1
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Fleming IR, Hannan JP, Swisher GH, Tesdahl CD, Martyr JG, Cordaro NJ, Erbse AH, Falke JJ. Binding of active Ras and its mutants to the Ras binding domain of PI-3-kinase: A quantitative approach to K D measurements. Anal Biochem 2023; 663:115019. [PMID: 36526022 PMCID: PMC9884175 DOI: 10.1016/j.ab.2022.115019] [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: 10/15/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Ras family GTPases (H/K/N-Ras) modulate numerous effectors, including the lipid kinase PI3K (phosphatidylinositol-3-kinase) that generates growth signal lipid PIP3 (phosphatidylinositol-3,4,5-triphosphate). Active GTP-Ras binds PI3K with high affinity, thereby stimulating PIP3 production. We hypothesize the affinity of this binding interaction could be significantly increased or decreased by Ras mutations at PI3K contact positions, with clinical implications since some Ras mutations at PI3K contact positions are disease-linked. To enable tests of this hypothesis, we have developed an approach combining UV spectral deconvolution, HPLC, and microscale thermophoresis to quantify the KD for binding. The approach measures the total Ras concentration, the fraction of Ras in the active state, and the affinity of active Ras binding to its docking site on PI3K Ras binding domain (RBD) in solution. The approach is illustrated by KD measurements for the binding of active H-Ras and representative mutants, each loaded with GTP or GMPPNP, to PI3Kγ RBD. The findings demonstrate that quantitation of the Ras activation state increases the precision of KD measurements, while also revealing that Ras mutations can increase (Q25L), decrease (D38E, Y40C), or have no effect (G13R) on PI3K binding affinity. Significant Ras affinity changes are predicted to alter PI3K regulation and PIP3 growth signals.
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Affiliation(s)
- Ian R Fleming
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Jonathan P Hannan
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - George Hayden Swisher
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Corey D Tesdahl
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Justin G Martyr
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Nicholas J Cordaro
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Annette H Erbse
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Joseph J Falke
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA.
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2
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Leonard AC, Weinstein JJ, Steiner PJ, Erbse AH, Fleishman SJ, Whitehead TA. Stabilization of the SARS-CoV-2 receptor binding domain by protein core redesign and deep mutational scanning. Protein Eng Des Sel 2022; 35:6553331. [PMID: 35325236 PMCID: PMC9077414 DOI: 10.1093/protein/gzac002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 11/22/2021] [Revised: 01/21/2022] [Accepted: 02/16/2022] [Indexed: 11/12/2022] Open
Abstract
Stabilizing antigenic proteins as vaccine immunogens or diagnostic reagents is a stringent case of protein engineering and design as the exterior surface must maintain recognition by receptor(s) and antigen-specific antibodies at multiple distinct epitopes. This is a challenge, as stability enhancing mutations must be focused on the protein core, whereas successful computational stabilization algorithms typically select mutations at solvent-facing positions. In this study, we report the stabilization of SARS-CoV-2 Wuhan Hu-1 Spike receptor binding domain using a combination of deep mutational scanning and computational design, including the FuncLib algorithm. Our most successful design encodes I358F, Y365W, T430I, and I513L receptor binding domain mutations, maintains recognition by the receptor ACE2 and a panel of different anti-receptor binding domain monoclonal antibodies, is between 1 and 2°C more thermally stable than the original receptor binding domain using a thermal shift assay, and is less proteolytically sensitive to chymotrypsin and thermolysin than the original receptor binding domain. Our approach could be applied to the computational stabilization of a wide range of proteins without requiring detailed knowledge of active sites or binding epitopes. We envision that this strategy may be particularly powerful for cases when there are multiple or unknown binding sites.
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Affiliation(s)
- Alison C Leonard
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80303, USA
| | - Jonathan J Weinstein
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Paul J Steiner
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80303, USA
| | - Annette H Erbse
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
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3
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Rudolph J, Muthurajan UM, Palacio M, Mahadevan J, Roberts G, Erbse AH, Dyer PN, Luger K. The BRCT domain of PARP1 binds intact DNA and mediates intrastrand transfer. Mol Cell 2021; 81:4994-5006.e5. [PMID: 34919819 PMCID: PMC8769213 DOI: 10.1016/j.molcel.2021.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 06/07/2021] [Revised: 09/15/2021] [Accepted: 11/12/2021] [Indexed: 12/18/2022]
Abstract
PARP1 is a key player in the response to DNA damage and is the target of clinical inhibitors for the treatment of cancers. Binding of PARP1 to damaged DNA leads to activation wherein PARP1 uses NAD+ to add chains of poly(ADP-ribose) onto itself and other nuclear proteins. PARP1 also binds abundantly to intact DNA and chromatin, where it remains enzymatically inactive. We show that intact DNA makes contacts with the PARP1 BRCT domain, which was not previously recognized as a DNA-binding domain. This binding mode does not result in the concomitant reorganization and activation of the catalytic domain. We visualize the BRCT domain bound to nucleosomal DNA by cryogenic electron microscopy and identify a key motif conserved from ancestral BRCT domains for binding phosphates on DNA and phospho-peptides. Finally, we demonstrate that the DNA-binding properties of the BRCT domain contribute to the "monkey-bar mechanism" that mediates DNA transfer of PARP1.
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Affiliation(s)
- Johannes Rudolph
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Uma M Muthurajan
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Megan Palacio
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Jyothi Mahadevan
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Genevieve Roberts
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Annette H Erbse
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Pamela N Dyer
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA.
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4
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Leonard AC, Weinstein JJ, Steiner PJ, Erbse AH, Fleishman SJ, Whitehead TA. Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning.. [PMID: 34845448 PMCID: PMC8629191 DOI: 10.1101/2021.11.22.469552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Stabilizing antigenic proteins as vaccine immunogens or diagnostic reagents is a stringent case of protein engineering and design as the exterior surface must maintain recognition by receptor(s) and antigen—specific antibodies at multiple distinct epitopes. This is a challenge, as stability-enhancing mutations must be focused on the protein core, whereas successful computational stabilization algorithms typically select mutations at solvent-facing positions. In this study we report the stabilization of SARS-CoV-2 Wuhan Hu-1 Spike receptor binding domain (S RBD) using a combination of deep mutational scanning and computational design, including the FuncLib algorithm. Our most successful design encodes I358F, Y365W, T430I, and I513L RBD mutations, maintains recognition by the receptor ACE2 and a panel of different anti-RBD monoclonal antibodies, is between 1–2°C more thermally stable than the original RBD using a thermal shift assay, and is less proteolytically sensitive to chymotrypsin and thermolysin than the original RBD. Our approach could be applied to the computational stabilization of a wide range of proteins without requiring detailed knowledge of active sites or binding epitopes, particularly powerful for cases when there are multiple or unknown binding sites.
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5
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Hannan JP, Swisher GH, Martyr JG, Cordaro NJ, Erbse AH, Falke JJ. HPLC method to resolve, identify and quantify guanine nucleotides bound to recombinant ras GTPase. Anal Biochem 2021; 631:114338. [PMID: 34433016 PMCID: PMC8511091 DOI: 10.1016/j.ab.2021.114338] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/31/2022]
Abstract
The Ras superfamily of small G proteins play central roles in diverse signaling pathways. Superfamily members act as molecular on-off switches defined by their occupancy with GTP or GDP, respectively. In vitro functional studies require loading with a hydrolysis-resistant GTP analogue to increase the on-state lifetime, as well as knowledge of fractional loading with activating and inactivating nucleotides. The present study describes a method combining elements of previous approaches with new, optimized features to analyze the bound nucleotide composition of a G protein loaded with activating (GMPPNP) or inactivating (GDP) nucleotide. After nucleotide loading, the complex is washed to remove unbound nucleotides then bound nucleotides are heat-extracted and subjected to ion-paired, reverse-phase HPLC-UV to resolve, identify and quantify the individual nucleotide components. These data enable back-calculation to the nucleotide composition and fractional activation of the original, washed G protein population prior to heat extraction. The method is highly reproducible. Application to multiple HRas preparations and mutants confirms its ability to fully extract and analyze bound nucleotides, and to resolve the fractional on- and off-state populations. Furthermore, the findings yield a novel hypothesis for the molecular disease mechanism of Ras mutations at the E63 and Y64 positions.
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Affiliation(s)
- Jonathan P Hannan
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - G Hayden Swisher
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Justin G Martyr
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Nicholas J Cordaro
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Annette H Erbse
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Joseph J Falke
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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6
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Swisher GH, Hannan JP, Cordaro NJ, Erbse AH, Falke JJ. Ras-guanine nucleotide complexes: A UV spectral deconvolution method to analyze protein concentration, nucleotide stoichiometry, and purity. Anal Biochem 2021; 618:114066. [PMID: 33485819 DOI: 10.1016/j.ab.2020.114066] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/31/2022]
Abstract
The many members of the Ras superfamily are small GTPases that serve as molecular switches. These proteins bind the guanine nucleotides GTP and GDP with picomolar affinities, thereby stabilizing on- and off-signaling states, respectively. Quantitative in vitro Ras studies require accurate determination of total protein, its fractional occupancy with guanine nucleotide, and spectroscopic purity. Yet the high nucleotide affinity of Ras and the overlapping UV spectra of the protein and bound nucleotide make such determinations challenging. Here we describe a generalizable UV spectral deconvolution method to analyze the total protein concentration, total nucleotide stoichiometry, and purity of Ras complexes.
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Affiliation(s)
- G Hayden Swisher
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States
| | - Jonathan P Hannan
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States
| | - Nicholas J Cordaro
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States
| | - Annette H Erbse
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States
| | - Joseph J Falke
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States.
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7
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Swisher GH, Cordaro NJ, Martyr JG, Erbse AH, Hannan JH, Kibby EM, Falke JJ. Binding of Ras to PI3K: Measuring Binding Affinity, and the Effects of Disease-Linked H-Ras Mutations on Affinity. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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8
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Wang X, Goodrich KJ, Conlon EG, Gao J, Erbse AH, Manley JL, Cech TR. C9orf72 and triplet repeat disorder RNAs: G-quadruplex formation, binding to PRC2 and implications for disease mechanisms. RNA 2019; 25:935-947. [PMID: 31048495 PMCID: PMC6633194 DOI: 10.1261/rna.071191.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/29/2019] [Indexed: 05/12/2023]
Abstract
Some neurological disorders, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), fragile X syndrome, Huntington's disease, myotonic dystrophy, and various ataxias, can be caused by expansions of short nucleic acid sequence repeats in specific genes. A possible disease mechanism involves the transcribed repeat RNA binding an RNA-binding protein (RBP), resulting in its sequestration and thus dysfunction. Polycomb repressive complex 2 (PRC2), the histone methyltransferase that deposits the H3K27me3 mark of epigenetically silenced chromatin, binds G-rich RNAs and has especially high affinity for G-quadruplex (G-Q) structures. Here, we find that PRC2 target genes are derepressed and the RNA binding subunit EZH2 largely insoluble in postmortem brain samples from ALS/FTD patients with C9ORF72 (C9) repeat expansions, leading to the hypothesis that the (G4C2)n repeat RNA might be sequestering PRC2. Contrary to this expectation, we found that C9 repeat RNAs (n = 6 or 10) bind weakly to purified PRC2, and studies with the G-Q specific BG4 antibody and circular dichroism studies both indicated that these C9 RNAs have little propensity to form G-Qs in vitro. Several GC-rich triplet-repeat expansion RNAs also have low affinity for PRC2 and do not appreciably form G-Qs in vitro. The results are consistent with these sequences forming hairpin structures that outcompete G-Q folding when the repeat length is sufficiently large. We suggest that binding of PRC2 to these GC-rich RNAs is fundamentally weak but may be modulated in vivo by protein factors that affect secondary structure, such as helicases and other RBPs.
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Affiliation(s)
- Xueyin Wang
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, USA
- BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Karen J Goodrich
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, USA
- BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Erin G Conlon
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Jianchao Gao
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Annette H Erbse
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Thomas R Cech
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, USA
- BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80309, USA
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9
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Brasino M, Roy S, Erbse AH, He L, Mao C, Park W, Cha JN, Goodwin AP. Anti-EGFR Affibodies with Site-Specific Photo-Cross-Linker Incorporation Show Both Directed Target-Specific Photoconjugation and Increased Retention in Tumors. J Am Chem Soc 2018; 140:11820-11828. [PMID: 30203972 PMCID: PMC6689236 DOI: 10.1021/jacs.8b07601] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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] [Indexed: 01/09/2023]
Abstract
A significant challenge for solid tumor treatment is ensuring that a sufficient concentration of therapeutic agent is delivered to the tumor site at doses that can be tolerated by the patient. Biomolecular targeting can bias accumulation in tumors by taking advantage of specific interactions with receptors overexpressed on cancerous cells. However, while antibody-based immunoconjugates show high binding to specific cells, their low dissociation constants ( KD) and large Stokes radii hinder their ability to penetrate deep into tumor tissue, leading to incomplete cell killing and tumor recurrence. To address this, we demonstrate the design and production of a photo-cross-linkable affibody that can form a covalent bond to epidermal growth factor receptor (EGFR) under near UV irradiation. Twelve cysteine mutations were created of an EGFR affibody and conjugated with maleimide-benzophenone. Of these only one exhibited photoconjugation to EGFR, as demonstrated by SDS-PAGE and Western blot. Next this modified affibody was shown to not only bind EGFR expressing cells but also show enhanced retention in a 3D tumor spheroid model, with minimal loss up to 24 h as compared to either unmodified EGFR-binding affibodies or nonbinding, photo-cross-linkable affibodies. Finally, in order to show utility of photo-cross-linking at clinically relevant wavelengths, upconverting nanoparticles (UCNPs) were synthesized that could convert 980 nm light to UV and blue light. In the presence of UCNPs, both direct photoconjugation to EGFR and enhanced retention in tumor spheroids could be obtained using near-infrared illumination. Thus, the photoactive affibodies developed here may be utilized as a platform technology for engineering new therapy conjugates that can penetrate deep into tumor tissue and be retained long enough for effective tumor therapy.
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Affiliation(s)
- Michael Brasino
- Department of Chemical and Biological Engineering, University of Colorado, 596 UCB, Boulder, Colorado 80303, United States
| | - Shambojit Roy
- Department of Chemical and Biological Engineering, University of Colorado, 596 UCB, Boulder, Colorado 80303, United States
| | - Annette H. Erbse
- Department of Chemistry and Biochemistry, University of Colorado, 596 UCB, Boulder, Colorado 80303, United States
| | - Liangcan He
- Department of Chemical and Biological Engineering, University of Colorado, 596 UCB, Boulder, Colorado 80303, United States
| | - Chenchen Mao
- Department of Electrical, Computer, and Energy Engineering, University of Colorado, 596 UCB, Boulder, Colorado 80303, United States
| | - Wounjhang Park
- Department of Electrical, Computer, and Energy Engineering, University of Colorado, 596 UCB, Boulder, Colorado 80303, United States
- Materials Science and Engineering Program, University of Colorado, 596 UCB, Boulder, Colorado 80303, United States
| | - Jennifer N. Cha
- Department of Chemical and Biological Engineering, University of Colorado, 596 UCB, Boulder, Colorado 80303, United States
- Materials Science and Engineering Program, University of Colorado, 596 UCB, Boulder, Colorado 80303, United States
| | - Andrew P. Goodwin
- Department of Chemical and Biological Engineering, University of Colorado, 596 UCB, Boulder, Colorado 80303, United States
- Materials Science and Engineering Program, University of Colorado, 596 UCB, Boulder, Colorado 80303, United States
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10
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Rudolph J, Erbse AH, Behlen LS, Copley SD. A radical intermediate in the conversion of pentachlorophenol to tetrachlorohydroquinone by Sphingobium chlorophenolicum. Biochemistry 2014; 53:6539-49. [PMID: 25238136 PMCID: PMC4204890 DOI: 10.1021/bi5010427] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Pentachlorophenol
(PCP) hydroxylase, the first enzyme in the pathway
for degradation of PCP in Sphingobium chlorophenolicum, is an unusually slow flavin-dependent monooxygenase (kcat = 0.02 s–1) that converts PCP to
a highly reactive product, tetrachlorobenzoquinone (TCBQ). Using stopped-flow
spectroscopy, we have shown that the steps up to and including formation
of TCBQ are rapid (5–30 s–1). Before products
can be released from the active site, the strongly oxidizing TCBQ
abstracts an electron from a donor at the active site, possibly a
cysteine residue, resulting in an off-pathway diradical state that
only slowly reverts to an intermediate capable of completing the catalytic
cycle. TCBQ reductase, the second enzyme in the PCP degradation pathway,
rescues this nonproductive complex via two fast sequential one-electron
transfers. These studies demonstrate how adoption of an ancestral
catalytic strategy for conversion of a substrate with different steric
and electronic properties can lead to subtle yet (literally) radical
changes in enzymatic reaction mechanisms.
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Affiliation(s)
- Johannes Rudolph
- Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, and ‡Department of Chemistry and Biochemistry, University of Colorado Boulder , Boulder, Colorado 80309, United States
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11
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Alzahrani AA, Erbse AH, Bowman CN. Evaluation and development of novel photoinitiator complexes for photoinitiating the copper-catalyzed azide–alkyne cycloaddition reaction. Polym Chem 2014. [DOI: 10.1039/c3py01064c] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Erbse AH, Berlinberg AJ, Falke JJ. Conformational Changes during Kinase On-Off Switching in the Chemosensory Signaling Array of the Bacterial Cell Membrane: Detection by One-Sample FRET. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.2471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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13
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Abstract
Fluorescence resonance energy transfer (FRET) is a powerful tool for studying macromolecular assemblies in vitro under near-physiological conditions. Here we present a new type of one-sample FRET (OS-FRET) method employing a novel, nonfluorescent methanethiosulfonate-linked acceptor that can be reversibly coupled to a target sulfhydryl residue via a disulfide bond. After the quenched donor emission is quantitated, the acceptor is removed by reduction, allowing measurement of unquenched donor emission in the same sample. Previous one-sample methods provide distinct advantages in specific FRET applications. The new OS-FRET method is a generalizable spectrochemical approach that can be applied to macromolecular systems lacking essential disulfide bonds and eliminates the potential systematic errors of some earlier one-sample methods. In addition, OS-FRET enables quantitative FRET measurements in virtually any fluorescence spectrometer or detection device. Compared to conventional multisample FRET methods, OS-FRET conserves sample, increases the precision of data, and shortens the time per measurement. The utility of the method is illustrated by its application to a protein complex of known structure formed by CheW and the P4-P5 fragment of CheA, both from Thermotoga maritima. The findings confirm the practicality and advantages of OS-FRET. Anticipated applications of OS-FRET include analysis of macromolecular structure, binding and conformational dynamics, and high-throughput screening for interactions and inhibitors.
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Affiliation(s)
- Annette H Erbse
- Department of Chemistry and Biochemistry and Molecular Biophysics Program, University of Colorado, Boulder, CO 80309-0215, USA
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14
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Abstract
The chemosensory pathway of bacterial chemotaxis forms a polar signaling cluster in which the fundamental signaling units, the ternary complexes, are arrayed in a highly cooperative, repeating lattice. The repeating ternary units are composed of transmembrane receptors, histidine-kinase CheA, and coupling protein CheW, but it is unknown how these three core proteins are interwoven in the assembled ultrasensitive lattice. Here, to further probe the nature of the lattice, we investigate its stability. The findings reveal that once the signaling cluster is assembled, CheA remains associated and active for days in vitro. All three core components are required for this ultrastable CheA binding and for receptor-controlled kinase activity. The stability is disrupted by low ionic strength or high pH, providing strong evidence that electrostatic repulsion between the highly acidic core components can lead to disassembly. We propose that ultrastability arises from the assembled lattice structure that establishes multiple linkages between the core components, thereby conferring thermodynamic or kinetic ultrastability to the bound state. An important, known function of the lattice structure is to facilitate receptor cooperativity, which in turn enhances pathway sensitivity. In the cell, however, the ultrastability of the lattice could lead to uncontrolled growth of the signaling complex until it fills the inner membrane. We hypothesize that such uncontrolled growth is prevented by an unidentified intracellular disassembly system that is lost when complexes are isolated from cells, thereby unmasking the intrinsic complex ultrastability. Possible biological functions of ultrastability are discussed.
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Affiliation(s)
- Annette H Erbse
- Department of Chemistry, and Biochemistry and Molecular Biophysics Program, University of Colorado, Boulder, Colorado 80309-0215, USA
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15
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Erbse AH, Wagner JN, Truscott KN, Spall SK, Kirstein J, Zeth K, Turgay K, Mogk A, Bukau B, Dougan DA. Conserved residues in the N-domain of the AAA+ chaperone ClpA regulate substrate recognition and unfolding. FEBS J 2008; 275:1400-1410. [PMID: 18279386 DOI: 10.1111/j.1742-4658.2008.06304.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Protein degradation in the cytosol of Escherichia coli is carried out by a variety of different proteolytic machines, including ClpAP. The ClpA component is a hexameric AAA+ (ATPase associated with various cellular activities) chaperone that utilizes the energy of ATP to control substrate recognition and unfolding. The precise role of the N-domains of ClpA in this process, however, remains elusive. Here, we have analysed the role of five highly conserved basic residues in the N-domain of ClpA by monitoring the binding, unfolding and degradation of several different substrates, including short unstructured peptides, tagged and untagged proteins. Interestingly, mutation of three of these basic residues within the N-domain of ClpA (H94, R86 and R100) did not alter substrate degradation. In contrast mutation of two conserved arginine residues (R90 and R131), flanking a putative peptide-binding groove within the N-domain of ClpA, specifically compromised the ability of ClpA to unfold and degrade selected substrates but did not prevent substrate recognition, ClpS-mediated substrate delivery or ClpP binding. In contrast, a highly conserved tyrosine residue lining the central pore of the ClpA hexamer was essential for the degradation of all substrate types analysed, including both folded and unstructured proteins. Taken together, these data suggest that ClpA utilizes two structural elements, one in the N-domain and the other in the pore of the hexamer, both of which are required for efficient unfolding of some protein substrates.
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Affiliation(s)
- Annette H Erbse
- Zentrum für Molekulare Biologie Heidelberg, Universität Heidelberg, Heidelberg, Germany
| | - Judith N Wagner
- Zentrum für Molekulare Biologie Heidelberg, Universität Heidelberg, Heidelberg, Germany
| | - Kaye N Truscott
- Department of Biochemistry, La Trobe University, Melbourne, Australia
| | - Sukhdeep K Spall
- Department of Biochemistry, La Trobe University, Melbourne, Australia
| | - Janine Kirstein
- Zentrum für Molekulare Biologie Heidelberg, Universität Heidelberg, Heidelberg, Germany., Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | | | - Kürsad Turgay
- Zentrum für Molekulare Biologie Heidelberg, Universität Heidelberg, Heidelberg, Germany., Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Axel Mogk
- Zentrum für Molekulare Biologie Heidelberg, Universität Heidelberg, Heidelberg, Germany
| | - Bernd Bukau
- Zentrum für Molekulare Biologie Heidelberg, Universität Heidelberg, Heidelberg, Germany
| | - David A Dougan
- Zentrum für Molekulare Biologie Heidelberg, Universität Heidelberg, Heidelberg, Germany., Department of Biochemistry, La Trobe University, Melbourne, Australia
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