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Binding Sites

  • 1.
    King S, Singh M. Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers. PLoS Comput Biol. 2023;19(3):e1010966. PMCID: PMC10035887
    Reference Link
  • 1.
    Roden C, Dai Y, Giannetti C, Seim I, Lee M, Sealfon R, McLaughlin G, Boerneke M, Iserman C, Wey S, Ekena J, Troyanskaya O, Weeks K, You L, Chilkoti A, Gladfelter A. Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures. Nucleic Acids Res. 2022;50(14):8168–8192. PMCID: PMC9371935
    Reference Link
  • 1.
    Kumar H, Jimah J, Misal S, Salinas N, Fried M, Schlesinger P, Tolia N. Implications of conformational flexibility, lipid binding, and regulatory domains in cell-traversal protein CelTOS for apicomplexan migration. J Biol Chem. 2022;298(9):102241. PMCID: PMC9400078
    Reference Link
  • 1.
    Colonnetta M, Abrahante J, Schedl P, Gohl D, Deshpande G. CLAMP regulates zygotic genome activation in Drosophila embryos. Genetics. 2021;219(2). PMCID: PMC8633140
    Reference Link
  • 1.
    Etzion-Fuchs A, Todd D, Singh M. dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. Nucleic Acids Res. 2021;49(13):e78. PMCID: PMC8287948
    Reference Link
  • 1.
    Duddy O, Huang X, Silpe J, Bassler B. Mechanism underlying the DNA-binding preferences of the Vibrio cholerae and vibriophage VP882 VqmA quorum-sensing receptors. PLoS Genet. 2021;17(7):e1009550. PMCID: PMC8284805
    Reference Link
  • 1.
    Balo A, Caruso A, Tao L, Tantillo D, Seyedsayamdost M, Britt D. Trapping a cross-linked lysine-tryptophan radical in the catalytic cycle of the radical SAM enzyme SuiB. Proc Natl Acad Sci U S A. 2021;118(21). PMCID: PMC8166192
    Reference Link
  • 1.
    Garrison C, Schwarzbauer J. Fibronectin fibril alignment is established upon initiation of extracellular matrix assembly. Mol Biol Cell. 2021;32(8):739–752. PMCID: PMC8108514
    Reference Link
  • 1.
    Pan Y, Ren Z, Gao S, Shen J, Wang L, Xu Z, Yu Y, Bachina P, Zhang H, Fan X, Laganowsky A, Yan N, Zhou M. Structural basis of ion transport and inhibition in ferroportin. Nat Commun. 2020;11(1):5686. PMCID: PMC7655804
    Reference Link
  • 1.
    Gao S, Yan N. Structural Basis of the Modulation of the Voltage-Gated Calcium Ion Channel Ca 1.1 by Dihydropyridine Compounds*. Angew Chem Int Ed Engl. 2021;60(6):3131–3137. PMCID: PMC7898392
    Reference Link
  • 1.
    Wang L, Qian H, Nian Y, Han Y, Ren Z, Zhang H, Hu L, Prasad B, Laganowsky A, Yan N, Zhou M. Structure and mechanism of human diacylglycerol O-acyltransferase 1. Nature. 2020;581(7808):329–332. PMCID: PMC7255049
    Reference Link
  • 1.
    Dao H, Dul B, Dann G, Liszczak G, Muir T. A basic motif anchoring ISWI to nucleosome acidic patch regulates nucleosome spacing. Nat Chem Biol. 2020;16(2):134–142. PMCID: PMC6982587
    Reference Link
  • 1.
    Zhao Y, Huang G, Wu J, Wu Q, Gao S, Yan Z, Lei J, Yan N. Molecular Basis for Ligand Modulation of a Mammalian Voltage-Gated Ca Channel. Cell. 2019;177(6):1495–1506.e12. PMID: 31150622
    Reference Link
  • 1.
    Huang X, Duddy O, Silpe J, Paczkowski J, Cong J, Henke B, Bassler B. Mechanism underlying autoinducer recognition in the DPO-VqmA quorum-sensing pathway. J Biol Chem. 2020;295(10):2916–2931. PMCID: PMC7062168
    Reference Link
  • 1.
    Arey R, Kaletsky R, Murphy C. Nervous system-wide profiling of presynaptic mRNAs reveals regulators of associative memory. Sci Rep. 2019;9(1):20314. PMCID: PMC6937282
    Reference Link
  • 1.
    Nechay M, Kleiner R. High-throughput approaches to profile RNA-protein interactions. Curr Opin Chem Biol. 2020;54:37–44. PMCID: PMC7131871
    Reference Link
  • 1.
    Diehl K, Ge E, Weinberg D, Jani K, Allis D, Muir T. PRC2 engages a bivalent H3K27M-H3K27me3 dinucleosome inhibitor. Proc Natl Acad Sci U S A. 2019;116(44):22152–22157. PMCID: PMC6825254
    Reference Link
  • 1.
    Zhao Y, Huang G, Wu Q, Wu K, Li R, Lei J, Pan X, Yan N. Cryo-EM structures of apo and antagonist-bound human Ca3.1. Nature. 2019;576(7787):492–497. PMCID: 18083096
    Reference Link
  • 1.
    Wetzel J, Singh M. Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination. Nucleic Acids Res. 2020;48(2):e9. PMCID: PMC7028011
    Reference Link
  • 1.
    Kobren S, Singh M. Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions. Nucleic Acids Res. 2019;47(2):582–593. PMCID: PMC6344845
    Reference Link
  • 1.
    Saunders J, Schwarzbauer J. Fibronectin matrix as a scaffold for procollagen proteinase binding and collagen processing. Mol Biol Cell. 2019;30(17):2218–2226. PMCID: PMC6743462
    Reference Link
  • 1.
    Gong D, Chi X, Wei J, Zhou G, Huang G, Zhang L, Wang R, Lei J, Chen S, Yan N. Modulation of cardiac ryanodine receptor 2 by calmodulin. Nature. 2019;572(7769):347–351. PMID: 31278385
    Reference Link
  • 1.
    Jani K, Jain S, Ge E, Diehl K, Lundgren S, Müller M, Lewis P, Muir T. Histone H3 tail binds a unique sensing pocket in EZH2 to activate the PRC2 methyltransferase. Proc Natl Acad Sci U S A. 2019;116(17):8295–8300. PMCID: PMC6486736
    Reference Link
  • 1.
    Fedotova A, Clendinen C, Bonchuk A, Mogila V, Aoki T, Georgiev P, Schedl P. Functional dissection of the developmentally restricted BEN domain chromatin boundary factor Insensitive. Epigenetics Chromatin. 2019;12(1):2. PMCID: PMC6317261
    Reference Link
  • 1.
    Shen H, Liu D, Wu K, Lei J, Yan N. Structures of human Na1.7 channel in complex with auxiliary subunits and animal toxins. Science. 2019;363(6433):1303–1308. PMID: 30765606
    Reference Link
  • 1.
    Munro D, Ghersi D, Singh M. Two critical positions in zinc finger domains are heavily mutated in three human cancer types. PLoS Comput Biol. 2018;14(6):e1006290. PMCID: PMC6040777
    Reference Link
  • 1.
    Gong X, Qian H, Cao P, Zhao X, Zhou Q, Lei J, Yan N. Structural basis for the recognition of Sonic Hedgehog by human Patched1. Science. 2018;361(6402). PMID: 29954986
    Reference Link
  • 1.
    Wojcik F, Dann G, Beh L, Debelouchina G, Hofmann R, Muir T. Functional crosstalk between histone H2B ubiquitylation and H2A modifications and variants. Nat Commun. 2018;9(1):1394. PMCID: PMC5895630
    Reference Link
  • 1.
    Raitman I, Huang M, Williams S, Friedman B, Godula K, Schwarzbauer J. Heparin-fibronectin interactions in the development of extracellular matrix insolubility. Matrix Biol. 2018;67:107–122. PMCID: PMC5910196
    Reference Link
  • 1.
    Hao Q, Yin P, Yan C, Yuan X, Li W, Zhang Z, Liu L, Wang J, Yan N. Functional mechanism of the abscisic acid agonist pyrabactin. J Biol Chem. 2010;285(37):28946–52. PMCID: PMC2937921
    Reference Link
  • 1.
    Yin P, Deng D, Yan C, Pan X, Xi J, Yan N, Shi Y. Specific DNA-RNA hybrid recognition by TAL effectors. Cell Rep. 2012;2(4):707–13. PMID: 23022487
    Reference Link
  • 1.
    Zhang X, Xia M, Li Y, Liu H, Jiang X, Ren W, Wu J, DeCaen P, Yu F, Huang S, He J, Clapham D, Yan N, Gong H. Analysis of the selectivity filter of the voltage-gated sodium channel Na(v)Rh. Cell Res. 2013;23(3):409–22. PMCID: PMC3587708
    Reference Link
  • 1.
    Madej G, Dang S, Yan N, Kaback R. Evolutionary mix-and-match with MFS transporters. Proc Natl Acad Sci U S A. 2013;110(15):5870–4. PMCID: PMC3625355
    Reference Link
  • 1.
    Yin P, Li Q, Yan C, Liu Y, Liu J, Yu F, Wang Z, Long J, He J, Wang H-W, Wang J, Zhu J-K, Shi Y, Yan N. Structural basis for the modular recognition of single-stranded RNA by PPR proteins. Nature. 2013;504(7478):168–71. PMID: 24162847
    Reference Link
  • 1.
    Madej G, Sun L, Yan N, Kaback R. Functional architecture of MFS D-glucose transporters. Proc Natl Acad Sci U S A. 2014;111(7):E719–27. PMCID: PMC3932877
    Reference Link
  • 1.
    Deng D, Yan C, Wu J, Pan X, Yan N. Revisiting the TALE repeat. Protein Cell. 2014;5(4):297–306. PMCID: PMC3978159
    Reference Link
  • 1.
    Deng D, Sun P, Yan C, Ke M, Jiang X, Xiong L, Ren W, Hirata K, Yamamoto M, Fan S, Yan N. Molecular basis of ligand recognition and transport by glucose transporters. Nature. 2015;526(7573):391–6. PMID: 26176916
    Reference Link
  • 1.
    Jiang X, Smirnova I, Kasho V, Wu J, Hirata K, Ke M, Pardon E, Steyaert J, Yan N, Kaback R. Crystal structure of a LacY-nanobody complex in a periplasmic-open conformation. Proc Natl Acad Sci U S A. 2016;113(44):12420–12425. PMCID: PMC5098631
    Reference Link
  • 1.
    Ducker G, Ghergurovich J, Mainolfi N, Suri V, Jeong S, Li S, Friedman A, Manfredi M, Gitai Z, Kim H, Rabinowitz J. Human SHMT inhibitors reveal defective glycine import as a targetable metabolic vulnerability of diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A. 2017;114(43):11404–11409. PMCID: PMC5664509
    Reference Link
  • 1.
    Kyrchanova O, Mogila V, Wolle D, Deshpande G, Parshikov A, Cleard F, Karch F, Schedl P, Georgiev P. Functional Dissection of the Blocking and Bypass Activities of the Fab-8 Boundary in the Drosophila Bithorax Complex. PLoS Genet. 2016;12(7):e1006188. PMCID: PMC4948906
    Reference Link
  • 1.
    Crow M, Cristea I. Human Antiviral Protein IFIX Suppresses Viral Gene Expression during Herpes Simplex Virus 1 (HSV-1) Infection and Is Counteracted by Virus-induced Proteasomal Degradation. Mol Cell Proteomics. 2017;16(4 suppl 1):S200-S214. PMCID: PMC5393386
    Reference Link
  • 1.
    Liszczak G, Brown Z, Kim S, Oslund R, David Y, Muir T. Genomic targeting of epigenetic probes using a chemically tailored Cas9 system. Proc Natl Acad Sci U S A. 2017;114(4):681–686. PMCID: PMC5278450
    Reference Link
  • 1.
    Boyaci H, Shah T, Hurley A, Kokona B, Li Z, Ventocilla C, Jeffrey P, Semmelhack M, Fairman R, Bassler B, Hughson F. Structure, Regulation, and Inhibition of the Quorum-Sensing Signal Integrator LuxO. PLoS Biol. 2016;14(5):e1002464. PMCID: PMC4878744
    Reference Link
  • 1.
    Frutos S, Jordan J, Bio M, Muir T, Thiel O, Vila-Perelló M. Access to site-specific Fc-cRGD peptide conjugates through streamlined expressed protein ligation. Org Biomol Chem. 2016;14(40):9549–9553. PMCID: PMC5978688
    Reference Link
  • 1.
    Blythe S, Wieschaus E. Establishment and maintenance of heritable chromatin structure during early embryogenesis. Elife. 2016;5. PMCID: PMC5156528
    Reference Link
  • 1.
    McDonald K, Guise A, Pourbozorgi-Langroudi P, Cristea I, Zakian V, Capra J, Sabouri N. Pfh1 Is an Accessory Replicative Helicase that Interacts with the Replisome to Facilitate Fork Progression and Preserve Genome Integrity. PLoS Genet. 2016;12(9):e1006238. PMCID: PMC5017727
    Reference Link
  • 1.
    Persikov A, Wetzel J, Rowland E, Oakes B, Xu D, Singh M, Noyes M. A systematic survey of the Cys2His2 zinc finger DNA-binding landscape. Nucleic Acids Res. 2015;43(3):1965–84. PMCID: PMC4330361
    Reference Link
  • 1.
    Jenni S, Goyal Y, von Grotthuss M, Shvartsman S, Klein D. Structural Basis of Neurohormone Perception by the Receptor Tyrosine Kinase Torso. Mol Cell. 2015;60(6):941–52. PMID: 26698662
    Reference Link
  • 1.
    Futran A, Kyin S, Shvartsman S, Link J. Mapping the binding interface of ERK and transcriptional repressor Capicua using photocrosslinking. Proc Natl Acad Sci U S A. 2015;112(28):8590–5. PMCID: PMC4507193
    Reference Link
  • 1.
    Carey J, Brynda J, Wolfová J, Grandori R, Gustavsson T, Ettrich R, Smatanová I. WrbA bridges bacterial flavodoxins and eukaryotic NAD(P)H:quinone oxidoreductases. Protein Sci. 2007;16(10):2301–5. PMCID: PMC2204128
    Reference Link

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