1
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Rao SPS, Gould MK, Noeske J, Saldivia M, Jumani RS, Ng PS, René O, Chen YL, Kaiser M, Ritchie R, Francisco AF, Johnson N, Patra D, Cheung H, Deniston C, Schenk AD, Cortopassi WA, Schmidt RS, Wiedemar N, Thomas B, Palkar R, Ghafar NA, Manoharan V, Luu C, Gable JE, Wan KF, Myburgh E, Mottram JC, Barnes W, Walker J, Wartchow C, Aziz N, Osborne C, Wagner J, Sarko C, Kelly JM, Manjunatha UH, Mäser P, Jiricek J, Lakshminarayana SB, Barrett MP, Diagana TT. Cyanotriazoles are selective topoisomerase II poisons that rapidly cure trypanosome infections. Science 2023; 380:1349-1356. [PMID: 37384702 DOI: 10.1126/science.adh0614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 02/22/2023] [Accepted: 05/24/2023] [Indexed: 07/01/2023]
Abstract
Millions who live in Latin America and sub-Saharan Africa are at risk of trypanosomatid infections, which cause Chagas disease and human African trypanosomiasis (HAT). Improved HAT treatments are available, but Chagas disease therapies rely on two nitroheterocycles, which suffer from lengthy drug regimens and safety concerns that cause frequent treatment discontinuation. We performed phenotypic screening against trypanosomes and identified a class of cyanotriazoles (CTs) with potent trypanocidal activity both in vitro and in mouse models of Chagas disease and HAT. Cryo-electron microscopy approaches confirmed that CT compounds acted through selective, irreversible inhibition of trypanosomal topoisomerase II by stabilizing double-stranded DNA:enzyme cleavage complexes. These findings suggest a potential approach toward successful therapeutics for the treatment of Chagas disease.
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Affiliation(s)
- Srinivasa P S Rao
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
| | - Matthew K Gould
- College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jonas Noeske
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Manuel Saldivia
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Rajiv S Jumani
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Pearly S Ng
- Novartis Institute for Tropical Diseases, Singapore
| | - Olivier René
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Yen-Liang Chen
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Ryan Ritchie
- College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Nila Johnson
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
| | - Debjani Patra
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Harry Cheung
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Colin Deniston
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | | | | | - Remo S Schmidt
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Natalie Wiedemar
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Bryanna Thomas
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Rima Palkar
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
| | | | | | - Catherine Luu
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Jonathan E Gable
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Kah Fei Wan
- Novartis Institute for Tropical Diseases, Singapore
| | - Elmarie Myburgh
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK
| | - Jeremy C Mottram
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Whitney Barnes
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - John Walker
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - Charles Wartchow
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Natasha Aziz
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Colin Osborne
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Juergen Wagner
- Novartis Institute for Tropical Diseases, Singapore
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Christopher Sarko
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - John M Kelly
- London School of Hygiene and Tropical Medicine, London, UK
| | - Ujjini H Manjunatha
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Jan Jiricek
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
| | - Suresh B Lakshminarayana
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
| | - Michael P Barrett
- College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Thierry T Diagana
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
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2
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Acker TM, Gable JE, Bohn MF, Jaishankar P, Thompson MC, Fraser JS, Renslo AR, Craik CS. Allosteric Inhibitors, Crystallography, and Comparative Analysis Reveal Network of Coordinated Movement across Human Herpesvirus Proteases. J Am Chem Soc 2017; 139:11650-11653. [PMID: 28759216 DOI: 10.1021/jacs.7b04030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Targeting of cryptic binding sites represents an attractive but underexplored approach to modulating protein function with small molecules. Using the dimeric protease (Pr) from Kaposi's sarcoma-associated herpesvirus (KSHV) as a model system, we sought to dissect a putative allosteric network linking a cryptic site at the dimerization interface to enzyme function. Five cryogenic X-ray structures were solved of the monomeric protease with allosteric inhibitors bound to the dimer interface site. Distinct coordinated movements captured by the allosteric inhibitors were also revealed as alternative states in room-temperature X-ray data and comparative analyses of other dimeric herpesvirus proteases. A two-step mechanism was elucidated through detailed kinetic analyses and suggests an enzyme isomerization model of inhibition. Finally, a representative allosteric inhibitor from this class was shown to be efficacious in a cellular model of viral infectivity. These studies reveal a coordinated dynamic network of atomic communication linking cryptic binding site occupancy and allosteric inactivation of KHSV Pr that can be exploited to target other members of this clinically relevant family of enzymes.
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Affiliation(s)
- Timothy M Acker
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States
| | - Jonathan E Gable
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States
| | - Markus-Frederik Bohn
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States
| | - Michael C Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California , San Francisco, California 94158, United States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California , San Francisco, California 94158, United States
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States
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3
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Gable JE, Lee GM, Acker TM, Hulce KR, Gonzalez ER, Schweigler P, Melkko S, Farady CJ, Craik CS. Fragment-Based Protein-Protein Interaction Antagonists of a Viral Dimeric Protease. ChemMedChem 2016; 11:862-9. [PMID: 26822284 DOI: 10.1002/cmdc.201500526] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 11/06/2015] [Indexed: 11/11/2022]
Abstract
Fragment-based drug discovery has shown promise as an approach for challenging targets such as protein-protein interfaces. We developed and applied an activity-based fragment screen against dimeric Kaposi's sarcoma-associated herpesvirus protease (KSHV Pr) using an optimized fluorogenic substrate. Dose-response determination was performed as a confirmation screen, and NMR spectroscopy was used to map fragment inhibitor binding to KSHV Pr. Kinetic assays demonstrated that several initial hits also inhibit human cytomegalovirus protease (HCMV Pr). Binding of these hits to HCMV Pr was also confirmed by NMR spectroscopy. Despite the use of a target-agnostic fragment library, more than 80 % of confirmed hits disrupted dimerization and bound to a previously reported pocket at the dimer interface of KSHV Pr, not to the active site. One class of fragments, an aminothiazole scaffold, was further explored using commercially available analogues. These compounds demonstrated greater than 100-fold improvement of inhibition. This study illustrates the power of fragment-based screening for these challenging enzymatic targets and provides an example of the potential druggability of pockets at protein-protein interfaces.
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Affiliation(s)
- Jonathan E Gable
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA.,Biophysics Graduate Group, University of California, San Francisco, CA, 94158-2280, USA
| | - Gregory M Lee
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA
| | - Timothy M Acker
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA
| | - Kaitlin R Hulce
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA.,Chemistry and Chemical Biology Graduate Group, University of California, San Francisco, CA, 94158-2280, USA
| | - Eric R Gonzalez
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA
| | - Patrick Schweigler
- Novartis Institutes for BioMedical Research, Forum 1, Novartis Campus, 4002, Basel, Switzerland
| | - Samu Melkko
- Novartis Institutes for BioMedical Research, Forum 1, Novartis Campus, 4002, Basel, Switzerland
| | - Christopher J Farady
- Novartis Institutes for BioMedical Research, Forum 1, Novartis Campus, 4002, Basel, Switzerland
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA.
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4
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Abstract
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Herpesviruses
rely on a homodimeric protease for viral capsid maturation.
A small molecule, DD2, previously shown to disrupt dimerization of
Kaposi’s sarcoma-associated herpesvirus protease (KSHV Pr)
by trapping an inactive monomeric conformation and two analogues generated
through carboxylate bioisosteric replacement (compounds 2 and 3) were shown to inhibit the associated proteases
of all three human herpesvirus (HHV) subfamilies (α, β,
and γ). Inhibition data reveal that compound 2 has
potency comparable to or better than that of DD2 against the tested
proteases. Nuclear magnetic resonance spectroscopy and a new application
of the kinetic analysis developed by Zhang and Poorman [Zhang, Z.
Y., Poorman, R. A., et al. (1991) J. Biol. Chem. 266, 15591–15594] show DD2, compound 2, and compound 3 inhibit HHV proteases by dimer disruption. All three compounds
bind the dimer interface of other HHV proteases in a manner analogous
to binding of DD2 to KSHV protease. The determination and analysis
of cocrystal structures of both analogues with the KSHV Pr monomer
verify and elaborate on the mode of binding for this chemical scaffold,
explaining a newly observed critical structure–activity relationship.
These results reveal a prototypical chemical scaffold for broad-spectrum
allosteric inhibition of human herpesvirus proteases and an approach
for the identification of small molecules that allosterically regulate
protein activity by targeting protein–protein interactions.
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Affiliation(s)
- Jonathan E Gable
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158-2280, United States
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5
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Lee GM, Shahian T, Baharuddin A, Gable JE, Craik CS. Enzyme inhibition by allosteric capture of an inactive conformation. J Mol Biol 2011; 411:999-1016. [PMID: 21723875 DOI: 10.1016/j.jmb.2011.06.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 06/15/2011] [Accepted: 06/16/2011] [Indexed: 10/18/2022]
Abstract
All members of the human herpesvirus protease (HHV Pr) family are active as weakly associating dimers but inactive as monomers. A small-molecule allosteric inhibitor of Kaposi's sarcoma-associated herpesvirus protease (KSHV Pr) traps the enzyme in an inactive monomeric state where the C-terminal helices are unfolded and the hydrophobic dimer interface is exposed. NMR titration studies demonstrate that the inhibitor binds to KSHV Pr monomers with low micromolar affinity. A 2.0-Å-resolution X-ray crystal structure of a C-terminal truncated KSHV Pr-inhibitor complex locates the binding pocket at the dimer interface and displays significant conformational perturbations at the active site, 15 Å from the allosteric site. NMR and CD data suggest that the small molecule inhibits human cytomegalovirus protease via a similar mechanism. As all HHV Prs are functionally and structurally homologous, the inhibitor represents a class of compounds that may be developed into broad-spectrum therapeutics that allosterically regulate enzymatic activity by disrupting protein-protein interactions.
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Affiliation(s)
- Gregory M Lee
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2280, USA
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6
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FIGUEREDO SHARELMENEZES, Gable JE, Kim JE, Ouellette AJ. Proximity of proregion anionic residues to the mature region maintains proCryptdin‐4 inhibition. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.521.2] [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: 11/11/2022]
Affiliation(s)
| | - Jonathan E Gable
- Department of Chemistry and BiochemistryUniversity of California at San DiegoLa JollaCA
| | - Judy E Kim
- Department of Chemistry and BiochemistryUniversity of California at San DiegoLa JollaCA
| | - Andre J Ouellette
- Pathology and Laboratory MedicineKeck School of Medicine of USCLos AngelesCA
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7
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Schlamadinger DE, Gable JE, Kim JE. Hydrogen bonding and solvent polarity markers in the uv resonance raman spectrum of tryptophan: application to membrane proteins. J Phys Chem B 2010; 113:14769-78. [PMID: 19817473 DOI: 10.1021/jp905473y] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ultraviolet resonance Raman (UVRR) spectra of tryptophan compounds in various solvents and a model peptide are presented and reveal systematic changes that reflect solvent polarity, hydrogen bond strength, and cation-pi interaction. The commonly utilized UVRR spectral marker for environment polarity that has been based on off-resonance Raman data, the tryptophan Fermi doublet ratio I1360/I1340, exhibits different values in on- and off-resonance Raman spectra as well as for different tryptophan derivatives. Specifically, the UVRR Fermi doublet ratio for indole ranges from 0.3 in polar solvents to 0.8 in nonpolar solvents, whereas the respective values reported here and previously for off-resonance Raman spectra are 0.5-1.3. UVRR Fermi doublet ratios for the more biologically relevant molecule, N-acetyl tryptophan ethyl ester (NATEE), are in a smaller range of 1.1 (polar solvent) to 1.7 (nonpolar solvent) and correlate to the solvent polarity/polarization parameters pi* and ETN. As has been reported previously, several UVRR modes are also sensitive to the hydrogen bond strength of the indole N-H moiety. Here, we report a new unambiguous marker for H-bonding: the ratio of the W10 (approximately 1237 cm-1) intensity to that of the W9 (approximately 1254 cm-1) mode (RW10). This ratio is 0.7 for NATEE in the absence of hydrogen bond acceptors and increases to 3.1 in the presence of strong hydrogen bond acceptors, with a value of 2.3 in water. The W8 and W17 modes shift more than +10 and approximately -5 cm-1 upon increase in hydrogen bond strength; this range for W17 is smaller than that reported previously and reflects a more realistic range for proteins and peptides in solution. Finally, our data provide evidence for change in the W18 and W16 relative intensity in the presence of cation-pi interactions. These UVRR markers are utilized to interpret spectra of model membrane-bound systems tryptophan octyl ester and the peptide toxin melittin. These spectra reveal the importance of intra- and intermolecular hydrogen bonding and cation-pi interactions that likely influence the partitioning of membrane-associated biomolecules to lipid bilayers or self-associated soluble oligomers. The UVRR analysis presented here modifies and augments prior reports and provides an unambiguous set of spectral makers that can be applied to elucidate the molecular microenvironment and structure of a wide range of complex systems, including anchoring tryptophan residues in membrane proteins and peptides.
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Affiliation(s)
- Diana E Schlamadinger
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
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8
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Kim JE, Sanchez KM, Schlamadinger DE, Gable JE, Wu B. Spectroscopic Study of Anchoring Aromatic Residues in Membrane Proteins and Peptides: Applications to Protein Folding and Vesicle Disruption. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.1297] [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: 11/16/2022] Open
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9
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Gable JE, Schlamadinger DE, Cogen AL, Gallo RL, Kim JE. Fluorescence and UV resonance Raman study of peptide-vesicle interactions of human cathelicidin LL-37 and its F6W and F17W mutants. Biochemistry 2009; 48:11264-72. [PMID: 19894716 DOI: 10.1021/bi900996q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
LL-37 is a broad-spectrum human antimicrobial peptide in the cathelicidin family. Potency assays in the form of minimal inhibitory concentration and vesicle leakage indicate that the single-tryptophan mutants, F6W and F17W, are as effective at killing bacteria and disrupting membranes as the native, tryptophan-free LL-37 peptide. Steady-state fluorescence and UV resonance Raman spectroscopy of F6W and F17W reveal molecular details of these tryptophan residues. The local environment polarity, hydrogen bond strength of the indole N-H moiety, and rotational freedom decrease for both F6W and F17W in the presence of carbonate ions relative to in pure distilled water; these results are consistent with burial of the hydrophobic region of alpha-helical LL-37 in oligomeric cores induced in the presence of carbonate ions. Differences in the spectroscopic properties of the carbonate-induced alpha-helical forms of F6W and F17W reflect the presence of a local lysine residue near F6W that makes the microenvironment of F6W more polar than that of F17W. In the presence of lipid vesicles, the mutants undergo additional loss of environment polarity, hydrogen bond strength, and rotational freedom. Quenching experiments utilizing brominated lipids reveal that the tryptophan residues in both mutants are essentially equidistant from the bilayer center and that bromines closer to the bilayer center, in the 9,10 positions, quench fluorescence more efficiently than those closer to the headgroups (6,7 positions). These results support carpeting or toroidal pore mechanisms of membrane disruption by LL-37 and demonstrate that the combination of tryptophan mutants and sensitive spectroscopic tools may provide important molecular clues about antimicrobial action.
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Affiliation(s)
- Jonathan E Gable
- Department of Chemistry and Biochemistry, University ofCalifornia at San Diego, La Jolla, California 92093, USA
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10
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Abstract
The innate immunity to pathogenic invasion of organisms in the plant and animal kingdoms relies upon cationic antimicrobial peptides (AMPs) as the first line of defense. In addition to these natural peptide antibiotics, similar cationic peptides, such as the bee venom toxin melittin, act as nonspecific toxins. Molecular details of AMP and peptide toxin action are not known, but the universal function of these peptides to disrupt cell membranes of pathogenic bacteria (AMPs) or a diverse set of eukaryotes and prokaryotes (melittin) is widely accepted. Here, we have utilized spectroscopic techniques to elucidate peptide-membrane interactions of alpha-helical human and mouse AMPs of the cathelicidin family as well as the peptide toxin melittin. The activity of these natural peptides and their engineered analogs was studied on eukaryotic and prokaryotic membrane mimics consisting of <200-nm bilayer vesicles composed of anionic and neutral lipids as well as cholesterol. Vesicle disruption, or peptide potency, was monitored with a sensitive fluorescence leakage assay. Detailed molecular information on peptide-membrane interactions and peptide structure was further gained through vibrational spectroscopy combined with circular dichroism. Finally, steady-state fluorescence experiments yielded insight into the local environment of native or engineered tryptophan residues in melittin and human cathelicidin embedded in bilayer vesicles. Collectively, our results provide clues to the functional structures of the engineered and toxic peptides and may impact the design of synthetic antibiotic peptides that can be used against the growing number of antibiotic-resistant pathogens.
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Affiliation(s)
- Diana E Schlamadinger
- Department of Chemistry and Biochemistry, University of California - San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Jonathan E Gable
- Department of Chemistry and Biochemistry, University of California - San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Judy E Kim
- Department of Chemistry and Biochemistry, University of California - San Diego, 9500 Gilman Drive, La Jolla, CA 92093
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11
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Sanchez KM, Gable JE, Schlamadinger DE, Kim JE. Effects of tryptophan microenvironment, soluble domain, and vesicle size on the thermodynamics of membrane protein folding: lessons from the transmembrane protein OmpA. Biochemistry 2008; 47:12844-52. [PMID: 18991402 PMCID: PMC2724591 DOI: 10.1021/bi800860k] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [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] [Indexed: 11/30/2022]
Abstract
Refolding curves of the integral membrane protein outer membrane protein A (OmpA) were measured to determine the conformational stabilities of this model system for membrane protein folding. Wild-type OmpA exhibits a free energy of unfolding (DeltaG degrees H2O) of 10.5 kcal/mol. Mutants, containing a single tryptophan residue at the native positions 7, 15, 57, 102, or 143, are less stable than wild-type OmpA, with DeltaG degrees H2O values of 6.7, 4.8, 2.4, 4.7, and 2.8 kcal/mol, respectively. The trend observed here is discussed in terms of noncovalent interactions, including aromatic interactions and hydrogen bonding. The effect of the soluble tail on the conformational stability of the transmembrane domain of OmpA was also investigated via truncated single-Trp mutants; DeltaG degrees H2O values for four of the five truncated mutants are greater by >2.7 kcal/mol relative to the full-length versions, suggesting that the absence of the soluble domain may destabilize the unfolded transmembrane domain. Finally, dynamic light scattering experiments were performed to measure the effects of urea and protein on vesicle size and stability. Urea concentrations greater than 1 M cause an increase in vesicle size, and these diameters are unaltered in the presence of protein. These dynamic light scattering results complement the fluorescence studies and illustrate the important effects of vesicle size on protein conformational stability.
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Affiliation(s)
- Katheryn M. Sanchez
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California, 92093
| | - Jonathan E. Gable
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California, 92093
| | - Diana E. Schlamadinger
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California, 92093
| | - Judy E. Kim
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California, 92093
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12
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Sanchez KM, Schlamadinger DE, Gable JE, Kim JE. Förster Resonance Energy Transfer and Conformational Stability of Proteins: An Advanced Biophysical Module for Physical Chemistry Students. J Chem Educ 2008; 85:1253-1256. [PMID: 19756254 PMCID: PMC2743118 DOI: 10.1021/ed085p1253] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Protein folding is an exploding area of research in biophysics and physical chemistry. Here, we describe the integration of several techniques, including absorption spectroscopy, fluorescence spectroscopy, and Förster resonance energy transfer (FRET) measurements, to probe important topics in protein folding. Cytochrome c is used as a model protein; comparison of conformational stabilities ( ΔGH2O∘) measured via two chemical denaturants, urea and guanidinium hydrochloride, illustrate important concepts in protein folding and intermolecular interactions. In addition, the determination of intraprotein distances based upon the FRET pair Trp-59 and the heme group for unfolded states of cytochrome c highlights the evolution of the protein structure under unfolding conditions. Analysis and discussion of these results provide opportunities to gain in-depth understanding of models for protein folding while enhancing students' skills with optical techniques. Collectively, the combination of optical spectroscopy, rigorous quantitative analysis, and a focus on biophysics illustrates the significance of fundamental research at the growing intersection of chemistry, biology, and physics.
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Affiliation(s)
- Katheryn M. Sanchez
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093
| | - Diana E. Schlamadinger
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093
| | - Jonathan E. Gable
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093
| | - Judy E. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093
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