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1.
PLoS Biol ; 19(12): e3001474, 2021 12.
Article in English | MEDLINE | ID: mdl-34879065

ABSTRACT

Endoplasmic reticulum-associated degradation (ERAD) is a protein quality control pathway of fundamental importance to cellular homeostasis. Although multiple ERAD pathways exist for targeting topologically distinct substrates, all pathways require substrate ubiquitination. Here, we characterize a key role for the UBE2G2 Binding Region (G2BR) of the ERAD accessory protein ancient ubiquitous protein 1 (AUP1) in ERAD pathways. This 27-amino acid (aa) region of AUP1 binds with high specificity and low nanomolar affinity to the backside of the ERAD ubiquitin-conjugating enzyme (E2) UBE2G2. The structure of the AUP1 G2BR (G2BRAUP1) in complex with UBE2G2 reveals an interface that includes a network of salt bridges, hydrogen bonds, and hydrophobic interactions essential for AUP1 function in cells. The G2BRAUP1 shares significant structural conservation with the G2BR found in the E3 ubiquitin ligase gp78 and in vitro can similarly allosterically activate ubiquitination in conjunction with ERAD E3s. In cells, AUP1 is uniquely required to maintain normal levels of UBE2G2; this is due to G2BRAUP1 binding to the E2 and preventing its rapid degradation. In addition, the G2BRAUP1 is required for both ER membrane recruitment of UBE2G2 and for its activation at the ER membrane. Thus, by binding to the backside of a critical ERAD E2, G2BRAUP1 plays multiple critical roles in ERAD.


Subject(s)
Endoplasmic Reticulum-Associated Degradation/genetics , Membrane Proteins/physiology , Ubiquitin-Conjugating Enzymes/physiology , Amino Acid Sequence/genetics , Cell Line, Tumor , Endoplasmic Reticulum/metabolism , Endoplasmic Reticulum-Associated Degradation/physiology , Humans , Membrane Proteins/genetics , Membrane Proteins/metabolism , Membrane Proteins/ultrastructure , Protein Binding/genetics , Protein Domains/genetics , Ubiquitin-Conjugating Enzymes/genetics , Ubiquitin-Conjugating Enzymes/metabolism , Ubiquitin-Conjugating Enzymes/ultrastructure , Ubiquitination
2.
Biochemistry ; 62(12): 1864-1877, 2023 06 20.
Article in English | MEDLINE | ID: mdl-37184593

ABSTRACT

The γ-crystallins are highly expressed structural lens proteins comprising four Greek key motifs arranged in two domains. Their globular structure and short-range spatial ordering are essential for lens transparency. Aromatic residues play a vital role in stabilizing Greek key folds by forming Greek key or non-Greek key pairs or tyrosine corners. We investigated the effects of the cataractogenic Y46D mutation in the second Greek key pair (Y46-Y51) of human γC-crystallin on its stability and aggregation. Wild-type and Y46D mutant human γC-crystallin were overexpressed in E. coli BL-21(DE3) PLysS cells, purified using ion-exchange and size-exclusion chromatography, and analyzed by fluorescence spectroscopy and circular dichroism spectroscopy. The Y46D mutation does not affect the γC-crystallin backbone conformation under benign conditions but alters the tryptophan microenvironment, exposing hydrophobic residues to the surface. The Y46D mutant undergoes a three-state transition under thermal stress with midpoints of 54.6 and 67.7 °C while the wild type shows a two-state transition with a midpoint of 77.6 °C. The Y46D mutant also shows a three-state transition under GuHCl stress with Cm values of 0.9 and 2.1 M while the wild type shows a two-state transition with a Cm of 2.4 M GuHCl. Mutant but not wild-type γC-crystallin forms light scattering particles upon heating at 65 °C. Overall, the Y46D CRYGS mutation leaves the protein fold intact under benign conditions but destabilizes the molecule by altering the tryptophan microenvironment and exposing hydrophobic residues to its surface, thus increasing its susceptibility to thermal and chemical stress with resultant self-aggregation, light scattering, and cataract.


Subject(s)
Cataract , gamma-Crystallins , Humans , gamma-Crystallins/chemistry , Escherichia coli/genetics , Escherichia coli/metabolism , Tryptophan/genetics , Cataract/genetics , Cataract/metabolism , Mutation
3.
Int J Mol Sci ; 24(18)2023 Sep 20.
Article in English | MEDLINE | ID: mdl-37762633

ABSTRACT

Aromatic residues forming tyrosine corners within Greek key motifs are critical for the folding, stability, and order of ßγ-crystallins and thus lens transparency. To delineate how a double amino acid substitution in an N-terminal-domain tyrosine corner of the CRYGS mutant p.F10_Y11delinsLN causes juvenile autosomal dominant cortical lamellar cataracts, human γS-crystallin c-DNA was cloned into pET-20b (+) and a p.F10_Y11delinsLN mutant was generated via site-directed mutagenesis, overexpressed, and purified using ion-exchange and size-exclusion chromatography. Structure, stability, and aggregation properties in solution under thermal and chemical stress were determined using spectrofluorimetry and circular dichroism. In benign conditions, the p.F10_Y11delinsLN mutation does not affect the protein backbone but alters its tryptophan microenvironment slightly. The mutant is less stable to thermal and GuHCl-induced stress, undergoing a two-state transition with a midpoint of 60.4 °C (wild type 73.1 °C) under thermal stress and exhibiting a three-state transition with midpoints of 1.25 and 2.59 M GuHCl (wild type: two-state transition with Cm = 2.72 M GuHCl). The mutant self-aggregates upon heating at 60 °C, which is inhibited by α-crystallin and reducing agents. Thus, the F10_Y11delinsLN mutation in human γS-crystallin impairs the protein's tryptophan microenvironment, weakening its stability under thermal and chemical stress, resulting in self-aggregation, lens opacification, and cataract.


Subject(s)
Cataract , gamma-Crystallins , Humans , gamma-Crystallins/chemistry , Tryptophan/genetics , Cataract/genetics , Cataract/metabolism , Mutation , Tyrosine/genetics
4.
Bioorg Med Chem ; 29: 115847, 2021 01 01.
Article in English | MEDLINE | ID: mdl-33199204

ABSTRACT

6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a key enzyme in the folate biosynthesis pathway. It catalyzes pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). HPPK is essential for microorganisms but absent in mammals; therefore, it is an attractive target for developing novel antimicrobial agents. Previously, based on our studies of the structure and mechanism of HPPK, we created first-generation bisubstrate inhibitors by linking 6-hydroxymethylpterin to adenosine through phosphate groups, and developed second-generation inhibitors by replacing the phosphate bridge with a linkage that contains a piperidine moiety. Here, we report third-generation inhibitors designed based on the piperidine-containing inhibitor, mimicking the transition state. We synthesized two such inhibitors, characterized their protein-binding and enzyme inhibition properties, and determined their crystal structures in complex with HPPK, advancing the development of such bisubstrate analog inhibitors.


Subject(s)
Enzyme Inhibitors/pharmacology , Piperidines/pharmacology , Adenosine Triphosphate/chemistry , Adenosine Triphosphate/metabolism , Binding Sites/drug effects , Crystallography, X-Ray , Diphosphotransferases , Dose-Response Relationship, Drug , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/chemistry , Escherichia coli/enzymology , Models, Molecular , Molecular Structure , Piperidines/chemical synthesis , Piperidines/chemistry , Pterins/chemistry , Pterins/metabolism , Structure-Activity Relationship
5.
Angew Chem Int Ed Engl ; 60(51): 26685-26693, 2021 12 13.
Article in English | MEDLINE | ID: mdl-34606673

ABSTRACT

Cyanine dyes are exceptionally useful probes for a range of fluorescence-based applications, but their photon output can be limited by trans-to-cis photoisomerization. We recently demonstrated that appending a ring system to the pentamethine cyanine ring system improves the quantum yield and extends the fluorescence lifetime. Here, we report an optimized synthesis of persulfonated variants that enable efficient labeling of nucleic acids and proteins. We demonstrate that a bifunctional sulfonated tertiary amide significantly improves the optical properties of the resulting bioconjugates. These new conformationally restricted cyanines are compared to the parent cyanine derivatives in a range of contexts. These include their use in the plasmonic hotspot of a DNA-nanoantenna, in single-molecule Förster-resonance energy transfer (FRET) applications, far-red fluorescence-lifetime imaging microscopy (FLIM), and single-molecule localization microscopy (SMLM). These efforts define contexts in which eliminating cyanine isomerization provides meaningful benefits to imaging performance.


Subject(s)
Carbocyanines/chemistry , Photons , Fluorescence Resonance Energy Transfer , Microscopy, Fluorescence , Molecular Conformation
6.
EMBO J ; 32(18): 2504-16, 2013 Sep 11.
Article in English | MEDLINE | ID: mdl-23942235

ABSTRACT

RING finger proteins constitute the large majority of ubiquitin ligases (E3s) and function by interacting with ubiquitin-conjugating enzymes (E2s) charged with ubiquitin. How low-affinity RING-E2 interactions result in highly processive substrate ubiquitination is largely unknown. The RING E3, gp78, represents an excellent model to study this process. gp78 includes a high-affinity secondary binding region for its cognate E2, Ube2g2, the G2BR. The G2BR allosterically enhances RING:Ube2g2 binding and ubiquitination. Structural analysis of the RING:Ube2g2:G2BR complex reveals that a G2BR-induced conformational effect at the RING:Ube2g2 interface is necessary for enhanced binding of RING to Ube2g2 or Ube2g2 conjugated to Ub. This conformational effect and a key ternary interaction with conjugated ubiquitin are required for ubiquitin transfer. Moreover, RING:Ube2g2 binding induces a second allosteric effect, disrupting Ube2g2:G2BR contacts, decreasing affinity and facilitating E2 exchange. Thus, gp78 is a ubiquitination machine where multiple E2-binding sites coordinately facilitate processive ubiquitination.


Subject(s)
Allosteric Regulation/physiology , Models, Molecular , Multiprotein Complexes/metabolism , Protein Conformation , Receptors, Autocrine Motility Factor/metabolism , Ubiquitin-Conjugating Enzymes/metabolism , Ubiquitination/physiology , Amino Acid Sequence , Cloning, Molecular , Crystallography, X-Ray , Escherichia coli , Humans , Magnetic Resonance Spectroscopy , Molecular Sequence Data , Protein Binding
7.
Mol Cell ; 34(6): 674-85, 2009 Jun 26.
Article in English | MEDLINE | ID: mdl-19560420

ABSTRACT

The activity of RING finger ubiquitin ligases (E3) is dependent on their ability to facilitate transfer of ubiquitin from ubiquitin-conjugating enzymes (E2) to substrates. The G2BR domain within the E3 gp78 binds selectively and with high affinity to the E2 Ube2g2. Through structural and functional analyses, we determine that this occurs on a region of Ube2g2 distinct from binding sites for ubiquitin-activating enzyme (E1) and RING fingers. Binding to the G2BR results in conformational changes in Ube2g2 that affect ubiquitin loading. The Ube2g2:G2BR interaction also causes an approximately 50-fold increase in affinity between the E2 and RING finger. This results in markedly increased ubiquitylation by Ube2g2 and the gp78 RING finger. The significance of this G2BR effect is underscored by enhanced ubiquitylation observed when Ube2g2 is paired with other RING finger E3s. These findings uncover a mechanism whereby allosteric effects on an E2 enhance E2-RING finger interactions and, consequently, ubiquitylation.


Subject(s)
Receptors, Cytokine/chemistry , Ubiquitin-Conjugating Enzymes/metabolism , Ubiquitin-Protein Ligases/chemistry , Amino Acid Sequence , Binding Sites , Crystallography, X-Ray , Humans , Models, Molecular , Molecular Sequence Data , Nuclear Magnetic Resonance, Biomolecular , Protein Structure, Tertiary , RING Finger Domains , Receptors, Autocrine Motility Factor , Receptors, Cytokine/metabolism , Receptors, Cytokine/physiology , Ubiquitin/metabolism , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Protein Ligases/physiology , Ubiquitination
8.
Biophys J ; 109(12): 2602-2613, 2015 Dec 15.
Article in English | MEDLINE | ID: mdl-26682817

ABSTRACT

Ras proteins are small GTPases that act as signal transducers between cell surface receptors and several intracellular signaling cascades. They contain highly homologous catalytic domains and flexible C-terminal hypervariable regions (HVRs) that differ across Ras isoforms. KRAS is among the most frequently mutated oncogenes in human tumors. Surprisingly, we found that the C-terminal HVR of K-Ras4B, thought to minimally impact the catalytic domain, directly interacts with the active site of the protein. The interaction is almost 100-fold tighter with the GDP-bound than the GTP-bound protein. HVR binding interferes with Ras-Raf interaction, modulates binding to phospholipids, and slightly slows down nucleotide exchange. The data indicate that contrary to previously suggested models of K-Ras4B signaling, HVR plays essential roles in regulation of signaling. High affinity binding of short peptide analogs of HVR to K-Ras active site suggests that targeting this surface with inhibitory synthetic molecules for the therapy of KRAS-dependent tumors is feasible.


Subject(s)
Catalytic Domain , Proto-Oncogene Proteins p21(ras)/chemistry , Proto-Oncogene Proteins p21(ras)/metabolism , ras Proteins/chemistry , ras Proteins/metabolism , Amino Acid Sequence , Biocatalysis , Guanosine Diphosphate/metabolism , Guanosine Triphosphate/metabolism , Molecular Dynamics Simulation , Molecular Sequence Data , Peptide Fragments/chemistry , Peptide Fragments/metabolism , Protein Binding
9.
J Immunol ; 191(2): 865-74, 2013 Jul 15.
Article in English | MEDLINE | ID: mdl-23776172

ABSTRACT

Alarmins are a group of structurally diverse host defense antimicrobial peptides that are important immune activators. In this article, we present a novel role for two potent alarmins, human ß-defensin 2 and 3 (HBD2 and 3), in promoting IFN-α production by human plasmacytoid dendritic cells. We demonstrate that HBD2 and 3 activate pDCs by enhancing the intracellular uptake of CpG and self DNA and promote DNA-induced IFN-α production in a TLR9-dependent manner. Both CpG and host DNA form aggregates that resemble DNA nets when combined with HBD2 and 3. Isothermal titration calorimetry studies to elucidate the nature of HBD3/CpG complexes demonstrate involvement of enthalpy-driven interactions, in addition to hydrophobic interactions, with the formation of complexes at a molar ratio of 2:1 defensin/CpG. The i.v. administration of HBD3/CpG complexes induced proinflammatory cytokines like IL-12, IFN-γ, IL-6, IFN-α, and IL-10 in serum, associated with an increased recruitment of APCs in the spleen. Subcutaneous injections of these complexes showed enhanced infiltration of inflammatory cells at the injection site, indicating a potential pathophysiological role for alarmin/DNA complexes in contributing to inflammation. Intraperitoneal immunization of HBD3/CpG complexes with OVA enhanced both cellular and humoral responses to OVA, compared with OVA/HBD3 or OVA/CPG alone, indicative of a much more potent adjuvant effect of the HBD3/CpG complexes. Thus, the ability of defensins to enhance cellular uptake of nucleic acids can lead to improved vaccine formulations by promoting their uptake by various cells, resulting in an enhanced immune response.


Subject(s)
Dendritic Cells/metabolism , Inflammation/immunology , Interferon-alpha/biosynthesis , beta-Defensins/metabolism , Adjuvants, Immunologic/pharmacology , Animals , Antigen-Presenting Cells/immunology , Biological Transport , Cells, Cultured , CpG Islands , DNA/metabolism , Dendritic Cells/immunology , Female , Humans , Hydrophobic and Hydrophilic Interactions , Interferon-alpha/blood , Interferon-gamma/blood , Interleukin-12/blood , Interleukin-6/blood , Mice , Mice, Inbred C57BL , Ovalbumin/immunology , Toll-Like Receptor 9/metabolism
10.
Proc Natl Acad Sci U S A ; 108(25): 10156-61, 2011 Jun 21.
Article in English | MEDLINE | ID: mdl-21646538

ABSTRACT

Era, composed of a GTPase domain and a K homology domain, is essential for bacterial cell viability. It is required for the maturation of 16S rRNA and assembly of the 30S ribosomal subunit. We showed previously that the protein recognizes nine nucleotides ( ) near the 3' end of 16S rRNA, and that this recognition stimulates GTP-hydrolyzing activity of Era. In all three kingdoms of life, the sequence and helix 45 (h45) (nucleotides 1506-1529) are highly conserved. It has been shown that the to double mutation severely affects the viability of bacteria. However, whether Era interacts with G1530 and/or h45 and whether such interactions (if any) contribute to the stimulation of Era's GTPase activity were not known. Here, we report two RNA structures that contain nucleotides 1506-1542 (RNA301), one in complex with Era and GDPNP (GNP), a nonhydrolysable GTP-analogue, and the other in complex with Era, GNP, and the KsgA methyltransferase. The structures show that Era recognizes 10 nucleotides, including G1530, and that Era also binds h45. Moreover, GTPase assay experiments show that G1530 does not stimulate Era's GTPase activity. Rather, A1531 and A1534 are most important for stimulation and h45 further contributes to the stimulation. Although G1530 does not contribute to the intrinsic GTPase activity of Era, its interaction with Era is important for binding and is essential for the protein to function, leading to the discovery of a new cold-sensitive phenotype of Era.


Subject(s)
Base Sequence , GTP-Binding Proteins/metabolism , RNA, Ribosomal, 16S/metabolism , RNA-Binding Proteins/metabolism , GTP-Binding Proteins/genetics , Methyltransferases/chemistry , Methyltransferases/genetics , Methyltransferases/metabolism , Models, Molecular , Molecular Sequence Data , Mutation , Nucleic Acid Conformation , Protein Binding , Protein Structure, Tertiary/genetics , RNA, Ribosomal, 16S/chemistry , RNA, Ribosomal, 16S/genetics , RNA-Binding Proteins/genetics
11.
Proc Natl Acad Sci U S A ; 108(24): 9798-803, 2011 Jun 14.
Article in English | MEDLINE | ID: mdl-21628584

ABSTRACT

Significant efforts have been devoted to the development of nanoparticular delivering systems targeting tumors. However, clinical application of nanoparticles is hampered by insufficient size homogeneity, difficulties in reproducible synthesis and manufacturing, frequent high uptake in the liver, systemic toxicity of the carriers (particularly for inorganic nanoparticles), and insufficient selectivity for tumor cells. We have found that properly modified synthetic analogs of transmembrane domains of membrane proteins can self-assemble into remarkably uniform spherical nanoparticles with innate biological activity. Self-assembly is driven by a structural transition of the peptide that adopts predominantly a beta-hairpin conformation in aqueous solutions, but folds into an alpha-helix upon spontaneous fusion of the nanoparticles with cell membrane. A 24-amino acid peptide corresponding to the second transmembrane helix of the CXCR4 forms self-assembled particles that inhibit CXCR4 function in vitro and hamper CXCR4-dependent tumor metastasis in vivo. Furthermore, such nanoparticles can encapsulate hydrophobic drugs, thus providing a delivery system with the potential for dual biological activity.


Subject(s)
Cell Membrane/chemistry , Membrane Proteins/chemistry , Nanoparticles/chemistry , Peptides/chemistry , Amino Acid Sequence , Animals , Cell Line, Tumor , Cell Membrane/metabolism , Cell Survival/drug effects , Circular Dichroism , Dose-Response Relationship, Drug , Female , Humans , Magnetic Resonance Spectroscopy , Mammary Neoplasms, Experimental/pathology , Mammary Neoplasms, Experimental/prevention & control , Membrane Proteins/metabolism , Mice , Mice, Nude , Microscopy, Confocal , Microscopy, Electron, Transmission , Molecular Sequence Data , Nanoparticles/ultrastructure , Particle Size , Peptides/metabolism , Peptides/pharmacology , Protein Binding , Receptors, CXCR4/antagonists & inhibitors , Receptors, CXCR4/chemistry , Receptors, CXCR4/metabolism
12.
Chem Sci ; 15(11): 4041-4053, 2024 Mar 13.
Article in English | MEDLINE | ID: mdl-38487241

ABSTRACT

Conformational switching is pervasively driven by protein interactions, particularly for intrinsically disordered binding partners. We developed a dually orthogonal fluorescence-based assay to monitor such events, exploiting environmentally sensitive fluorophores. This assay is applied to E3 ligase E6AP, as its AZUL domain induces a disorder-to-order switch in an intrinsically disordered region of the proteasome, the so-named Rpn10 AZUL-binding domain (RAZUL). By testing various fluorophores, we developed an assay appropriate for high-throughput screening of Rpn10:E6AP-disrupting ligands. We found distinct positions in RAZUL for fluorophore labeling with either acrylodan or Atto610, which had disparate spectral responses to E6AP binding. E6AP caused a hypsochromic shift with increased fluorescence of acrylodan-RAZUL while decreasing fluorescence intensity of Atto610-RAZUL. Combining RAZUL labeled with either acrylodan or Atto610 into a common sample achieved robust and orthogonal measurement of the E6AP-induced conformational switch. This approach is generally applicable to disorder-to-order (or vice versa) transitions mediated by molecular interactions.

13.
J Biol Chem ; 287(17): 14192-200, 2012 Apr 20.
Article in English | MEDLINE | ID: mdl-22378781

ABSTRACT

Phosphorylation of signal transducer and activator of transcription 3 (STAT3) on a single tyrosine residue in response to growth factors, cytokines, interferons, and oncogenes activates its dimerization, translocation to the nucleus, binding to the interferon γ (gamma)-activated sequence (GAS) DNA-binding site and activation of transcription of target genes. STAT3 is constitutively phosphorylated in various cancers and drives gene expression from GAS-containing promoters to promote tumorigenesis. Recently, roles for unphosphorylated STAT3 (U-STAT3) have been described in response to cytokine stimulation, in cancers, and in maintenance of heterochromatin stability. However, the mechanisms underlying U-STAT3 binding to DNA has not been fully investigated. Here, we explore STAT3-DNA interactions by atomic force microscopy (AFM) imaging. We observed that U-STAT3 molecules bind to the GAS DNA-binding site as dimers and monomers. In addition, we observed that U-STAT3 binds to AT-rich DNA sequence sites and recognizes specific DNA structures, such as 4-way junctions and DNA nodes, within negatively supercoiled plasmid DNA. These structures are important for chromatin organization and our data suggest a role for U-STAT3 as a chromatin/genome organizer. Unexpectedly, we found that a C-terminal truncated 67.5-kDa STAT3 isoform recognizes single-stranded spacers within cruciform structures that also have a role in chromatin organization and gene expression. This isoform appears to be abundant in the nuclei of cancer cells and, therefore, may have a role in regulation of gene expression. Taken together, our data highlight novel mechanisms by which U-STAT3 binds to DNA and supports U-STAT3 function as a transcriptional activator and a chromatin/genomic organizer.


Subject(s)
Chromatin/chemistry , DNA/chemistry , STAT3 Transcription Factor/metabolism , Binding Sites , Cell Line, Tumor , Female , Gene Expression Regulation, Neoplastic , Humans , Kinetics , Male , Microscopy, Atomic Force/methods , Phosphorylation , Plasmids/metabolism , Protein Binding , Protein Isoforms , Protein Structure, Tertiary , Subcellular Fractions
14.
Nucleic Acids Res ; 39(17): 7803-15, 2011 Sep 01.
Article in English | MEDLINE | ID: mdl-21652641

ABSTRACT

Processive transcription antitermination requires the assembly of the complete antitermination complex, which is initiated by the formation of the ternary NusB-NusE-BoxA RNA complex. We have elucidated the crystal structure of this complex, demonstrating that the BoxA RNA is composed of 8 nt that are recognized by the NusB-NusE heterodimer. Functional biologic and biophysical data support the structural observations and establish the relative significance of key protein-protein and protein-RNA interactions. Further crystallographic investigation of a NusB-NusE-dsRNA complex reveals a heretofore unobserved dsRNA binding site contiguous with the BoxA binding site. We propose that the observed dsRNA represents BoxB RNA, as both single-stranded BoxA and double-stranded BoxB components are present in the classical lambda antitermination site. Combining these data with known interactions amongst antitermination factors suggests a specific model for the assembly of the complete antitermination complex.


Subject(s)
Bacterial Proteins/chemistry , Escherichia coli Proteins/chemistry , RNA-Binding Proteins/chemistry , RNA/chemistry , Ribosomal Proteins/chemistry , Transcription Factors/chemistry , Amino Acid Sequence , Bacterial Proteins/genetics , Binding Sites , Escherichia coli Proteins/genetics , Genetic Complementation Test , Models, Molecular , Molecular Sequence Data , Mutation , Phenotype , Protein Multimerization , RNA, Double-Stranded/metabolism , RNA-Binding Proteins/genetics , Ribosomal Proteins/genetics , Transcription Factors/genetics , Transcription, Genetic
15.
Front Oncol ; 13: 1144153, 2023.
Article in English | MEDLINE | ID: mdl-37182134

ABSTRACT

STAT3 N-terminal domain is a promising molecular target for cancer treatment and modulation of immune responses. However, STAT3 is localized in the cytoplasm, mitochondria, and nuclei, and thus, is inaccessible to therapeutic antibodies. Its N-terminal domain lacks deep pockets on the surface and represents a typical "non-druggable" protein. In order to successfully identify potent and selective inhibitors of the domain, we have used virtual screening of billion structure-sized virtual libraries of make-on-demand screening samples. The results suggest that the expansion of accessible chemical space by cutting-edge ultra-large virtual compound databases can lead to successful development of small molecule drugs for hard-to-target intracellular proteins.

16.
Proc Natl Acad Sci U S A ; 106(12): 4665-70, 2009 Mar 24.
Article in English | MEDLINE | ID: mdl-19255450

ABSTRACT

The oncoproteins MDM2 and MDMX negatively regulate the activity and stability of the tumor suppressor protein p53--a cellular process initiated by MDM2 and/or MDMX binding to the N-terminal transactivation domain of p53. MDM2 and MDMX in many tumors confer p53 inactivation and tumor survival, and are important molecular targets for anticancer therapy. We screened a duodecimal peptide phage library against site-specifically biotinylated p53-binding domains of human MDM2 and MDMX chemically synthesized via native chemical ligation, and identified several peptide inhibitors of the p53-MDM2/MDMX interactions. The most potent inhibitor (TSFAEYWNLLSP), termed PMI, bound to MDM2 and MDMX at low nanomolar affinities--approximately 2 orders of magnitude stronger than the wild-type p53 peptide of the same length (ETFSDLWKLLPE). We solved the crystal structures of synthetic MDM2 and MDMX, both in complex with PMI, at 1.6 A resolution. Comparative structural analysis identified an extensive, tightened intramolecular H-bonding network in bound PMI that contributed to its conformational stability, thus enhanced binding to the 2 oncogenic proteins. Importantly, the C-terminal residue Pro of PMI induced formation of a hydrophobic cleft in MDMX previously unseen in the structures of p53-bound MDM2 or MDMX. Our findings deciphered the structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMX, shedding new light on structure-based rational design of different classes of p53 activators for potential therapeutic use.


Subject(s)
Nuclear Proteins/chemistry , Nuclear Proteins/metabolism , Oligopeptides/pharmacology , Peptides/pharmacology , Proto-Oncogene Proteins c-mdm2/chemistry , Proto-Oncogene Proteins c-mdm2/metabolism , Proto-Oncogene Proteins/chemistry , Proto-Oncogene Proteins/metabolism , Tumor Suppressor Protein p53/chemistry , Tumor Suppressor Protein p53/metabolism , Amino Acid Sequence , Cell Cycle Proteins , Humans , Models, Molecular , Molecular Sequence Data , Oligopeptides/chemistry , Oligopeptides/metabolism , Peptide Library , Peptides/chemistry , Peptides/metabolism , Protein Binding/drug effects , Protein Structure, Secondary , Structure-Activity Relationship
17.
J Biol Chem ; 285(25): 19572-81, 2010 Jun 18.
Article in English | MEDLINE | ID: mdl-20382735

ABSTRACT

A retro-inverso peptide is made up of d-amino acids in a reversed sequence and, when extended, assumes a side chain topology similar to that of its parent molecule but with inverted amide peptide bonds. Despite their limited success as antigenic mimicry, retro-inverso isomers generally fail to emulate the protein-binding activities of their parent peptides of an alpha-helical nature. In studying the interaction between the tumor suppressor protein p53 and its negative regulator MDM2, Sakurai et al. (Sakurai, K., Chung, H. S., and Kahne, D. (2004) J. Am. Chem. Soc. 126, 16288-16289) made a surprising finding that the retro-inverso isomer of p53(15-29) retained the same binding activity as the wild type peptide as determined by inhibition enzyme-linked immunosorbent assay. The authors attributed the unusual outcome to the ability of the D-peptide to adopt a right-handed helical conformation upon MDM2 binding. Using a battery of biochemical and biophysical tools, we found that retro-inverso isomerization diminished p53 (15-29) binding to MDM2 or MDMX by 3.2-3.3 kcal/mol. Similar results were replicated with the C-terminal domain of HIV-1 capsid protein (3.0 kcal/mol) and the Src homology 3 domain of Abl tyrosine kinase (3.4 kcal/mol). CD and NMR spectroscopic as well as x-ray crystallographic studies showed that D-peptide ligands of MDM2 invariably adopted left-handed helical conformations in both free and bound states. Our findings reinforce that the retro-inverso strategy works poorly in molecular mimicry of biologically active helical peptides, due to inherent differences at the secondary and tertiary structure levels between an l-peptide and its retro-inverso isomer despite their similar side chain topologies at the primary structure level.


Subject(s)
Enzyme-Linked Immunosorbent Assay/methods , Peptides/chemistry , Capsid/chemistry , Cell Cycle Proteins , Crystallography, X-Ray/methods , HIV-1/metabolism , Humans , Models, Molecular , Molecular Mimicry/drug effects , Nuclear Proteins/chemistry , Protein Binding , Protein Conformation , Protein Structure, Tertiary , Proto-Oncogene Proteins/chemistry , Proto-Oncogene Proteins c-mdm2/chemistry , Tumor Suppressor Protein p53/chemistry , Ubiquitin-Protein Ligases/chemistry
18.
Chembiochem ; 12(6): 914-21, 2011 Apr 11.
Article in English | MEDLINE | ID: mdl-21365731

ABSTRACT

Isolated protein motifs that are involved in interactions with their binding partners can be used to inhibit these interactions. However, peptides corresponding to protein fragments tend to have no defined secondary or tertiary structure in the absence of scaffolding by the rest of protein molecule. This results in low inhibitor potency. NMR and CD spectroscopy studies of lipopeptide inhibitors of the Hedgehog pathway revealed that membrane anchoring allows the cell membrane to function as a scaffold and facilitate the folding of short peptides. In addition, lipidation enhances cell permeability and increases the concentration of the compounds near the membrane, thus facilitating potent inhibition. The general applicability of this rational approach was further confirmed by the generation of selective antagonists of the insulin-like growth factor 1 receptor with GI(50) values in the nanomolar range. Lipopeptides corresponding to protein fragments were found to serve as potent and selective inhibitors of a number of nondruggable molecular targets.


Subject(s)
Hedgehog Proteins/antagonists & inhibitors , Peptides/chemistry , Amino Acid Sequence , Cell Line, Tumor , Cell Membrane Permeability/drug effects , Circular Dichroism , Hedgehog Proteins/metabolism , Humans , Magnetic Resonance Spectroscopy , Molecular Sequence Data , Peptides/pharmacology , Protein Structure, Tertiary , Receptor, IGF Type 1/antagonists & inhibitors , Receptor, IGF Type 1/metabolism
19.
Methods Mol Biol ; 2208: 135-148, 2021.
Article in English | MEDLINE | ID: mdl-32856260

ABSTRACT

Synthetic analogs of the second transmembrane domain (TM) containing a portion of the extracellular loop 1 of G-protein-coupled receptors (GPCR) can serve as biased antagonists of the corresponding receptor. Analogs with negative charges added to the extracellular end self-assemble into round structures. Addition of polyethylene glycol chains of defined length to the C-terminus of the peptides prevents super aggregation and results in highly uniform particles that can fuse with cell membranes spontaneously. Added PEG chains slow down cell fusion, while attachment of receptor ligands to the surface of particles results in receptor-mediated membrane fusion and cell-selective delivery. Critical assembly concentration of TM peptide particles is in the nanomolar range and thus requires nontraditional methods of determination. In this chapter, we outline sequence selection and design of self-assembling GPCR antagonists, methods of the preparation of the nanoparticles, and biophysical methods of particle characterization. The protocols allow for straightforward rational design, generation, and characterization of self-assembling GPCR antagonists for a variety of applications.


Subject(s)
Peptides/chemistry , Receptors, G-Protein-Coupled/antagonists & inhibitors , Receptors, G-Protein-Coupled/chemistry , Amino Acid Sequence , Cell Membrane/chemistry , Nanoparticles/chemistry , Polyethylene Glycols/chemistry , Protein Domains
20.
Nat Commun ; 12(1): 7318, 2021 12 16.
Article in English | MEDLINE | ID: mdl-34916494

ABSTRACT

Proteasome substrate receptor hRpn13 is a promising anti-cancer target. By integrated in silico and biophysical screening, we identified a chemical scaffold that binds hRpn13 with non-covalent interactions that mimic the proteasome and a weak electrophile for Michael addition. hRpn13 Pru domain binds proteasomes and ubiquitin whereas its DEUBAD domain binds deubiquitinating enzyme UCHL5. NMR revealed lead compound XL5 to interdigitate into a hydrophobic pocket created by lateral movement of a Pru ß-hairpin with an exposed end for Proteolysis Targeting Chimeras (PROTACs). Implementing XL5-PROTACs as chemical probes identified a DEUBAD-lacking hRpn13 species (hRpn13Pru) present naturally with cell type-dependent abundance. XL5-PROTACs preferentially target hRpn13Pru, causing its ubiquitination. Gene-editing and rescue experiments established hRpn13 requirement for XL5-PROTAC-triggered apoptosis. These data establish hRpn13 as an anti-cancer target for multiple myeloma and introduce an hRpn13-targeting scaffold that can be optimized for preclinical trials against hRpn13Pru-producing cancer types.


Subject(s)
Intracellular Signaling Peptides and Proteins/chemistry , Intracellular Signaling Peptides and Proteins/metabolism , Multiple Myeloma/metabolism , Ubiquitination , Apoptosis , Cell Line, Tumor , Gene Expression Regulation, Neoplastic , Humans , Intracellular Signaling Peptides and Proteins/genetics , Multiple Myeloma/genetics , Proteasome Endopeptidase Complex/metabolism , Transcription Factors/metabolism , Transcriptional Activation , Ubiquitin/metabolism
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