weitao Yang
- Department of ChemistryDuke UniversityDurhamNorth CarolinaUnited States
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials ScienceDuke UniversityDurhamNorth CarolinaUnited States
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6
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Gracia B, Montes P, Gutierrez AM, Arun B, Karras GI. Protein-Folding Chaperones Predict Structure-Function Relationships and Cancer Risk in BRCA1 Mutation Carriers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557795. [PMID: 37745493 PMCID: PMC10515940 DOI: 10.1101/2023.09.14.557795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Identifying pathogenic mutations and predicting their impact on protein structure, function and phenotype remain major challenges in genome sciences. Protein-folding chaperones participate in structure-function relationships by facilitating the folding of protein variants encoded by mutant genes. Here, we utilize a high-throughput protein-protein interaction assay to test HSP70 and HSP90 chaperone interactions as predictors of pathogenicity for variants in the tumor suppressor BRCA1. Chaperones bind 77% of pathogenic BRCA1-BRCT variants, most of which engaged HSP70 more than HSP90. Remarkably, the magnitude of chaperone binding to variants is proportional to the degree of structural and phenotypic defect induced by BRCA1 mutation. Quantitative chaperone interactions identified BRCA1-BRCT separation-of-function variants and hypomorphic alleles missed by pathogenicity prediction algorithms. Furthermore, increased chaperone binding signified greater cancer risk in human BRCA1 carriers. Altogether, our study showcases the utility of chaperones as quantitative cellular biosensors of variant folding and phenotypic severity. HIGHLIGHTS Chaperones detect an abundance of pathogenic folding variants of BRCA1-BRCT.Degree of chaperone binding reflects severity of structural and phenotypic defect.Chaperones identify separation-of-function and hypomorphic variants. Chaperone interactions indicate penetrance and expressivity of BRCA1 alleles.
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7
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Nordquist E, Zhang G, Barethiya S, Ji N, White KM, Han L, Jia Z, Shi J, Cui J, Chen J. Incorporating physics to overcome data scarcity in predictive modeling of protein function: A case study of BK channels. PLoS Comput Biol 2023; 19:e1011460. [PMID: 37713443 PMCID: PMC10529646 DOI: 10.1371/journal.pcbi.1011460] [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: 06/24/2023] [Revised: 09/27/2023] [Accepted: 08/24/2023] [Indexed: 09/17/2023] Open
Abstract
Machine learning has played transformative roles in numerous chemical and biophysical problems such as protein folding where large amount of data exists. Nonetheless, many important problems remain challenging for data-driven machine learning approaches due to the limitation of data scarcity. One approach to overcome data scarcity is to incorporate physical principles such as through molecular modeling and simulation. Here, we focus on the big potassium (BK) channels that play important roles in cardiovascular and neural systems. Many mutants of BK channel are associated with various neurological and cardiovascular diseases, but the molecular effects are unknown. The voltage gating properties of BK channels have been characterized for 473 site-specific mutations experimentally over the last three decades; yet, these functional data by themselves remain far too sparse to derive a predictive model of BK channel voltage gating. Using physics-based modeling, we quantify the energetic effects of all single mutations on both open and closed states of the channel. Together with dynamic properties derived from atomistic simulations, these physical descriptors allow the training of random forest models that could reproduce unseen experimentally measured shifts in gating voltage, ∆V1/2, with a RMSE ~ 32 mV and correlation coefficient of R ~ 0.7. Importantly, the model appears capable of uncovering nontrivial physical principles underlying the gating of the channel, including a central role of hydrophobic gating. The model was further evaluated using four novel mutations of L235 and V236 on the S5 helix, mutations of which are predicted to have opposing effects on V1/2 and suggest a key role of S5 in mediating voltage sensor-pore coupling. The measured ∆V1/2 agree quantitatively with prediction for all four mutations, with a high correlation of R = 0.92 and RMSE = 18 mV. Therefore, the model can capture nontrivial voltage gating properties in regions where few mutations are known. The success of predictive modeling of BK voltage gating demonstrates the potential of combining physics and statistical learning for overcoming data scarcity in nontrivial protein function prediction.
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Affiliation(s)
- Erik Nordquist
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Guohui Zhang
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Shrishti Barethiya
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Nathan Ji
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Kelli M. White
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Lu Han
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Zhiguang Jia
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Jingyi Shi
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Jianmin Cui
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
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8
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Nordquist E, Zhang G, Barethiya S, Ji N, White KM, Han L, Jia Z, Shi J, Cui J, Chen J. Incorporating physics to overcome data scarcity in predictive modeling of protein function: a case study of BK channels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.24.546384. [PMID: 37425916 PMCID: PMC10327070 DOI: 10.1101/2023.06.24.546384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Machine learning has played transformative roles in numerous chemical and biophysical problems such as protein folding where large amount of data exists. Nonetheless, many important problems remain challenging for data-driven machine learning approaches due to the limitation of data scarcity. One approach to overcome data scarcity is to incorporate physical principles such as through molecular modeling and simulation. Here, we focus on the big potassium (BK) channels that play important roles in cardiovascular and neural systems. Many mutants of BK channel are associated with various neurological and cardiovascular diseases, but the molecular effects are unknown. The voltage gating properties of BK channels have been characterized for 473 site-specific mutations experimentally over the last three decades; yet, these functional data by themselves remain far too sparse to derive a predictive model of BK channel voltage gating. Using physics-based modeling, we quantify the energetic effects of all single mutations on both open and closed states of the channel. Together with dynamic properties derived from atomistic simulations, these physical descriptors allow the training of random forest models that could reproduce unseen experimentally measured shifts in gating voltage, ΔV 1/2 , with a RMSE ∼ 32 mV and correlation coefficient of R ∼ 0.7. Importantly, the model appears capable of uncovering nontrivial physical principles underlying the gating of the channel, including a central role of hydrophobic gating. The model was further evaluated using four novel mutations of L235 and V236 on the S5 helix, mutations of which are predicted to have opposing effects on V 1/2 and suggest a key role of S5 in mediating voltage sensor-pore coupling. The measured ΔV 1/2 agree quantitatively with prediction for all four mutations, with a high correlation of R = 0.92 and RMSE = 18 mV. Therefore, the model can capture nontrivial voltage gating properties in regions where few mutations are known. The success of predictive modeling of BK voltage gating demonstrates the potential of combining physics and statistical learning for overcoming data scarcity in nontrivial protein function prediction. Author Summary Deep machine learning has brought many exciting breakthroughs in chemistry, physics and biology. These models require large amount of training data and struggle when the data is scarce. The latter is true for predictive modeling of the function of complex proteins such as ion channels, where only hundreds of mutational data may be available. Using the big potassium (BK) channel as a biologically important model system, we demonstrate that a reliable predictive model of its voltage gating property could be derived from only 473 mutational data by incorporating physics-derived features, which include dynamic properties from molecular dynamics simulations and energetic quantities from Rosetta mutation calculations. We show that the final random forest model captures key trends and hotspots in mutational effects of BK voltage gating, such as the important role of pore hydrophobicity. A particularly curious prediction is that mutations of two adjacent residues on the S5 helix would always have opposite effects on the gating voltage, which was confirmed by experimental characterization of four novel mutations. The current work demonstrates the importance and effectiveness of incorporating physics in predictive modeling of protein function with scarce data.
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Affiliation(s)
- Erik Nordquist
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Guohui Zhang
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shrishti Barethiya
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Nathan Ji
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, USA
| | - Kelli M. White
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Lu Han
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Zhiguang Jia
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Jingyi Shi
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jianmin Cui
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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9
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Chen X, Hutchinson RB, Cavagnero S. Distribution and solvent exposure of Hsp70 chaperone binding sites across the Escherichia coli proteome. Proteins 2023; 91:665-678. [PMID: 36539330 PMCID: PMC10073276 DOI: 10.1002/prot.26456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/01/2022] [Accepted: 12/13/2022] [Indexed: 01/02/2023]
Abstract
Many proteins must interact with molecular chaperones to achieve their native state in the cell. Yet, how chaperone binding-site characteristics affect the folding process is poorly understood. The ubiquitous Hsp70 chaperone system prevents client-protein aggregation by holding unfolded conformations and by unfolding misfolded states. Hsp70 binding sites of client proteins comprise a nonpolar core surrounded by positively charged residues. However, a detailed analysis of Hsp70 binding sites on a proteome-wide scale is still lacking. Further, it is not known whether proteins undergo some degree of folding while chaperone bound. Here, we begin to address the above questions by identifying Hsp70 binding sites in 2258 Escherichia coli (E. coli) proteins. We find that most proteins bear at least one Hsp70 binding site and that the number of Hsp70 binding sites is directly proportional to protein size. Aggregation propensity upon release from the ribosome correlates with number of Hsp70 binding sites only in the case of large proteins. Interestingly, Hsp70 binding sites are more solvent-exposed than other nonpolar sites, in protein native states. Our findings show that the majority of E. coli proteins are systematically enabled to interact with Hsp70 even if this interaction only takes place during a fraction of the protein lifetime. In addition, our data suggest that some conformational sampling may take place within Hsp70-bound states, due to the solvent exposure of some chaperone binding sites in native proteins. In all, we propose that Hsp70-chaperone-binding traits have evolved to favor Hsp70-assisted protein folding devoid of aggregation.
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Affiliation(s)
- Xi Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biophysics and Physiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Rachel B Hutchinson
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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10
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Abildgaard AB, Voutsinos V, Petersen SD, Larsen FB, Kampmeyer C, Johansson KE, Stein A, Ravid T, Andréasson C, Jensen MK, Lindorff-Larsen K, Hartmann-Petersen R. HSP70-binding motifs function as protein quality control degrons. Cell Mol Life Sci 2023; 80:32. [PMID: 36609589 PMCID: PMC11072582 DOI: 10.1007/s00018-022-04679-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023]
Abstract
Protein quality control (PQC) degrons are short protein segments that target misfolded proteins for proteasomal degradation, and thus protect cells against the accumulation of potentially toxic non-native proteins. Studies have shown that PQC degrons are hydrophobic and rarely contain negatively charged residues, features which are shared with chaperone-binding regions. Here we explore the notion that chaperone-binding regions may function as PQC degrons. When directly tested, we found that a canonical Hsp70-binding motif (the APPY peptide) functioned as a dose-dependent PQC degron both in yeast and in human cells. In yeast, Hsp70, Hsp110, Fes1, and the E3 Ubr1 target the APPY degron. Screening revealed that the sequence space within the chaperone-binding region of APPY that is compatible with degron function is vast. We find that the number of exposed Hsp70-binding sites in the yeast proteome correlates with a reduced protein abundance and half-life. Our results suggest that when protein folding fails, chaperone-binding sites may operate as PQC degrons, and that the sequence properties leading to PQC-linked degradation therefore overlap with those of chaperone binding.
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Affiliation(s)
- Amanda B Abildgaard
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Vasileios Voutsinos
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Søren D Petersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Fia B Larsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Kampmeyer
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer E Johansson
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Amelie Stein
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Tommer Ravid
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark.
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11
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Singh A, Rief M, Žoldák G. Direct observation of chemo-mechanical coupling in DnaK by single-molecule force experiments. Biophys J 2022; 121:4729-4739. [PMID: 36196054 PMCID: PMC9748191 DOI: 10.1016/j.bpj.2022.09.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/16/2022] [Accepted: 09/29/2022] [Indexed: 12/15/2022] Open
Abstract
Protein allostery requires a communication channel for functional regulation between distal sites within a protein. In the molecular chaperone Hsp70, a two-domain enzyme, the ATP/ADP status of an N-terminal nucleotide-binding domain regulates the substrate affinity of a C-terminal substrate-binding domain. Recently available three-dimensional structures of Hsp70 in ATP/ADP states have provided deep insights into molecular pathways of allosteric signals. However, direct mechanical probing of long-range allosteric coupling between the ATP hydrolysis step and domain states is missing. Using laser optical tweezers, we examined the mechanical properties of a truncated two-domain DnaK(1-552ye) in apo/ADP/ATP- and peptide-bound states. We find that in the apo and ADP states, DnaK domains are mechanically stable and rigid. However, in the ATP state, substrate-binding domain (SBD)∗ye is mechanically destabilized as the result of interdomain docking followed by the unfolding of the α-helical lid. By observing the folding state of the SBD, we could observe the continuous ATP/ADP cycling of the enzyme in real time with a single molecule. The SBD lid closure is strictly coupled to the chemical steps of the ATP hydrolysis cycle even in the presence of peptide substrate.
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Affiliation(s)
- Anubhuti Singh
- Center for Functional Protein Assemblies (CPA), Physik Department, Technische Universität München, Garching, Germany
| | - Matthias Rief
- Center for Functional Protein Assemblies (CPA), Physik Department, Technische Universität München, Garching, Germany.
| | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University, Košice, Slovakia; Center for Interdisciplinary Biosciences, Cassovia New Industry Cluster (CNIC), Trieda SNP 1, 040 11, Košice, Slovakia.
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12
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Curreli S, Benedetti F, Yuan W, Munawwar A, Cocchi F, Gallo RC, Sherman NE, Zella D. Characterization of the interactome profiling of Mycoplasma fermentans DnaK in cancer cells reveals interference with key cellular pathways. Front Microbiol 2022; 13:1022704. [PMID: 36386669 PMCID: PMC9651203 DOI: 10.3389/fmicb.2022.1022704] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/03/2022] [Indexed: 06/10/2024] Open
Abstract
Chaperone proteins are redundant in nature and, to achieve their function, they bind a large repertoire of client proteins. DnaK is a bacterial chaperone protein that recognizes misfolded and aggregated proteins and drives their folding and intracellular trafficking. Some Mycoplasmas are associated with cancers, and we demonstrated that infection with a strain of Mycoplasma fermentans isolated in our lab promoted lymphoma in a mouse model. Its DnaK is expressed intracellularly in infected cells, it interacts with key proteins to hamper essential pathways related to DNA repair and p53 functions and uninfected cells can take-up extracellular DnaK. We profile here for the first time the eukaryotic proteins interacting with DnaK transiently expressed in five cancer cell lines. A total of 520 eukaryotic proteins were isolated by immunoprecipitation and identified by Liquid Chromatography Mass Spectrometry (LC-MS) analysis. Among the cellular DnaK-binding partners, 49 were shared between the five analyzed cell lines, corroborating the specificity of the interaction of DnaK with these proteins. Enrichment analysis revealed multiple RNA biological processes, DNA repair, chromatin remodeling, DNA conformational changes, protein-DNA complex subunit organization, telomere organization and cell cycle as the most significant ontology terms. This is the first study to show that a bacterial chaperone protein interacts with key eukaryotic components thus suggesting DnaK could become a perturbing hub for the functions of important cellular pathways. Given the close interactions between bacteria and host cells in the local microenvironment, these results provide a foundation for future mechanistic studies on how bacteria interfere with essential cellular processes.
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Affiliation(s)
- Sabrina Curreli
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Francesca Benedetti
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Weirong Yuan
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Arshi Munawwar
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Fiorenza Cocchi
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Robert C. Gallo
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Nicholas E. Sherman
- Biomolecular Analysis Facility Core, School of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Davide Zella
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, United States
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13
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Yi W, Sun A, Liu M, Liu X, Zhang W, Dai Q. Comparative Study on Feature Selection in Protein Structure and Function Prediction. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:1650693. [PMID: 36267316 PMCID: PMC9578875 DOI: 10.1155/2022/1650693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/14/2022] [Indexed: 11/18/2022]
Abstract
Many effective methods extract and fuse different protein features to study the relationship between protein sequence, structure, and function, but different methods have preferences in solving the research of protein structure and function, which requires selecting valuable and contributing features to design more effective prediction methods. This work mainly focused on the feature selection methods in the study of protein structure and function, and systematically compared and analyzed the efficiency of different feature selection methods in the prediction of protein structures, protein disorders, protein molecular chaperones, and protein solubility. The results show that the feature selection method based on nonlinear SVM performs best in protein structure prediction, protein solubility prediction, protein molecular chaperone prediction, and protein solubility prediction. After selection, the accuracy of features is improved by 13.16% ~71%, especially the Kmer features and PSSM features of proteins.
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Affiliation(s)
- Wenjing Yi
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Ao Sun
- College of Informatics Science and Technology, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Manman Liu
- College of Informatics Science and Technology, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xiaoqing Liu
- College of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Wei Zhang
- College of Informatics Science and Technology, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Qi Dai
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
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14
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Hassell D, Denney A, Singer E, Benson A, Roth A, Ceglowski J, Steingesser M, McMurray M. Chaperone requirements for de novo folding of Saccharomyces cerevisiae septins. Mol Biol Cell 2022; 33:ar111. [PMID: 35947497 PMCID: PMC9635297 DOI: 10.1091/mbc.e22-07-0262] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/02/2022] [Indexed: 11/11/2022] Open
Abstract
Polymers of septin protein complexes play cytoskeletal roles in eukaryotic cells. The specific subunit composition within complexes controls functions and higher-order structural properties. All septins have globular GTPase domains. The other eukaryotic cytoskeletal NTPases strictly require assistance from molecular chaperones of the cytosol, particularly the cage-like chaperonins, to fold into oligomerization-competent conformations. We previously identified cytosolic chaperones that bind septins and influence the oligomerization ability of septins carrying mutations linked to human disease, but it was unknown to what extent wild-type septins require chaperone assistance for their native folding. Here we use a combination of in vivo and in vitro approaches to demonstrate chaperone requirements for de novo folding and complex assembly by budding yeast septins. Individually purified septins adopted nonnative conformations and formed nonnative homodimers. In chaperonin- or Hsp70-deficient cells, septins folded slower and were unable to assemble posttranslationally into native complexes. One septin, Cdc12, was so dependent on cotranslational chaperonin assistance that translation failed without it. Our findings point to distinct translation elongation rates for different septins as a possible mechanism to direct a stepwise, cotranslational assembly pathway in which general cytosolic chaperones act as key intermediaries.
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Affiliation(s)
- Daniel Hassell
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Ashley Denney
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Emily Singer
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Aleyna Benson
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Andrew Roth
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Julia Ceglowski
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Marc Steingesser
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Michael McMurray
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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15
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Nordquist EB, Clerico EM, Chen J, Gierasch LM. Computationally-Aided Modeling of Hsp70-Client Interactions: Past, Present, and Future. J Phys Chem B 2022; 126:6780-6791. [PMID: 36040440 PMCID: PMC10309085 DOI: 10.1021/acs.jpcb.2c03806] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hsp70 molecular chaperones play central roles in maintaining a healthy cellular proteome. Hsp70s function by binding to short peptide sequences in incompletely folded client proteins, thus preventing them from misfolding and/or aggregating, and in many cases holding them in a state that is competent for subsequent processes like translocation across membranes. There is considerable interest in predicting the sites where Hsp70s may bind their clients, as the ability to do so sheds light on the cellular functions of the chaperone. In addition, the capacity of the Hsp70 chaperone family to bind to a broad array of clients and to identify accessible sequences that enable discrimination of those that are folded from those that are not fully folded, which is essential to their cellular roles, is a fascinating puzzle in molecular recognition. In this article we discuss efforts to harness computational modeling with input from experimental data to develop a predictive understanding of the promiscuous yet selective binding of Hsp70 molecular chaperones to accessible sequences within their client proteins. We trace how an increasing understanding of the complexities of Hsp70-client interactions has led computational modeling to new underlying assumptions and design features. We describe the trend from purely data-driven analysis toward increased reliance on physics-based modeling that deeply integrates structural information and sequence-based functional data with physics-based binding energies. Notably, new experimental insights are adding to our understanding of the molecular origins of "selective promiscuity" in substrate binding by Hsp70 chaperones and challenging the underlying assumptions and design used in earlier predictive models. Taking the new experimental findings together with exciting progress in computational modeling of protein structures leads us to foresee a bright future for a predictive understanding of selective-yet-promiscuous binding exploited by Hsp70 molecular chaperones; the resulting new insights will also apply to substrate binding by other chaperones and by signaling proteins.
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Affiliation(s)
- Erik B. Nordquist
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, 01003, United States
| | - Eugenia M. Clerico
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, 01003, United States
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, 01003, United States
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, 01003, United States
| | - Lila M. Gierasch
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, 01003, United States
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, 01003, United States
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16
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Shoup D, Roth A, Puchalla J, Rye HS. The Impact of Hidden Structure on Aggregate Disassembly by Molecular Chaperones. Front Mol Biosci 2022; 9:915307. [PMID: 35874607 PMCID: PMC9302491 DOI: 10.3389/fmolb.2022.915307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Protein aggregation, or the uncontrolled self-assembly of partially folded proteins, is an ever-present danger for living organisms. Unimpeded, protein aggregation can result in severe cellular dysfunction and disease. A group of proteins known as molecular chaperones is responsible for dismantling protein aggregates. However, how protein aggregates are recognized and disassembled remains poorly understood. Here we employ a single particle fluorescence technique known as Burst Analysis Spectroscopy (BAS), in combination with two structurally distinct aggregate types grown from the same starting protein, to examine the mechanism of chaperone-mediated protein disaggregation. Using the core bi-chaperone disaggregase system from Escherichia coli as a model, we demonstrate that, in contrast to prevailing models, the overall size of an aggregate particle has, at most, a minor influence on the progression of aggregate disassembly. Rather, we show that changes in internal structure, which have no observable impact on aggregate particle size or molecular chaperone binding, can dramatically limit the ability of the bi-chaperone system to take aggregates apart. In addition, these structural alterations progress with surprising speed, rendering aggregates resistant to disassembly within minutes. Thus, while protein aggregate structure is generally poorly defined and is often obscured by heterogeneous and complex particle distributions, it can have a determinative impact on the ability of cellular quality control systems to process protein aggregates.
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Affiliation(s)
- Daniel Shoup
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Andrew Roth
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Jason Puchalla
- Department of Physics, Princeton University, Princeton, NJ, United States
| | - Hays S. Rye
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
- *Correspondence: Hays S. Rye,
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17
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Johnson OT, Gestwicki JE. Multivalent protein-protein interactions are pivotal regulators of eukaryotic Hsp70 complexes. Cell Stress Chaperones 2022; 27:397-415. [PMID: 35670950 PMCID: PMC9346034 DOI: 10.1007/s12192-022-01281-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022] Open
Abstract
Heat shock protein 70 (Hsp70) is a molecular chaperone and central regulator of protein homeostasis (proteostasis). Paramount to this role is Hsp70's binding to client proteins and co-chaperones to produce distinct complexes, such that understanding the protein-protein interactions (PPIs) of Hsp70 is foundational to describing its function and dysfunction in disease. Mounting evidence suggests that these PPIs include both "canonical" interactions, which are universally conserved, and "non-canonical" (or "secondary") contacts that seem to have emerged in eukaryotes. These two categories of interactions involve discrete binding surfaces, such that some clients and co-chaperones engage Hsp70 with at least two points of contact. While the contributions of canonical interactions to chaperone function are becoming increasingly clear, it can be challenging to deconvolute the roles of secondary interactions. Here, we review what is known about non-canonical contacts and highlight examples where their contributions have been parsed, giving rise to a model in which Hsp70's secondary contacts are not simply sites of additional avidity but are necessary and sufficient to impart unique functions. From this perspective, we propose that further exploration of non-canonical contacts will generate important insights into the evolution of Hsp70 systems and inspire new approaches for developing small molecules that tune Hsp70-mediated proteostasis.
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Affiliation(s)
- Oleta T Johnson
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, 94158, USA.
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18
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Nissley DA, Jiang Y, Trovato F, Sitarik I, Narayan KB, To P, Xia Y, Fried SD, O'Brien EP. Universal protein misfolding intermediates can bypass the proteostasis network and remain soluble and less functional. Nat Commun 2022; 13:3081. [PMID: 35654797 PMCID: PMC9163053 DOI: 10.1038/s41467-022-30548-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 05/05/2022] [Indexed: 01/12/2023] Open
Abstract
Some misfolded protein conformations can bypass proteostasis machinery and remain soluble in vivo. This is an unexpected observation, as cellular quality control mechanisms should remove misfolded proteins. Three questions, then, are: how do long-lived, soluble, misfolded proteins bypass proteostasis? How widespread are such misfolded states? And how long do they persist? We address these questions using coarse-grain molecular dynamics simulations of the synthesis, termination, and post-translational dynamics of a representative set of cytosolic E. coli proteins. We predict that half of proteins exhibit misfolded subpopulations that bypass molecular chaperones, avoid aggregation, and will not be rapidly degraded, with some misfolded states persisting for months or longer. The surface properties of these misfolded states are native-like, suggesting they will remain soluble, while self-entanglements make them long-lived kinetic traps. In terms of function, we predict that one-third of proteins can misfold into soluble less-functional states. For the heavily entangled protein glycerol-3-phosphate dehydrogenase, limited-proteolysis mass spectrometry experiments interrogating misfolded conformations of the protein are consistent with the structural changes predicted by our simulations. These results therefore provide an explanation for how proteins can misfold into soluble conformations with reduced functionality that can bypass proteostasis, and indicate, unexpectedly, this may be a wide-spread phenomenon.
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Affiliation(s)
- Daniel A Nissley
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Fabio Trovato
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Ian Sitarik
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Karthik B Narayan
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Philip To
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Yingzi Xia
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA.
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
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19
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François-Moutal L, Scott DD, Ambrose AJ, Zerio CJ, Rodriguez-Sanchez M, Dissanayake K, May DG, Carlson JM, Barbieri E, Moutal A, Roux KJ, Shorter J, Khanna R, Barmada SJ, McGurk L, Khanna M. Heat shock protein Grp78/BiP/HspA5 binds directly to TDP-43 and mitigates toxicity associated with disease pathology. Sci Rep 2022; 12:8140. [PMID: 35581326 PMCID: PMC9114370 DOI: 10.1038/s41598-022-12191-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 05/04/2022] [Indexed: 11/09/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with no cure or effective treatment in which TAR DNA Binding Protein of 43 kDa (TDP-43) abnormally accumulates into misfolded protein aggregates in affected neurons. It is widely accepted that protein misfolding and aggregation promotes proteotoxic stress. The molecular chaperones are a primary line of defense against proteotoxic stress, and there has been long-standing interest in understanding the relationship between chaperones and aggregated protein in ALS. Of particular interest are the heat shock protein of 70 kDa (Hsp70) family of chaperones. However, defining which of the 13 human Hsp70 isoforms is critical for ALS has presented many challenges. To gain insight into the specific Hsp70 that modulates TDP-43, we investigated the relationship between TDP-43 and the Hsp70s using proximity-dependent biotin identification (BioID) and discovered several Hsp70 isoforms associated with TDP-43 in the nucleus, raising the possibility of an interaction with native TDP-43. We further found that HspA5 bound specifically to the RNA-binding domain of TDP-43 using recombinantly expressed proteins. Moreover, in a Drosophila strain that mimics ALS upon TDP-43 expression, the mRNA levels of the HspA5 homologue (Hsc70.3) were significantly increased. Similarly we observed upregulation of HspA5 in prefrontal cortex neurons from human ALS patients. Finally, overexpression of HspA5 in Drosophila rescued TDP-43-induced toxicity, suggesting that upregulation of HspA5 may have a compensatory role in ALS pathobiology.
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Affiliation(s)
- Liberty François-Moutal
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA.,Center for Innovation in Brain Science, Tucson, AZ, 85721, USA
| | - David Donald Scott
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA.,Center for Innovation in Brain Science, Tucson, AZ, 85721, USA
| | - Andrew J Ambrose
- Pharmacology and Toxicology, School of Pharmacy, University of Arizona, Tucson, AZ, 85724, USA
| | - Christopher J Zerio
- Pharmacology and Toxicology, School of Pharmacy, University of Arizona, Tucson, AZ, 85724, USA
| | | | - Kumara Dissanayake
- Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Danielle G May
- Enabling Technologies Group, Sanford Research, Sioux Falls, SD, USA
| | - Jacob M Carlson
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA.,Center for Innovation in Brain Science, Tucson, AZ, 85721, USA
| | - Edward Barbieri
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Aubin Moutal
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA.,Center for Innovation in Brain Science, Tucson, AZ, 85721, USA
| | - Kyle J Roux
- Enabling Technologies Group, Sanford Research, Sioux Falls, SD, USA.,Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA
| | - James Shorter
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA
| | - Rajesh Khanna
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA.,Center for Innovation in Brain Science, Tucson, AZ, 85721, USA
| | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Leeanne McGurk
- Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - May Khanna
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA. .,Center for Innovation in Brain Science, Tucson, AZ, 85721, USA. .,Department of Molecular Pathobiology, NYU, New York, NY, USA. .,Department of Molecular Pathobiology, College of Dentistry, NYU, 433 1st Ave, New York, NY, 10010, USA.
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20
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Tawde M, Bior A, Feiss M, Teng F, Freimuth P. A polypeptide model for toxic aberrant proteins induced by aminoglycoside antibiotics. PLoS One 2022; 17:e0258794. [PMID: 35486612 PMCID: PMC9053816 DOI: 10.1371/journal.pone.0258794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 03/01/2022] [Indexed: 11/24/2022] Open
Abstract
Aminoglycoside antibiotics interfere with the selection of cognate tRNAs during translation, resulting in the synthesis of aberrant proteins that are the ultimate cause of cell death. However, the toxic potential of aberrant proteins and how they avoid degradation by the cell’s protein quality control (QC) machinery are not understood. Here we report that levels of the heat shock (HS) transcription factor σ32 increased sharply following exposure of Escherichia coli to the aminoglycoside kanamycin (Kan), suggesting that at least some of the aberrant proteins synthesized in these cells were recognized as substrates by DnaK, a molecular chaperone that regulates the HS response, the major protein QC pathway in bacteria. To further investigate aberrant protein toxic potential and interaction with cell QC factors, we studied an acutely toxic 48-residue polypeptide (ARF48) that is encoded by an alternate reading frame in a plant cDNA. As occurred in cells exposed to Kan, σ32 levels were strongly elevated following ARF48 expression, suggesting that ARF48 was recognized as a substrate by DnaK. Paradoxically, an internal 10-residue region that was tightly bound by DnaK in vitro also was required for the ARF48 toxic effect. Despite the increased levels of σ32, levels of several HS proteins were unchanged following ARF48 expression, suggesting that the HS response had been aborted. Nucleoids were condensed and cell permeability increased rapidly following ARF48 expression, together suggesting that ARF48 disrupts DNA-membrane interactions that could be required for efficient gene expression. Our results are consistent with earlier studies showing that aberrant proteins induced by aminoglycoside antibiotics disrupt cell membrane integrity. Insights into the mechanism for this effect could be gained by further study of the ARF48 model system.
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Affiliation(s)
- Mangala Tawde
- Department of Biological Sciences and Geology, Queensborough Community College, City University of New York, Bayside, New York, United States of America
| | - Abdelaziz Bior
- Department of Natural and Applied Sciences, Cheyney University of Pennsylvania, Cheyney, Pennsylvania, United States of America
| | - Michael Feiss
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, Iowa, United States of America
| | - Feiyue Teng
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Paul Freimuth
- Biology Department, Brookhaven National Laboratory, Upton, New York, United States of America
- * E-mail:
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21
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Active unfolding of the glucocorticoid receptor by the Hsp70/Hsp40 chaperone system in single-molecule mechanical experiments. Proc Natl Acad Sci U S A 2022; 119:e2119076119. [PMID: 35377810 PMCID: PMC9169861 DOI: 10.1073/pnas.2119076119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
One of the key unresolved questions in the field of molecular chaperones is how they can actively unfold proteins. In this study, we discovered that the Hsp70/Hsp40 chaperone system completely unfolds a native soluble substrate protein, the ligand-binding domain of the glucocorticoid receptor, in a concerted action. Our high-resolution optical tweezers data show in real time how the substrate is attacked by the chaperone machinery. As soon as the hormone has left the binding pocket, up to five Hsp70/Hsp40 complexes bind and unfold the protein in a stepwise manner. This finding constitutes direct evidence that the chaperone machinery can bind to the folded core of the receptor, thus providing a mechanism for Hsp70-induced protein unfolding. The glucocorticoid receptor (GR) is an important transcription factor and drug target linked to a variety of biological functions and diseases. It is one of the most stringent physiological clients of the Hsp90/Hsp70/Hsp40 chaperone system. In this study, we used single-molecule force spectroscopy by optical tweezers to observe the interaction of the GR’s ligand-binding domain (GR-LBD) with the Hsp70/Hsp40 chaperone system (Hsp70/40). We show in real time that Hsp70/40 can unfold the complete GR-LBD in a stepwise manner. Each unfolding step involves binding of an Hsp70 to the GR-LBD and subsequent adenosine triphosphate (ATP) hydrolysis, stimulated by Hsp40. The kinetics of chaperone-mediated unfolding depend on chaperone concentrations as well as the presence of the nucleotide exchange factor BAG1. We find that Hsp70/40 can stabilize new unfolding intermediates, showing that Hsp70/40 can directly interact with the folded core of the protein when working as an unfoldase. Our results support an unfolding mechanism where Hsp70 can directly bind to folded protein structures and unfold them upon ATP hydrolysis. These results provide important insights into the regulation of GR by Hsp70/40.
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22
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Berhanu S, Ueda T, Alix JH. The E. coli DnaK chaperone stimulates the α-complementation of β-galactosidase. J Basic Microbiol 2022; 62:669-688. [PMID: 35289419 DOI: 10.1002/jobm.202100487] [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: 09/29/2021] [Revised: 01/11/2022] [Accepted: 02/20/2022] [Indexed: 11/09/2022]
Abstract
pUC18 and pUC19 are well-known high copy-number plasmid vectors routinely used for DNA cloning purposes. We show here that, in E. coli transformed by native pUC18, the α-complementation of β-galactosidase (i.e., mediated by the peptide LacZα18) is intrinsically weak and slow, but is greatly stimulated by the DnaK/DnaJ/GrpE chaperone system. In contrast, the α-complementation mediated by the peptide LacZα19 (in E. coli transformed by the native pUC19) is much more efficient, and therefore does not require the assistance of the DnaK chaperone machinery. The marked difference between these two LacZα peptides is reproduced in cell-free protein expression system coupled with α-complementation. We conclude that: (i) α-complementation of β-galactosidase is DnaK-mediated depending upon the LacZα peptide donor. (ii) DnaK, sensu stricto, is not necessary for α-complementation, but can enhance it to a great extent. (iii) this observation could be used to establish an easy and inexpensive method for screening small molecules libraries in search of DnaK inhibitors and also for deciphering the DnaK-mediated protein quality control mechanism. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Samuel Berhanu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba Prefecture, Japan
| | - Takuya Ueda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba Prefecture, Japan
| | - Jean-Hervé Alix
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba Prefecture, Japan
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23
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Nordquist EB, English CA, Clerico EM, Sherman W, Gierasch LM, Chen J. Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones. PLoS Comput Biol 2021; 17:e1009567. [PMID: 34735438 PMCID: PMC8604352 DOI: 10.1371/journal.pcbi.1009567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 11/19/2021] [Accepted: 10/15/2021] [Indexed: 11/18/2022] Open
Abstract
To help cells cope with protein misfolding and aggregation, Hsp70 molecular chaperones selectively bind a variety of sequences ("selective promiscuity"). Statistical analyses from substrate-derived peptide arrays reveal that DnaK, the E. coli Hsp70, binds to sequences containing three to five branched hydrophobic residues, although otherwise the specific amino acids can vary considerably. Several high-resolution structures of the substrate -binding domain (SBD) of DnaK bound to peptides reveal a highly conserved configuration of the bound substrate and further suggest that the substrate-binding cleft consists of five largely independent sites for interaction with five consecutive substrate residues. Importantly, both substrate backbone orientations (N- to C- and C- to N-) allow essentially the same backbone hydrogen-bonding and side-chain interactions with the chaperone. In order to rationalize these observations, we performed atomistic molecular dynamics simulations to sample the interactions of all 20 amino acid side chains in each of the five sites of the chaperone in the context of the conserved substrate backbone configurations. The resulting interaction energetics provide the basis set for deriving a predictive model that we call Paladin (Physics-based model of DnaK-Substrate Binding). Trained using available peptide array data, Paladin can distinguish binders and nonbinders of DnaK with accuracy comparable to existing predictors and further predicts the detailed configuration of the bound sequence. Tested using existing DnaK-peptide structures, Paladin correctly predicted the binding register in 10 out of 13 substrate sequences that bind in the N- to C- orientation, and the binding orientation in 16 out of 22 sequences. The physical basis of the Paladin model provides insight into the origins of how Hsp70s bind substrates with a balance of selectivity and promiscuity. The approach described here can be extended to other Hsp70s where extensive peptide array data is not available.
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Affiliation(s)
- Erik B. Nordquist
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Charles A. English
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- Impact, New York City, New York, United States of America
| | - Eugenia M. Clerico
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Woody Sherman
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- Roivant Sciences, Boston, Massachusetts, United States of America
| | - Lila M. Gierasch
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- * E-mail: (LMG); (JC)
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- * E-mail: (LMG); (JC)
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24
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Alam MS, Saleh MA, Mozibullah M, Riham AT, Solayman M, Gan SH. Computational algorithmic and molecular dynamics study of functional and structural impacts of non-synonymous single nucleotide polymorphisms in human DHFR gene. Comput Biol Chem 2021; 95:107587. [PMID: 34710812 DOI: 10.1016/j.compbiolchem.2021.107587] [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: 07/02/2021] [Revised: 08/21/2021] [Accepted: 10/01/2021] [Indexed: 11/26/2022]
Abstract
Human dihydrofolate reductase (DHFR) is a conserved enzyme that is central to folate metabolism and is widely targeted in pathogenic diseases as well as cancers. Although studies have reported the fact that genetic mutations in DHFR leads to a rare autosomal recessive inborn error of folate metabolism and drug resistance, there is a lack of an extensive study on how the deleterious non-synonymous SNPs (nsSNPs) disrupt its phenotypic effects. In this study, we aim at discovering the structural and functional consequences of nsSNPs in DHFR by employing a combined computational approach consisting of ten recently developed in silico tools for identification of damaging nsSNPs and molecular dynamics (MD) simulation for getting deeper insights into the magnitudes of damaging effects. Our study revealed the presence of 12 most deleterious nsSNPs affecting the native phenotypic effects, with three (R71T, G118D, Y122D) identified in the co-factor and ligand binding active sites. MD simulations also suggested that these three SNPs particularly Y122D, alter the overall structural flexibility and dynamics of the native DHFR protein which can provide more understandings into the crucial roles of these mutants in influencing the loss of DHFR function.
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Affiliation(s)
- Md Shahed Alam
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md Abu Saleh
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md Mozibullah
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Ashik Tanvir Riham
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md Solayman
- Institute for Glycomics, Griffith University, Parklands Dr. Southport, QLD 4222, Australia.
| | - Siew Hua Gan
- School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Selangor Darul Ehsan, Malaysia
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25
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Zutz A, Hamborg L, Pedersen LE, Kassem MM, Papaleo E, Koza A, Herrgård MJ, Jensen SI, Teilum K, Lindorff-Larsen K, Nielsen AT. A dual-reporter system for investigating and optimizing protein translation and folding in E. coli. Nat Commun 2021; 12:6093. [PMID: 34667164 PMCID: PMC8526717 DOI: 10.1038/s41467-021-26337-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 10/01/2021] [Indexed: 01/29/2023] Open
Abstract
Strategies for investigating and optimizing the expression and folding of proteins for biotechnological and pharmaceutical purposes are in high demand. Here, we describe a dual-reporter biosensor system that simultaneously assesses in vivo protein translation and protein folding, thereby enabling rapid screening of mutant libraries. We have validated the dual-reporter system on five different proteins and find an excellent correlation between reporter signals and the levels of protein expression and solubility of the proteins. We further demonstrate the applicability of the dual-reporter system as a screening assay for deep mutational scanning experiments. The system enables high throughput selection of protein variants with high expression levels and altered protein stability. Next generation sequencing analysis of the resulting libraries of protein variants show a good correlation between computationally predicted and experimentally determined protein stabilities. We furthermore show that the mutational experimental data obtained using this system may be useful for protein structure calculations.
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Affiliation(s)
- Ariane Zutz
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Louise Hamborg
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Maher M Kassem
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Elena Papaleo
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Anna Koza
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark.
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26
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Selective promiscuity in the binding of E. coli Hsp70 to an unfolded protein. Proc Natl Acad Sci U S A 2021; 118:2016962118. [PMID: 34625496 DOI: 10.1073/pnas.2016962118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2021] [Indexed: 01/16/2023] Open
Abstract
Heat shock protein 70 (Hsp70) chaperones bind many different sequences and discriminate between incompletely folded and folded clients. Most research into the origins of this "selective promiscuity" has relied on short peptides as substrates to dissect the binding, but much less is known about how Hsp70s bind full-length client proteins. Here, we connect detailed structural analyses of complexes between the Escherichia coli Hsp70 (DnaK) substrate-binding domain (SBD) and peptides encompassing five potential binding sites in the precursor to E. coli alkaline phosphatase (proPhoA) with SBD binding to full-length unfolded proPhoA. Analysis of SBD complexes with proPhoA peptides by a combination of X-ray crystallography, methyl-transverse relaxation optimized spectroscopy (methyl-TROSY), and paramagnetic relaxation enhancement (PRE) NMR and chemical cross-linking experiments provided detailed descriptions of their binding modes. Importantly, many sequences populate multiple SBD binding modes, including both the canonical N to C orientation and a C to N orientation. The favored peptide binding mode optimizes substrate residue side-chain compatibility with the SBD binding pockets independent of backbone orientation. Relating these results to the binding of the SBD to full-length proPhoA, we observe that multiple chaperones may bind to the protein substrate, and the binding sites, well separated in the proPhoA sequence, behave independently. The hierarchy of chaperone binding to sites on the protein was generally consistent with the apparent binding affinities observed for the peptides corresponding to these sites. Functionally, these results reveal that Hsp70s "read" sequences without regard to the backbone direction and that both binding orientations must be considered in current predictive algorithms.
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27
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Houben B, Rousseau F, Schymkowitz J. Protein structure and aggregation: a marriage of necessity ruled by aggregation gatekeepers. Trends Biochem Sci 2021; 47:194-205. [PMID: 34561149 DOI: 10.1016/j.tibs.2021.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/25/2021] [Accepted: 08/31/2021] [Indexed: 12/27/2022]
Abstract
Protein aggregation propensity is a pervasive and seemingly inescapable property of proteomes. Strikingly, a significant fraction of the proteome is supersaturated, meaning that, for these proteins, their native conformation is less stable than the aggregated state. Maintaining the integrity of a proteome under such conditions is precarious and requires energy-consuming proteostatic regulation. Why then is aggregation propensity maintained at such high levels over long evolutionary timescales? Here, we argue that the conformational stability of the native and aggregated states are correlated thermodynamically and that codon usage strengthens this correlation. As a result, the folding of stable proteins requires kinetic control to avoid aggregation, provided by aggregation gatekeepers. These unique residues are evolutionarily selected to kinetically favor native folding, either on their own or by coopting chaperones.
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Affiliation(s)
- Bert Houben
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| | - Joost Schymkowitz
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
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28
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Akmal MA, Hussain W, Rasool N, Khan YD, Khan SA, Chou KC. Using CHOU'S 5-Steps Rule to Predict O-Linked Serine Glycosylation Sites by Blending Position Relative Features and Statistical Moment. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2045-2056. [PMID: 31985438 DOI: 10.1109/tcbb.2020.2968441] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Glycosylation of proteins in eukaryote cells is an important and complicated post-translation modification due to its pivotal role and association with crucial physiological functions within most of the proteins. Identification of glycosylation sites in a polypeptide chain is not an easy task due to multiple impediments. Analytical identification of these sites is expensive and laborious. There is a dire need to develop a reliable computational method for precise determination of such sites which can help researchers to save time and effort. Herein, we propose a novel predictor namely iGlycoS-PseAAC by integrating the Chou's Pseudo Amino Acid Composition (PseAAC) and relative/absolute position-based features. The self-consistency results show that the accuracy revealed by the model using the benchmark dataset for prediction of O-linked glycosylation having serine sites is 98.8 percent. The overall accuracy of predictor achieved through 10-fold cross validation by combining the positive and negative results is 97.2 percent. The overall accuracy achieved through Jackknife test is 96.195 percent by aggregating of all the prediction results. Thus the proposed predictor can help in predicting the O-linked glycosylated serine sites in an efficient and accurate way. The overall results show that the accuracy of the iGlycoS-PseAAC is higher than the existing tools.
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29
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Hamborg L, Granata D, Olsen JG, Roche JV, Pedersen LE, Nielsen AT, Lindorff-Larsen K, Teilum K. Synergistic stabilization of a double mutant in chymotrypsin inhibitor 2 from a library screen in E. coli. Commun Biol 2021; 4:980. [PMID: 34408246 PMCID: PMC8373930 DOI: 10.1038/s42003-021-02490-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022] Open
Abstract
Most single point mutations destabilize folded proteins. Mutations that stabilize a protein typically only have a small effect and multiple mutations are often needed to substantially increase the stability. Multiple point mutations may act synergistically on the stability, and it is often not straightforward to predict their combined effect from the individual contributions. Here, we have applied an efficient in-cell assay in E. coli to select variants of the barley chymotrypsin inhibitor 2 with increased stability. We find two variants that are more than 3.8 kJ mol-1 more stable than the wild-type. In one case, the increased stability is the effect of the single substitution D55G. The other case is a double mutant, L49I/I57V, which is 5.1 kJ mol-1 more stable than the sum of the effects of the individual mutations. In addition to demonstrating the strength of our selection system for finding stabilizing mutations, our work also demonstrate how subtle conformational effects may modulate stability.
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Affiliation(s)
- Louise Hamborg
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Lyngby, Denmark
| | - Daniele Granata
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Johan G Olsen
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Jennifer Virginia Roche
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Lyngby, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
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30
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Powers ET, Gierasch LM. The Proteome Folding Problem and Cellular Proteostasis. J Mol Biol 2021; 433:167197. [PMID: 34391802 DOI: 10.1016/j.jmb.2021.167197] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 12/16/2022]
Abstract
Stunning advances have been achieved in addressing the protein folding problem, providing deeper understanding of the mechanisms by which proteins navigate energy landscapes to reach their native states and enabling powerful algorithms to connect sequence to structure. However, the realities of the in vivo protein folding problem remain a challenge to reckon with. Here, we discuss the concept of the "proteome folding problem"-the problem of how organisms build and maintain a functional proteome-by admitting that folding energy landscapes are characterized by many misfolded states and that cells must deploy a network of chaperones and degradation enzymes to minimize deleterious impacts of these off-pathway species. The resulting proteostasis network is an inextricable part of in vivo protein folding and must be understood in detail if we are to solve the proteome folding problem. We discuss how the development of computational models for the proteostasis network's actions and the relationship to the biophysical properties of the proteome has begun to offer new insights and capabilities.
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Affiliation(s)
- Evan T Powers
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Lila M Gierasch
- Departments of Biochemistry & Molecular Biology and Chemistry, University of Massachusetts-Amherst, Amherst, MA 01003, USA.
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31
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Kohler V, Andréasson C. Hsp70-mediated quality control: should I stay or should I go? Biol Chem 2021; 401:1233-1248. [PMID: 32745066 DOI: 10.1515/hsz-2020-0187] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/11/2020] [Indexed: 12/30/2022]
Abstract
Chaperones of the 70 kDa heat shock protein (Hsp70) superfamily are key components of the cellular proteostasis system. Together with its co-chaperones, Hsp70 forms proteostasis subsystems that antagonize protein damage during physiological and stress conditions. This function stems from highly regulated binding and release cycles of protein substrates, which results in a flow of unfolded, partially folded and misfolded species through the Hsp70 subsystem. Specific factors control how Hsp70 makes decisions regarding folding and degradation fates of the substrate proteins. In this review, we summarize how the flow of Hsp70 substrates is controlled in the cell with special emphasis on recent advances regarding substrate release mechanisms.
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Affiliation(s)
- Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91 Stockholm, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91 Stockholm, Sweden
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32
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Ambrose AJ, Chapman E. Function, Therapeutic Potential, and Inhibition of Hsp70 Chaperones. J Med Chem 2021; 64:7060-7082. [PMID: 34009983 DOI: 10.1021/acs.jmedchem.0c02091] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hsp70s are among the most highly conserved proteins in all of biology. Through an iterative binding and release of exposed hydrophobic residues on client proteins, Hsp70s can prevent aggregation and promote folding to the native state of their client proteins. The human proteome contains eight canonical Hsp70s. Because Hsp70s are relatively promiscuous they play a role in folding a large proportion of the proteome. Hsp70s are implicated in disease through their ability to regulate protein homeostasis. In recent years, researchers have attempted to develop selective inhibitors of Hsp70 isoforms to better understand the role of individual isoforms in biology and as potential therapeutics. Selective inhibitors have come from rational design, forced localization, and serendipity, but the development of completely selective inhibitors remains elusive. In the present review, we discuss the Hsp70 structure and function, the known Hsp70 client proteins, the role of Hsp70s in disease, and current efforts to discover Hsp70 modulators.
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Affiliation(s)
- Andrew J Ambrose
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Eli Chapman
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
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33
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Lang BJ, Guerrero ME, Prince TL, Okusha Y, Bonorino C, Calderwood SK. The functions and regulation of heat shock proteins; key orchestrators of proteostasis and the heat shock response. Arch Toxicol 2021; 95:1943-1970. [PMID: 34003342 DOI: 10.1007/s00204-021-03070-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 05/03/2021] [Indexed: 12/14/2022]
Abstract
Cells respond to protein-damaging (proteotoxic) stress by activation of the Heat Shock Response (HSR). The HSR provides cells with an enhanced ability to endure proteotoxic insults and plays a crucial role in determining subsequent cell death or survival. The HSR is, therefore, a critical factor that influences the toxicity of protein stress. While named for its vital role in the cellular response to heat stress, various components of the HSR system and the molecular chaperone network execute essential physiological functions as well as responses to other diverse toxic insults. The effector molecules of the HSR, the Heat Shock Factors (HSFs) and Heat Shock Proteins (HSPs), are also important regulatory targets in the progression of neurodegenerative diseases and cancers. Modulation of the HSR and/or its extended network have, therefore, become attractive treatment strategies for these diseases. Development of effective therapies will, however, require a detailed understanding of the HSR, important features of which continue to be uncovered and are yet to be completely understood. We review recently described and hallmark mechanistic principles of the HSR, the regulation and functions of HSPs, and contexts in which the HSR is activated and influences cell fate in response to various toxic conditions.
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Affiliation(s)
- Benjamin J Lang
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Martin E Guerrero
- Laboratory of Oncology, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), 5500, Mendoza, Argentina
| | - Thomas L Prince
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Yuka Okusha
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Cristina Bonorino
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brasil.,Department of Surgery, School of Medicine, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Stuart K Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
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34
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Gersing SK, Wang Y, Grønbæk-Thygesen M, Kampmeyer C, Clausen L, Willemoës M, Andréasson C, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Mapping the degradation pathway of a disease-linked aspartoacylase variant. PLoS Genet 2021; 17:e1009539. [PMID: 33914734 PMCID: PMC8084241 DOI: 10.1371/journal.pgen.1009539] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 04/06/2021] [Indexed: 11/19/2022] Open
Abstract
Canavan disease is a severe progressive neurodegenerative disorder that is characterized by swelling and spongy degeneration of brain white matter. The disease is genetically linked to polymorphisms in the aspartoacylase (ASPA) gene, including the substitution C152W. ASPA C152W is associated with greatly reduced protein levels in cells, yet biophysical experiments suggest a wild-type like thermal stability. Here, we use ASPA C152W as a model to investigate the degradation pathway of a disease-causing protein variant. When we expressed ASPA C152W in Saccharomyces cerevisiae, we found a decreased steady state compared to wild-type ASPA as a result of increased proteasomal degradation. However, molecular dynamics simulations of ASPA C152W did not substantially deviate from wild-type ASPA, indicating that the native state is structurally preserved. Instead, we suggest that the C152W substitution interferes with the de novo folding pathway resulting in increased proteasomal degradation before reaching its stable conformation. Systematic mapping of the protein quality control components acting on misfolded and aggregation-prone species of C152W, revealed that the degradation is highly dependent on the molecular chaperone Hsp70, its co-chaperone Hsp110 as well as several quality control E3 ubiquitin-protein ligases, including Ubr1. In addition, the disaggregase Hsp104 facilitated refolding of aggregated ASPA C152W, while Cdc48 mediated degradation of insoluble ASPA protein. In human cells, ASPA C152W displayed increased proteasomal turnover that was similarly dependent on Hsp70 and Hsp110. Our findings underscore the use of yeast to determine the protein quality control components involved in the degradation of human pathogenic variants in order to identify potential therapeutic targets.
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Affiliation(s)
- Sarah K. Gersing
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yong Wang
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Grønbæk-Thygesen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Kampmeyer
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lene Clausen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Willemoës
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Amelie Stein
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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35
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Chilukoti N, Sil TB, Sahoo B, Deepa S, Cherakara S, Maddheshiya M, Garai K. Hsp70 Inhibits Aggregation of IAPP by Binding to the Heterogeneous Prenucleation Oligomers. Biophys J 2021; 120:476-488. [PMID: 33417920 PMCID: PMC7895988 DOI: 10.1016/j.bpj.2020.12.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022] Open
Abstract
Molecular chaperone Hsp70 plays important roles in the pathology of amyloid diseases by inhibiting aberrant aggregation of proteins. However, the biophysical mechanism of the interaction of Hsp70 with the intrinsically disordered proteins (IDPs) is unclear. Here, we report that Hsp70 inhibits aggregation of islet amyloid polypeptide (IAPP) at substoichiometric concentrations under diverse solution conditions, including in the absence of ATP. The inhibitory effect is strongest if Hsp70 is added in the beginning of aggregation but progressively less if added later, indicating a role for Hsp70 in preventing nucleation of IAPP. However, ensemble measurement of the binding affinity suggests poor interactions between Hsp70 and IAPP. Therefore, we hypothesize that the interaction must involve a rare species (e.g., the oligomeric intermediates of IAPP). Size exclusion chromatography and field flow fractionation are then used to fractionate the constituent species. Multiangle light scattering and fluorescence correlation spectroscopy measurements indicate that the dominant fraction in size exclusion chromatography contains a few nanomolar Hsp70-IAPP complexes amid several μmoles of free Hsp70. Using single-particle two-color coincidence detection measurements, we detected a minor fraction that exhibits fluorescence bursts arising from heterogeneous oligomeric complexes of IAPP and Hsp70. Taken together, our results indicate that Hsp70 interacts poorly with the monomers but strongly with oligomers of IAPP. This is likely a generic feature of the interactions of Hsp70 chaperones with the amyloidogenic IDPs. Whereas high-affinity interactions with the oligomers prevent aberrant aggregation, poor interaction with the monomers averts interference with the physiological functions of the IDPs.
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Affiliation(s)
- Neeraja Chilukoti
- Tata Institute of Fundamental Research, Serilingampally, Hyderabad, India
| | - Timir Baran Sil
- Tata Institute of Fundamental Research, Serilingampally, Hyderabad, India
| | - Bankanidhi Sahoo
- Tata Institute of Fundamental Research, Serilingampally, Hyderabad, India
| | - S Deepa
- Tata Institute of Fundamental Research, Serilingampally, Hyderabad, India
| | | | - Mithun Maddheshiya
- Tata Institute of Fundamental Research, Serilingampally, Hyderabad, India
| | - Kanchan Garai
- Tata Institute of Fundamental Research, Serilingampally, Hyderabad, India.
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36
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Yazar M, Özbek P. In Silico Tools and Approaches for the Prediction of Functional and Structural Effects of Single-Nucleotide Polymorphisms on Proteins: An Expert Review. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 25:23-37. [PMID: 33058752 DOI: 10.1089/omi.2020.0141] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) are single-base variants that contribute to human biological variation and pathogenesis of many human diseases. Among all SNP types, nonsynonymous single-nucleotide polymorphisms (nsSNPs) can alter many structural, biochemical, and functional features of a protein such as folding characteristics, charge distribution, stability, dynamics, and interactions with other proteins/nucleotides. These modifications in the protein structure can lead nsSNPs to be closely associated with many multifactorial diseases such as cancer, diabetes, and neurodegenerative diseases. Predicting structural and functional effects of nsSNPs with experimental approaches can be time-consuming and costly; hence, computational prediction tools and algorithms are being widely and increasingly utilized in biology and medical research. This expert review examines the in silico tools and algorithms for the prediction of functional or structural effects of SNP variants, in addition to the description of the phenotypic effects of nsSNPs on protein structure, association between pathogenicity of variants, and functional or structural features of disease-associated variants. Finally, case studies investigating the functional and structural effects of nsSNPs on selected protein structures are highlighted. We conclude that creating a consistent workflow with a combination of in silico approaches or tools should be considered to increase the performance, accuracy, and precision of the biological and clinical predictions made in silico.
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Affiliation(s)
- Metin Yazar
- Department of Bioengineering, Marmara University, Göztepe, İstanbul, Turkey.,Department of Genetics and Bioengineering, Istanbul Okan University, Tuzla, Istanbul, Turkey
| | - Pemra Özbek
- Department of Bioengineering, Marmara University, Göztepe, İstanbul, Turkey
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37
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Claes F, Rudyak S, Laird AS, Louros N, Beerten J, Debulpaep M, Michiels E, van der Kant R, Van Durme J, De Baets G, Houben B, Ramakers M, Yuan K, Gwee SSL, Hernandez S, Broersen K, Oliveberg M, Moahamed B, Kirstein J, Robberecht W, Rousseau F, Schymkowitz J. Exposure of a cryptic Hsp70 binding site determines the cytotoxicity of the ALS-associated SOD1-mutant A4V. Protein Eng Des Sel 2020; 32:443-457. [PMID: 32399571 DOI: 10.1093/protein/gzaa008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/21/2020] [Indexed: 12/11/2022] Open
Abstract
The accumulation of toxic protein aggregates is thought to play a key role in a range of degenerative pathologies, but it remains unclear why aggregation of polypeptides into non-native assemblies is toxic and why cellular clearance pathways offer ineffective protection. We here study the A4V mutant of SOD1, which forms toxic aggregates in motor neurons of patients with familial amyotrophic lateral sclerosis (ALS). A comparison of the location of aggregation prone regions (APRs) and Hsp70 binding sites in the denatured state of SOD1 reveals that ALS-associated mutations promote exposure of the APRs more than the strongest Hsc/Hsp70 binding site that we could detect. Mutations designed to increase the exposure of this Hsp70 interaction site in the denatured state promote aggregation but also display an increased interaction with Hsp70 chaperones. Depending on the cell type, in vitro this resulted in cellular inclusion body formation or increased clearance, accompanied with a suppression of cytotoxicity. The latter was also observed in a zebrafish model in vivo. Our results suggest that the uncontrolled accumulation of toxic SOD1A4V aggregates results from insufficient detection by the cellular surveillance network.
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Affiliation(s)
- Filip Claes
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium
| | - Stanislav Rudyak
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Leninskiy Prospekt, 14, Moscow 119991, Russia
| | - Angela S Laird
- VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, Herestraat 49, Leuven, Belgium.,Center for Motor Neuron Disease Research, Department of Biomedical Science, Faculty of Medicine, Macquarie University, Balaclava Rd, Macquarie Park, Sydney NSW 2109, Australia
| | - Nikolaos Louros
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium
| | - Jacinte Beerten
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,Applied Stem Cell Technologies, University of Twente, Technical Medical Centre, Drienerlolaan 5, Enschede, The Netherlands
| | - Maja Debulpaep
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,Applied Stem Cell Technologies, University of Twente, Technical Medical Centre, Drienerlolaan 5, Enschede, The Netherlands
| | - Emiel Michiels
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium
| | - Rob van der Kant
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium
| | - Joost Van Durme
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium.,Applied Stem Cell Technologies, University of Twente, Technical Medical Centre, Drienerlolaan 5, Enschede, The Netherlands
| | - Greet De Baets
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium.,Applied Stem Cell Technologies, University of Twente, Technical Medical Centre, Drienerlolaan 5, Enschede, The Netherlands
| | - Bert Houben
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium
| | - Meine Ramakers
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium
| | - Kristy Yuan
- Center for Motor Neuron Disease Research, Department of Biomedical Science, Faculty of Medicine, Macquarie University, Balaclava Rd, Macquarie Park, Sydney NSW 2109, Australia
| | - Serene S L Gwee
- Center for Motor Neuron Disease Research, Department of Biomedical Science, Faculty of Medicine, Macquarie University, Balaclava Rd, Macquarie Park, Sydney NSW 2109, Australia
| | - Sara Hernandez
- VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, Herestraat 49, Leuven, Belgium
| | - Kerensa Broersen
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,Applied Stem Cell Technologies, University of Twente, Technical Medical Centre, Drienerlolaan 5, Enschede, The Netherlands
| | - Mikael Oliveberg
- Stockholm University, Department of Biochemistry and Biophysics, Frescativägen, 114 19 Stockholm, Sweden
| | - Barbara Moahamed
- Universität Bremen, Fachbereich 2 Biologie/ Chemie, Postfach 330 440, Bremen, Germany
| | - Janine Kirstein
- Universität Bremen, Fachbereich 2 Biologie/ Chemie, Postfach 330 440, Bremen, Germany
| | - Wim Robberecht
- VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, Herestraat 49, Leuven, Belgium
| | - Frederic Rousseau
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium
| | - Joost Schymkowitz
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium
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38
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Houben B, Michiels E, Ramakers M, Konstantoulea K, Louros N, Verniers J, van der Kant R, De Vleeschouwer M, Chicória N, Vanpoucke T, Gallardo R, Schymkowitz J, Rousseau F. Autonomous aggregation suppression by acidic residues explains why chaperones favour basic residues. EMBO J 2020; 39:e102864. [PMID: 32237079 PMCID: PMC7265246 DOI: 10.15252/embj.2019102864] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 12/13/2022] Open
Abstract
Many chaperones favour binding to hydrophobic sequences that are flanked by basic residues while disfavouring acidic residues. However, the origin of this bias in protein quality control remains poorly understood. Here, we show that while acidic residues are the most efficient aggregation inhibitors, they are also less compatible with globular protein structure than basic amino acids. As a result, while acidic residues allow for chaperone-independent control of aggregation, their use is structurally limited. Conversely, we find that, while being more compatible with globular structure, basic residues are not sufficient to autonomously suppress protein aggregation. Using Hsp70, we show that chaperones with a bias towards basic residues are structurally adapted to prioritize aggregating sequences whose structural context forced the use of the less effective basic residues. The hypothesis that emerges from our analysis is that the bias of many chaperones for basic residues results from fundamental thermodynamic and kinetic constraints of globular structure. This also suggests the co-evolution of basic residues and chaperones allowed for an expansion of structural variety in the protein universe.
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Affiliation(s)
- Bert Houben
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Emiel Michiels
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Meine Ramakers
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Katerina Konstantoulea
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Nikolaos Louros
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Joffré Verniers
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Rob van der Kant
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Matthias De Vleeschouwer
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Nuno Chicória
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Thomas Vanpoucke
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Rodrigo Gallardo
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
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39
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Dalphin MD, Stangl AJ, Liu Y, Cavagnero S. KLR-70: A Novel Cationic Inhibitor of the Bacterial Hsp70 Chaperone. Biochemistry 2020; 59:1946-1960. [PMID: 32326704 DOI: 10.1021/acs.biochem.0c00320] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The heat-shock factor Hsp70 and other molecular chaperones play a central role in nascent protein folding. Elucidating the task performed by individual chaperones within the complex cellular milieu, however, has been challenging. One strategy for addressing this goal has been to monitor protein biogenesis in the absence and presence of inhibitors of a specific chaperone, followed by analysis of folding outcomes under both conditions. In this way, the role of the chaperone of interest can be discerned. However, development of chaperone inhibitors, including well-known proline-rich antimicrobial peptides, has been fraught with undesirable side effects, including decreased protein expression yields. Here, we introduce KLR-70, a rationally designed cationic inhibitor of the Escherichia coli Hsp70 chaperone (also known as DnaK). KLR-70 is a 14-amino acid peptide bearing naturally occurring residues and engineered to interact with the DnaK substrate-binding domain. The interaction of KLR-70 with DnaK is enantioselective and is characterized by high affinity in a buffered solution. Importantly, KLR-70 does not significantly interact with the DnaJ and GroEL/ES chaperones, and it does not alter nascent protein biosynthesis yields across a wide concentration range. Some attenuation of the anti-DnaK activity of KLR-70, however, has been observed in the complex E. coli cell-free environment. Interestingly, the d enantiomer D-KLR-70, unlike its all-L KLR-70 counterpart, does not bind the DnaK and DnaJ chaperones, yet it strongly inhibits translation. This outcome suggests that the two enantiomers (KLR-70 and D-KLR-70) may serve as orthogonal inhibitors of chaperone binding and translation. In summary, KLR-70 is a novel chaperone inhibitor with high affinity and selectivity for bacterial Hsp70 and with considerable potential to help in parsing out the role of Hsp70 in nascent protein folding.
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Affiliation(s)
- Matthew D Dalphin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Andrew J Stangl
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Yue Liu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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40
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Srinivasan E, Natarajan N, Rajasekaran R. TTRMDB: A database for structural and functional analysis on the impact of SNPs over transthyretin (TTR) using bioinformatic tools. Comput Biol Chem 2020; 87:107290. [PMID: 32512488 DOI: 10.1016/j.compbiolchem.2020.107290] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/14/2020] [Accepted: 05/21/2020] [Indexed: 12/21/2022]
Abstract
Hereditary Transthyretin-associated amyloidosis (ATTR) is an autosomal dominant protein-folding disorder with adult-onset caused by mutation of transthyretin (TTR). TTR is characterized by extracellular deposition of amyloid, leading to loss of autonomy and finally, death. More than 100 distinct mutations in TTR gene have been reported from variable age of onset, clinical expression and penetrance data. Besides, the cure for the disease remains still obscure. Further, the prioritizing of mutations concerning the characteristic features governing the stability and pathogenicity of TTR mutant proteins remains unanswered, to date and thus, a complex state of study for researchers. Herein, we provide a full report encompassing the effects of every reported mutant model of TTR protein about the stability, functionality and pathogenicity using various computational tools. In addition, the results obtained from our study were used to create TTRMDB (Transthyretin mutant database), which could be easy access to researchers at http://vit.ac.in/ttrmdb.
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Affiliation(s)
- E Srinivasan
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore 632014, Tamil Nadu, India
| | - Nandhini Natarajan
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore 632014, Tamil Nadu, India
| | - R Rajasekaran
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore 632014, Tamil Nadu, India.
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41
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Srinivasan E, Rajasekaran R. A Systematic and Comprehensive Review on Disease-Causing Genes in Amyotrophic Lateral Sclerosis. J Mol Neurosci 2020; 70:1742-1770. [PMID: 32415434 DOI: 10.1007/s12031-020-01569-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder and is characterized by degeneration and axon loss from the upper motor neuron, that descends from the lower motor neuron in the brain. Over the period, assorted outcomes from medical findings, molecular pathogenesis, and structural and biophysical studies have abetted in providing thoughtful insights underlying the importance of disease-causing genes in ALS. Consequently, numerous mechanisms were proposed for the pathogenesis of ALS, considering protein mutations, aggregation, and misfolding. Besides, the answers to the majority of ALS cases that happen to be sporadic still remain obscure. The application in discovering susceptibility factors in ALS contemplating the genetic factors is to be further dissevered in the future years with innovation in research studies. Hence, this review targets in revisiting the breakthroughs on the disease-causing genes related with ALS.
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Affiliation(s)
- E Srinivasan
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (deemed to be university), Vellore, Tamil Nadu, 632014, India
| | - R Rajasekaran
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (deemed to be university), Vellore, Tamil Nadu, 632014, India.
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42
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Baaklini I, Gonçalves CDC, Lukacs GL, Young JC. Selective Binding of HSC70 and its Co-Chaperones to Structural Hotspots on CFTR. Sci Rep 2020; 10:4176. [PMID: 32144307 PMCID: PMC7060200 DOI: 10.1038/s41598-020-61107-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/07/2020] [Indexed: 12/17/2022] Open
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) channel cause cystic fibrosis. Chaperones, including HSC70, DNAJA1 and DNAJA2, play key roles in both the folding and degradation of wild-type and mutant CFTR at multiple cellular locations. DNAJA1 and HSC70 promote the folding of newly synthesized CFTR at the endoplasmic reticulum (ER), but are required for the rapid turnover of misfolded channel at the plasma membrane (PM). DNAJA2 and HSC70 are also involved in the ER-associated degradation (ERAD) of misfolded CFTR, while they assist the refolding of destabilized channel at the PM. These outcomes may depend on the binding of chaperones to specific sites within CFTR, which would be exposed in non-native states. A CFTR peptide library was used to identify binding sites for HSC70, DNAJA1 and DNAJA2, validated by competition and functional assays. Each chaperone had a distinct binding pattern, and sites were distributed between the surfaces of the CFTR cytosolic domains, and domain interfaces known to be important for channel assembly. The accessibility of sites to chaperones will depend on the degree of CFTR folding or unfolding. Different folded states may be recognized by unique combinations of HSC70, DNAJA1 and DNAJA2, leading to divergent biological effects.
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Affiliation(s)
- Imad Baaklini
- McGill University, Department of Biochemistry, Montreal, H3G 1Y6, Canada
| | | | - Gergely L Lukacs
- McGill University, Department of Biochemistry, Montreal, H3G 1Y6, Canada.,McGill University, Department of Physiology, Montreal, H3G 1Y6, Canada
| | - Jason C Young
- McGill University, Department of Biochemistry, Montreal, H3G 1Y6, Canada.
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43
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Jong WSP, Ten Hagen-Jongman CM, Vikström D, Dontje W, Abdallah AM, de Gier JW, Bitter W, Luirink J. Mutagenesis-Based Characterization and Improvement of a Novel Inclusion Body Tag. Front Bioeng Biotechnol 2020; 7:442. [PMID: 31998707 PMCID: PMC6965018 DOI: 10.3389/fbioe.2019.00442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/11/2019] [Indexed: 12/13/2022] Open
Abstract
Whereas, bacterial inclusion bodies (IBs) for long were regarded as undesirable aggregates emerging during recombinant protein production, they currently receive attention as promising nanoparticulate biomaterials with diverse applications in biotechnology and biomedicine. We previously identified ssTorA, a signal sequence that normally directs protein export via the Tat pathway in E. coli, as a tag that induces the accumulation of fused proteins into IBs under overexpression conditions. Here, we used targeted mutagenesis to identify features and motifs being either critical or dispensable for IB formation. We found that IB formation is neither related to the function of ssTorA as a Tat-signal sequence nor is it a general feature of this family of signal sequences. IB formation was inhibited by co-overexpression of ssTorA binding chaperones TorD and DnaK and by amino acid substitutions that affect the propensity of ssTorA to form an α-helix. Systematic deletion experiments identified a minimal region of ssTorA required for IB formation in the center of the signal sequence. Unbiased genetic screening of a library of randomly mutagenized ssTorA sequences for reduced aggregation properties allowed us to pinpoint residues that are critical to sustain insoluble expression. Together, the data point to possible mechanisms for the aggregation of ssTorA fusions. Additionally, they led to the design of a tag with superior IB-formation properties compared to the original ssTorA sequence.
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Affiliation(s)
- Wouter S P Jong
- Abera Bioscience AB, Solna, Sweden.,Department of Molecular Microbiology, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), Vrije Universiteit, Amsterdam, Netherlands
| | - Corinne M Ten Hagen-Jongman
- Department of Molecular Microbiology, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), Vrije Universiteit, Amsterdam, Netherlands
| | | | - Wendy Dontje
- Department of Clinical Immunology and Rheumatology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Abdallah M Abdallah
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar.,Bioscience Core Laboratory, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden
| | - Wilbert Bitter
- Department of Molecular Microbiology, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), Vrije Universiteit, Amsterdam, Netherlands.,Medical Microbiology and Infection Control, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Joen Luirink
- Abera Bioscience AB, Solna, Sweden.,Department of Molecular Microbiology, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), Vrije Universiteit, Amsterdam, Netherlands
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44
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Imamoglu R, Balchin D, Hayer-Hartl M, Hartl FU. Bacterial Hsp70 resolves misfolded states and accelerates productive folding of a multi-domain protein. Nat Commun 2020; 11:365. [PMID: 31953415 PMCID: PMC6969021 DOI: 10.1038/s41467-019-14245-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/17/2019] [Indexed: 11/09/2022] Open
Abstract
The ATP-dependent Hsp70 chaperones (DnaK in E. coli) mediate protein folding in cooperation with J proteins and nucleotide exchange factors (E. coli DnaJ and GrpE, respectively). The Hsp70 system prevents protein aggregation and increases folding yields. Whether it also enhances the rate of folding remains unclear. Here we show that DnaK/DnaJ/GrpE accelerate the folding of the multi-domain protein firefly luciferase (FLuc) ~20-fold over the rate of spontaneous folding measured in the absence of aggregation. Analysis by single-pair FRET and hydrogen/deuterium exchange identified inter-domain misfolding as the cause of slow folding. DnaK binding expands the misfolded region and thereby resolves the kinetically-trapped intermediates, with folding occurring upon GrpE-mediated release. In each round of release DnaK commits a fraction of FLuc to fast folding, circumventing misfolding. We suggest that by resolving misfolding and accelerating productive folding, the bacterial Hsp70 system can maintain proteins in their native states under otherwise denaturing stress conditions.
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Affiliation(s)
- Rahmi Imamoglu
- Max Planck Institute of Biochemistry, Department of Cellular Biochemistry, Martinsried, Germany
| | - David Balchin
- Max Planck Institute of Biochemistry, Department of Cellular Biochemistry, Martinsried, Germany.
| | - Manajit Hayer-Hartl
- Max Planck Institute of Biochemistry, Department of Cellular Biochemistry, Martinsried, Germany.
| | - F Ulrich Hartl
- Max Planck Institute of Biochemistry, Department of Cellular Biochemistry, Martinsried, Germany.
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45
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Abstract
Adaptive mutations play an important role in molecular evolution. However, the frequency and nature of these mutations at the intramolecular level are poorly understood. To address this, we analyzed the impact of protein architecture on the rate of adaptive substitutions, aiming to understand how protein biophysics influences fitness and adaptation. Using Drosophila melanogaster and Arabidopsis thaliana population genomics data, we fitted models of distribution of fitness effects and estimated the rate of adaptive amino-acid substitutions both at the protein and amino-acid residue level. We performed a comprehensive analysis covering genome, gene, and protein structure, by exploring a multitude of factors with a plausible impact on the rate of adaptive evolution, such as intron number, protein length, secondary structure, relative solvent accessibility, intrinsic protein disorder, chaperone affinity, gene expression, protein function, and protein-protein interactions. We found that the relative solvent accessibility is a major determinant of adaptive evolution, with most adaptive mutations occurring at the surface of proteins. Moreover, we observe that the rate of adaptive substitutions differs between protein functional classes, with genes encoding for protein biosynthesis and degradation signaling exhibiting the fastest rates of protein adaptation. Overall, our results suggest that adaptive evolution in proteins is mainly driven by intermolecular interactions, with host-pathogen coevolution likely playing a major role.
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Affiliation(s)
- Ana Filipa Moutinho
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Fernanda Fontes Trancoso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Julien Yann Dutheil
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Unité Mixte de Recherche 5554 Institut des Sciences de l'Evolution, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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46
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Gershenson A, Gosavi S, Faccioli P, Wintrode PL. Successes and challenges in simulating the folding of large proteins. J Biol Chem 2020; 295:15-33. [PMID: 31712314 PMCID: PMC6952611 DOI: 10.1074/jbc.rev119.006794] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Computational simulations of protein folding can be used to interpret experimental folding results, to design new folding experiments, and to test the effects of mutations and small molecules on folding. However, whereas major experimental and computational progress has been made in understanding how small proteins fold, research on larger, multidomain proteins, which comprise the majority of proteins, is less advanced. Specifically, large proteins often fold via long-lived partially folded intermediates, whose structures, potentially toxic oligomerization, and interactions with cellular chaperones remain poorly understood. Molecular dynamics based folding simulations that rely on knowledge of the native structure can provide critical, detailed information on folding free energy landscapes, intermediates, and pathways. Further, increases in computational power and methodological advances have made folding simulations of large proteins practical and valuable. Here, using serpins that inhibit proteases as an example, we review native-centric methods for simulating the folding of large proteins. These synergistic approaches range from Gō and related structure-based models that can predict the effects of the native structure on folding to all-atom-based methods that include side-chain chemistry and can predict how disease-associated mutations may impact folding. The application of these computational approaches to serpins and other large proteins highlights the successes and limitations of current computational methods and underscores how computational results can be used to inform experiments. These powerful simulation approaches in combination with experiments can provide unique insights into how large proteins fold and misfold, expanding our ability to predict and manipulate protein folding.
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Affiliation(s)
- Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003; Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003.
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore-560065, India.
| | - Pietro Faccioli
- Dipartimento di Fisica, Universitá degli Studi di Trento, 38122 Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, 38123 Povo (Trento), Italy.
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201.
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47
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Assenza S, Sassi AS, Kellner R, Schuler B, De Los Rios P, Barducci A. Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones. eLife 2019; 8:e48491. [PMID: 31845888 PMCID: PMC7000219 DOI: 10.7554/elife.48491] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 12/17/2019] [Indexed: 11/13/2022] Open
Abstract
Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here, we combine complementary theoretical approaches to elucidate the structural and thermodynamic details of the chaperone-induced expansion of a substrate protein, with a particular emphasis on the critical role played by ATP hydrolysis. We first determine the conformational free-energy cost of the substrate expansion due to the binding of multiple chaperones using coarse-grained molecular simulations. We then exploit this result to implement a non-equilibrium rate model which estimates the degree of expansion as a function of the free energy provided by ATP hydrolysis. Our results are in quantitative agreement with recent single-molecule FRET experiments and highlight the stark non-equilibrium nature of the process, showing that Hsp70s are optimized to effectively convert chemical energy into mechanical work close to physiological conditions.
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Affiliation(s)
- Salvatore Assenza
- Laboratory of Food and Soft MaterialsETH ZürichZürichSwitzerland
- Departmento de Física Teórica de la Materia CondensadaUniversidad Autónoma de MadridMadridSpain
| | - Alberto Stefano Sassi
- Institute of Physics, School of Basic SciencesÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- IBM TJ Watson Research CenterYorktown HeightsNew YorkUnited States
| | - Ruth Kellner
- Department of BiochemistryUniversity of ZurichZurichSwitzerland
| | - Benjamin Schuler
- Department of BiochemistryUniversity of ZurichZurichSwitzerland
- Department of PhysicsUniversity of ZurichZurichSwitzerland
| | - Paolo De Los Rios
- Institute of Physics, School of Basic SciencesÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Alessandro Barducci
- Centre de Biochimie Structurale (CBS)INSERM, CNRS, Université de MontpellierMontpellierFrance
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48
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Guin D, Gelman H, Wang Y, Gruebele M. Heat shock-induced chaperoning by Hsp70 is enabled in-cell. PLoS One 2019; 14:e0222990. [PMID: 31557226 PMCID: PMC6762143 DOI: 10.1371/journal.pone.0222990] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Recent work has shown that weak protein-protein interactions are susceptible to the cellular milieu. One case in point is the binding of heat shock proteins (Hsps) to substrate proteins in cells under stress. Upregulation of the Hsp70 chaperone machinery at elevated temperature was discovered in the 1960s, and more recent studies have shown that ATPase activity in one Hsp70 domain is essential for control of substrate binding by the other Hsp70 domain. Although there are several denaturant-based assays of Hsp70 activity, reports of ATP-dependent binding of Hsp70 to a globular protein substrate under heat shock are scarce. Here we show that binding of heat-inducible Hsp70 to phosphoglycerate kinase (PGK) is remarkably different in vitro compared to in-cell. We use fluorescent-labeled mHsp70 and ePGK, and begin by showing that mHsp70 passes the standard β-galactosidase assay, and that it does not self-aggregate until 50°C in presence of ATP. Yet during denaturant refolding or during in vitro heat shock, mHsp70 shows only ATP-independent non-specific sticking to ePGK, as evidenced by nearly identical results with an ATPase activity-deficient K71M mutant of Hsp70 as a control. Addition of Hsp40 (co-factor) or Ficoll (crowder) does not reduce non-specific sticking, but cell lysate does. Therefore, Hsp70 does not act as an ATP-dependent chaperone on its substrate PGK in vitro. In contrast, we observe only specific ATP-dependent binding of mHsp70 to ePGK in mammalian cells, when compared to the inactive Hsp70 K71M mutant. We hypothesize that enhanced in-cell activity is not due to an unknown co-factor, but simply to a favorable shift in binding equilibrium caused by the combination of crowding and osmolyte/macromolecular interactions present in the cell. One candidate mechanism for such a favorable shift in binding equilibrium is the proven ability of Hsp70 to bind near-native states of substrate proteins in vitro. We show evidence for early onset of binding in-cell. Our results suggest that Hsp70 binds PGK preemptively, prior to its full unfolding transition, thus stabilizing it against further unfolding. We propose a "preemptive holdase" mechanism for Hsp70-substrate binding. Given our result for PGK, more proteins than one might think based on in vitro assays may be chaperoned by Hsp70 in vivo. The cellular environment thus plays an important role in maintaining proper Hsp70 function.
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Affiliation(s)
- Drishti Guin
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Hannah Gelman
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Yuhan Wang
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Martin Gruebele
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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49
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The Hsp70 Chaperone System Stabilizes a Thermo-sensitive Subproteome in E. coli. Cell Rep 2019; 28:1335-1345.e6. [DOI: 10.1016/j.celrep.2019.06.081] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/01/2019] [Accepted: 06/21/2019] [Indexed: 01/05/2023] Open
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50
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Bui LM, Geraldi A, Nguyen TT, Lee JH, Lee JY, Cho BK, Kim SC. mRNA Engineering for the Efficient Chaperone-Mediated Co-Translational Folding of Recombinant Proteins in Escherichia coli. Int J Mol Sci 2019; 20:ijms20133163. [PMID: 31261687 PMCID: PMC6651523 DOI: 10.3390/ijms20133163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 12/22/2022] Open
Abstract
The production of soluble, functional recombinant proteins by engineered bacterial hosts is challenging. Natural molecular chaperone systems have been used to solubilize various recombinant proteins with limited success. Here, we attempted to facilitate chaperone-mediated folding by directing the molecular chaperones to their protein substrates before the co-translational folding process completed. To achieve this, we either anchored the bacterial chaperone DnaJ to the 3ʹ untranslated region of a target mRNA by fusing with an RNA-binding domain in the chaperone-recruiting mRNA scaffold (CRAS) system, or coupled the expression of DnaJ and a target recombinant protein using the overlapping stop-start codons 5ʹ-TAATG-3ʹ between the two genes in a chaperone-substrate co-localized expression (CLEX) system. By engineering the untranslated and intergenic sequences of the mRNA transcript, bacterial molecular chaperones are spatially constrained to the location of protein translation, expressing selected aggregation-prone proteins in their functionally active, soluble form. Our mRNA engineering methods surpassed the in-vivo solubilization efficiency of the simple DnaJ chaperone co-overexpression method, thus providing more effective tools for producing soluble therapeutic proteins and enzymes.
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Affiliation(s)
- Le Minh Bui
- KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- NTT Hi-Tech Institute, Nguyen Tat Thanh University (NTTU), Ho Chi Minh City 700000, Vietnam
| | - Almando Geraldi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Biology Department, Science and Technology Faculty, Universitas Airlangga Mulyorejo, Surabaya 60115, Indonesia
| | - Thi Thuy Nguyen
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jun Hyoung Lee
- KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Ju Young Lee
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44429, Korea
| | - Byung-Kwan Cho
- KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Intelligent Synthetic Biology Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
| | - Sun Chang Kim
- KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Intelligent Synthetic Biology Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
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