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List of works by Titia Sixma

"4D Biology for health and disease" workshop report

scientific article published on 15 October 2010

A conserved two-step binding for the UAF1 regulator to the USP12 deubiquitinating enzyme

scientific article

A deubiquitylating complex required for neosynthesis of a yeast mitochondrial ATP synthase subunit

scientific article

A genomic and functional inventory of deubiquitinating enzymes

scientific article

A glia-derived acetylcholine-binding protein that modulates synaptic transmission.

scientific article

AChBP-targeted α-conotoxin correlates distinct binding orientations with nAChR subtype selectivity

scientific article

ARP/wARP and molecular replacement: the next generation

scientific article published on 05 December 2007

ATP increases the affinity between MutS ATPase domains. Implications for ATP hydrolysis and conformational changes.

scientific article

Acetylcholine binding protein (AChBP) as template for hierarchical in silico screening procedures to identify structurally novel ligands for the nicotinic receptors

scientific article

Acetylcholine binding protein (AChBP): a secreted glial protein that provides a high-resolution model for the extracellular domain of pentameric ligand-gated ion channels.

scientific article

Acetylcholine-binding proteins: functional and structural homologs of nicotinic acetylcholine receptors

scientific article published on 01 January 2006

Active site alanine mutations convert deubiquitinases into high-affinity ubiquitin-binding proteins

scientific article published on 27 August 2018

Active site alanine substitutions can convert deubiquitinating enzymes into avid ubiquitin-binding domains

Akt-mediated phosphorylation of Bmi1 modulates its oncogenic potential, E3 ligase activity, and DNA damage repair activity in mouse prostate cancer.

scientific article published on 16 April 2012

Assembly of a π–π stack of ligands in the binding site of an acetylcholine-binding protein

scientific article

BAP1/ASXL1 recruitment and activation for H2A deubiquitination.

scientific article published on 7 January 2016

Chemical Trapping of the Dynamic MutS-MutL Complex Formed in DNA Mismatch Repair in Escherichia coli ⬇️

scientific article published on March 15, 2011

Chemical synthesis of ubiquitin, ubiquitin-based probes, and diubiquitin

scientific article published on December 2010

Co-expression of protein complexes in prokaryotic and eukaryotic hosts: experimental procedures, database tracking and case studies

scientific article published on 19 September 2006

Crystal structure of acetylcholine-binding protein from Bulinus truncatus reveals the conserved structural scaffold and sites of variation in nicotinic acetylcholine receptors.

scientific article

Crystal structure of an ACh-binding protein reveals the ligand-binding domain of nicotinic receptors

scientific article

Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system

scientific article

Crystal structure of nicotinic acetylcholine receptor homolog AChBP in complex with an alpha-conotoxin PnIA variant.

scientific article published on 12 June 2005

Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA

scientific article

Crystal structure of the specific DNA-binding domain of Tc3 transposase of C.elegans in complex with transposon DNA.

scientific article published on October 1997

DNA mismatch repair: MutS structures bound to mismatches.

scientific article

Dimeric  -Cobratoxin X-ray Structure: LOCALIZATION OF INTERMOLECULAR DISULFIDES AND POSSIBLE MODE OF BINDING TO NICOTINIC ACETYLCHOLINE RECEPTORS

scientific article

Divide and conquer: the E2 active site

scientific article published on 01 June 2006

Dual role of MutS glutamate 38 in DNA mismatch discrimination and in the authorization of repair.

scientific article

E3 ligase Rad18 promotes monoubiquitination rather than ubiquitin chain formation by E2 enzyme Rad6

scientific article

Effect of cobratoxin binding on the normal mode vibration within acetylcholine binding protein

scientific article

Enabling high-throughput ligation-independent cloning and protein expression for the family of ubiquitin specific proteases

scientific article published on 29 March 2011

Erratum: The nucleosome acidic patch plays a critical role in RNF168-dependent ubiquitination of histone H2A.

scientific article published on 24 April 2014

Eukaryotic expression: developments for structural proteomics.

scientific article published on 19 September 2006

First steps towards effective methods in exploiting high-throughput technologies for the determination of human protein structures of high biomedical value.

scientific article published on 19 September 2006

Fragment growing induces conformational changes in acetylcholine-binding protein: a structural and thermodynamic analysis

scientific article

Functional characterization of Rad18 domains for Rad6, ubiquitin, DNA binding and PCNA modification

scientific article

Galactose-binding site in Escherichia coli heat-labile enterotoxin (LT) and cholera toxin (CT)

scientific article

Histone H1 couples initiation and amplification of ubiquitin signalling after DNA damage.

scientific article published on 21 October 2015

Histone ubiquitination in the DNA damage response

scientific article

Human RAD18 interacts with ubiquitylated chromatin components and facilitates RAD9 recruitment to DNA double strand breaks

scientific article

Human Wrnip1 is localized in replication factories in a ubiquitin-binding zinc finger-dependent manner

scientific article published on 7 October 2008

Identification of cross-linked peptides for protein interaction studies using mass spectrometry and 18O labeling

scientific article published on 01 September 2002

Insight in nAChR subtype selectivity from AChBP crystal structures.

scientific article published on July 2009

Interaction of alpha-conotoxin ImII and its analogs with nicotinic receptors and acetylcholine-binding proteins: additional binding sites on Torpedo receptor

scientific article published on 27 August 2009

Intermolecular interactions between the A and B subunits of heat-labile enterotoxin from Escherichia coli promote holotoxin assembly and stability in vivo ⬇️

scientific article published on December 15, 1992

Interplay among nucleosomal DNA, histone tails, and corepressor CoREST underlies LSD1-mediated H3 demethylation

scientific article

Intrinsic flexibility of ubiquitin on proliferating cell nuclear antigen (PCNA) in translesion synthesis.

scientific article published on 18 September 2012

Kinetic analysis of multistep USP7 mechanism shows critical role for target protein in activity

scientific article published in Nature Communications

LNA modification of single-stranded DNA oligonucleotides allows subtle gene modification in mismatch-repair-proficient cells

scientific article published on 7 March 2016

Lactose binding to heat-labile enterotoxin revealed by X-ray crystallography ⬇️

scientific article published on February 6, 1992

Layers of DUB regulation.

scientific article published on 11 June 2015

Lysine-targeting specificity in ubiquitin and ubiquitin-like modification pathways.

scientific article published on April 2014

Magnesium Coordination Controls the Molecular Switch Function of DNA Mismatch Repair Protein MutS

scientific article

Make them, break them, and catch them: studying rare ubiquitin chains.

scientific article published in April 2015

Mechanism of UCH-L5 activation and inhibition by DEUBAD domains in RPN13 and INO80G.

scientific article published on 19 February 2015

Mechanism of USP7/HAUSP activation by its C-terminal ubiquitin-like domain and allosteric regulation by GMP-synthetase

scientific article

MutS/MutL crystal structure reveals that the MutS sliding clamp loads MutL onto DNA.

scientific article published on 11 July 2015

Native mass spectrometry provides direct evidence for DNA mismatch-induced regulation of asymmetric nucleotide binding in mismatch repair protein MutS.

scientific article

Nicotine and carbamylcholine binding to nicotinic acetylcholine receptors as studied in AChBP crystal structures

scientific article (publication date: 25 March 2004)

Nicotinic receptor structure emerging slowly

scientific article published on 01 August 2007

Noncovalent interaction between Ubc9 and SUMO promotes SUMO chain formation

scientific article

Nonhydrolyzable ubiquitin-isopeptide isosteres as deubiquitinating enzyme probes.

scientific article published in July 2010

Preparation of sumoylated substrates for biochemical analysis.

scientific article published on January 2009

Protein engineering: making ubiquitin specific

scientific article published on 01 January 2013

Protein-protein interactions regulate Ubl conjugation

scientific article published on 15 October 2007

Proteomic analysis identifies novel binding partners of BAP1

scientific article published on 30 September 2021

Quantitative analysis of USP activity in vitro

scientific article published on 23 February 2019

RBR E3-ligases at work

scientific article published on 27 January 2014

RNF168 ubiquitinates K13-15 on H2A/H2AX to drive DNA damage signaling

scientific article

RNF8- and RNF168-dependent degradation of KDM4A/JMJD2A triggers 53BP1 recruitment to DNA damage sites

scientific article

Regulation of USP7: A High Incidence of E3 Complexes.

scientific article published on 4 June 2017

SUMO assay with peptide arrays on solid support: insights into SUMO target sites.

scientific article

SUMO modification of the ubiquitin-conjugating enzyme E2-25K

Sharp kinking of a coiled-coil in MutS allows DNA binding and release

scientific article published on 01 September 2019

Structural Characterization of Binding Mode of Smoking Cessation Drugs to Nicotinic Acetylcholine Receptors through Study of Ligand Complexes with Acetylcholine-binding Protein

scientific article

Structural analysis of the LDL receptor-interacting FERM domain in the E3 ubiquitin ligase IDOL reveals an obscured substrate binding site

scientific article published on 29 July 2020

Structural analysis of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA.

scientific article

Structural aspects of multi-domain RING/Ubox E3 ligases in DNA repair.

scientific article published on 26 February 2009

Structural basis for dual excitation and photoisomerization of the Aequorea victoria green fluorescent protein

scientific article

Structural basis of specific H2A K13/K15 ubiquitination by RNF168

scientific article published on 15 April 2019

Structural determinants of selective alpha-conotoxin binding to a nicotinic acetylcholine receptor homolog AChBP.

scientific article

Structure and E3-ligase activity of the Ring-Ring complex of polycomb proteins Bmi1 and Ring1b

scientific article

Structure and function of AChBP, homologue of the ligand-binding domain of the nicotinic acetylcholine receptor

scientific article published on September 2003

Structure of UBE2Z Enzyme Provides Functional Insight into Specificity in the FAT10 Protein Conjugation Machinery

scientific article published on 10 November 2015

Structure of USP7 catalytic domain and three Ubl-domains reveals a connector α-helix with regulatory role

scientific article

Structure of partially-activated E. coli heat-labile enterotoxin (LT) at 2.6 A resolution

scientific article

Structures of Escherichia coli DNA mismatch repair enzyme MutS in complex with different mismatches: a common recognition mode for diverse substrates

scientific article

Symmetry and asymmetry of the RING-RING dimer of Rad18

scientific article

Target specificity of the E3 ligase LUBAC for ubiquitin and NEMO relies on different minimal requirements.

scientific article published on 12 September 2013

The 2.7 A structure of AChBP, homologue of the ligand-binding domain of the nicotinic acetylcholine receptor

scientific article

The DUSP-Ubl domain of USP4 enhances its catalytic efficiency by promoting ubiquitin exchange

scientific article published on 18 November 2014

The Differential Modulation of USP Activity by Internal Regulatory Domains, Interactors and Eight Ubiquitin Chain Types

scientific article published on 01 December 2011

The E3 ligase HOIP specifies linear ubiquitin chain assembly through its RING-IBR-RING domain and the unique LDD extension.

scientific article published on 3 August 2012

The RanBP2 SUMO E3 ligase is neither HECT- nor RING-type

scientific journal article

The alternating ATPase domains of MutS control DNA mismatch repair

scientific article

The conserved molecular machinery in DNA mismatch repair enzyme structures

scientific article

The crystal structure of DNA mismatch repair protein MutS binding to a G x T mismatch

scientific article

The nucleosome acidic patch plays a critical role in RNF168-dependent ubiquitination of histone H2A.

scientific article published on January 2014

The role of UBL domains in ubiquitin-specific proteases

scientific article

The seven wonders of ubiquitin: a multi-interview: Personal insights into the ubiquitin field. Interview by Nonia Pariente

scientific article

The ubiquitin ligase Triad1 inhibits myelopoiesis through UbcH7 and Ubc13 interacting domains

scientific article

The unstructured linker arms of MutL enable GATC site incision beyond roadblocks during initiation of DNA mismatch repair

scientific article published on 01 December 2019

Touch, act and go: landing and operating on nucleosomes

scientific article published on 19 January 2016

Transient transfection coupled to baculovirus infection for rapid protein expression screening in insect cells

scientific article

USP4 inhibits SMAD4 monoubiquitination and promotes activin and BMP signaling.

scientific article

USP48 restrains resection by site-specific cleavage of the BRCA1 ubiquitin mark from H2A.

scientific article published on 15 January 2018

Ubc9 sumoylation regulates SUMO target discrimination

scientific article

Ubiquitin-specific protease 4 is inhibited by its ubiquitin-like domain ⬇️

scientific article published on 18 March 2011

Use of Single-Cysteine Variants for Trapping Transient States in DNA Mismatch Repair

scientific article published on 22 May 2017

Use of acetylcholine binding protein in the search for novel alpha7 nicotinic receptor ligands. In silico docking, pharmacological screening, and X-ray analysis

scientific article

Using stable MutS dimers and tetramers to quantitatively analyze DNA mismatch recognition and sliding clamp formation

scientific article

Usp39 is essential for mitotic spindle checkpoint integrity and controls mRNA-levels of aurora B.

scientific article

Variations on the ABC

scientific article published on 01 April 2005

Variety in the USP deubiquitinase catalytic mechanism

scientific article published in 2024

X-ray studies reveal lanthanide binding sites at the A/B5 interface of E. coli heat labile enterotoxin

scientific article published on February 3, 1992

ZUFSP Deubiquitylates K63-Linked Polyubiquitin Chains to Promote Genome Stability.

scientific article published on 9 March 2018

wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models

scientific article (publication date: July 1997)

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