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List of works by Yunyu Shi

1H, 13C and 15N resonance assignments and secondary structure of the human PHF6-ePHD1 domain

scientific article published on 19 August 2015

1H, 13C and 15N resonance assignments and the secondary structures of human coactosin like protein (hCLP) D123N.

scientific article published in July 2004

3D local structure around Zn in Kti11p as a representative Zn-(Cys)4 motif as obtained by MXAN.

scientific article published on 9 July 2008

A conserved dimer interface connects ERH and YTH family proteins to promote gene silencing

scientific article published in Nature Communications

A large intrinsically disordered region in SKIP and its disorder-order transition induced by PPIL1 binding revealed by NMR

scientific journal article

A novel RNA-binding mode of the YTH domain reveals the mechanism for recognition of determinant of selective removal by Mmi1.

scientific article published on 15 December 2015

A novel short-chain peptide BmKX from the Chinese scorpion Buthus martensi Karsch, sequencing, gene cloning and structure determination

scientific article

A systematic investigation of Escherichia coli central carbon metabolism in response to superoxide stress ⬇️

scientific article published on September 1, 2010

A systematic study of the cellular metabolic regulation of Jhdm1b in tumor cells.

scientific article

Application of NMR Spectroscopy to Determine Small RNA Structure

scientific article published on 01 January 2020

Backbone and side chain assignments of human Peptidylprolyl Isomerase Like 1 (hPPIL1).

scientific article

Binding model of human coactosin-like protein with filament actin revealed by mutagenesis

scientific article

Chromatin protein HP1 interacts with the mitotic regulator borealin protein and specifies the centromere localization of the chromosomal passenger complex

scientific article

Cloning, expression, secondary structure characterization of HMG box 1 of hUBF from E. coli and its binding to DNA.

scientific article

Combinatorial readout of unmodified H3R2 and acetylated H3K14 by the tandem PHD finger of MOZ reveals a regulatory mechanism for HOXA9 transcription

scientific article

Compact molten globule-like state of hUBF HMG Box1 at extremely low pH.

scientific article

Conformational Selection in Ligand Recognition by the First Tudor Domain of PHF20L1

scientific article published on 04 September 2020

Conformational change upon ligand binding and dynamics of the PDZ domain from leukemia-associated Rho guanine nucleotide exchange factor

scientific article published on 14 April 2008

Cooperation of Escherichia coli Hfq hexamers in DsrA binding

scientific article

Crystal Structure of Arginine Methyltransferase 6 from Trypanosoma brucei

scientific article

Crystal Structure of Human SSRP1 Middle Domain Reveals a Role in DNA Binding

scientific article

Crystal structure and functional characterization of the human RBM25 PWI domain and its flanking basic region ⬇️

scientific article published on February 15, 2013

Crystal structure of Arabidopsis terminal uridylyl transferase URT1

scientific article published on 31 January 2020

Crystal structure of human BS69 Bromo-ZnF-PWWP reveals its role in H3K36me3 nucleosome binding

scientific article

Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate

scientific article

Crystal structure of triple-BRCT-domain of ECT2 and insights into the binding characteristics to CYK-4

scientific article

Domain-swapped dimerization of the second PDZ domain of ZO2 may provide a structural basis for the polymerization of claudins

scientific article

Dynamic Nature of CTCF Tandem 11 Zinc Fingers in Multivalent Recognition of DNA As Revealed by NMR Spectroscopy

scientific article published on 06 July 2018

EB1 acetylation by P300/CBP-associated factor (PCAF) ensures accurate kinetochore-microtubule interactions in mitosis.

scientific article

Expression, purification, crystallization and preliminary X-ray characterization of the GRP carbohydrate-recognition domain from Homo sapiens

scientific article

Hfq-bridged ternary complex is important for translation activation of rpoS by DsrA

scientific article

How well can we predict native contacts in proteins based on decoy structures and their energies?

scientific article

Identification and structural basis for a novel interaction between Vav2 and Arap3

scientific article

Identification of a potent inhibitor of human dual-specific phosphatase, VHR, from computer-aided and NMR-based screening to cellular effects.

scientific article

Improving metabolic flux estimation via evolutionary optimization for convex solution space

scientific article published in March 2007

Increasing the accuracy of mass isotopomer analysis through calibration curves constructed using biologically synthesized compounds

scientific article

Insight into the binding properties of MEKK3 PB1 to MEK5 PB1 from its solution structure

scientific article

Insights into the Structure of Dimeric RNA Helicase CsdA and Indispensable Role of Its C-Terminal Regions.

scientific article

Insights into the molecular recognition of the granuphilin C2A domain with PI(4,5)P2.

scientific article published on 13 January 2015

Interesting structural and dynamical behaviors exhibited by the AF-6 PDZ domain upon Bcr peptide binding.

scientific article

Investigation of the four cooperative unfolding units existing in the MICAL-1 CH domain

scientific article

Investigation of the structural stability of hUBF HMG box 5 by native-state hydrogen exchange

scientific article published on 01 February 2007

Metabolic flux ratio analysis and multi-objective optimization revealed a globally conserved and coordinated metabolic response of E. coli to paraquat-induced oxidative stress ⬇️

scientific article published on November 6, 2012

Mitosis-specific acetylation tunes Ran effector binding for chromosome segregation.

scientific article published on 6 October 2017

Molecular dynamics simulation of the unfolding of the human prion protein domain under low pH and high temperature conditions

scientific article published in May 2003

Molecular dynamics simulations of peptides and proteins with amplified collective motions

scientific article

NMR Fragment-Based Screening against Tandem RNA Recognition Motifs of TDP-43

scientific article published on 30 June 2019

NMR structure and regulated expression in APL cell of human SH3BGRL3.

scientific article

Polo-like kinase 1 coordinates biosynthesis during cell cycle progression by directly activating pentose phosphate pathway

scientific article published on 15 November 2017

Recognition of unmodified histone H3 by the first PHD finger of bromodomain-PHD finger protein 2 provides insights into the regulation of histone acetyltransferases monocytic leukemic zinc-finger protein (MOZ) and MOZ-related factor (MORF)

scientific article

Repurposing Low-Molecular-Weight Drugs Against the Main Protease of Severe Acute Respiratory Syndrome Coronavirus 2

scientific article published on 28 July 2020

Repurposing low–molecular-weight drugs against the main protease of severe acute respiratory syndrome coronavirus 2

scientific article published on 07 May 2020

SUMO-1 modification increases human SOD1 stability and aggregation

scientific article published on 23 June 2006

Solution Structure of Tandem SH2 Domains from Spt6 Protein and Their Binding to the Phosphorylated RNA Polymerase II C-terminal Domain ⬇️

scientific article published on June 15, 2011

Solution Structure of the Second RRM Domain of RBM5 and Its Unusual Binding Characters for Different RNA Targets ⬇️

scientific article published on August 8, 2012

Solution structure and DNA binding property of the fifth HMG box domain in comparison with the first HMG box domain in human upstream binding factor

scientific article (publication date: 25 February 2003)

Solution structure and backbone dynamics of the AF-6 PDZ domain/Bcr peptide complex

scientific article

Solution structure of AF-6 PDZ domain and its interaction with the C-terminal peptides from Neurexin and Bcr

scientific article published on 31 January 2005

Solution structure of BRD7 bromodomain and its interaction with acetylated peptides from histone H3 and H4

scientific article

Solution structure of BmBKTx1, a new BKCa1 channel blocker from the Chinese scorpion Buthus martensi Karsch

scientific article published in April 2004

Solution structure of GOPC PDZ domain and its interaction with the C-terminal motif of neuroligin

scientific article

Solution structure of Kti11p from Saccharomyces cerevisiae reveals a novel zinc-binding module.

scientific article

Solution structure of S. cerevisiae PDCD5-like protein and its promoting role in H(2)O(2)-induced apoptosis in yeast.

scientific article

Solution structure of Urm1 and its implications for the origin of protein modifiers

scientific article (publication date: August 2006)

Solution structure of an atypical PHD finger in BRPF2 and its interaction with DNA

scientific article published in October 2012

Solution structure of calponin homology domain of Human MICAL-1

scientific article published on 17 October 2006

Solution structure of human Brg1 bromodomain and its specific binding to acetylated histone tails

scientific article

Solution structure of human DESR1, a CSL zinc-binding protein

scientific article

Solution structure of human SUMO-3 C47S and its binding surface for Ubc9

scientific article (publication date: March 2005)

Solution structure of human peptidyl prolyl isomerase-like protein 1 and insights into its interaction with SKIP

scientific article

Solution structure of the Pdp1 PWWP domain reveals its unique binding sites for methylated H4K20 and DNA

scientific article

Solution structure of the first HMG box domain in human upstream binding factor

scientific article

Solution structure of the first SH3 domain of human vinexin and its interaction with vinculin peptides

scientific article

Solution structure of the second PDZ domain of Zonula Occludens 1

scientific article

Solution structure of the second SH3 domain of human CMS and a newly identified binding site at the C-terminus of c-Cbl

scientific article

Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails

scientific article

Specific recognition of phosphorylated tail of H2AX by the tandem BRCT domains of MCPH1 revealed by complex structure

scientific article published in February 2012

Stabilization of PML nuclear localization by conjugation and oligomerization of SUMO-3.

scientific article published in August 2005

Sterical Hindrance Promotes Selectivity of the Autophagy Cargo Receptor NDP52 for the Danger Receptor Galectin-8 in Antibacterial Autophagy ⬇️

scientific article published on February 5, 2013

Structural Analysis of Rtt106p Reveals a DNA Binding Role Required for Heterochromatin Silencing

scientific article

Structural Basis for the Specific Recognition of RhoA by the Dual GTPase-activating Protein ARAP3.

scientific article published on 15 June 2016

Structural Basis of Plant Homeodomain Finger 6 (PHF6) Recognition by the Retinoblastoma Binding Protein 4 (RBBP4) Component of the Nucleosome Remodeling and Deacetylase (NuRD) Complex

scientific article

Structural Insights into ceNAP1 Chaperoning Activity toward ceH2A-H2B

scientific article published on 22 October 2019

Structural analysis of Stc1 provides insights into the coupling of RNAi and chromatin modification

scientific article

Structural and biochemical insights into human zinc finger protein AEBP2 reveals interactions with RBBP4.

scientific article published on 13 November 2017

Structural and dynamic characterization of the acid-unfolded state of hUBF HMG box 1 provides clues for the early events in protein folding

scientific article published on 01 June 2005

Structural and dynamic properties of the C-terminal region of the Escherichia coli RNA chaperone Hfq: integrative experimental and computational studies

scientific article

Structural and functional characterization of hMEX-3C Ring finger domain as an E3 ubiquitin ligase

scholarly article by Sayed Ala Moududee published in September 2018

Structural and functional insights into the human Börjeson-Forssman-Lehmann syndrome-associated protein PHF6.

scientific article

Structural basis and binding properties of the second bromodomain of Brd4 with acetylated histone tails

scientific article

Structural basis for SUMO-E2 interaction revealed by a complex model using docking approach in combination with NMR data

scientific article

Structural basis for the specific recognition of 18S rRNA by APUM23.

scientific article

Structural basis of γH2AX recognition by human PTIP BRCT5-BRCT6 domains in the DNA damage response pathway ⬇️

scientific article published on November 3, 2011

Structural determinants for the strict monomethylation activity by trypanosoma brucei protein arginine methyltransferase 7

scientific article

Structural insight into the unique dsDNA binding topology of the human ORC2 wing helix domain

scientific article published on 19 April 2019

Structural insights into a unique preference for 3' terminal guanine of mirtron in Drosophila TUTase tailor

scientific article published in January 2019

Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function

scientific article published on 01 August 2019

Structural insights into substrate selectivity of ribosomal RNA methyltransferase RlmCD.

scientific article published on 26 September 2017

Structural insights into the recognition of phosphorylated FUNDC1 by LC3B in mitophagy.

scientific article published on 18 October 2016

Structural insights into the recognition of phosphorylated Hop1 by Mek1

scientific article published on 02 October 2018

Structural insights into the recognition of the internal A-rich linker from OxyS sRNA by Escherichia coli Hfq.

scientific article

Structural insights into the recognition of γ-globin gene promoter by BCL11A

scientific article published on 29 August 2019

Structural insights on mouse L-threonine dehydrogenase: A regulatory role of Arg180 in catalysis

scientific article

Structural insights reveal the specific recognition of roX RNA by the dsRNA-binding domains of the RNA helicase MLE and its indispensable role in dosage compensation in Drosophila

Structural investigation of the interaction between the tandem SH3 domains of c-Cbl-associated protein and vinculin

scientific article

Structure and function of the two tandem WW domains of the pre-mRNA splicing factor FBP21 (formin-binding protein 21)

scientific article

Structure of C-terminal Tandem BRCT Repeats of Rtt107 Protein Reveals Critical Role in Interaction with Phosphorylated Histone H2A during DNA Damage Repair ⬇️

scientific article published on January 19, 2012

Structure of a CENP-A-histone H4 heterodimer in complex with chaperone HJURP

scientific article

Structure of the YTH domain of human YTHDF2 in complex with an m(6)A mononucleotide reveals an aromatic cage for m(6)A recognition

scientific article

Structure-guided activity enhancement and catalytic mechanism of yeast grx8

scientific article

TRIM66 reads unmodified H3R2K4 and H3K56ac to respond to DNA damage in embryonic stem cells

scientific article published on 19 September 2019

Temperature-induced partially unfolded state of hUBF HMG Box-5: conformational and dynamic investigations of the Box-5 thermal intermediate ensemble

scientific article

The 1.9Å crystal structure of Prp20p from Saccharomyces cerevisiae and its binding properties to Gsp1p and histones ⬇️

scientific article published on November 18, 2010

The 11th C2H2 zinc finger and an adjacent C-terminal arm are responsible for TZAP recognition of telomeric DNA.

scientific article published on 14 November 2017

The Methyltransferase NSD3 Has Chromatin-binding Motifs, PHD5-C5HCH, That Are Distinct from Other NSD (Nuclear Receptor SET Domain) Family Members in Their Histone H3 Recognition ⬇️

scientific article published on December 26, 2012

The human RNA-binding protein and E3 ligase MEX-3C binds the MEX-3-recognition element (MRE) motif with high affinity

scientific article published on 14 August 2017

The important conformational plasticity of DsrA sRNA for adapting multiple target regulation

scientific article

Unveiling the structural features that determine the dual methyltransferase activities of Streptococcus pneumoniae RlmCD

scientific article published on 02 November 2018

ZBTB10 binds the telomeric variant repeat TTGGGG and interacts with TRF2

scientific article published on 01 February 2019

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