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1.
Cell ; 184(9): 2471-2486.e20, 2021 04 29.
Article in English | MEDLINE | ID: mdl-33878291

ABSTRACT

Metastasis has been considered as the terminal step of tumor progression. However, recent genomic studies suggest that many metastases are initiated by further spread of other metastases. Nevertheless, the corresponding pre-clinical models are lacking, and underlying mechanisms are elusive. Using several approaches, including parabiosis and an evolving barcode system, we demonstrated that the bone microenvironment facilitates breast and prostate cancer cells to further metastasize and establish multi-organ secondary metastases. We uncovered that this metastasis-promoting effect is driven by epigenetic reprogramming that confers stem cell-like properties on cancer cells disseminated from bone lesions. Furthermore, we discovered that enhanced EZH2 activity mediates the increased stemness and metastasis capacity. The same findings also apply to single cell-derived populations, indicating mechanisms distinct from clonal selection. Taken together, our work revealed an unappreciated role of the bone microenvironment in metastasis evolution and elucidated an epigenomic reprogramming process driving terminal-stage, multi-organ metastases.


Subject(s)
Bone Neoplasms/secondary , Breast Neoplasms/pathology , Neoplasm Metastasis , Prostatic Neoplasms/pathology , Tumor Microenvironment , Animals , Apoptosis , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Bone Neoplasms/genetics , Bone Neoplasms/metabolism , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Cell Proliferation , Disease Progression , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Male , Mice , Mice, Inbred C57BL , Mice, Inbred NOD , Mice, Nude , Mice, SCID , Prostatic Neoplasms/genetics , Prostatic Neoplasms/metabolism , Tumor Cells, Cultured , Xenograft Model Antitumor Assays
2.
J Am Chem Soc ; 146(27): 18292-18297, 2024 Jul 10.
Article in English | MEDLINE | ID: mdl-38941563

ABSTRACT

We investigated the metal-substituted catalytic activity of human cysteamine dioxygenase (ADO), an enzyme pivotal in regulating thiol metabolism and contributing to oxygen homeostasis. Our findings demonstrate the catalytic competence of cobalt(II)- and nickel(II)-substituted ADO in cysteamine oxygenation. Notably, Co(II)-ADO exhibited superiority over Ni(II)-ADO despite remaining significantly less active than the natural enzyme. Structural analyses through X-ray crystallography and cobalt K-edge excitation confirmed successful metal substitution with minimal structural perturbations. This provided a robust structural basis, supporting a conserved catalytic mechanism tailored to distinct metal centers. This finding challenges the proposed high-valent ferryl-based mechanism for thiol dioxygenases, suggesting a non-high-valent catalytic pathway in the native enzyme. Further investigation of the cysteamine-bound or a peptide mimic of N-terminus RGS5 bound Co(II)-ADO binary complex revealed the metal center's high-spin (S = 3/2) state. Upon reaction with O2, a kinetically and spectroscopically detectable intermediate emerged with a ground spin state of S = 1/2. This intermediate exhibits a characteristic 59Co hyperfine splitting (A = 67 MHz) structure in the EPR spectrum alongside UV-vis features, consistent with known low-spin Co(III)-superoxo complexes. This observation, unique for protein-bound thiolate-ligated cobalt centers in a protein, unveils the capacities for O2 activation in such metal environments. These findings provide valuable insights into the non-heme iron-dependent thiol dioxygenase mechanistic landscape, furthering our understanding of thiol metabolism regulation. The exploration of metal-substituted ADO sheds light on the intricate interplay between metal and catalytic activity in this essential enzyme.


Subject(s)
Cobalt , Dioxygenases , Cobalt/chemistry , Cobalt/metabolism , Dioxygenases/metabolism , Dioxygenases/chemistry , Humans , Oxygen/chemistry , Oxygen/metabolism , Crystallography, X-Ray , Models, Molecular , Coordination Complexes/chemistry , Coordination Complexes/metabolism
3.
Angew Chem Int Ed Engl ; : e202407018, 2024 Sep 19.
Article in English | MEDLINE | ID: mdl-39300819

ABSTRACT

Bifunctional catalase-peroxidase (KatG) features a posttranslational methionine-tyrosine-tryptophan (MYW) crosslinked cofactor crucial for its catalase function, enabling pathogens to neutralize hydrogen peroxide during infection. We discovered the presence of indole nitrogen-linked hydroperoxyl adduct (MYW-OOH) in Mycobacterium tuberculosis KatG in the solution state under ambient conditions, suggesting its natural occurrence. By isolating predominantly MYW-OOH-containing KatG protein, we investigated the chemical stability and functional impact of MYW-OOH. We discovered that MYW-OOH inhibits catalase activity, presenting a unique temporary lock. Exposure to peroxide or increased temperature removes the hydroperoxyl adduct from the protein cofactor, converting MYW-OOH to MYW and restoring the detoxifying ability of the enzyme against hydrogen peroxide. Thus, the N-linked hydroperoxyl group is releasable. KatG with MYW-OOH represents a catalase dormant, but primed, state of the enzyme. These findings provide insight into chemical strategies targeting the bifunctional enzyme KatG in pathogens, highlighting the role of N-linked hydroperoxyl modifications in enzymatic function.

4.
J Biol Chem ; 297(4): 101176, 2021 10.
Article in English | MEDLINE | ID: mdl-34508780

ABSTRACT

Cysteamine dioxygenase (ADO) plays a vital role in regulating thiol metabolism and preserving oxygen homeostasis in humans by oxidizing the sulfur of cysteamine and N-terminal cysteine-containing proteins to their corresponding sulfinic acids using O2 as a cosubstrate. However, as the only thiol dioxygenase that processes both small-molecule and protein substrates, how ADO handles diverse substrates of disparate sizes to achieve various reactions is not understood. The knowledge gap is mainly due to the three-dimensional structure not being solved, as ADO cannot be directly compared with other known thiol dioxygenases. Herein, we report the first crystal structure of human ADO at a resolution of 1.78 Å with a nickel-bound metal center. Crystallization was achieved through both metal substitution and C18S/C239S double mutations. The metal center resides in a tunnel close to an entry site flanked by loops. While ADO appears to use extensive flexibility to handle substrates of different sizes, it also employs proline and proline pairs to maintain the core protein structure and to retain the residues critical for catalysis in place. This feature distinguishes ADO from thiol dioxygenases that only oxidize small-molecule substrates, possibly explaining its divergent substrate specificity. Our findings also elucidate the structural basis for ADO functioning as an oxygen sensor by modifying N-degron substrates to transduce responses to hypoxia. Thus, this work fills a gap in structure-function relationships of the thiol dioxygenase family and provides a platform for further mechanistic investigation and therapeutic intervention targeting impaired oxygen sensing.


Subject(s)
Dioxygenases/chemistry , Oxygen/chemistry , Amino Acid Substitution , Dioxygenases/genetics , Dioxygenases/metabolism , Humans , Mutation, Missense , Nickel/chemistry , Nickel/metabolism , Oxygen/metabolism , Protein Domains , Structure-Activity Relationship
5.
Molecules ; 26(3)2021 Jan 21.
Article in English | MEDLINE | ID: mdl-33494451

ABSTRACT

HupZ is an expected heme degrading enzyme in the heme acquisition and utilization pathway in Group A Streptococcus. The isolated HupZ protein containing a C-terminal V5-His6 tag exhibits a weak heme degradation activity. Here, we revisited and characterized the HupZ-V5-His6 protein via biochemical, mutagenesis, protein quaternary structure, UV-vis, EPR, and resonance Raman spectroscopies. The results show that the ferric heme-protein complex did not display an expected ferric EPR signal and that heme binding to HupZ triggered the formation of higher oligomeric states. We found that heme binding to HupZ was an O2-dependent process. The single histidine residue in the HupZ sequence, His111, did not bind to the ferric heme, nor was it involved with the weak heme-degradation activity. Our results do not favor the heme oxygenase assignment because of the slow binding of heme and the newly discovered association of the weak heme degradation activity with the His6-tag. Altogether, the data suggest that the protein binds heme by its His6-tag, resulting in a heme-induced higher-order oligomeric structure and heme stacking. This work emphasizes the importance of considering exogenous tags when interpreting experimental observations during the study of heme utilization proteins.


Subject(s)
Bacterial Proteins/chemistry , Heme/chemistry , Streptococcus pyogenes/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Heme/genetics , Heme/metabolism , Protein Binding , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Streptococcus pyogenes/genetics , Streptococcus pyogenes/metabolism
6.
J Am Chem Soc ; 142(44): 18753-18757, 2020 11 04.
Article in English | MEDLINE | ID: mdl-33091303

ABSTRACT

Galactose oxidase (GAO) contains a Cu(II)-ligand radical cofactor. The cofactor, which is autocatalytically generated through the oxidation of the copper, consists of a cysteine-tyrosine radical (Cys-Tyr•) as a copper ligand. The formation of the cross-linked thioether bond is accompanied by a C-H bond scission on Tyr272 with few details known thus far. Here, we report the genetic incorporation of 3,5-dichlorotyrosine (Cl2-Tyr) and 3,5-difluorotyrosine (F2-Tyr) to replace Tyr272 in the GAOV previously optimized for expression through directed evolution. The proteins with an unnatural tyrosine residue are catalytically competent. We determined the high-resolution crystal structures of the GAOV, Cl2-Tyr272, and F2-Tyr272 incorporated variants at 1.48, 1.23, and 1.80 Šresolution, respectively. The structural data showed only one halogen remained in the cofactor, indicating that an oxidative carbon-chlorine/fluorine bond scission has occurred during the autocatalytic process of cofactor biogenesis. Using hydroxyurea as a radical scavenger, the spin-coupled hidden Cu(II) was observed by EPR spectroscopy. Thus, the structurally defined catalytic center with genetic unnatural tyrosine substitution is in the radical containing form as in the wild-type, i.e., Cu(II)-(Cl-Tyr•-Cys) or Cu(II)-(F-Tyr•-Cys). These findings illustrate a previously unobserved C-F/C-Cl bond cleavage in biology mediated by a mononuclear copper center.


Subject(s)
Carbon/chemistry , Copper/chemistry , Fluorine/chemistry , Free Radicals/chemistry , Galactose Oxidase/metabolism , Tyrosine/chemistry , Catalysis , Crystallography, X-Ray , Directed Molecular Evolution , Electron Spin Resonance Spectroscopy , Galactose Oxidase/chemistry , Galactose Oxidase/genetics , Kinetics , Ligands , Mutagenesis, Site-Directed , Oxidation-Reduction , Protein Structure, Tertiary , Tyrosine/analogs & derivatives , Tyrosine/metabolism
7.
Nat Chem Biol ; 14(9): 853-860, 2018 09.
Article in English | MEDLINE | ID: mdl-29942080

ABSTRACT

Cysteine dioxygenase (CDO) plays an essential role in sulfur metabolism by regulating homeostatic levels of cysteine. Human CDO contains a post-translationally generated Cys93-Tyr157 cross-linked cofactor. Here, we investigated this Cys-Tyr cross-linking by incorporating unnatural tyrosines in place of Tyr157 via a genetic method. The catalytically active variants were obtained with a thioether bond between Cys93 and the halogen-substituted Tyr157, and we determined the crystal structures of both wild-type and engineered CDO variants in the purely uncross-linked form and with a mature cofactor. Along with mass spectrometry and 19F NMR, these data indicated that the enzyme could catalyze oxidative C-F or C-Cl bond cleavage, resulting in a substantial conformational change of both Cys93 and Tyr157 during cofactor assembly. These findings provide insights into the mechanism of Cys-Tyr cofactor biogenesis and may aid the development of bioinspired aromatic carbon-halogen bond activation.


Subject(s)
Carbon/metabolism , Cysteine Dioxygenase/metabolism , Fluorine/metabolism , Protein Engineering , Biocatalysis , Carbon/chemistry , Crystallography, X-Ray , Cysteine Dioxygenase/analysis , Fluorine/chemistry , Humans , Models, Molecular
8.
Biochemistry ; 58(17): 2218-2227, 2019 04 30.
Article in English | MEDLINE | ID: mdl-30946568

ABSTRACT

Cysteine dioxygenase (CDO) is a nonheme iron enzyme that adds two oxygen atoms from dioxygen to the sulfur atom of l-cysteine. Adjacent to the iron site of mammalian CDO, there is a post-translationally generated Cys-Tyr cofactor, whose presence substantially enhances the oxygenase activity. The formation of the Cys-Tyr cofactor in CDO is an autocatalytic process, and it is challenging to study by traditional techniques because the cross-linking reaction is a side, uncoupled, single-turnover oxidation buried among multiple turnovers of l-cysteine oxygenation. Here, we take advantage of our recent success in obtaining a purely uncross-linked human CDO due to site-specific incorporation of 3,5-difluoro-l-tyrosine (F2-Tyr) at the cross-linking site through the genetic code expansion strategy. Using EPR spectroscopy, we show that nitric oxide (•NO), an oxygen surrogate, similarly binds to uncross-linked F2-Tyr157 CDO as in wild-type human CDO. We determined X-ray crystal structures of uncross-linked F2-Tyr157 CDO and mature wild-type CDO in complex with both l-cysteine and •NO. These structural data reveal that the active site cysteine (Cys93 in the human enzyme), rather than the generally expected tyrosine (i.e., Tyr157), is well-aligned to be oxidized should the normal oxidation reaction uncouple. This structure-based understanding is further supported by a computational study with models built on the uncross-linked ternary complex structure. Together, these results strongly suggest that the first target to oxidize during the iron-assisted Cys-Tyr cofactor biogenesis is Cys93. Based on these data, a plausible reaction mechanism implementing a cysteine radical involved in the cross-link formation is proposed.


Subject(s)
Cysteine Dioxygenase/chemistry , Dipeptides/chemistry , Protein Conformation , Tyrosine/analogs & derivatives , Catalytic Domain , Cross-Linking Reagents/chemistry , Crystallography, X-Ray , Cysteine/chemistry , Cysteine/genetics , Cysteine/metabolism , Cysteine Dioxygenase/genetics , Cysteine Dioxygenase/metabolism , Dipeptides/metabolism , Electron Spin Resonance Spectroscopy , Humans , Models, Molecular , Nitric Oxide/chemistry , Nitric Oxide/metabolism , Oxidation-Reduction , Oxygen/chemistry , Oxygen/metabolism , Protein Binding , Tyrosine/chemistry , Tyrosine/genetics , Tyrosine/metabolism
9.
Optom Vis Sci ; 95(4): 299-308, 2018 04.
Article in English | MEDLINE | ID: mdl-29561496

ABSTRACT

SIGNIFICANCE: Measured corneal biomechanical properties are driven by intraocular pressure, tissue thickness, and inherent material properties. We demonstrate tissue thickness as an important factor in the measurement of corneal biomechanics that can confound short-term effects due to UV riboflavin cross-linking (CXL) treatment. PURPOSE: We isolate the effects of tissue thickness on the measured corneal biomechanical properties using optical coherence elastography by experimentally altering the tissue hydration state and stiffness. METHODS: Dynamic optical coherence elastography was performed using phase-sensitive optical coherence tomography imaging to quantify the tissue deformation dynamics resulting from a spatially discrete, low-force air pulse (150-µm spot size; 0.8-millisecond duration; <10 Pa [<0.08 mmHg]). The time-dependent surface deformation is characterized by a viscoelastic tissue recovery response, quantified by an exponential decay constant-relaxation rate. Ex vivo rabbit globes (n = 10) with fixed intraocular pressure (15 mmHg) were topically instilled every 5 minutes with 0.9% saline for 60 minutes and 20% dextran for another 60 minutes. Measurements were made after every 20 minutes to determine the central corneal thickness (CCT) and the relaxation rates. Cross-linking treatment was performed on another 13 eyes, applying isotonic riboflavin (n = 6) and hypertonic riboflavin (n = 7) every 5 minutes for 30 minutes, followed by UV irradiation (365 nm, 3 mW/cm) for 30 minutes while instilling riboflavin. Central corneal thickness and relaxation rates were obtained before and after CXL treatment. RESULTS: Corneal thickness was positively correlated (R = 0.9) with relaxation rates. In the CXL-treated eyes, isotonic riboflavin did not affect CCT and showed a significant increase in relaxation rates (+10%; P = .01) from 2.29 ms to 2.53 ms. Hypertonic riboflavin showed a significant CCT decrease (-31%; P = .01) from 618 µm to 429 µm but showed little change in relaxation rates after CXL treatment. CONCLUSIONS: Corneal thickness and stiffness are correlated positively. A higher relaxation rate implied stiffer material properties after isotonic CXL treatment. Hypertonic CXL treatment results in a stiffness decrease that offsets the stiffness increase with CXL treatment.


Subject(s)
Cornea/physiopathology , Elasticity Imaging Techniques , Elasticity/physiology , Photosensitizing Agents/pharmacology , Riboflavin/pharmacology , Animals , Biomechanical Phenomena , Collagen/metabolism , Cornea/diagnostic imaging , Corneal Stroma/drug effects , Corneal Stroma/metabolism , Cross-Linking Reagents , Intraocular Pressure/drug effects , Organ Size , Osmolar Concentration , Rabbits , Tomography, Optical Coherence , Tonometry, Ocular , Ultraviolet Rays
10.
Angew Chem Int Ed Engl ; 57(27): 8149-8153, 2018 07 02.
Article in English | MEDLINE | ID: mdl-29752763

ABSTRACT

Cysteamine dioxygenase (ADO) is a thiol dioxygenase whose study has been stagnated by the ambiguity as to whether or not it possesses an anticipated protein-derived cofactor. Reported herein is the discovery and elucidation of a Cys-Tyr cofactor in human ADO, crosslinked between Cys220 and Tyr222 through a thioether (C-S) bond. By genetically incorporating an unnatural amino acid, 3,5-difluoro-tyrosine (F2 -Tyr), specifically into Tyr222 of human ADO, an autocatalytic oxidative carbon-fluorine bond activation and fluoride release were identified by mass spectrometry and 19 F NMR spectroscopy. These results suggest that the cofactor biogenesis is executed by a powerful oxidant during an autocatalytic process. Unlike that of cysteine dioxygenase, the crosslinking results in a minimal structural change of the protein and it is not detectable by routine low-resolution techniques. Finally, a new sequence motif, C-X-Y-Y(F), is proposed for identifying the Cys-Tyr crosslink.


Subject(s)
Dioxygenases/metabolism , Tyrosine/metabolism , Amino Acid Motifs , Carbon/chemistry , Catalytic Domain , Cysteine/chemistry , Cysteine/metabolism , Cysteine Dioxygenase/chemistry , Cysteine Dioxygenase/metabolism , Dioxygenases/chemistry , Fluorine/chemistry , Humans , Nuclear Magnetic Resonance, Biomolecular , Oxidation-Reduction , Protein Structure, Tertiary , Tyrosine/chemistry
11.
J Biol Inorg Chem ; 22(2-3): 395-405, 2017 04.
Article in English | MEDLINE | ID: mdl-28084551

ABSTRACT

Molecular oxygen is utilized in numerous metabolic pathways fundamental for life. Mononuclear nonheme iron-dependent oxygenase enzymes are well known for their involvement in some of these pathways, activating O2 so that oxygen atoms can be incorporated into their primary substrates. These reactions often initiate pathways that allow organisms to use stable organic molecules as sources of carbon and energy for growth. From the myriad of reactions in which these enzymes are involved, this perspective recounts the general mechanisms of aromatic dihydroxylation and oxidative ring cleavage, both of which are ubiquitous chemical reactions found in life-sustaining processes. The organic substrate provides all four electrons required for oxygen activation and insertion in the reactions mediated by extradiol and intradiol ring-cleaving catechol dioxygenases. In contrast, two of the electrons are provided by NADH in the cis-dihydroxylation mechanism of Rieske dioxygenases. The catalytic nonheme Fe center, with the aid of active site residues, facilitates these electron transfers to O2 as key elements of the activation processes. This review discusses some general questions for the catalytic strategies of oxygen activation and insertion into aromatic compounds employed by mononuclear nonheme iron-dependent dioxygenases. These include: (1) how oxygen is activated, (2) whether there are common intermediates before oxygen transfer to the aromatic substrate, and (3) are these key intermediates unique to mononuclear nonheme iron dioxygenases?


Subject(s)
Dioxygenases/metabolism , Hydrocarbons, Aromatic/metabolism , Iron/metabolism , Oxygen/metabolism , Enzyme Activation
12.
Article in English | MEDLINE | ID: mdl-27547022

ABSTRACT

The mechanical properties of tissues can provide valuable information about tissue integrity and health and can assist in detecting and monitoring the progression of diseases such as keratoconus. Optical coherence elastography (OCE) is a rapidly emerging technique, which can assess localized mechanical contrast in tissues with micrometer spatial resolution. In this work we present a noncontact method of optical coherence elastography to evaluate the changes in the mechanical properties of the cornea after UV-induced collagen cross-linking. A focused air-pulse induced a low amplitude (µm scale) elastic wave, which then propagated radially and was imaged in three dimensions by a phase-stabilized swept source optical coherence tomography (PhS-SSOCT) system. The elastic wave velocity was translated to Young's modulus in agar phantoms of various concentrations. Additionally, the speed of the elastic wave significantly changed in porcine cornea before and after UV-induced corneal collagen cross-linking (CXL). Moreover, different layers of the cornea, such as the anterior stroma, posterior stroma, and inner region, could be discerned from the phase velocities of the elastic wave. Therefore, because of noncontact excitation and imaging, this method may be useful for in vivo detection of ocular diseases such as keratoconus and evaluation of therapeutic interventions such as CXL.

13.
J Am Chem Soc ; 137(23): 7270-3, 2015 Jun 17.
Article in English | MEDLINE | ID: mdl-26020364

ABSTRACT

Electron transfer (ET) is widely used for driving the processes that underlie the chemistry of life. However, our abilities to probe electron transfer mechanisms in proteins and design redox enzymes are limited, due to the lack of methods to site-specifically insert electron acceptors into proteins in vivo. Here we describe the synthesis and genetic incorporation of 4-fluoro-3-nitrophenylalanine (FNO2Phe), which has similar reduction potentials to NAD(P)H and ferredoxin, the most important biological reductants. Through the genetic incorporation of FNO2Phe into green fluorescent protein (GFP) and femtosecond transient absorption measurement, we show that photoinduced electron transfer (PET) from the GFP chromophore to FNO2Phe occurs very fast (within 11 ps), which is comparable to that of the first electron transfer step in photosystem I, from P700* to A0. This genetically encoded, low-reduction potential unnatural amino acid (UAA) can significantly improve our ability to investigate electron transfer mechanisms in complex reductases and facilitate the design of miniature proteins that mimic their functions.


Subject(s)
Green Fluorescent Proteins/chemistry , Green Fluorescent Proteins/genetics , Phenylalanine/analogs & derivatives , Electron Transport , Green Fluorescent Proteins/metabolism , Models, Molecular , Molecular Structure , Phenylalanine/chemistry , Phenylalanine/metabolism , Photochemical Processes
14.
J Am Chem Soc ; 137(14): 4594-7, 2015 Apr 15.
Article in English | MEDLINE | ID: mdl-25672571

ABSTRACT

While a conserved tyrosine (Tyr) is found in oxidases, the roles of phenol ring pKa and reduction potential in O2 reduction have not been defined despite many years of research on numerous oxidases and their models. These issues represent major challenges in our understanding of O2 reduction mechanism in bioenergetics. Through genetic incorporation of unnatural amino acid analogs of Tyr, with progressively decreasing pKa of the phenol ring and increasing reduction potential, in the active site of a functional model of oxidase in myoglobin, a linear dependence of both the O2 reduction activity and the fraction of H2O formation with the pKa of the phenol ring has been established. By using these unnatural amino acids as spectroscopic probe, we have provided conclusive evidence for the location of a Tyr radical generated during reaction with H2O2, by the distinctive hyperfine splitting patterns of the halogenated tyrosines and one of its deuterated derivatives incorporated at the 33 position of the protein. These results demonstrate for the first time that enhancing the proton donation ability of the Tyr enhances the oxidase activity, allowing the Tyr analogs to augment enzymatic activity beyond that of natural Tyr.


Subject(s)
Oxidoreductases/chemistry , Oxidoreductases/metabolism , Protein Engineering , Tyrosine/analogs & derivatives , Tyrosine/metabolism , Catalytic Domain , Methanocaldococcus/enzymology , Models, Molecular , Oxidation-Reduction , Oxidoreductases/genetics
15.
Opt Lett ; 40(11): 2588-91, 2015 Jun 01.
Article in English | MEDLINE | ID: mdl-26030564

ABSTRACT

Shear-wave imaging optical coherence elastography (SWI-OCE) is an emerging method for 3D quantitative assessment of tissue local mechanical properties based on imaging and analysis of elastic wave propagation. Current methods for SWI-OCE involve multiple temporal optical coherence tomography scans (M-mode) at different spatial locations across tissue surface (B- and C-modes). This requires an excitation for each measurement position leading to clinically unacceptable long acquisition times up to tens of minutes. In this Letter, we demonstrate, for the first time, noncontact true kilohertz frame-rate OCE by combining a Fourier domain mode-locked swept source laser with an A-scan rate of ∼1.5 MHz and a focused air-pulse as an elastic wave excitation source. The propagation of the elastic wave in the sample was imaged at a frame rate of ∼7.3 kHz. Therefore, to quantify the elastic wave propagation velocity in a single direction, only a single excitation was needed. This method was validated by quantifying the elasticity of tissue-mimicking agar phantoms as well as of a porcine cornea ex vivo at different intraocular pressures. The results demonstrate that this method can reduce the acquisition time of an elastogram to milliseconds.


Subject(s)
Elasticity Imaging Techniques/methods , Optical Devices , Animals , Cornea/cytology , Elasticity Imaging Techniques/instrumentation , Phantoms, Imaging , Swine
16.
Opt Lett ; 40(20): 4791-4, 2015 Oct 15.
Article in English | MEDLINE | ID: mdl-26469621

ABSTRACT

High-resolution three-dimensional (3D) imaging of cardiovascular dynamics in mouse embryos is greatly desired to study mammalian congenital cardiac defects. Here, we demonstrate direct four-dimensional (4D) imaging of the cardiovascular structure and function in live mouse embryos at a ∼43 Hz volume rate using an optical coherence tomography (OCT) system with a ∼1.5 MHz Fourier domain mode-locking swept laser source. Combining ultrafast OCT imaging with live mouse embryo culture protocols, 3D volumes of the embryo are directly and continuously acquired over time for a cardiodynamics analysis without the application of any synchronization algorithms. We present the time-resolved measurements of the heart wall motion based on the 4D structural data, report 4D speckle variance and Doppler imaging of the vascular system, and quantify spatially resolved blood flow velocity over time. These results indicate that the ultra-high-speed 4D imaging approach could be a useful tool for efficient cardiovascular phenotyping of mouse embryos.


Subject(s)
Heart/embryology , Heart/physiology , Imaging, Three-Dimensional/methods , Tomography, Optical Coherence/methods , Animals , Female , Mice
17.
Angew Chem Int Ed Engl ; 54(15): 4597-602, 2015 Apr 07.
Article in English | MEDLINE | ID: mdl-25694369

ABSTRACT

Advances in RNA research and RNA nanotechnology depend on the ability to manipulate and probe RNA with high precision through chemical approaches, both in vitro and in mammalian cells. However, covalent RNA labeling methods with scope and versatility comparable to those of current protein labeling strategies are underdeveloped. A method is reported for the site- and sequence-specific covalent labeling of RNAs in mammalian cells by using tRNA(Ile2) -agmatidine synthetase (Tias) and click chemistry. The crystal structure of Tias in complex with an azide-bearing agmatine analogue was solved to unravel the structural basis for Tias/substrate recognition. The unique RNA sequence specificity and plastic Tias/substrate recognition enable the site-specific transfer of azide/alkyne groups to an RNA molecule of interest in vitro and in mammalian cells. Subsequent click chemistry reactions facilitate the versatile labeling, functionalization, and visualization of target RNA.


Subject(s)
Alkynes/chemistry , Azides/chemistry , Click Chemistry , Cytidine/analogs & derivatives , Fluorescent Dyes/chemistry , RNA, Transfer/analysis , Animals , Archaea/enzymology , Cell Line , Cytidine/chemistry , Cytidine/metabolism , Humans , Ligases/metabolism , Models, Molecular , Optical Imaging , RNA, Transfer/metabolism , Staining and Labeling
18.
J Am Chem Soc ; 136(38): 13094-7, 2014 Sep 24.
Article in English | MEDLINE | ID: mdl-25197956

ABSTRACT

Photo-induced electron transfer (PET) is ubiquitous for photosynthesis and fluorescent sensor design. However, genetically coded PET sensors are underdeveloped, due to the lack of methods to site-specifically install PET probes on proteins. Here we describe a family of acid and Mn(III) turn-on fluorescent protein (FP) sensors, named iLovU, based on PET and the genetic incorporation of superior PET quenchers in the fluorescent flavoprotein iLov. Using the iLovU PET sensors, we monitored the cytoplasmic acidification process, and achieved Mn(III) fluorescence sensing for the first time. The iLovU sensors should be applicable for studying pH changes in living cells, monitoring biogentic Mn(III) in the environment, and screening for efficient manganese peroxidase, which is highly desirable for lignin degradation and biomass conversion. Our work establishes a platform for many more protein PET sensors, facilitates the de novo design of metalloenzymes harboring redox active residues, and expands our ability to probe protein conformational dynamics.


Subject(s)
Arabidopsis/chemistry , Biosensing Techniques/methods , Cytoplasm/chemistry , Flavoproteins/chemistry , Luminescent Proteins/chemistry , Magnesium/analysis , Plant Proteins/chemistry , Arabidopsis/genetics , Electron Transport , Electrons , Flavoproteins/genetics , Fluorescent Dyes/chemistry , Hydrogen-Ion Concentration , Luminescent Proteins/genetics , Models, Molecular , Plant Proteins/genetics , Protein Engineering
19.
Methods Enzymol ; 703: 147-166, 2024.
Article in English | MEDLINE | ID: mdl-39260994

ABSTRACT

Mammalian cysteamine dioxygenase (ADO), a mononuclear non-heme Fe(II) enzyme with three histidine ligands, plays a key role in cysteamine catabolism and regulation of the N-degron signaling pathway. Despite its importance, the catalytic mechanism of ADO remains elusive. Here, we describe an HPLC-MS assay for characterizing thiol dioxygenase catalytic activities and a metal-substitution approach for mechanistic investigation using human ADO as a model. Two proposed mechanisms for ADO differ in oxygen activation: one involving a high-valent ferryl-oxo intermediate. We hypothesized that substituting iron with a metal that has a disfavored tendency to form high-valent states would discriminate between mechanisms. This chapter details the expression, purification, preparation, and characterization of cobalt-substituted ADO. The new HPLC-MS assay precisely measures enzymatic activity, revealing retained reactivity in the cobalt-substituted enzyme. The results obtained favor the concurrent dioxygen transfer mechanism in ADO. This combined approach provides a powerful tool for studying other non-heme iron thiol oxidizing enzymes.


Subject(s)
Mass Spectrometry , Chromatography, High Pressure Liquid/methods , Humans , Mass Spectrometry/methods , Cobalt/chemistry , Cobalt/metabolism , Dioxygenases/metabolism , Dioxygenases/chemistry , Enzyme Assays/methods , Oxygen/metabolism , Oxidation-Reduction , Liquid Chromatography-Mass Spectrometry
20.
Med Phys ; 50(1): 30-37, 2023 Jan.
Article in English | MEDLINE | ID: mdl-36342301

ABSTRACT

BACKGROUND: Postballoon expansion is considered as an appropriate procedure for adequate stent expansion for coronary bifurcation lesions. Two postballoon expansion procedures are currently recommended: proximal optimization technique (POT)/side/POT and POT/kiss/POT. However, the effects of the two postballoon expansion treatments are different. There is a lack of biomechanical study to quantify the difference. PURPOSE: It is recognized that biomechanical factors influence the occurrence of Major Cardiovascular Adverse Events (MACE), which includes recurrent angina pectoris, acute myocardial infarction and coronary heart disease death. The current paper evaluated the two postexpansion strategies and quantified biomechanical parameters to provide a basis for clinical decisions. METHODS: Based on the CT angiography (CTA) data of a patient diagnosed with coronary bifurcation lesions, a personalized coronary bifurcation lesion model was constructed, and the surgical procedure after two expansions was simulated. The POT/side/POT and POT/kiss/POT expansion procedures were analyzed from the perspective of biomechanics through finite element analysis. The biomechanics factors, including the percentage of stent malapposition and stent occlusion at the side branch (SB) opening, the stent ellipse index of proximal main vessel (PMV) segment, the minimum lumen area of the stent vessel segment and the stress distribution of the vessel wall, were used to quantify clinician concerns about factors affecting patient outcomes. The factors include stent adhesion, SB open stent occlusion, poor stent deformation, patency effect of vessel stenosis, and vessel wall damage. RESULTS: Both postexpansion procedures were successfully simulated. The malapposition rate during POT/side/POT was larger (1.2% vs. 0.42%) and stent occlusion at the SB opening from the cross-section perpendicular to the SB opening after the POT/side/POT procedure was 0.20%, compared with 0.00% after POT/kiss/POT. POT/kiss/POT produced a larger PMV segment stent ellipse index. Minimum lumen area after POT/side/POT was 5.6 mm2 and after POT/kiss/POT 5.9 mm2 . POT/kiss/POT produces an effect of greater vascular stress than POT/side/POT. CONCLUSION: Numerical simulations provide a quantitative analysis to inform clinicians of the differences between preoperative planning and surgical procedures. Biomechanical analysis of the differences between the two postexpansion strategies found that the POT/kiss/POT procedure resulted in better stent fit, less occlusion of the SB open stent and better vascular patency but also resulted in poor stent deformation and caused greater vessel wall stress. The current study informs rationales for clinical understanding of postexpansion strategies.


Subject(s)
Myocardial Infarction , Stents , Humans , Coronary Angiography/methods , Finite Element Analysis , Treatment Outcome
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