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Matsui T, Rajkovic I, Mooers BHM, Liu P, Weiss TM. Adaptable SEC-SAXS data collection for higher quality structure analysis in solution. Protein Sci 2024; 33:e4946. [PMID: 38501481 PMCID: PMC10949327 DOI: 10.1002/pro.4946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/31/2024] [Accepted: 02/10/2024] [Indexed: 03/20/2024]
Abstract
The two major challenges in synchrotron size-exclusion chromatography coupled in-line with small-angle x-ray scattering (SEC-SAXS) experiments are the overlapping peaks in the elution profile and the fouling of radiation-damaged materials on the walls of the sample cell. In recent years, many post-experimental analyses techniques have been developed and applied to extract scattering profiles from these problematic SEC-SAXS data. Here, we present three modes of data collection at the BioSAXS Beamline 4-2 of the Stanford Synchrotron Radiation Lightsource (SSRL BL4-2). The first mode, the High-Resolution mode, enables SEC-SAXS data collection with excellent sample separation and virtually no additional peak broadening from the UHPLC UV detector to the x-ray position by taking advantage of the low system dispersion of the UHPLC. The small bed volume of the analytical SEC column minimizes sample dilution in the column and facilitates data collection at higher sample concentrations with excellent sample economy equal to or even less than that of the conventional equilibrium SAXS method. Radiation damage problems during SEC-SAXS data collection are evaded by additional cleaning of the sample cell after buffer data collection and avoidance of unnecessary exposures through the use of the x-ray shutter control options, allowing sample data collection with a clean sample cell. Therefore, accurate background subtraction can be performed at a level equivalent to the conventional equilibrium SAXS method without requiring baseline correction, thereby leading to more reliable downstream structural analysis and quicker access to new science. The two other data collection modes, the High-Throughput mode and the Co-Flow mode, add agility to the planning and execution of experiments to efficiently achieve the user's scientific objectives at the SSRL BL4-2.
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Affiliation(s)
- Tsutomu Matsui
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Ivan Rajkovic
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Blaine H. M. Mooers
- Department of Biochemistry and PhysiologyUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
- Stephenson Cancer CenterUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
- Laboratory of Biomolecular Structure and FunctionUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
| | - Ping Liu
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
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2
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Nguyen RC, Stagliano C, Liu A. Structural insights into the half-of-sites reactivity in homodimeric and homotetrameric metalloenzymes. Curr Opin Chem Biol 2023; 75:102332. [PMID: 37269676 PMCID: PMC10528533 DOI: 10.1016/j.cbpa.2023.102332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 04/24/2023] [Accepted: 04/29/2023] [Indexed: 06/05/2023]
Abstract
Half-of-sites reactivity in many homodimeric and homotetrameric metalloenzymes has been known for half a century, yet its benefit remains poorly understood. A recently reported cryo-electron microscopy structure has given some clues on the less optimized reactivity of Escherichia coli ribonucleotide reductase with an asymmetric association of α2β2 subunits during catalysis. Moreover, nonequivalence of enzyme active sites has been reported in many other enzymes, possibly as a means of regulation. They are often induced by substrate binding or caused by a critical component introduced from a neighboring subunit in response to substrate loadings, such as in prostaglandin endoperoxide H synthase, cytidine triphosphate synthase, glyoxalase, tryptophan dioxygenase, and several decarboxylases or dehydrogenases. Overall, half-of-sites reactivity is likely not an act of wasting resources but rather a method devised in nature to accommodate catalytic or regulatory needs.
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Affiliation(s)
- Romie C Nguyen
- Department of Chemistry, University of Texas, San Antonio, TX, 78249, USA
| | - Cassadee Stagliano
- Department of Chemistry, University of Texas, San Antonio, TX, 78249, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas, San Antonio, TX, 78249, USA.
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3
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Newton A, McCann L, Huo L, Liu A. Kynurenine Pathway Regulation at Its Critical Junctions with Fluctuation of Tryptophan. Metabolites 2023; 13:metabo13040500. [PMID: 37110158 PMCID: PMC10143591 DOI: 10.3390/metabo13040500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/14/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
The kynurenine pathway (KP) is the primary route for the catabolism of the essential amino acid tryptophan. The central KP metabolites are neurologically active molecules or biosynthetic precursors to critical molecules, such as NAD+. Within this pathway are three enzymes of interest, HAO, ACMSD, and AMSDH, whose substrates and/or products can spontaneously cyclize to form side products such as quinolinic acid (QA or QUIN) and picolinic acid. Due to their unstable nature for spontaneous autocyclization, it might be expected that the levels of these side products would be dependent on tryptophan intake; however, this is not the case in healthy individuals. On top of that, the regulatory mechanisms of the KP remain unknown, even after a deeper understanding of the structure and mechanism of the enzymes that handle these unstable KP metabolic intermediates. Thus, the question arises, how do these enzymes compete with the autocyclization of their substrates, especially amidst increased tryptophan levels? Here, we propose the formation of a transient enzyme complex as a regulatory mechanism for metabolite distribution between enzymatic and non-enzymatic routes during periods of increased metabolic intake. Amid high levels of tryptophan, HAO, ACMSD, and AMSDH may bind together, forming a tunnel to shuttle the metabolites through each enzyme, consequently regulating the autocyclization of their products. Though further research is required to establish the formation of transient complexation as a solution to the regulatory mysteries of the KP, our docking model studies support this new hypothesis.
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Affiliation(s)
- Ashley Newton
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Luree McCann
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Lu Huo
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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4
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Cianci M, Giacchè N, Cialabrini L, Carotti A, Liscio P, Rosatelli E, De Franco F, Gasparrini M, Robertson J, Amici A, Raffaelli N, Pellicciari R. Structural Basis of Human Dimeric α-Amino-β-Carboxymuconate-ε-Semialdehyde Decarboxylase Inhibition With TES-1025. Front Mol Biosci 2022; 9:834700. [PMID: 35463964 PMCID: PMC9021598 DOI: 10.3389/fmolb.2022.834700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Human α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD) stands at a branch point of the de novo NAD+ synthesis pathway and plays an important role in maintaining NAD+ homeostasis. It has been recently identified as a novel therapeutic target for a wide range of diseases, including inflammatory, metabolic disorders, and aging. So far, in absence of potent and selective enzyme inhibitors, only a crystal structure of the complex of human dimeric ACMSD with pseudo-substrate dipicolinic acid has been resolved. In this study, we report the crystal structure of the complex of human dimeric ACMSD with TES-1025, the first nanomolar inhibitor of this target, which shows a binding conformation different from the previously published predicted binding mode obtained by docking experiments. The inhibitor has a Ki value of 0.85 ± 0.22 nM and binds in the catalytic site, interacting with the Zn2+ metal ion and with residues belonging to both chains of the dimer. The results provide new structural information about the mechanism of inhibition exerted by a novel class of compounds on the ACMSD enzyme, a novel therapeutic target for liver and kidney diseases.
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Affiliation(s)
- Michele Cianci
- Biochemistry and Structural Biology Laboratory, Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
- *Correspondence: Michele Cianci, ; Nicola Giacchè,
| | - Nicola Giacchè
- TES Pharma S.r.l, Perugia, Italy
- *Correspondence: Michele Cianci, ; Nicola Giacchè,
| | - Lucia Cialabrini
- Biochemistry and Structural Biology Laboratory, Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Andrea Carotti
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | | | | | | | - Massimiliano Gasparrini
- Biochemistry and Structural Biology Laboratory, Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | | | - Adolfo Amici
- Department of Clinical Sciences DISCO, Section of Biochemistry, Polytechnic University of Marche, Ancona, Italy
| | - Nadia Raffaelli
- Biochemistry and Structural Biology Laboratory, Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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5
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Kropp C, Bruckmann A, Babinger P. Controlling Enzymatic Activity by Modulating the Oligomerization State via Chemical Rescue and Optical Control. Chembiochem 2021; 23:e202100490. [PMID: 34633135 PMCID: PMC9298306 DOI: 10.1002/cbic.202100490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/08/2021] [Indexed: 12/22/2022]
Abstract
Selective switching of enzymatic activity has been a longstanding goal in synthetic biology. Drastic changes in activity upon mutational manipulation of the oligomerization state of enzymes have frequently been reported in the literature, but scarcely exploited for switching. Using geranylgeranylglyceryl phosphate synthase as a model, we demonstrate that catalytic activity can be efficiently controlled by exogenous modulation of the association state. We introduced a lysine‐to‐cysteine mutation, leading to the breakdown of the active hexamer into dimers with impaired catalytic efficiency. Addition of bromoethylamine chemically rescued the enzyme by restoring hexamerization and activity. As an alternative method, we incorporated the photosensitive unnatural amino acid o‐nitrobenzyl‐O‐tyrosine (ONBY) into the hexamerization interface. This again led to inactive dimers, but the hexameric state and activity could be recovered by UV‐light induced cleavage of ONBY. For both approaches, we obtained switching factors greater than 350‐fold, which compares favorably with previously reported activity changes that were caused by site‐directed mutagenesis.
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Affiliation(s)
- Cosimo Kropp
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040, Regensburg, Germany
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology, Regensburg Center for Biochemistry, University of Regensburg, 93040, Regensburg, Germany
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040, Regensburg, Germany
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6
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Yang Y, Borel T, de Azambuja F, Johnson D, Sorrentino JP, Udokwu C, Davis I, Liu A, Altman RA. Diflunisal Derivatives as Modulators of ACMS Decarboxylase Targeting the Tryptophan-Kynurenine Pathway. J Med Chem 2020; 64:797-811. [PMID: 33369426 DOI: 10.1021/acs.jmedchem.0c01762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In the kynurenine pathway for tryptophan degradation, an unstable metabolic intermediate, α-amino-β-carboxymuconate-ε-semialdehyde (ACMS), can nonenzymatically cyclize to form quinolinic acid, the precursor for de novo biosynthesis of nicotinamide adenine dinucleotide (NAD+). In a competing reaction, ACMS is decarboxylated by ACMS decarboxylase (ACMSD) for further metabolism and energy production. Therefore, the inhibition of ACMSD increases NAD+ levels. In this study, an Food and Drug Administration (FDA)-approved drug, diflunisal, was found to competitively inhibit ACMSD. The complex structure of ACMSD with diflunisal revealed a previously unknown ligand-binding mode and was consistent with the results of inhibition assays, as well as a structure-activity relationship (SAR) study. Moreover, two synthesized diflunisal derivatives showed half-maximal inhibitory concentration (IC50) values 1 order of magnitude better than diflunisal at 1.32 ± 0.07 μM (22) and 3.10 ± 0.11 μM (20), respectively. The results suggest that diflunisal derivatives have the potential to modulate NAD+ levels. The ligand-binding mode revealed here provides a new direction for developing inhibitors of ACMSD.
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Affiliation(s)
- Yu Yang
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Timothy Borel
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | | | - David Johnson
- Computational Chemical Biology Core and Molecular Graphics and Modeling Laboratory, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Jacob P Sorrentino
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Chinedum Udokwu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Ian Davis
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Ryan A Altman
- Department of Medicinal Chemistry and Molecular Pharmacology and Department of Chemistry, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
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Wang Y, Liu KF, Yang Y, Davis I, Liu A. Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens. Proc Natl Acad Sci U S A 2020; 117:19720-19730. [PMID: 32732435 PMCID: PMC7443976 DOI: 10.1073/pnas.2005327117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The synthesis of quinolinic acid from tryptophan is a critical step in the de novo biosynthesis of nicotinamide adenine dinucleotide (NAD+) in mammals. Herein, the nonheme iron-based 3-hydroxyanthranilate-3,4-dioxygenase responsible for quinolinic acid production was studied by performing time-resolved in crystallo reactions monitored by UV-vis microspectroscopy, electron paramagnetic resonance (EPR) spectroscopy, and X-ray crystallography. Seven catalytic intermediates were kinetically and structurally resolved in the crystalline state, and each accompanies protein conformational changes at the active site. Among them, a monooxygenated, seven-membered lactone intermediate as a monodentate ligand of the iron center at 1.59-Å resolution was captured, which presumably corresponds to a substrate-based radical species observed by EPR using a slurry of small-sized single crystals. Other structural snapshots determined at around 2.0-Å resolution include monodentate and subsequently bidentate coordinated substrate, superoxo, alkylperoxo, and two metal-bound enol tautomers of the unstable dioxygenase product. These results reveal a detailed stepwise O-atom transfer dioxygenase mechanism along with potential isomerization activity that fine-tunes product profiling and affects the production of quinolinic acid at a junction of the metabolic pathway.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Yu Yang
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Ian Davis
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249;
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