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Article ; Online: Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED.

Zhu, Lan / Bu, Guanhong / Jing, Liang / Shi, Dan / Lee, Ming-Yue / Gonen, Tamir / Liu, Wei / Nannenga, Brent L

Structure (London, England : 1993)

2020 Volume 28, Issue 10, Page(s) 1149–1159.e4

Abstract: The lipidic cubic phase (LCP) technique has proved to facilitate the growth of high-quality crystals that are otherwise difficult to grow by other methods. However, the crystal size optimization process could be time and resource consuming, if it ever ... ...

Abstract	The lipidic cubic phase (LCP) technique has proved to facilitate the growth of high-quality crystals that are otherwise difficult to grow by other methods. However, the crystal size optimization process could be time and resource consuming, if it ever happens. Therefore, improved techniques for structure determination using these small crystals is an important strategy in diffraction technology development. Microcrystal electron diffraction (MicroED) is a technique that uses a cryo-transmission electron microscopy to collect electron diffraction data and determine high-resolution structures from very thin micro- and nanocrystals. In this work, we have used modified LCP and MicroED protocols to analyze crystals embedded in LCP converted by 2-methyl-2,4-pentanediol or lipase, including Proteinase K crystals grown in solution, cholesterol crystals, and human adenosine A
MeSH term(s)	Cholesterol/chemistry ; Cryoelectron Microscopy/methods ; Crystallization/methods ; Endopeptidase K/chemistry ; Glycols/chemistry ; Lipids/chemistry ; Microscopy, Electron, Transmission/methods ; Nanoparticles/chemistry ; Receptor, Adenosine A2A/chemistry
Chemical Substances	ADORA2A protein, human ; Glycols ; Lipids ; Receptor, Adenosine A2A ; Cholesterol (97C5T2UQ7J) ; Endopeptidase K (EC 3.4.21.64) ; hexylene glycol (KEH0A3F75J)
Language	English
Publishing date	2020-07-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2020.07.006
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Article: Overview of Biochemical Assays in Lipidic Cubic Phase.

Lan, Zhu / Lee, Ming-Yue / Chun, Eugene / Liu, Bin / Liu, Wei

Trends in biochemical sciences

2018 Volume 44, Issue 4, Page(s) 295–299

Abstract: The development of novel biochemical methods to efficiently characterize membrane protein (MP) properties in lipidic cubic phase (LCP) is important for studying complicated MPs and their multimeric complexes. Here, we summarize recent LCP-related assays ... ...

Abstract	The development of novel biochemical methods to efficiently characterize membrane protein (MP) properties in lipidic cubic phase (LCP) is important for studying complicated MPs and their multimeric complexes. Here, we summarize recent LCP-related assays and provide an outlook on their applications in structure and function studies of MPs.
MeSH term(s)	Crystallography, X-Ray ; Lipids/chemistry ; Membrane Proteins/chemistry ; Membrane Proteins/metabolism ; Models, Molecular
Chemical Substances	Lipids ; Membrane Proteins
Language	English
Publishing date	2018-09-19
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	194216-5
ISSN	1362-4326 ; 0968-0004 ; 0376-5067
ISSN (online)	1362-4326
ISSN	0968-0004 ; 0376-5067
DOI	10.1016/j.tibs.2018.08.008
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Article ; Online: Evidence that specific interactions play a role in the cholesterol sensitivity of G protein-coupled receptors.

Geiger, James / Sexton, Rick / Al-Sahouri, Zina / Lee, Ming-Yue / Chun, Eugene / Harikumar, Kaleeckal G / Miller, Laurence J / Beckstein, Oliver / Liu, Wei

Biochimica et biophysica acta. Biomembranes

2021 Volume 1863, Issue 9, Page(s) 183557

Abstract: G protein-coupled receptors (GPCRs) are known to be modulated by membrane cholesterol levels, but whether or not the effects are caused by specific receptor-cholesterol interactions or cholesterol's general effects on the membrane is not well-understood. ...

Abstract	G protein-coupled receptors (GPCRs) are known to be modulated by membrane cholesterol levels, but whether or not the effects are caused by specific receptor-cholesterol interactions or cholesterol's general effects on the membrane is not well-understood. We performed coarse-grained molecular dynamics (CGMD) simulations coupled with structural bioinformatics approaches on the β
MeSH term(s)	Cholesterol/chemistry ; Models, Molecular ; Receptors, G-Protein-Coupled/chemistry
Chemical Substances	Receptors, G-Protein-Coupled ; Cholesterol (97C5T2UQ7J)
Language	English
Publishing date	2021-01-11
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	60-7
ISSN	1879-2642 ; 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2642 ; 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbamem.2021.183557
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Article ; Online: Insight into the molecular basis of aromatic polyketide cyclization: crystal structure and in vitro characterization of WhiE-ORFVI.

Lee, Ming-Yue / Ames, Brian D / Tsai, Shiou-Chuan

Biochemistry

2012 Volume 51, Issue 14, Page(s) 3079–3091

Abstract: Aromatic polyketides are biologically active natural products. Many important pharmaceuticals are derived from aromatic polyketides. Especially important in aromatic polyketide biosynthesis is the regiospecific cyclization of a linear, preassembled ... ...

Abstract	Aromatic polyketides are biologically active natural products. Many important pharmaceuticals are derived from aromatic polyketides. Especially important in aromatic polyketide biosynthesis is the regiospecific cyclization of a linear, preassembled polyketide chain catalyzed by aromatase/cyclase (ARO/CYC), which serves as a key control point in aromatic ring formation. How different ARO/CYCs promote different cyclization patterns is not well understood. The whiE locus of Streptomyces coelicolor A3(2) is responsible for the biosynthesis of an aromatic polyketide precursor to the gray spore pigment. The WhiE ARO/CYC catalyzes the regiospecific C9-C14 and C7-C16 cyclization and aromatization of a 24-carbon polyketide chain. WhiE ARO/CYC shares a high degree of similarity to another nonreducing PKS ARO/CYC, TcmN ARO/CYC. This paper presents the apo crystal structure of WhiE ARO/CYC, and cocrystal structures of WhiE and TcmN ARO/CYCs bound with polycyclic aromatic compounds that mimic the respective ARO/CYC products. Site-directed mutagenesis coupled with in vitro PKS reconstitution assays was used to characterize the interior pocket residues of WhiE ARO/CYC. The results confirmed that the interior pocket of ARO/CYCs is a critical determinant of polyketide cyclization specificity. A unified ARO/CYC-mediated cyclization mechanism is proposed on the basis of these structural and functional results.
MeSH term(s)	Amino Acid Sequence ; Aromatase/chemistry ; Aromatase/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Crystallography, X-Ray ; Cyclization ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Polyketide Synthases/chemistry ; Polyketide Synthases/metabolism ; Polyketides/chemistry ; Polyketides/metabolism ; Protein Conformation ; Sequence Alignment ; Streptomyces coelicolor/enzymology ; Streptomyces coelicolor/metabolism
Chemical Substances	Bacterial Proteins ; Polyketides ; Polyketide Synthases (79956-01-7) ; Aromatase (EC 1.14.14.1)
Language	English
Publishing date	2012-03-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/bi201705q
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Article: Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase.

Lee, Ming-Yue / Geiger, James / Ishchenko, Andrii / Han, Gye Won / Barty, Anton / White, Thomas A / Gati, Cornelius / Batyuk, Alexander / Hunter, Mark S / Aquila, Andrew / Boutet, Sébastien / Weierstall, Uwe / Cherezov, Vadim / Liu, Wei

IUCrJ

2020 Volume 7, Issue Pt 6, Page(s) 976–984

Abstract: Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has ... ...

Abstract	Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has limitations. Here we attempt to address some of these limitations related to the use of a vacuum chamber and the need for attenuation of the XFEL beam, in order to further improve the efficiency of this method. Using an optimized SFX experimental setup in a helium atmosphere, the room-temperature structure of the adenosine A
Language	English
Publishing date	2020-10-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2754953-7
ISSN	2052-2525
ISSN	2052-2525
DOI	10.1107/S2052252520012701
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Article ; Online: Structural Basis of the Activation of Heterotrimeric Gs-Protein by Isoproterenol-Bound β

Su, Minfei / Zhu, Lan / Zhang, Yixiao / Paknejad, Navid / Dey, Raja / Huang, Jianyun / Lee, Ming-Yue / Williams, Dewight / Jordan, Kelsey D / Eng, Edward T / Ernst, Oliver P / Meyerson, Joel R / Hite, Richard K / Walz, Thomas / Liu, Wei / Huang, Xin-Yun

Molecular cell

2020 Volume 80, Issue 1, Page(s) 59–71.e4

Abstract: Cardiac disease remains the leading cause of morbidity and mortality worldwide. The ... ...

Abstract	Cardiac disease remains the leading cause of morbidity and mortality worldwide. The β
MeSH term(s)	Animals ; Binding Sites ; Cattle ; Cell Line ; GTP-Binding Protein alpha Subunits, Gs/chemistry ; GTP-Binding Protein alpha Subunits, Gs/metabolism ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/metabolism ; Isoproterenol/metabolism ; Models, Molecular ; Protein Binding ; Protein Domains ; Protein Structure, Secondary ; Receptors, Adrenergic, beta-1/chemistry ; Receptors, Adrenergic, beta-1/metabolism
Chemical Substances	Receptors, Adrenergic, beta-1 ; Guanosine Diphosphate (146-91-8) ; Guanosine Triphosphate (86-01-1) ; GTP-Binding Protein alpha Subunits, Gs (EC 3.6.5.1) ; Isoproterenol (L628TT009W)
Language	English
Publishing date	2020-08-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2020.08.001
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Zs.A 5055: Show issues

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Article ; Online: Modeling, Synthesis, and Biological Evaluation of Potential Retinoid-X-Receptor (RXR) Selective Agonists: Analogs of 4-[1-(3,5,5,8,8-Pentamethyl-5,6,7,8-tetrahyro-2-naphthyl)ethynyl]benzoic Acid (Bexarotene) and 6-(Ethyl(4-isobutoxy-3-isopropylphenyl)amino)nicotinic Acid (NEt-4IB).

International journal of molecular sciences

2021 Volume 22, Issue 22

Abstract: Five novel analogs of 6-(ethyl)(4-isobutoxy-3-isopropylphenyl)amino)nicotinic acid-or NEt-4IB-in addition to seven novel analogs of 4-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydro-2-naphthyl)ethynyl]benzoic acid (bexarotene) were prepared and evaluated ... ...

Abstract	Five novel analogs of 6-(ethyl)(4-isobutoxy-3-isopropylphenyl)amino)nicotinic acid-or NEt-4IB-in addition to seven novel analogs of 4-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydro-2-naphthyl)ethynyl]benzoic acid (bexarotene) were prepared and evaluated for selective retinoid-X-receptor (RXR) agonism alongside bexarotene (
MeSH term(s)	Animals ; Antineoplastic Agents/chemical synthesis ; Antineoplastic Agents/pharmacology ; Apolipoproteins E/genetics ; Apolipoproteins E/metabolism ; Bexarotene/analogs & derivatives ; Bexarotene/chemical synthesis ; Bexarotene/pharmacology ; Cell Line, Tumor ; Dose-Response Relationship, Drug ; Gene Expression ; Humans ; Leukocytes/drug effects ; Leukocytes/metabolism ; Leukocytes/pathology ; Nicotinic Acids/chemical synthesis ; Nicotinic Acids/pharmacology ; Retinoid X Receptor alpha/agonists ; Retinoid X Receptor alpha/genetics ; Retinoid X Receptor alpha/metabolism ; Structure-Activity Relationship
Chemical Substances	Antineoplastic Agents ; ApoE protein, human ; Apolipoproteins E ; Nicotinic Acids ; RXRA protein, human ; Retinoid X Receptor alpha ; Bexarotene (A61RXM4375)
Language	English
Publishing date	2021-11-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms222212371
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Article: Insight into the Molecular Basis of Aromatic Polyketide Cyclization: Crystal Structure and in Vitro Characterization of WhiE-ORFVI

Lee, Ming-Yue / Ames Brian D / Tsai Shiou-Chuan

Biochemistry. 2012 Apr. 10, v. 51, no. 14

2012

Abstract	Aromatic polyketides are biologically active natural products. Many important pharmaceuticals are derived from aromatic polyketides. Especially important in aromatic polyketide biosynthesis is the regiospecific cyclization of a linear, preassembled polyketide chain catalyzed by aromatase/cyclase (ARO/CYC), which serves as a key control point in aromatic ring formation. How different ARO/CYCs promote different cyclization patterns is not well understood. The whiE locus of Streptomyces coelicolor A3(2) is responsible for the biosynthesis of an aromatic polyketide precursor to the gray spore pigment. The WhiE ARO/CYC catalyzes the regiospecific C9âC14 and C7âC16 cyclization and aromatization of a 24-carbon polyketide chain. WhiE ARO/CYC shares a high degree of similarity to another nonreducing PKS ARO/CYC, TcmN ARO/CYC. This paper presents the apo crystal structure of WhiE ARO/CYC, and cocrystal structures of WhiE and TcmN ARO/CYCs bound with polycyclic aromatic compounds that mimic the respective ARO/CYC products. Site-directed mutagenesis coupled with in vitro PKS reconstitution assays was used to characterize the interior pocket residues of WhiE ARO/CYC. The results confirmed that the interior pocket of ARO/CYCs is a critical determinant of polyketide cyclization specificity. A unified ARO/CYC-mediated cyclization mechanism is proposed on the basis of these structural and functional results.
Keywords	Streptomyces coelicolor ; aromatase ; biosynthesis ; crystal structure ; drugs ; loci ; polyketides ; site-directed mutagenesis ; spores
Language	English
Dates of publication	2012-0410
Size	p. 3079-3091.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/bi201705q
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Zs.A 217: Show issues

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Article ; Online: High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions.

Broecker, Jana / Morizumi, Takefumi / Ou, Wei-Lin / Klingel, Viviane / Kuo, Anling / Kissick, David J / Ishchenko, Andrii / Lee, Ming-Yue / Xu, Shenglan / Makarov, Oleg / Cherezov, Vadim / Ogata, Craig M / Ernst, Oliver P

Nature protocols

2018 Volume 13, Issue 2, Page(s) 260–292

Abstract: Protein crystallography has significantly advanced in recent years, with in situ data collection, in which crystals are placed in the X-ray beam within their growth medium, being a major point of focus. In situ methods eliminate the need to harvest ... ...

Abstract	Protein crystallography has significantly advanced in recent years, with in situ data collection, in which crystals are placed in the X-ray beam within their growth medium, being a major point of focus. In situ methods eliminate the need to harvest crystals, a previously unavoidable drawback, particularly for often small membrane-protein crystals. Here, we present a protocol for the high-throughput in situ X-ray screening of and data collection from soluble and membrane-protein crystals at room temperature (20-25°C) and under cryogenic conditions. The Mylar in situ method uses Mylar-based film sandwich plates that are inexpensive, easy to make, and compatible with automated imaging, and that show very low background scattering. They support crystallization in microbatch and vapor-diffusion modes, as well as in lipidic cubic phases (LCPs). A set of 3D-printed holders for differently sized patches of Mylar sandwich films makes the method robust and versatile, allows for storage and shipping of crystals, and enables automated mounting at synchrotrons, as well as goniometer-based screening and data collection. The protocol covers preparation of in situ plates and setup of crystallization trials; 3D printing and assembly of holders; opening of plates, isolation of film patches containing crystals, and loading them onto holders; basic screening and data-collection guidelines; and unloading of holders, as well as reuse and recycling of them. In situ plates are prepared and assembled in 1 h; holders are 3D-printed and assembled in ≤90 min; and an in situ plate is opened, and a film patch containing crystals is isolated and loaded onto a holder in 5 min.
MeSH term(s)	Crystallization ; Crystallography, X-Ray/methods ; Data Collection ; High-Throughput Screening Assays/instrumentation ; High-Throughput Screening Assays/methods ; Lipids ; Membrane Proteins/analysis ; Polyethylene Terephthalates/chemistry ; Proteins/chemistry ; Temperature ; X-Rays
Chemical Substances	Lipids ; Membrane Proteins ; Polyethylene Terephthalates ; Proteins ; Lavsan (25038-59-9)
Language	English
Publishing date	2018-01-04
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2244966-8
ISSN	1750-2799 ; 1754-2189
ISSN (online)	1750-2799
ISSN	1754-2189
DOI	10.1038/nprot.2017.135
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Article: Allosteric Coupling of Drug Binding and Intracellular Signaling in the A2A Adenosine Receptor

Eddy, Matthew T / Lee, Ming-Yue / Gao, Zhan-Guo / White, Kate L / Didenko, Tatiana / Horst, Reto / Audet, Martin / Stanczak, Pawel / McClary, Kyle M / Han, Gye Won / Jacobson, Kenneth A / Stevens, Raymond C / Wüthrich, Kurt

Elsevier Inc. Cell. 2018 Jan. 11, v. 172, no. 1-2

2018

Abstract: Signaling across cellular membranes, the 826 human G protein-coupled receptors (GPCRs) govern a wide range of vital physiological processes, making GPCRs prominent drug targets. X-ray crystallography provided GPCR molecular architectures, which also ... ...

Abstract	Signaling across cellular membranes, the 826 human G protein-coupled receptors (GPCRs) govern a wide range of vital physiological processes, making GPCRs prominent drug targets. X-ray crystallography provided GPCR molecular architectures, which also revealed the need for additional structural dynamics data to support drug development. Here, nuclear magnetic resonance (NMR) spectroscopy with the wild-type-like A2A adenosine receptor (A2AAR) in solution provides a comprehensive characterization of signaling-related structural dynamics. All six tryptophan indole and eight glycine backbone 15N–1H NMR signals in A2AAR were individually assigned. These NMR probes provided insight into the role of Asp522.50 as an allosteric link between the orthosteric drug binding site and the intracellular signaling surface, revealing strong interactions with the toggle switch Trp 2466.48, and delineated the structural response to variable efficacy of bound drugs across A2AAR. The present data support GPCR signaling based on dynamic interactions between two semi-independent subdomains connected by an allosteric switch at Asp522.50.
Keywords	G-protein coupled receptors ; X-ray diffraction ; binding sites ; cell membranes ; drugs ; humans ; nuclear magnetic resonance spectroscopy ; tryptophan
Language	English
Dates of publication	2018-0111
Size	p. 68-80.e12.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2017.12.004
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