1
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Dudley JA, Park S, Cho O, Wells NGM, MacDonald ME, Blejec KM, Fetene E, Zanderigo E, Houliston S, Liddle JC, Dashnaw CM, Sabo TM, Shaw BF, Balsbaugh JL, Rocklin GJ, Smith CA. Heat-induced structural and chemical changes to a computationally designed miniprotein. Protein Sci 2024; 33:e4991. [PMID: 38757381 PMCID: PMC11099715 DOI: 10.1002/pro.4991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 05/18/2024]
Abstract
The de novo design of miniprotein inhibitors has recently emerged as a new technology to create proteins that bind with high affinity to specific therapeutic targets. Their size, ease of expression, and apparent high stability makes them excellent candidates for a new class of protein drugs. However, beyond circular dichroism melts and hydrogen/deuterium exchange experiments, little is known about their dynamics, especially at the elevated temperatures they seemingly tolerate quite well. To address that and gain insight for future designs, we have focused on identifying unintended and previously overlooked heat-induced structural and chemical changes in a particularly stable model miniprotein, EHEE_rd2_0005. Nuclear magnetic resonance (NMR) studies suggest the presence of dynamics on multiple time and temperature scales. Transiently elevating the temperature results in spontaneous chemical deamidation visible in the NMR spectra, which we validate using both capillary electrophoresis and mass spectrometry (MS) experiments. High temperatures also result in greatly accelerated intrinsic rates of hydrogen exchange and signal loss in NMR heteronuclear single quantum coherence spectra from local unfolding. These losses are in excellent agreement with both room temperature hydrogen exchange experiments and hydrogen bond disruption in replica exchange molecular dynamics simulations. Our analysis reveals important principles for future miniprotein designs and the potential for high stability to result in long-lived alternate conformational states.
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Affiliation(s)
- Joshua A. Dudley
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Sojeong Park
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Oliver Cho
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | | | | | | | - Emmanuel Fetene
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Eric Zanderigo
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Scott Houliston
- Structural Genomics ConsortiumUniversity of TorontoTorontoOntarioCanada
| | - Jennifer C. Liddle
- Proteomics and Metabolomics FacilityUniversity of ConnecticutStorrsConnecticutUSA
| | - Chad M. Dashnaw
- Department of Chemistry and BiochemistryBaylor UniversityWacoTexasUSA
| | - T. Michael Sabo
- Department of Medicine and Brown Cancer CenterUniversity of LouisvilleLouisvilleKentuckyUSA
| | - Bryan F. Shaw
- Department of Chemistry and BiochemistryBaylor UniversityWacoTexasUSA
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics FacilityUniversity of ConnecticutStorrsConnecticutUSA
| | - Gabriel J. Rocklin
- Department of Pharmacology and Center for Synthetic BiologyNorthwestern UniversityEvanstonIllinoisUSA
| | - Colin A. Smith
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
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2
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Hossain MA, Sarin R, Donnelly DP, Miller BC, Weiss A, McAlary L, Antonyuk SV, Salisbury JP, Amin J, Conway JB, Watson SS, Winters JN, Xu Y, Alam N, Brahme RR, Shahbazian H, Sivasankar D, Padmakumar S, Sattarova A, Ponmudiyan AC, Gawde T, Verrill DE, Yang W, Kannapadi S, Plant LD, Auclair JR, Makowski L, Petsko GA, Ringe D, Agar NYR, Greenblatt DJ, Ondrechen MJ, Chen Y, Yerbury JJ, Manetsch R, Hasnain SS, Brown RH, Agar JN. Evaluating protein cross-linking as a therapeutic strategy to stabilize SOD1 variants in a mouse model of familial ALS. PLoS Biol 2024; 22:e3002462. [PMID: 38289969 PMCID: PMC10826971 DOI: 10.1371/journal.pbio.3002462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/05/2023] [Indexed: 02/01/2024] Open
Abstract
Mutations in the gene encoding Cu-Zn superoxide dismutase 1 (SOD1) cause a subset of familial amyotrophic lateral sclerosis (fALS) cases. A shared effect of these mutations is that SOD1, which is normally a stable dimer, dissociates into toxic monomers that seed toxic aggregates. Considerable research effort has been devoted to developing compounds that stabilize the dimer of fALS SOD1 variants, but unfortunately, this has not yet resulted in a treatment. We hypothesized that cyclic thiosulfinate cross-linkers, which selectively target a rare, 2 cysteine-containing motif, can stabilize fALS-causing SOD1 variants in vivo. We created a library of chemically diverse cyclic thiosulfinates and determined structure-cross-linking-activity relationships. A pre-lead compound, "S-XL6," was selected based upon its cross-linking rate and drug-like properties. Co-crystallographic structure clearly establishes the binding of S-XL6 at Cys 111 bridging the monomers and stabilizing the SOD1 dimer. Biophysical studies reveal that the degree of stabilization afforded by S-XL6 (up to 24°C) is unprecedented for fALS, and to our knowledge, for any protein target of any kinetic stabilizer. Gene silencing and protein degrading therapeutic approaches require careful dose titration to balance the benefit of diminished fALS SOD1 expression with the toxic loss-of-enzymatic function. We show that S-XL6 does not share this liability because it rescues the activity of fALS SOD1 variants. No pharmacological agent has been proven to bind to SOD1 in vivo. Here, using a fALS mouse model, we demonstrate oral bioavailability; rapid engagement of SOD1G93A by S-XL6 that increases SOD1G93A's in vivo half-life; and that S-XL6 crosses the blood-brain barrier. S-XL6 demonstrated a degree of selectivity by avoiding off-target binding to plasma proteins. Taken together, our results indicate that cyclic thiosulfinate-mediated SOD1 stabilization should receive further attention as a potential therapeutic approach for fALS.
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Affiliation(s)
- Md Amin Hossain
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
- Department of Neurosurgery and Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richa Sarin
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Biogen Inc, Cambridge, Massachusetts, United States of America
| | - Daniel P. Donnelly
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Brandon C. Miller
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Alexandra Weiss
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Luke McAlary
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Department of Biochemistry & Systems Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Joseph P. Salisbury
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Jakal Amin
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Jeremy B. Conway
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Samantha S. Watson
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Jenifer N. Winters
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Yu Xu
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - Novera Alam
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Rutali R. Brahme
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Haneyeh Shahbazian
- School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Durgalakshmi Sivasankar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Swathi Padmakumar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Aziza Sattarova
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - Aparna C. Ponmudiyan
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Tanvi Gawde
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - David E. Verrill
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Wensheng Yang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Sunanda Kannapadi
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Leigh D. Plant
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - Jared R. Auclair
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Lee Makowski
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, United States of America
| | - Gregory A. Petsko
- Ann Romney Center for Neurologic Diseases at Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Departments of Chemistry and Biochemistry, and Rosenstiel Center for Basic Medical Research, Brandeis University, Waltham, Massachusetts, United States of America
| | - Dagmar Ringe
- Departments of Chemistry and Biochemistry, and Rosenstiel Center for Basic Medical Research, Brandeis University, Waltham, Massachusetts, United States of America
| | - Nathalie Y. R. Agar
- Department of Neurosurgery and Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David J. Greenblatt
- School of Medicine, Tufts University, Boston, Massachusetts, United States of America
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Yunqiu Chen
- Biogen Inc, Cambridge, Massachusetts, United States of America
| | - Justin J. Yerbury
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Roman Manetsch
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - S. Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry & Systems Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Robert H. Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jeffrey N. Agar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
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3
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Kamelnia R, Goliaei B, Peyman Shariatpanahi S, Mehrnejad F, Ghasemi A, Zare Karizak A, Ebrahim-Habibi A. Chemical Modification of the Amino Groups of Human Insulin: Investigating Structural Properties and Amorphous Aggregation of Acetylated Species. Protein J 2023:10.1007/s10930-023-10131-7. [PMID: 37395911 DOI: 10.1007/s10930-023-10131-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2023] [Indexed: 07/04/2023]
Abstract
The efficacy of human recombinant insulin can be affected by its aggregation. Effects of acetylation were observed on insulin structure, stability, and aggregation at 37 and 50 °C and pH of 5.0 and 7.4 with the use of spectroscopy, circular dichroism (CD), dynamic light scattering (DLS), and atomic force microscopy (AFM). Raman and FTIR results were indicative of structural changes in AC-INS, and CD analyses showed a slight increase in β-sheet content in AC-INS. Melting temperature (Tm) measurements indicated an overall more stable structure and spectroscopic assessment showed a more compact one. Formation of amorphous aggregates was followed over time and kinetics parameters showed a longer nucleation phase (higher t* amount) and lower aggregates amount (lower Alim) for acetylated insulin (AC-INS) compared to native (N-INS) in all tested conditions. The results of amyloid-specific probes approved the formation of amorphous aggregates. Size particle and microscopic analysis suggested that AC-INS was less prone to form aggregates, which were smaller if formed. In conclusion, this study has demonstrated that controlled acetylation of insulin may lead to its higher stability and lower propensity toward amorphous aggregation and has provided insight into the result of this type of post-translational protein modification.
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Affiliation(s)
- Reyhane Kamelnia
- Laboratory of Biophysics and Molecular Biology, Departments of Biophysics, Institute of Biochemistry and Biophysics, University of Tehran, 16th Azar St., Enghelab Sq., P.O. Box 13145-1384, Tehran, Iran
| | - Bahram Goliaei
- Laboratory of Biophysics and Molecular Biology, Departments of Biophysics, Institute of Biochemistry and Biophysics, University of Tehran, 16th Azar St., Enghelab Sq., P.O. Box 13145-1384, Tehran, Iran.
| | - Seyed Peyman Shariatpanahi
- Laboratory of Biophysics and Molecular Biology, Departments of Biophysics, Institute of Biochemistry and Biophysics, University of Tehran, 16th Azar St., Enghelab Sq., P.O. Box 13145-1384, Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Atiyeh Ghasemi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ashkan Zare Karizak
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Azadeh Ebrahim-Habibi
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Jalal Al Ahmad Highway, Tehran, 1411713137, Iran.
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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4
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Koone JC, Dashnaw CM, Gonzalez M, Shaw BF. A method for quantifying how the activity of an enzyme is affected by the net charge of its nearest crowded neighbor. Protein Sci 2022. [PMCID: PMC9601770 DOI: 10.1002/pro.4384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The electrostatic effects of protein crowding have not been systematically explored. Rather, protein crowding is generally studied with co‐solvents or crowders that are electrostatically neutral, with no methods to measure how the net charge (Z) of a crowder affects protein function. For example, can the activity of an enzyme be affected electrostatically by the net charge of its neighbor in crowded milieu? This paper reports a method for crowding proteins of different net charge to an enzyme via semi‐random chemical crosslinking. As a proof of concept, RNase A was crowded (at distances ≤ the Debye length) via crosslinking to different heme proteins with Z = +8.50 ± 0.04, Z = +6.39 ± 0.12, or Z = −10.30 ± 1.32. Crosslinking did not disrupt the structure of proteins, according to amide H/D exchange, and did not inhibit RNase A activity. For RNase A, we found that the electrostatic environment of each crowded neighbor had significant effects on rates of RNA hydrolysis. Crowding with cationic cytochrome c led to increases in activity, while crowding with anionic “supercharged” cytochrome c or myoglobin diminished activity. Surprisingly, electrostatic crowding effects were amplified at high ionic strength (I = 0.201 M) and attenuated at low ionic strength (I = 0.011 M). This salt dependence might be caused by a unique set of electric double layers at the dimer interspace (maximum distance of 8 Å, which cannot accommodate four layers). This new method of crowding via crosslinking can be used to search for electrostatic effects in protein crowding.
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Affiliation(s)
- Jordan C. Koone
- Department of Chemistry and Biochemistry Baylor University Waco Texas USA
| | - Chad M. Dashnaw
- Department of Chemistry and Biochemistry Baylor University Waco Texas USA
| | - Mayte Gonzalez
- Department of Chemistry and Biochemistry Baylor University Waco Texas USA
| | - Bryan F. Shaw
- Department of Chemistry and Biochemistry Baylor University Waco Texas USA
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5
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Latif S, Kang YS. Change in Cationic Amino Acid Transport System and Effect of Lysine Pretreatment on Inflammatory State in Amyotrophic Lateral Sclerosis Cell Model. Biomol Ther (Seoul) 2021; 29:498-505. [PMID: 33935047 PMCID: PMC8411026 DOI: 10.4062/biomolther.2021.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 11/21/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a lethal neurological disorder characterized by the deterioration of motor neurons. The aim of this study was to investigate alteration of cationic amino acid transporter (CAT-1) activity in the transport of lysine and the pretreatment effect of lysine on pro-inflammatory states in an amyotrophic lateral sclerosis cell line. The mRNA expression of cationic amino acid transporter 1 was lower in NSC-34/hSOD1G93A (MT) than the control cell line (WT), lysine transport is mediated by CAT-1 in NSC-34 cell lines. The uptake of [3H]L-lysine was Na+-independent, voltage-sensitive, and strongly inhibited by inhibitors and substrates of cationic amino acid transporter 1 (system y+). The transport process involved two saturable processes in both cell lines. In the MT cell line, at a high-affinity site, the affinity was 9.4-fold higher and capacity 24-fold lower than that in the WT; at a low-affinity site, the capacity was 2.3-fold lower than that in the WT cell line. Donepezil and verapamil competitively inhibited [3H]L-lysine uptake in the NSC-34 cell lines. Pretreatment with pro-inflammatory cytokines decreased the uptake of [3H]L-lysine and mRNA expression levels in both cell lines; however, the addition of L-lysine restored the transport activity in the MT cell lines. L-Lysine exhibited neuroprotective effects against pro-inflammatory states in the ALS disease model cell lines. In conclusion, studying the alteration in the expression of transporters and characteristics of lysine transport in ALS can lead to the development of new therapies for neurodegenerative diseases.
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Affiliation(s)
- Sana Latif
- College of Pharmacy and Drug Information Research Institute, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Young-Sook Kang
- College of Pharmacy and Drug Information Research Institute, Sookmyung Women's University, Seoul 04310, Republic of Korea
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6
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Baumer KM, Cook CD, Zahler CT, Beard AA, Chen Z, Koone JC, Dashnaw CM, Villacob RA, Solouki T, Wood JL, Borchelt DR, Shaw BF. Supercharging Prions via Amyloid‐Selective Lysine Acetylation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Katelyn M. Baumer
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | | | - Collin T. Zahler
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | | | - Zhijuan Chen
- Department of Neuroscience University of Florida Gainesville FL USA
| | - Jordan C. Koone
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | - Chad M. Dashnaw
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | - Raul A. Villacob
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | - John L. Wood
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | | | - Bryan F. Shaw
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
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7
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Baumer KM, Cook CD, Zahler CT, Beard AA, Chen Z, Koone JC, Dashnaw CM, Villacob RA, Solouki T, Wood JL, Borchelt DR, Shaw BF. Supercharging Prions via Amyloid-Selective Lysine Acetylation. Angew Chem Int Ed Engl 2021; 60:15069-15079. [PMID: 33876528 DOI: 10.1002/anie.202103548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 11/10/2022]
Abstract
Repulsive electrostatic forces between prion-like proteins are a barrier against aggregation. In neuropharmacology, however, a prion's net charge (Z) is not a targeted parameter. Compounds that selectively boost prion Z remain unreported. Here, we synthesized compounds that amplified the negative charge of misfolded superoxide dismutase-1 (SOD1) by acetylating lysine-NH3 + in amyloid-SOD1, without acetylating native-SOD1. Compounds resembled a "ball and chain" mace: a rigid amyloid-binding "handle" (benzothiazole, stilbene, or styrylpyridine); an aryl ester "ball"; and a triethylene glycol chain connecting ball to handle. At stoichiometric excess, compounds acetylated up to 9 of 11 lysine per misfolded subunit (ΔZfibril =-8100 per 103 subunits). Acetylated amyloid-SOD1 seeded aggregation more slowly than unacetylated amyloid-SOD1 in vitro and organotypic spinal cord (these effects were partially due to compound binding). Compounds exhibited reactivity with other amyloid and non-amyloid proteins (e.g., fibrillar α-synuclein was peracetylated; serum albumin was partially acetylated; carbonic anhydrase was largely unacetylated).
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Affiliation(s)
- Katelyn M Baumer
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Christopher D Cook
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Collin T Zahler
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Alexandra A Beard
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Zhijuan Chen
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
| | - Jordan C Koone
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Chad M Dashnaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Raul A Villacob
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - John L Wood
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - David R Borchelt
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
| | - Bryan F Shaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
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8
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Dashnaw CM, Koone JC, Abdolvahabi A, Shaw BF. Measuring how two proteins affect each other's net charge in a crowded environment. Protein Sci 2021; 30:1594-1605. [PMID: 33928693 DOI: 10.1002/pro.4092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/23/2021] [Indexed: 12/19/2022]
Abstract
Theory predicts that the net charge (Z) of a protein can be altered by the net charge of a neighboring protein as the two approach one another below the Debye length. This type of charge regulation suggests that a protein's charge and perhaps function might be affected by neighboring proteins without direct binding. Charge regulation during protein crowding has never been directly measured due to analytical challenges. Here, we show that lysine specific protein crosslinkers (NHS ester-Staudinger pairs) can be used to mimic crowding by linking two non-interacting proteins at a maximal distance of ~7.9 Å. The net charge of the regioisomeric dimers and preceding monomers can then be determined with lysine-acyl "protein charge ladders" and capillary electrophoresis. As a proof of concept, we covalently linked myoglobin (Zmonomer = -0.43 ± 0.01) and α-lactalbumin (Zmonomer = -4.63 ± 0.05). Amide hydrogen/deuterium exchange and circular dichroism spectroscopy demonstrated that crosslinking did not significantly alter the structure of either protein or result in direct binding (thus mimicking crowding). Ultimately, capillary electrophoretic analysis of the dimeric charge ladder detected a change in charge of ΔZ = -0.04 ± 0.09 upon crowding by this pair (Zdimer = -5.10 ± 0.07). These small values of ΔZ are not necessarily general to protein crowding (qualitatively or quantitatively) but will vary per protein size, charge, and solvent conditions.
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Affiliation(s)
- Chad M Dashnaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Jordan C Koone
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Alireza Abdolvahabi
- Mass Spectrometry Core Facility, School of Pharmacy, University of Southern California, Los Angeles, California, USA
| | - Bryan F Shaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
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9
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Trist BG, Hilton JB, Hare DJ, Crouch PJ, Double KL. Superoxide Dismutase 1 in Health and Disease: How a Frontline Antioxidant Becomes Neurotoxic. Angew Chem Int Ed Engl 2021; 60:9215-9246. [PMID: 32144830 PMCID: PMC8247289 DOI: 10.1002/anie.202000451] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Indexed: 12/11/2022]
Abstract
Cu/Zn superoxide dismutase (SOD1) is a frontline antioxidant enzyme catalysing superoxide breakdown and is important for most forms of eukaryotic life. The evolution of aerobic respiration by mitochondria increased cellular production of superoxide, resulting in an increased reliance upon SOD1. Consistent with the importance of SOD1 for cellular health, many human diseases of the central nervous system involve perturbations in SOD1 biology. But far from providing a simple demonstration of how disease arises from SOD1 loss-of-function, attempts to elucidate pathways by which atypical SOD1 biology leads to neurodegeneration have revealed unexpectedly complex molecular characteristics delineating healthy, functional SOD1 protein from that which likely contributes to central nervous system disease. This review summarises current understanding of SOD1 biology from SOD1 genetics through to protein function and stability.
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Affiliation(s)
- Benjamin G. Trist
- Brain and Mind Centre and Discipline of PharmacologyThe University of Sydney, CamperdownSydneyNew South Wales2050Australia
| | - James B. Hilton
- Department of Pharmacology and TherapeuticsThe University of MelbourneParkvilleVictoria3052Australia
| | - Dominic J. Hare
- Brain and Mind Centre and Discipline of PharmacologyThe University of Sydney, CamperdownSydneyNew South Wales2050Australia
- School of BioSciencesThe University of MelbourneParkvilleVictoria3052Australia
- Atomic Medicine InitiativeThe University of Technology SydneyBroadwayNew South Wales2007Australia
| | - Peter J. Crouch
- Department of Pharmacology and TherapeuticsThe University of MelbourneParkvilleVictoria3052Australia
| | - Kay L. Double
- Brain and Mind Centre and Discipline of PharmacologyThe University of Sydney, CamperdownSydneyNew South Wales2050Australia
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10
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Trist BG, Hilton JB, Hare DJ, Crouch PJ, Double KL. Superoxide Dismutase 1 in Health and Disease: How a Frontline Antioxidant Becomes Neurotoxic. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Benjamin G. Trist
- Brain and Mind Centre and Discipline of Pharmacology The University of Sydney, Camperdown Sydney New South Wales 2050 Australia
| | - James B. Hilton
- Department of Pharmacology and Therapeutics The University of Melbourne Parkville Victoria 3052 Australia
| | - Dominic J. Hare
- Brain and Mind Centre and Discipline of Pharmacology The University of Sydney, Camperdown Sydney New South Wales 2050 Australia
- School of BioSciences The University of Melbourne Parkville Victoria 3052 Australia
- Atomic Medicine Initiative The University of Technology Sydney Broadway New South Wales 2007 Australia
| | - Peter J. Crouch
- Department of Pharmacology and Therapeutics The University of Melbourne Parkville Victoria 3052 Australia
| | - Kay L. Double
- Brain and Mind Centre and Discipline of Pharmacology The University of Sydney, Camperdown Sydney New South Wales 2050 Australia
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11
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McAlary L, Chew YL, Lum JS, Geraghty NJ, Yerbury JJ, Cashman NR. Amyotrophic Lateral Sclerosis: Proteins, Proteostasis, Prions, and Promises. Front Cell Neurosci 2020; 14:581907. [PMID: 33328890 PMCID: PMC7671971 DOI: 10.3389/fncel.2020.581907] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is characterized by the progressive degeneration of the motor neurons that innervate muscle, resulting in gradual paralysis and culminating in the inability to breathe or swallow. This neuronal degeneration occurs in a spatiotemporal manner from a point of onset in the central nervous system (CNS), suggesting that there is a molecule that spreads from cell-to-cell. There is strong evidence that the onset and progression of ALS pathology is a consequence of protein misfolding and aggregation. In line with this, a hallmark pathology of ALS is protein deposition and inclusion formation within motor neurons and surrounding glia of the proteins TAR DNA-binding protein 43, superoxide dismutase-1, or fused in sarcoma. Collectively, the observed protein aggregation, in conjunction with the spatiotemporal spread of symptoms, strongly suggests a prion-like propagation of protein aggregation occurs in ALS. In this review, we discuss the role of protein aggregation in ALS concerning protein homeostasis (proteostasis) mechanisms and prion-like propagation. Furthermore, we examine the experimental models used to investigate these processes, including in vitro assays, cultured cells, invertebrate models, and murine models. Finally, we evaluate the therapeutics that may best prevent the onset or spread of pathology in ALS and discuss what lies on the horizon for treating this currently incurable disease.
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Affiliation(s)
- Luke McAlary
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Yee Lian Chew
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Jeremy Stephen Lum
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Nicholas John Geraghty
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Justin John Yerbury
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Neil R. Cashman
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
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Abstract
The misfolding, aggregation, and deposition of specific proteins is the key hallmark of most progressive neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis (ALS). ALS is characterized by the rapid and progressive degenerations of motor neurons in the spinal cord and motor cortex, resulting in paralysis of those who suffer from it. Pathologically, there are three major aggregating proteins associated with ALS, including TAR DNA-binding protein of 43kDa (TDP-43), superoxide dismutase-1 (SOD1), and fused in sarcoma (FUS). While there are ALS-associated mutations found in each of these proteins, the most prevalent aggregation pathology is that of wild-type TDP-43 (97% of cases), with the remaining split between mutant forms of SOD1 (~2%) and FUS (~1%). Considering the progressive nature of ALS and its association with the aggregation of specific proteins, a growing notion is that the spread of pathology and symptoms can be explained by a prion-like mechanism. Prion diseases are a group of highly infectious neurodegenerative disorders caused by the misfolding, aggregation, and spread of a transmissible conformer of prion protein (PrP). Pathogenic PrP is capable of converting healthy PrP into a toxic form through template-directed misfolding. Application of this finding to other neurodegenerative disorders, and in particular ALS, has revolutionized our understanding of cause and progression of these disorders. In this chapter, we first provide a background on ALS pathology and genetic origin. We then detail and discuss the evidence supporting a prion-like propagation of protein misfolding and aggregation in ALS with a particular focus on SOD1 and TDP-43 as these are the most well-established models in the field.
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Affiliation(s)
- L McAlary
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia; Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - J J Yerbury
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia; Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - N R Cashman
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada.
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13
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Dantas LS, Viviani LG, Inague A, Piccirillo E, Rezende LD, Ronsein GE, Augusto O, Medeiros MHG, Amaral ATD, Miyamoto S. Lipid aldehyde hydrophobicity affects apo-SOD1 modification and aggregation. Free Radic Biol Med 2020; 156:157-167. [PMID: 32598986 DOI: 10.1016/j.freeradbiomed.2020.05.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/30/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022]
Abstract
Unsaturated lipids are oxidized by reactive oxygen species and enzymes, leading to the increased formation of lipid hydroperoxides and several electrophilic products. Lipid-derived electrophiles can modify macromolecules, such as proteins, resulting in the loss of function and/or aggregation. The accumulation of Cu,Zn-superoxide dismutase (SOD1) aggregates has been associated with familial cases of amyotrophic lateral sclerosis (ALS). The protein aggregation mechanisms in motor neurons remain unclear, although recent studies have shown that lipids and oxidized lipid derivatives may play roles in this process. Here, we aimed to compare the effects of different lipid aldehydes on the induction of SOD1 modifications and aggregation, in vitro. Human recombinant apo-SOD1 was incubated with 4-hydroxy-2-hexenal (HHE), 4-hydroxy-2-nonenal (HNE), 2-hexen-1-al (HEX), 2,4-nonadienal (NON), 2,4-decadienal (DEC), or secosterol aldehydes (SECO-A or SECO-B). High-molecular-weight apo-SOD1 aggregates dramatically increased in the presence of highly hydrophobic aldehydes (LogPcalc > 3). Notably, several Lys residues were modified by exposure to all aldehydes. The observed modifications were primarily observed on Lys residues located near the dimer interface (K3 and K9) and at the electrostatic loop (K122, K128, and K136). Moreover, HHE and HNE induced extensive apo-SOD1 modifications, by forming Schiff bases or Michael adducts with Lys, His, and Cys residues. However, these aldehydes were unable to induce large protein aggregates. Overall, our data shed light on the importance of lipid aldehyde hydrophobicity on the induction of apo-SOD1 aggregation and identified preferential sites of lipid aldehyde-induced modifications.
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Affiliation(s)
- Lucas S Dantas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Lucas G Viviani
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Alex Inague
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Erika Piccirillo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil; Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Leandro de Rezende
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Graziella E Ronsein
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ohara Augusto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Marisa H G Medeiros
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Antonia T do Amaral
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Sayuri Miyamoto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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Pineau H, Sim V. POSCAbilities: The Application of the Prion Organotypic Slice Culture Assay to Neurodegenerative Disease Research. Biomolecules 2020; 10:E1079. [PMID: 32698402 DOI: 10.3390/biom10071079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/06/2020] [Accepted: 07/16/2020] [Indexed: 12/14/2022] Open
Abstract
Prion diseases are fatal, transmissible neurodegenerative disorders whose pathogenesis is driven by the misfolding, self-templating and cell-to-cell spread of the prion protein. Other neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis and Huntington’s disease, share some of these prion-like features, with different aggregation-prone proteins. Consequently, researchers have begun to apply prion-specific techniques, like the prion organotypic slice culture assay (POSCA), to these disorders. In this review we explore the ways in which the prion phenomenon has been used in organotypic cultures to study neurodegenerative diseases from the perspective of protein aggregation and spreading, strain propagation, the role of glia in pathogenesis, and efficacy of drug treatments. We also present an overview of the advantages and disadvantages of this culture system compared to in vivo and in vitro models and provide suggestions for new directions.
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15
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Mercado-Uribe H, Andrade-Medina M, Espinoza-Rodríguez JH, Carrillo-Tripp M, Scheckhuber CQ. Analyzing structural alterations of mitochondrial intermembrane space superoxide scavengers cytochrome-c and SOD1 after methylglyoxal treatment. PLoS One 2020; 15:e0232408. [PMID: 32353034 PMCID: PMC7192434 DOI: 10.1371/journal.pone.0232408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/14/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are quantitatively the most important sources of reactive oxygen species (ROS) which are formed as by-products during cellular respiration. ROS generation occurs when single electrons are transferred to molecular oxygen. This leads to a number of different ROS types, among them superoxide. Although most studies focus on ROS generation in the mitochondrial matrix, the intermembrane space (IMS) is also important in this regard. The main scavengers for the detoxification of superoxide in the IMS are Cu, Zn superoxide dismutase (SOD1) and cytochrome-c. Similar to ROS, certain reactive carbonyl species are known for their high reactivity. The consequences are deleterious modifications to essential components compromising cellular functions and contributing to the etiology of severe pathological conditions like cancer, diabetes and neurodegeneration. In this study, we investigated the susceptibility of SOD1 and cytochrome-c to in vitro glycation by the dicarbonyl methylglyoxal (MGO) and the resulting effects on their structure. We utilized experimental techniques like immunodetection of the MGO-mediated modification 5-hydro-5-methylimidazolone, differential scanning calorimetry, fluorescence emission and circular dichroism measurements. We found that glycation of cytochrome-c leads to monomer aggregation, an altered secondary structure (increase in alpha helical content) and slightly more compact folding. In addition to structural changes, glycated cytochrome-c displays an altered thermal unfolding behavior. Subjecting SOD1 to MGO does not influence its secondary structure. However, similar to cytochrome-c, subunit aggregation is observed under denaturating conditions. Furthermore, the appearance of a second peak in the calorimetry diagram indirectly suggests de-metallation of SOD1 when high MGO levels are used. In conclusion, our data demonstrate that MGO has the potential to alter several structural parameters in important proteins of energy metabolism (cytochrome-c) and antioxidant defense (cytochrome-c, SOD1).
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Affiliation(s)
- Hilda Mercado-Uribe
- Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional Unidad Monterrey, Parque PIIT, Apodaca, Nuevo León, México
| | - Mariana Andrade-Medina
- Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional Unidad Monterrey, Parque PIIT, Apodaca, Nuevo León, México
| | | | - Mauricio Carrillo-Tripp
- Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional Unidad Monterrey, Parque PIIT, Apodaca, Nuevo León, México
| | - Christian Quintus Scheckhuber
- Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional Unidad Monterrey, Parque PIIT, Apodaca, Nuevo León, México
- * E-mail:
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16
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Schaffert LN, Carter WG. Do Post-Translational Modifications Influence Protein Aggregation in Neurodegenerative Diseases: A Systematic Review. Brain Sci 2020; 10:E232. [PMID: 32290481 DOI: 10.3390/brainsci10040232] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
The accumulation of abnormal protein aggregates represents a universal hallmark of neurodegenerative diseases (NDDs). Post-translational modifications (PTMs) regulate protein structure and function. Dysregulated PTMs may influence the propensity for protein aggregation in NDD-proteinopathies. To investigate this, we systematically reviewed the literature to evaluate effects of PTMs on aggregation propensity for major proteins linked to the pathogenesis and/or progression of NDDs. A search of PubMed, MEDLINE, EMBASE, and Web of Science Core Collection was conducted to retrieve studies that investigated an association between PTMs and protein aggregation in seven NDDs: Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), amyotrophic lateral sclerosis (ALS), spinocerebellar ataxias, transmissible spongiform encephalopathy, and multiple sclerosis. Together, 1222 studies were identified, of which 69 met eligibility criteria. We identified that the following PTMs, in isolation or combination, potentially act as modulators of proteinopathy in NDDs: isoaspartate formation in Aβ, phosphorylation of Aβ or tau in AD; acetylation, 4-hydroxy-2-neonal modification, O-GlcNAcylation or phosphorylation of α-synuclein in PD; acetylation or phosphorylation of TAR DNA-binding protein-43 in ALS, and SUMOylation of superoxide dismutase-1 in ALS; and phosphorylation of huntingtin in HD. The potential pharmacological manipulation of these aggregation-modulating PTMs represents an as-yet untapped source of therapy to treat NDDs.
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Abstract
Few proteins have come under such intense scrutiny as superoxide dismutase-1 (SOD1). For almost a century, scientists have dissected its form, function and then later its malfunction in the neurodegenerative disease amyotrophic lateral sclerosis (ALS). We now know SOD1 is a zinc and copper metalloenzyme that clears superoxide as part of our antioxidant defence and respiratory regulation systems. The possibility of reduced structural integrity was suggested by the first crystal structures of human SOD1 even before deleterious mutations in the sod1 gene were linked to the ALS. This concept evolved in the intervening years as an impressive array of biophysical studies examined the characteristics of mutant SOD1 in great detail. We now recognise how ALS-related mutations perturb the SOD1 maturation processes, reduce its ability to fold and reduce its thermal stability and half-life. Mutant SOD1 is therefore predisposed to monomerisation, non-canonical self-interactions, the formation of small misfolded oligomers and ultimately accumulation in the tell-tale insoluble inclusions found within the neurons of ALS patients. We have also seen that several post-translational modifications could push wild-type SOD1 down this toxic pathway. Recently we have come to view ALS as a prion-like disease where both the symptoms, and indeed SOD1 misfolding itself, are transmitted to neighbouring cells. This raises the possibility of intervention after the initial disease presentation. Several small-molecule and biologic-based strategies have been devised which directly target the SOD1 molecule to change the behaviour thought to be responsible for ALS. Here we provide a comprehensive review of the many biophysical advances that sculpted our view of SOD1 biology and the recent work that aims to apply this knowledge for therapeutic outcomes in ALS.
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18
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Abstract
SOD1 is commonly known for its ROS scavenging activity, but recent work has uncovered additional roles in modulating metabolism, maintaining redox balance, and regulating transcription. This new paradigm of expanded SOD1 function raises questions regarding the regulation of SOD1 and the cellular partitioning of its biological roles. Despite decades of research on SOD1, much of which focuses on its pathogenic role in amyotrophic lateral sclerosis, relatively little is known about its regulation by post-translational modifications (PTMs). However, over the last decade, advancements in mass spectrometry have led to a boom in PTM discovery across the proteome, which has also revealed new mechanisms of SOD1 regulation by PTMs and an array of SOD1 PTMs with high likelihood of biological function. In this review, we address emerging mechanisms of SOD1 regulation by post-translational modifications, many of which begin to shed light on how the various functions of SOD1 are regulated within the cell.
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Affiliation(s)
- C J Banks
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - J L Andersen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
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Zhang W, Wu H, Zhang R, Fang X, Xu W. Structure and effective charge characterization of proteins by a mobility capillary electrophoresis based method. Chem Sci 2019; 10:7779-7787. [PMID: 31588326 PMCID: PMC6761862 DOI: 10.1039/c9sc02039j] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/02/2019] [Indexed: 12/18/2022] Open
Abstract
The integration of Taylor dispersion analysis (TDA) into mobility capillary electrophoresis allows protein separation, effective charge and hydrodynamic radius measurements.
Measuring the conformations and effective charges of proteins in solution is critical for investigating protein bioactivity, but their rapid analysis remains a challenging problem. Here we report a mobility capillary electrophoresis (MCE) based method for the rapid analysis of protein stereo-structures and effective charges in different solution environments. With the capability of mixture separation, MCE measures the hydrodynamic radius of a protein through Taylor dispersion analysis and its effective charge through ion mobility analysis. The experimental results acquired from MCE are then utilized to restrain molecular dynamics simulations, so that the most probable conformation of that protein can be obtained. As proof-of-concept demonstrations, the charge states and structures of five proteins were analyzed under close to native environments. The conformation transitions and charge state variations of bovine serum albumin and lysozyme under different pH conditions were also investigated. This method is promising for high-throughput protein analysis, which could potentially be coupled with mass spectrometry for investigating protein stereo-structures and functions in top-down proteomics.
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Affiliation(s)
- Wenjing Zhang
- School of Life Science , Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian Dist , Beijing , China .
| | - Haimei Wu
- School of Life Science , Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian Dist , Beijing , China .
| | - Rongkai Zhang
- School of Life Science , Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian Dist , Beijing , China .
| | - Xiang Fang
- National Institute of Metrology , No. 18, Bei San Huan Dong Lu, Chaoyang Dist , Beijing , China
| | - Wei Xu
- School of Life Science , Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian Dist , Beijing , China .
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20
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Wang W, Wu S, Wang J, Li Z, Cui H, Lin S, Zhu J, Chen Q. Superoxide dismutase transcellular shuttle constructed from dendritic MOF and charge reversible protein derivatives. Chem Sci 2019; 10:4476-4485. [PMID: 31057775 PMCID: PMC6482591 DOI: 10.1039/c8sc04160a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 03/07/2019] [Indexed: 11/21/2022] Open
Abstract
The development of molecular biology has led to the identification of protein-based therapeutics as an intriguing approach for the treatment of a wide range of diseases. To manufacture transcellular protein delivery shuttles, we attempted charge reversal chemistry on native proteins [e.g., superoxide dismutase (SOD): an enzyme capable of scavenging detrimental reactive oxygen species] by the selective conversion of the positively charged amino residues of native SOD to conjugated negatively charged citraconic moieties, eliciting overall negatively charged polyelectrolytes for the subsequent electrostatic self-assembly with cationic metal-organic framework (MOF) derivatives into protein delivery systems. Please note that the charge conversion was reversible, restoring the original amino groups in intracellular acidic endosome compartments (pH 5), which afforded facile charge reversible functions to reclaim the active SOD in the cell interior. In particular, the strategic manufacture of dendritic MOF supramolecular architectures as transcellular shuttles for the aforementioned charge-reversible SOD derivatives is noteworthy. The MOF was surface-functionalized with several polycationic segments, thus contributing to the hyper-charged architecture for the easy accommodation of the negatively charged SOD derivatives. Consequently, the SOD derivatives managed to internalize into cells by hitchhiking via endocytosis of the positively charged MOF. Once they resided in the acidic endosomes, the charge reversal of the SOD derivatives could occur smoothly and result in reduced interactions between the charged-reversed SOD and MOF, leading to the release of active SOD. Simultaneously, the dendritic MOF due to protein release presented a highly positive-charged architecture to provoke endosome membrane disruption, consequently spurring the translocation of SOD to the cytosol for the execution of its enzymatic activities. Herein, the intracellular ROS level of the activated macrophages was validated to be markedly suppressed by our proposed transcellular SOD shuttles, thereby indicating their wide availability to diverse functional proteins for biomedical applications.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Fine Chemicals , Dalian University of Technology , No. 2 Linggong Road , Dalian 116024 , China .
- School of Life Science and Biotechnology , Dalian University of Technology , No. 2 Linggong Road , Dalian 116024 , China
| | - Sudong Wu
- Academy for Advanced Interdisciplinary Studies , Southern University of Science and Technology , Shenzhen 518055 , China
- Department of Materials Science and Engineering , Southern University of Science and Technology , Shenzhen 518055 , China
| | - Jingyun Wang
- State Key Laboratory of Fine Chemicals , Dalian University of Technology , No. 2 Linggong Road , Dalian 116024 , China .
- School of Life Science and Biotechnology , Dalian University of Technology , No. 2 Linggong Road , Dalian 116024 , China
| | - Zhen Li
- College of Pharmacy , Dalian Medical University , No. 9 West Section Lvshun South Road , Dalian 116044 , China
| | - Hongyan Cui
- School of Life Science and Biotechnology , Dalian University of Technology , No. 2 Linggong Road , Dalian 116024 , China
| | - Shuseng Lin
- School of Life Science and Biotechnology , Dalian University of Technology , No. 2 Linggong Road , Dalian 116024 , China
| | - Jingyi Zhu
- School of Life Science and Biotechnology , Dalian University of Technology , No. 2 Linggong Road , Dalian 116024 , China
| | - Qixian Chen
- State Key Laboratory of Fine Chemicals , Dalian University of Technology , No. 2 Linggong Road , Dalian 116024 , China .
- School of Life Science and Biotechnology , Dalian University of Technology , No. 2 Linggong Road , Dalian 116024 , China
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Kumar Ghosh D, Nanaji Shrikondawar A, Ranjan A. Local structural unfolding at the edge-strands of beta sheets is the molecular basis for instability and aggregation of G85R and G93A mutants of superoxide dismutase 1. J Biomol Struct Dyn 2019; 38:647-659. [DOI: 10.1080/07391102.2019.1584125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Debasish Kumar Ghosh
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Akshaykumar Nanaji Shrikondawar
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, India
- Graduate Studies, Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Akash Ranjan
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, India
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22
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Abdolvahabi A, Rasouli S, Croom CM, Plewman DL. High-Throughput Microplate-Based Fluorescence Assays for Studying Stochastic Aggregation of Superoxide Dismutase-1. Methods Mol Biol 2019; 1873:93-108. [PMID: 30341605 DOI: 10.1007/978-1-4939-8820-4_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Investigating in vitro kinetics of superoxide dismutase-1 (SOD1) aggregation with high-throughput microplate-based assays provides valuable information regarding SOD1 pathogenesis in amyotrophic lateral sclerosis (ALS) and opens venues for the development of effective therapies. In this chapter, we first explain the step-by-step purification and demetallation of wild-type (WT) and ALS-variant SOD1 proteins from Saccharomyces cerevisiae (baker's yeast). We then describe the methodology for a microplate-based fluorescence assay that is used to study real-time kinetics of metal-free (apo)-SOD1 aggregation. This technique is highly sensitive, semiautomated, requires minimum modifications to protein, and produces a plethora of data in a short period of time. We also describe a new approach for extracting clinically relevant information from SOD1 aggregation data using Kaplan-Meier estimators.
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Affiliation(s)
- Alireza Abdolvahabi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Sanaz Rasouli
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
- Institute of Biomedical Studies, Baylor University, Waco, TX, USA
| | - Corbin M Croom
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Devon L Plewman
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
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23
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Pokrishevsky E, McAlary L, Farrawell NE, Zhao B, Sher M, Yerbury JJ, Cashman NR. Tryptophan 32-mediated SOD1 aggregation is attenuated by pyrimidine-like compounds in living cells. Sci Rep 2018; 8:15590. [PMID: 30349065 PMCID: PMC6197196 DOI: 10.1038/s41598-018-32835-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/14/2018] [Indexed: 12/19/2022] Open
Abstract
Over 160 mutations in superoxide dismutase 1 (SOD1) are associated with familial amyotrophic lateral sclerosis (fALS), where the main pathological feature is deposition of SOD1 into proteinaceous cytoplasmic inclusions. We previously showed that the tryptophan residue at position 32 (W32) mediates the prion-like propagation of SOD1 misfolding in cells, and that a W32S substitution blocks this phenomenon. Here, we used in vitro protein assays to demonstrate that a W32S substitution in SOD1-fALS mutants significantly diminishes their propensity to aggregate whilst paradoxically decreasing protein stability. We also show SOD1-W32S to be resistant to seeded aggregation, despite its high abundance of unfolded protein. A cell-based aggregation assay demonstrates that W32S substitution significantly mitigates inclusion formation. Furthermore, this assay reveals that W32 in SOD1 is necessary for the formation of a competent seed for aggregation under these experimental conditions. Following the observed importance of W32 for aggregation, we established that treatment of living cells with the W32-interacting 5-Fluorouridine (5-FUrd), and its FDA approved analogue 5-Fluorouracil (5-FU), substantially attenuate inclusion formation similarly to W32S substitution. Altogether, we highlight W32 as a significant contributor to SOD1 aggregation, and propose that 5-FUrd and 5-FU present promising lead drug candidates for the treatment of SOD1-associated ALS.
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Affiliation(s)
- Edward Pokrishevsky
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Luke McAlary
- Faculty of Science Medicine and Health, University of Wollongong, Wollongong, NSW, 2522, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Natalie E Farrawell
- Faculty of Science Medicine and Health, University of Wollongong, Wollongong, NSW, 2522, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Beibei Zhao
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Mine Sher
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Justin J Yerbury
- Faculty of Science Medicine and Health, University of Wollongong, Wollongong, NSW, 2522, Australia. .,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia.
| | - Neil R Cashman
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
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Rasouli S, Abdolvahabi A, Croom CM, Plewman DL, Shi Y, Shaw BF. Glycerolipid Headgroups Control Rate and Mechanism of Superoxide Dismutase-1 Aggregation and Accelerate Fibrillization of Slowly Aggregating Amyotrophic Lateral Sclerosis Mutants. ACS Chem Neurosci 2018; 9:1743-1756. [PMID: 29649360 DOI: 10.1021/acschemneuro.8b00086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Interactions between superoxide dismutase-1 (SOD1) and lipid membranes might be directly involved in the toxicity and intercellular propagation of aggregated SOD1 in amyotrophic lateral sclerosis (ALS), but the chemical details of lipid-SOD1 interactions and their effects on SOD1 aggregation remain unclear. This paper determined the rate and mechanism of nucleation of fibrillar apo-SOD1 catalyzed by liposomal surfaces with identical hydrophobic chains (RCH2(O2C18H33)2), but headgroups of different net charge and hydrophobicity (i.e., R(CH2)N+(CH3)3, RPO4-(CH2)2N+(CH3)3, and RPO4-). Under semiquiescent conditions (within a 96 well microplate, without a gyrating bead), the aggregation of apo-SOD1 into thioflavin-T-positive (ThT(+)) amyloid fibrils did not occur over 120 h in the absence of liposomal surfaces. Anionic liposomes triggered aggregation of apo-SOD1 into ThT(+) amyloid fibrils; cationic liposomes catalyzed fibrillization but at slower rates and across a narrower lipid concentration; zwitterionic liposomes produced nonfibrillar (amorphous) aggregates. The inability of zwitterionic liposomes to catalyze fibrillization and the dependence of fibrillization rate on anionic lipid concentration suggests that membranes catalyze SOD1 fibrillization by a primary nucleation mechanism. Membrane-catalyzed fibrillization was also examined for eight ALS variants of apo-SOD1, including G37R, G93R, D90A, and E100G apo-SOD1 that nucleate slower than or equal to WT SOD1 in lipid-free, nonquiescent amyloid assays. All ALS variants (with one exception) nucleated faster than WT SOD1 in the presence of anionic liposomes, wherein the greatest acceleratory effects were observed among variants with lower net negative surface charge (G37R, G93R, D90A, E100G). The exception was H46R apo-SOD1, which did not form ThT(+) species.
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Affiliation(s)
- Sanaz Rasouli
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
- Institute of Biomedical Studies, Baylor University, Waco, Texas 76706, United States
| | - Alireza Abdolvahabi
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Corbin M. Croom
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Devon L. Plewman
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Yunhua Shi
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Bryan F. Shaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
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25
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Zahler CT, Zhou H, Abdolvahabi A, Holden RL, Rasouli S, Tao P, Shaw BF. Direct Measurement of Charge Regulation in Metalloprotein Electron Transfer. Angew Chem Int Ed Engl 2018; 57:5364-5368. [PMID: 29451960 PMCID: PMC6033162 DOI: 10.1002/anie.201712306] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/15/2018] [Indexed: 12/16/2022]
Abstract
Determining whether a protein regulates its net electrostatic charge during electron transfer (ET) will deepen our mechanistic understanding of how polypeptides tune rates and free energies of ET (e.g., by affecting reorganization energy, and/or redox potential). Charge regulation during ET has never been measured for proteins because few tools exist to measure the net charge of a folded protein in solution at different oxidation states. Herein, we used a niche analytical tool (protein charge ladders analyzed with capillary electrophoresis) to determine that the net charges of myoglobin, cytochrome c, and azurin change by 0.62±0.06, 1.19±0.02, and 0.51±0.04 units upon single ET. Computational analysis predicts that these fluctuations in charge arise from changes in the pKa values of multiple non-coordinating residues (predominantly histidine) that involve between 0.42-0.90 eV. These results suggest that ionizable residues can tune the reactivity of redox centers by regulating the net charge of the entire protein-cofactor-solvent complex.
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Affiliation(s)
- Collin T. Zahler
- Department of Chemistry and BiochemistryBaylor University1301 S University Parks Dr.WacoTX76706USA
| | - Hongyu Zhou
- Department of ChemistrySouthern Methodist University6425 Boaz LaneDallasTX75205USA
| | - Alireza Abdolvahabi
- Department of Chemistry and BiochemistryBaylor University1301 S University Parks Dr.WacoTX76706USA
| | - Rebecca L. Holden
- Department of Chemistry and BiochemistryBaylor University1301 S University Parks Dr.WacoTX76706USA
| | - Sanaz Rasouli
- Department of Chemistry and BiochemistryBaylor University1301 S University Parks Dr.WacoTX76706USA
- Institute of Biomedical StudiesBaylor University1301 S University Parks Dr.WacoTX76706USA
| | - Peng Tao
- Department of ChemistrySouthern Methodist University6425 Boaz LaneDallasTX75205USA
| | - Bryan F. Shaw
- Department of Chemistry and BiochemistryBaylor University1301 S University Parks Dr.WacoTX76706USA
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26
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Zahler CT, Zhou H, Abdolvahabi A, Holden RL, Rasouli S, Tao P, Shaw BF. Direct Measurement of Charge Regulation in Metalloprotein Electron Transfer. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712306] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Collin T. Zahler
- Department of Chemistry and Biochemistry Baylor University 1301 S University Parks Dr. Waco TX 76706 USA
| | - Hongyu Zhou
- Department of Chemistry Southern Methodist University 6425 Boaz Lane Dallas TX 75205 USA
| | - Alireza Abdolvahabi
- Department of Chemistry and Biochemistry Baylor University 1301 S University Parks Dr. Waco TX 76706 USA
| | - Rebecca L. Holden
- Department of Chemistry and Biochemistry Baylor University 1301 S University Parks Dr. Waco TX 76706 USA
| | - Sanaz Rasouli
- Department of Chemistry and Biochemistry Baylor University 1301 S University Parks Dr. Waco TX 76706 USA
- Institute of Biomedical Studies Baylor University 1301 S University Parks Dr. Waco TX 76706 USA
| | - Peng Tao
- Department of Chemistry Southern Methodist University 6425 Boaz Lane Dallas TX 75205 USA
| | - Bryan F. Shaw
- Department of Chemistry and Biochemistry Baylor University 1301 S University Parks Dr. Waco TX 76706 USA
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