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A disordered linker in the Polycomb protein Polyhomeotic tunes phase separation and oligomerization

Molecular cell 2025年第11期85卷 2128-2146.e15页

作者： Tim M Gemeinhardt Roshan M Regy Tien M phan Nanu Pal Jyoti Sharma Olga Senkovich Andrea J Mendiola Heather J Ledterman Amy Henrickson daniel Lopes Utkarsh Kapoor Ashish Bihani djamouna Sihou Young C Kim david Jeruzalmi Borries demeler Chongwoo A Kim Jeetain Mittal Nicole J Francis Montreal Clinical Research Institute (IRCM) Montreal QC Canada Division of Experimental Medicine McGill University Montreal QC Canada. Artie McFerrin Department of Chemical Engineering Texas A&M University College Station TX USA. Department of Biochemistry and Molecular Medicine University of Montreal Montreal QC Canada. Montreal Clinical Research Institute (IRCM) Montreal QC Canada. Department of Biochemistry and Molecular Genetics Midwestern University Glendale AZ USA. Department of Chemistry and Biochemistry The University of Lethbridge Lethbridge AB Canada. Department of Chemistry and Biochemistry City College of New York New York NY USA. Department of Chemical and Biomedical Engineering University of Wyoming Laramie WY USA. Center for Materials Physics and Technology Naval Research Laboratory Washington DC USA. Department of Chemistry and Biochemistry City College of New York New York NY USA Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New York NY USA Ph.D. Program in Biology The Graduate Center of the City University of New York New York NY USA Ph.D. Program in Chemistry The Graduate Center of the City University of New York New York NY USA. Department of Chemistry and Biochemistry The University of Lethbridge Lethbridge AB Canada Department of Chemistry and Biochemistry University of Montana Missoula MT USA. Artie McFerrin Department of Chemical Engineering Texas A&M University College Station TX USA Department of Chemistry Texas A&M University College Station TX USA Interdisciplinary Graduate Program in Genetics and Genomics Texas A&M University College Station TX USA. Electronic address: jeetain@tamu.edu. Division of Experimental Medicine McGill University Montreal QC Canada Department of Biochemistry and Molecular Medicine University of Montreal Montreal QC Canada. Electronic address: nicole.francis@ircm.qc.ca.

Biomolecular condensates are increasingly recognized as key regulators of chromatin organization, yet how their formation and properties arise from protein sequences remains incompletely understood. Cross-species comparisons can reveal both conserved functions and significant evolutionary differences. Here, we integrate in vitro reconstitution, molecular dynamics simulations, and cell-based assays to examine how drosophila and human variants of Polyhomeotic (ph)-a subunit of the PRC1 chromatin regulatory complex-drive condensate formation through their sterile alpha motif (SAM) oligomerization domains. We identify divergent interactions between SAM and the disordered linker connecting it to the rest of ph. These interactions enhance oligomerization and modulate both the formation and properties of reconstituted condensates. Oligomerization influences condensate dynamics but minimally impacts condensate formation. Linker-SAM interactions also affect condensate formation in drosophila and human cells and growth in drosophila imaginal discs. Our findings show how evolutionary changes in disordered linkers can fine-tune condensate properties, providing insights into sequence-function relationships.

关键词： CRISPR drosophila Polycomb analytical ultracentrifugation biochemistry biomolecular condensates gene regulation intrinsically disordered regions molecular dynamics simulations oligomerization phase separation sterile alpha motif

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Water-Vapor Responsive Metallo-Peptide Nanofibers

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Angewandte Chemie 2024年第47期136卷

作者： Avishek dey Elma Naranjo Ranajit Saha Sheng Zhang Maya Narayanan Nair Tai-de Li Xi Chen Rein V. Ulijn Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York New York New York 10031 USA Department of Chemical Engineering The City College of New York 275 Convent Ave New York NY 10031 USA Department of Chemistry Cooch Behar Panchanan Barma University Cooch Behar West Bengal 736101 India Department of Physics City College of New York of City University of New York New York NY 10031 USA Ph.D. Program in Physics The Graduate Center of the City University of New York 365 5th Ave New York NY 10016 USA Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 5th Ave New York NY 10016 USA Department of Chemistry Hunter College City University of New York New York New York 10065 USA Ph.D. Program in Biochemistry The Graduate Center of the City University of New York 365 5th Ave New York NY 10016 USA

Short peptides are versatile molecules for the construction of supramolecular materials. Most reported peptide materials are hydrophobic, stiff, and show limited response to environmental conditions in the solid-state. Herein, we describe a design strategy for minimalistic supramolecular metallo-peptide nanofibers that, depending on their sequence, change stiffness, or reversibly assemble in the solid-state, in response to changes in relative humidity (RH). We tested a series of histidine (H) containing dipeptides with varying hydrophobicity, XH, where X is G, A, L, Y (glycine, alanine, leucine, and tyrosine). The one-dimensional fiber formation is supported by metal coordination and dynamic H-bonds. Solvent conditions were identified where GH/Zn and AH/Zn formed gels that upon air-drying gave rise to nanofibers. Upon exposure of the nanofiber networks to increasing RH, a reduction in stiffness was observed with GH/Zn fibers reversibly (dis-)assembled at 60–70 % RH driven by a rebalancing of hydrogen bonding interactions between peptides and water. When these metallo-peptide nanofibers were deposited on the surface of polyimide films and exposed to varying RH, peptide/water-vapor interactions in the solid-state mechanically transferred to the polymer film, leading to the rapid and reversible folding-unfolding of the films, thus demonstrating RH-responsive actuation.

关键词： Metallopeptide Actuation Humidity Responsive Assembly-disassembly Water Vapor Responsive

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Correction to: Current clinical applications of Cerenkov luminescence for intraoperative molecular imaging

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European journal of nuclear medicine and molecular imaging 2024年第12期51卷 3809页

作者： Natalie Boykoff Jan Grimm Department of Chemistry and Biochemistry The City College of New York 160 Convent Avenue New York NY 10031 USA. Ph.D. Program in Chemistry The Graduate Center of the City University of New York New York NY 10016 USA. Molecular Pharmacology Program Memorial Sloan Kettering Cancer Center New York NY 10065 USA. Department of Radiology Memorial Sloan Kettering Cancer Center New York NY 10065 USA. Molecular Pharmacology Program Memorial Sloan Kettering Cancer Center New York NY 10065 USA. grimmj@***. Department of Radiology Memorial Sloan Kettering Cancer Center New York NY 10065 USA. grimmj@***. Pharmacology Program Weill Cornell Medical College New York NY 10021 USA. grimmj@***. Department of Radiology Weill Cornell Medical College New York NY 10021 USA. grimmj@***.

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Perturbation Potentials to Overcome Order/disorder Transitions in Alchemical Binding Free Energy Calculations

arXiv

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arXiv 2019年

作者： Pal, Rajat K. Gallicchio, Emilio Department of Chemistry Brooklyn College of the City University of New York New YorkNY United States Ph.D. Program in Biochemistry Graduate Center of the City University of New York New YorkNY United States Ph.D. Program in Chemistry The Graduate Center of the City University of New York New YorkNY United States

We investigate the role of order/disorder transitions in alchemical simulations of protein-ligand absolute binding free energies. We show, in the context of a potential of mean force description, that for a benchmarking system (the complex between the L99A mutant of T4 lysozyme and 3-iodotoluene) and for a more challenging system relevant for medicinal applications (the complex of the farnesoid X receptor and inhibitor 26 from a recent d3R challenge) that order/disorder transitions can significantly hamper Hamiltonian replica exchange sampling efficiency and slow down the rate of equilibration of binding free energy estimates. We further show that our analytical model of alchemical binding combined with the formalism developed by Straub et al. for the treatment of order/disorder transitions of molecular systems can be successfully employed to analyze the transitions and help design alchemical schedules and soft-core functions that avoid or reduce the adverse effects of rare binding/unbinding transitions. The results of this work pave the way for the application of these techniques to the alchemical estimation with explicit solvation of hydration free energies and absolute binding free energies of systems undergoing order/disorder transitions. Copyright © 2019, The Authors. All rights reserved.

关键词： Binding energy

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Cover Feature: Conformational Sensing by a Mammalian Olfactory Receptor (Chem. Eur. J. 50/2020)

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chemistry – A European Journal 2020年第50期26卷 11346-11346页

作者： Min Ting Liu dr. Mihwa Na dr. Yadi Li Prof. Mark R. Biscoe Prof. Kevin Ryan Department of Chemistry and Biochemistry The City College of New York New York NY 10031 USA Ph.D. Program in Chemistry The Graduate Center of the City University of New York New York NY 10016 USA Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New York NY 10016 USA

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Facile Modifications at the C4 Position of Pyrimidine Nucleosides via In Situ Amide Activation with 1H-Benzotriazol-1-yloxy-tris(dimethyl-amino)phosphonium Hexafluorophosphate

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Current Protocols in Nucleic Acid chemistry 2019年第1期76卷 e73页

作者： Akula, Hari K. Lakshman, Mahesh K. Department of Chemistry and Biochemistry The City College of New York New York NY United States The Ph.D. Program in Chemistry The Graduate Center of the City University of New York New York NY United States

Two approaches for C4 modifications of silyl-protected thymidine, 2′-deoxyuridine, and 3′-azido-2′,3′-dideoxythymidine (AZT) are described. In both, nucleoside amide activation with 1H-benzotriazol-1-yloxy-tris(dimethylamino)phosphonium hexafluorophosphate (BOP) and dBU yields O ⁴ -(benzotriazol-1-yl) derivatives. These in situ–formed intermediates are reacted with various nucleophiles, resulting in C4 modifications. In the two-step, one-pot approach, the O ⁴ -(benzotriazol-1-yl) nucleoside intermediates are initially produced by reactions of the nucleosides with BOP and dBU in THF. This step is fast and typically complete within 30 min. Subsequently, the O ⁴ -(benzotriazol-1-yl) derivatives are reacted with nucleophiles, such as aliphatic and aromatic amines, thiols, and alcohols, under appropriate conditions. Workup, isolation, and purification lead to the desired C4-modified pyrimidine nucleosides in good to excellent yields. In the one-step approach, the nucleosides are reacted with BOP and dBU, in the presence of the nucleophile (only aliphatic and aromatic amines, and thiols have been tested). Where comparisons are possible, the one-step approach is generally superior. © 2019 by John Wiley & Sons, Inc. © 2019 John Wiley & Sons, Inc.

关键词： 1H-benzotriazol-1-yloxy-tris(dimethylamino)phosphonium hexafluorophosphate (BOP) 2′-deoxyuridine 3′-azido-2′,3′-dideoxythymidine (AZT) amide activation nucleoside modification pyrimidine nucleosides thymidine

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Remote Participation during Glycosylation Reactions of Galactose Building Blocks: direct Evidence from Cryogenic Vibrational Spectroscopy

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Advanced Materials 2020年第15期132卷 6224-6229页

作者： Marianski, Mateusz Mucha, Eike Greis, Kim Moon, Sooyeon Pardo, Alonso Kirschbaum, Carla Thomas, daniel A. Meijer, Gerard von Helden, Gert Gilmore, Kerry Seeherger, Peter H. Pagel, Kevin Department of Chemistry and Biochemistry Hunter College 695 Park Ave New YorkNY10065 United States The Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 5th Ave New YorkNY10016 United States Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 Berlin14195 Germany Max-Planck-lnstitut für Kolloid und Grenzflächenforschun Am Mühlenberg 1 Potsdam14476 Germany Institut für Chemie und Biochemie Freie Universität Berlin Takustraße 3 Berlin14195 Germany

The stereoselective formation of 1,2-cis-glycosidic bonds is challenging. However, 1,2-cis-selectivity can be induced by remote participation of C4 or C6 ester groups. Reactions involving remote participation are believed to proceed via a key ionic intermediate, the glycosyl cation. Although mechanistic pathways were postulated many years ago, the structure of the reaction intermediates remained elusive owing to their short-lived nature. Herein, we unravel the structure of glycosyl cations involved in remote participation reactions via cryogenic vibrational spectroscopy and first principles theory. Acetyl groups at C4 ensure α-selective galactosylations by forming a covalent bond to the anomeric carbon in dioxolenium-type ions. Unexpectedly, also benzyl ether protecting groups can engage in remote participation and promote the stereoselective formation of 1,2-cis-glycosidic bonds. © 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

关键词： Positive ions

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Cover Feature: Singlet Oxygen Oxidation of the Radical Cations of 8-Oxo-2′-deoxyguanosine and Its 9-Methyl Analogue: dynamics, Potential Energy Surface, and Products Mediated by C5-O2-Addition (ChemPlusChem 9/2021)

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ChemPlusChem 2021年第9期86卷

作者： May Myat Moe Prof. dr. Midas Tsai Prof. dr. Jianbo Liu Department of Chemistry and Biochemistry Queens College of the City University of New York 65-30 Kissena Blvd. Queens NY 11367 USA Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 5th Ave. New York NY 10016 USA Department of Natural Sciences LaGuardia Community College 31-10 Thomson Ave. Long Island City NY 11101 USA

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Atomistic mechanisms underlying the activation of the G protein-coupled sweet receptor heterodimer by sugar alcohol recognition (vol 9, 10205, 2019)

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SCIENTIFIC REPORTS 2019年第1期9卷 1-11页

作者： Mahalapbutr, Panupong darai, Nitchakan Panman, Wanwisa Opasmahakul, Aunchan Kungwan, Nawee Hannongbua, Supot Rungrotmongkol, Thanyada Structural and Computational Biology Research Unit Department of Biochemistry Faculty of Science Chulalongkorn University 10330 Bangkok Thailand Program in Biotechnology Faculty of Science Chulalongkorn University 10330 Bangkok Thailand Multidisciplinary Program of Petrochemistry and Polymer Science Faculty of Science Chulalongkorn University 10330 Bangkok Thailand Computational Chemistry Center of Excellent Department of Chemistry Faculty of Science Chulalongkorn University 10330 Bangkok Thailand Department of Chemistry Faculty of Science Chiang Mai University 50200 Chiang Mai Thailand Center of Excellence in Materials Science and Technology Chiang Mai University 50200 Chiang Mai Thailand Ph.D. Program in Bioinformatics and Computational Biology Faculty of Science Chulalongkorn University 10330 Bangkok Thailand Molecular Sensory Science Center Faculty of Science Chulalongkorn University 10330 Bangkok Thailand

The human T1R2-T1R3 sweet taste receptor (STR) plays an important role in recognizing various low-molecular-weight sweet-tasting sugars and proteins, resulting in the release of intracellular heterotrimeric G protein that in turn leads to the sweet taste perception. Xylitol and sorbitol, which are naturally occurring sugar alcohols (polyols) found in many fruits and vegetables, exhibit the potential caries-reducing effect and are widely used for diabetic patients as low-calorie sweeteners. In the present study, computational tools were applied to investigate the structural details of binary complexes formed between these two polyols and the T1R2-T1R3 heterodimeric STR. Principal component analysis revealed that the Venus flytrap domain (VFd) of T1R2 monomer was adapted by the induced-fit mechanism to accommodate the focused polyols, in which α-helical residues 233–268 moved significantly closer to stabilize ligands. This finding likely suggested that these structural transformations might be the important mechanisms underlying polyols-STR recognitions. The calculated free energies also supported the VFd of T1R2 monomer as the preferential binding site for such polyols, rather than T1R3 region, in accord with the lower number of accessible water molecules in the T1R2 pocket. The E302 amino acid residue in T1R2 was found to be the important recognition residue for polyols binding through a strongly formed hydrogen bond. Additionally, the binding affinity of xylitol toward the T1R2 monomer was significantly higher than that of sorbitol, making it a sweeter tasting molecule. [ABSTRACT FROM AUTHOR]

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Publisher Correction: Atomistic mechanisms underlying the activation of the G protein-coupled sweet receptor heterodimer by sugar alcohol recognition

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Scientific reports 2019年第1期9卷 18996页

作者： Panupong Mahalapbutr Nitchakan darai Wanwisa Panman Aunchan Opasmahakul Nawee Kungwan Supot Hannongbua Thanyada Rungrotmongkol Structural and Computational Biology Research Unit Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. Program in Biotechnology Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. Multidisciplinary Program of Petrochemistry and Polymer Science Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. Computational Chemistry Center of Excellent Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. Department of Chemistry Faculty of Science Chiang Mai University Chiang Mai 50200 Thailand. Center of Excellence in Materials Science and Technology Chiang Mai University Chiang Mai 50200 Thailand. Structural and Computational Biology Research Unit Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. t.rungrotmongkol@***. Ph.D. Program in Bioinformatics and Computational Biology Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. t.rungrotmongkol@***. Molecular Sensory Science Center Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. t.rungrotmongkol@***.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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