6 results on '"Cheng, Yi-Qiang"'
Search Results
2. Activation of ClpP protease by ADEP antibiotics: insights from hydrogen exchange mass spectrometry.
- Author
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Sowole MA, Alexopoulos JA, Cheng YQ, Ortega J, and Konermann L
- Subjects
- Allosteric Regulation, Amino Acid Sequence, Depsipeptides metabolism, Depsipeptides pharmacology, Endopeptidase Clp metabolism, Enzyme Activation drug effects, Hydrogen chemistry, Hydrogen Bonding, Hydrophobic and Hydrophilic Interactions, Kinetics, Mass Spectrometry, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Conformation, Protein Multimerization, Depsipeptides chemistry, Endopeptidase Clp chemistry
- Abstract
The bacterial protease ClpP consists of 14 subunits that assemble into two stacked heptameric rings. The central degradation chamber can be accessed via axial pores. In free ClpP, these pores are obstructed by the N-terminal regions of the seven subunits at either end of the barrel. Acyldepsipeptides (ADEPs) are antibacterial compounds that bind in hydrophobic clefts surrounding the pore region, causing the pores to open up. The ensuing uncontrolled degradation of intracellular proteins is responsible for the antibiotic activity of ADEPs. Recently published X-ray structures yielded conflicting models regarding the conformation adopted by the N-terminal regions in the open state. Here, we use hydrogen/deuterium exchange (HDX) mass spectrometry to obtain complementary insights into the ClpP behavior with and without ADEP1. Ligand binding causes rigidification of the equatorial belt, accompanied by destabilization in the vicinity of the binding clefts. The N-terminal regions undergo rapid deuteration with only minor changes after ADEP1 binding, revealing a lack of stable H-bonding. Our data point to a mechanism where the pore opening mechanism is mediated primarily by changes in the packing of N-terminal nonpolar side chains. We propose that a "hydrophobic plug" causes pore blockage in ligand-free ClpP. ADEP1 binding provides new hydrophobic anchor points that nonpolar N-terminal residues can interact with. In this way, ADEP1 triggers the transition to an open conformation, where nonpolar moieties are clustered around the rim of the pore. This proposed mechanism helps reconcile the conflicting models that had been put forward earlier., (© 2013.)
- Published
- 2013
- Full Text
- View/download PDF
3. Activators of cylindrical proteases as antimicrobials: identification and development of small molecule activators of ClpP protease.
- Author
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Leung E, Datti A, Cossette M, Goodreid J, McCaw SE, Mah M, Nakhamchik A, Ogata K, El Bakkouri M, Cheng YQ, Wodak SJ, Eger BT, Pai EF, Liu J, Gray-Owen S, Batey RA, and Houry WA
- Subjects
- Anti-Bacterial Agents pharmacology, Binding Sites, Computer Simulation, Endopeptidase Clp genetics, Endopeptidase Clp metabolism, Enzyme Activation drug effects, Escherichia coli enzymology, Escherichia coli Proteins genetics, Escherichia coli Proteins metabolism, Microbial Sensitivity Tests, Molecular Chaperones metabolism, Protein Structure, Tertiary, Recombinant Proteins chemistry, Recombinant Proteins genetics, Recombinant Proteins metabolism, Small Molecule Libraries chemistry, Small Molecule Libraries pharmacology, Anti-Bacterial Agents chemistry, Endopeptidase Clp chemistry, Escherichia coli Proteins chemistry
- Abstract
ClpP is a cylindrical serine protease whose ability to degrade proteins is regulated by the unfoldase ATP-dependent chaperones. ClpP on its own can only degrade small peptides. Here, we used ClpP as a target in a high-throughput screen for compounds, which activate the protease and allow it to degrade larger proteins, hence, abolishing the specificity arising from the ATP-dependent chaperones. Our screen resulted in five distinct compounds, which we designate as Activators of Self-Compartmentalizing Proteases 1 to 5 (ACP1 to 5). The compounds are found to stabilize the ClpP double-ring structure. The ACP1 chemical structure was considered to have drug-like characteristics and was further optimized to give analogs with bactericidal activity. Hence, the ACPs represent classes of compounds that can activate ClpP and that can be developed as potential novel antibiotics., (Copyright © 2011 Elsevier Ltd. All rights reserved.)
- Published
- 2011
- Full Text
- View/download PDF
4. Acyldepsipeptide antibiotics induce the formation of a structured axial channel in ClpP: A model for the ClpX/ClpA-bound state of ClpP.
- Author
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Li DH, Chung YS, Gloyd M, Joseph E, Ghirlando R, Wright GD, Cheng YQ, Maurizi MR, Guarné A, and Ortega J
- Subjects
- ATPases Associated with Diverse Cellular Activities, Adenosine Triphosphatases chemistry, Adenosine Triphosphatases metabolism, Endopeptidase Clp metabolism, Escherichia coli enzymology, Escherichia coli Proteins metabolism, Kinetics, Molecular Chaperones chemistry, Molecular Chaperones metabolism, Protein Binding, Protein Folding, Protein Structure, Tertiary, Substrate Specificity, Anti-Bacterial Agents chemistry, Depsipeptides chemistry, Endopeptidase Clp chemistry, Escherichia coli Proteins chemistry, Models, Molecular
- Abstract
In ClpXP and ClpAP complexes, ClpA and ClpX use the energy of ATP hydrolysis to unfold proteins and translocate them into the self-compartmentalized ClpP protease. ClpP requires the ATPases to degrade folded or unfolded substrates, but binding of acyldepsipeptide antibiotics (ADEPs) to ClpP bypasses this requirement with unfolded proteins. We present the crystal structure of Escherichia coli ClpP bound to ADEP1 and report the structural changes underlying ClpP activation. ADEP1 binds in the hydrophobic groove that serves as the primary docking site for ClpP ATPases. Binding of ADEP1 locks the N-terminal loops of ClpP in a β-hairpin conformation, generating a stable pore through which extended polypeptides can be threaded. This structure serves as a model for ClpP in the holoenzyme ClpAP and ClpXP complexes and provides critical information to further develop this class of antibiotics., (Copyright © 2010 Elsevier Ltd. All rights reserved.)
- Published
- 2010
- Full Text
- View/download PDF
5. An FAD-dependent pyridine nucleotide-disulfide oxidoreductase is involved in disulfide bond formation in FK228 anticancer depsipeptide.
- Author
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Wang C, Wesener SR, Zhang H, and Cheng YQ
- Subjects
- Antibiotics, Antineoplastic chemistry, Chromobacterium enzymology, Chromobacterium genetics, Depsipeptides biosynthesis, Depsipeptides chemistry, Kinetics, Molecular Sequence Data, Multigene Family, Mutant Proteins genetics, Mutant Proteins metabolism, NADH, NADPH Oxidoreductases classification, NADH, NADPH Oxidoreductases genetics, Phylogeny, Antibiotics, Antineoplastic metabolism, Depsipeptides metabolism, Disulfides metabolism, Flavin-Adenine Dinucleotide metabolism, NADH, NADPH Oxidoreductases metabolism
- Abstract
Disulfide bonds are rare in bacterial natural products, and the mechanism of disulfide bond formation in those products is unknown. Here we characterize a gene and its product critical for a disulfide bond formation in FK228 anticancer depsipeptide in Chromobacterium violaceum. Deletion of depH drastically reduced FK228 production, whereas complementation of the depH-deletion mutant with a copy of depH on a medium copy-number plasmid not only fully restored the FK228 production but also significantly increased the FK228 yield. Purified 6xHis-tagged DepH fusion protein in native form is a homodimer of 71.0 kDa, with each monomer containing one molecule of FAD. DepH efficiently converts an immediate FK228 precursor to FK228 in the presence of NADP(+). We conclude that DepH is an FAD-dependent pyridine nucleotide-disulfide oxidoreductase, specifically and efficiently catalyzing a disulfide bond formation in FK228.
- Published
- 2009
- Full Text
- View/download PDF
6. Leinamycin biosynthesis revealing unprecedented architectural complexity for a hybrid polyketide synthase and nonribosomal peptide synthetase.
- Author
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Tang GL, Cheng YQ, and Shen B
- Subjects
- Amino Acid Sequence, Cloning, Molecular, Genes, Regulator, Models, Genetic, Molecular Sequence Data, Phylogeny, Sequence Alignment, Sequence Analysis, Streptomyces enzymology, Streptomyces metabolism, Antibiotics, Antineoplastic biosynthesis, Genes, Bacterial, Lactams, Macrolides metabolism, Multienzyme Complexes genetics, Multigene Family, Peptide Synthases genetics, Streptomyces genetics, Thiazoles metabolism, Thiones metabolism
- Abstract
A 135,638 bp DNA region that encompasses the leinamycin (LNM) biosynthetic gene cluster was sequenced from Streptomyces atroolivaceus S-140. The boundaries of the lnm cluster were defined by systematic inactivation of open reading frames within the sequenced region. The lnm cluster spans 61.3 kb of DNA and consists of 27 genes encoding nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), hybrid NRPS-PKS, resistance, regulatory, and tailoring enzymes, as well as proteins of unknown function. A model for LNM biosynthesis is proposed, central to which is the LNM hybrid NRPS-PKS megasynthetase consisting of discrete (LnmQ and LnmP) and modular (LnmI) NRPS, acyltransferase-less PKS (LnmG, LnmI, and LnmJ), and PKS modules with unusual domain organization. These studies unveil an unprecedented architectural complexity for the LNM hybrid NRPS-PKS megasynthetase and set the stage to investigate the molecular basis for LNM biosynthesis.
- Published
- 2004
- Full Text
- View/download PDF
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