Publications in Ylva Ivarsson Group

Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions

Kassa, Eszter; Jamshidi, Sara; Mihalič, Filip; Simonetti, Leandro et al.

Part of Analytical Biochemistry, 2023.

DOI for Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions Download full text (pdf) of Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions

A Syntenin Inhibitor Blocks Endosomal Entry of SARS-CoV-2 and a Panel of RNA Viruses

Lindqvist, Richard; Benz, Caroline; Sereikaite, Vita; Maassen, Lars et al.

Part of Viruses, 2022.

DOI for A Syntenin Inhibitor Blocks Endosomal Entry of SARS-CoV-2 and a Panel of RNA Viruses Download full text (pdf) of A Syntenin Inhibitor Blocks Endosomal Entry of SARS-CoV-2 and a Panel of RNA Viruses

Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition

Li, Yitong; Balakrishnan, Vijaya Kumar; Rowse, Michael; Wu, Cheng-Guo et al.

Part of eLIFE, 2022.

DOI for Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition Download full text (pdf) of Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition

How viral proteins bind short linear motifs and intrinsically disordered domains

Madhu, Priyanka; Davey, Norman E.; Ivarsson, Ylva

Part of Essays in Biochemistry, p. 935-944, 2022.

DOI for How viral proteins bind short linear motifs and intrinsically disordered domains

Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets

Mihalic, Filip; Benz, Caroline; Kassa, Eszter; Lindqvist, Richard et al.

Part of Nature Structural & Molecular Biology, 2022.

p Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs

Kliche, Johanna; Ivarsson, Ylva

Part of Biochemical Journal, p. 1-22, 2022.

DOI for p Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs Download full text (pdf) of p Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs

ProP-PD for proteome-wide motif-mediated interaction discovery

Davey, Norman E.; Simonetti, Leandro; Ivarsson, Ylva

Part of TIBS -Trends in Biochemical Sciences. Regular ed., p. 547-548, 2022.

DOI for ProP-PD for proteome-wide motif-mediated interaction discovery Download full text (pdf) of ProP-PD for proteome-wide motif-mediated interaction discovery

Proteome-scale mapping of binding sites in the unstructured regions of the human proteome

Benz, Caroline; Ali, Muhammad; Krystkowiak, Izabella; Simonetti, Leandro et al.

Part of Molecular Systems Biology, 2022.

DOI for Proteome-scale mapping of binding sites in the unstructured regions of the human proteome Download full text (pdf) of Proteome-scale mapping of binding sites in the unstructured regions of the human proteome

A High-Affinity Peptide Ligand Targeting Syntenin Inhibits Glioblastoma

Haugaard-Kedström, Linda M.; Clemmensen, Louise S.; Sereikaite, Vita; Jin, Zeyu et al.

Part of Journal of Medicinal Chemistry, p. 1423-1434, 2021.

DOI for A High-Affinity Peptide Ligand Targeting Syntenin Inhibits Glioblastoma

Cytoplasmic short linear motifs in ACE2 and integrin beta(3) link SARS-CoV-2 host cell receptors to mediators of endocytosis and autophagy

Kliche, Johanna; Kuss, Hanna; Ali, Muhammad; Ivarsson, Ylva

Part of Science Signaling, 2021.

DOI for Cytoplasmic short linear motifs in ACE2 and integrin beta(3) link SARS-CoV-2 host cell receptors to mediators of endocytosis and autophagy

Integrated analysis of Shank1 PDZ interactions with C-terminal and internal binding motifs

Ali, Muhammad; McAuley, Mishal Mariam; Lüchow, Susanne; Knapp, Stefan et al.

Part of Current Research in Structural Biology, p. 41-50, 2021.

DOI for Integrated analysis of Shank1 PDZ interactions with C-terminal and internal binding motifs Download full text (pdf) of Integrated analysis of Shank1 PDZ interactions with C-terminal and internal binding motifs

Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities

Kruse, Thomas; Benz, Caroline; Garvanska, Dimitriya H.; Lindqvist, Richard et al.

Part of Nature Communications, 2021.

DOI for Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities Download full text (pdf) of Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities

Deciphering the Unexpected Binding Capacity of the Third PDZ Domain of Whirlin to Various Cochlear Hair Cell Partners

Zhu, Yanlei; Delhommel, Florent; Cordier, Florence; Lüchow, Susanne et al.

Part of Journal of Molecular Biology, p. 5920-5937, 2020.

DOI for Deciphering the Unexpected Binding Capacity of the Third PDZ Domain of Whirlin to Various Cochlear Hair Cell Partners

Genetically Encoded Cyclic Peptide Phage Display Libraries

Simonetti, Leandro; Ivarsson, Ylva

Part of ACS CENTRAL SCIENCE, p. 336-338, 2020.

DOI for Genetically Encoded Cyclic Peptide Phage Display Libraries Download full text (pdf) of Genetically Encoded Cyclic Peptide Phage Display Libraries

Profiling calcium-dependent interactions between Sorcin and intrinsically disordered regions of human proteome

Genovese, Ilaria; Carotti, Andrea; Ilari, Andrea; Fiorillo, Annarita et al.

Part of Biochimica et Biophysica Acta - General Subjects, 2020.

DOI for Profiling calcium-dependent interactions between Sorcin and intrinsically disordered regions of human proteome

Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling

Wigington, Callie P.; Roy, Jagoree; Damle, Nikhil P.; Yadav, Vikash K. et al.

Part of Molecular Cell, p. 342-+, 2020.

DOI for Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling

A Consensus Binding Motif for the PP4 Protein Phosphatase

Ueki, Yumi; Kruse, Thomas; Weisser, Melanie Bianca; Sundell, Gustav N. et al.

Part of Molecular Cell, p. 953-964.e6, 2019.

DOI for A Consensus Binding Motif for the PP4 Protein Phosphatase

Affinity and specificity of motif-based protein-protein interactions

Ivarsson, Ylva; Jemth, Per

Part of Current opinion in structural biology, p. 26-33, 2019.

DOI for Affinity and specificity of motif-based protein-protein interactions Download full text (pdf) of Affinity and specificity of motif-based protein-protein interactions

Editorial overview: Folding and binding

Ivarsson, Ylva; Jemth, Per

Part of Current opinion in structural biology, p. 139-140, 2019.

DOI for Editorial overview: Folding and binding

Systematic identification of recognition motifs for the hub protein LC8

Jespersen, Nathan; Estelle, Aidan; Waugh, Nathan; Davey, Norman E. et al.

Part of Life Science Alliance, 2019.

DOI for Systematic identification of recognition motifs for the hub protein LC8 Download full text (pdf) of Systematic identification of recognition motifs for the hub protein LC8

High-throughput discovery of functional disordered regions

Ali, Muhammad; Ivarsson, Ylva

Part of Molecular Systems Biology, 2018.

DOI for High-throughput discovery of functional disordered regions

Proteome‐wide analysis of phospho‐regulated PDZ domain interactions

Sundell, Gustav; Arnold, Roland; Ali, Muhammad; Naksukpaiboon, Piangfan et al.

Part of Molecular Systems Biology, 2018.

DOI for Proteome‐wide analysis of phospho‐regulated PDZ domain interactions Download full text (pdf) of Proteome‐wide analysis of phospho‐regulated PDZ domain interactions

The Sign of Nuclear Magnetic Resonance Chemical Shift Difference as a Determinant of the Origin of Binding Selectivity: Elucidation of the Position Dependence of Phosphorylation in Ligands Binding to Scribble PDZ1

Sundell, Gustav; Vögeli, Beat; Ivarsson, Ylva; Chi, Celestine N.

Part of Biochemistry, p. 66-71, 2018.

DOI for The Sign of Nuclear Magnetic Resonance Chemical Shift Difference as a Determinant of the Origin of Binding Selectivity: Elucidation of the Position Dependence of Phosphorylation in Ligands Binding to Scribble PDZ1 Download full text (pdf) of The Sign of Nuclear Magnetic Resonance Chemical Shift Difference as a Determinant of the Origin of Binding Selectivity: Elucidation of the Position Dependence of Phosphorylation in Ligands Binding to Scribble PDZ1

A novel role for the Calcineurin phosphatase at the nuclear pore

Wigington, C. P.; Roy, J.; Damle, N. P.; Ulengin-Talkish, I. et al.

Part of Molecular Biology of the Cell, p. 3727-3727, 2017.

DOI for A novel role for the Calcineurin phosphatase at the nuclear pore

Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome

Davey, Norman E.; Seo, Moon-Hyeong; Yadav, Vikash Kumar; Jeon, Jouhyun et al.

Part of The FEBS Journal, p. 485-498, 2017.

DOI for Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome Download full text (pdf) of Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome

Investigating the phospho-regulation of ER shaping protein RTN1A (Reticulon-1A) by the Calcineurin phosphatase.

Cho, S. Ei; Roy, J.; Ivarsson, Ylva; Cyert, M. S.

Part of Molecular Biology of the Cell, p. 3727-3727, 2017.

DOI for Investigating the phospho-regulation of ER shaping protein RTN1A (Reticulon-1A) by the Calcineurin phosphatase.

Mapping the human calcineurin phosphatase signaling network through global identification of short linear motifs that mediate substrate recognition

Roy, J.; Wigington, C. P.; Damle, N. P.; Ulengin-Talkish, I. et al.

Part of Molecular Biology of the Cell, p. 3727-3727, 2017.

DOI for Mapping the human calcineurin phosphatase signaling network through global identification of short linear motifs that mediate substrate recognition

PP2A-B' holoenzyme substrate recognition, regulation and role in cytokinesis

Wu, Cheng-Guo; Chen, Hui; Guo, Feng; Yadav, Vikash K et al.

Part of Cell Discovery, 2017.

DOI for PP2A-B' holoenzyme substrate recognition, regulation and role in cytokinesis Download full text (pdf) of PP2A-B' holoenzyme substrate recognition, regulation and role in cytokinesis

Uncovering Novel Substrates and Functions for the Calcineurin Phosphatase in Human Cells

Wigington, Callie P.; Roy, Jagoree; Damle, Nikhil P.; El Cho, Shein et al.

Part of The FASEB Journal, 2017.

Frizzled 7 and PIP2 binding by syntenin PDZ2 domain supports Frizzled 7 trafficking and signalling

Egea-Jimenez, Antonio Luis; Gallardo, Rodrigo; Garcia-Pino, Abel; Ivarsson, Ylva et al.

Part of Nature Communications, 2016.

DOI for Frizzled 7 and PIP2 binding by syntenin PDZ2 domain supports Frizzled 7 trafficking and signalling Download full text (pdf) of Frizzled 7 and PIP2 binding by syntenin PDZ2 domain supports Frizzled 7 trafficking and signalling

Improved affinity at the cost of decreased specificity: a recurring theme in PDZ-peptide interactions.

Karlsson, O Andreas; Sundell, Gustav N; Andersson, Eva; Ivarsson, Ylva et al.

Part of Scientific Reports, 2016.

DOI for Improved affinity at the cost of decreased specificity: a recurring theme in PDZ-peptide interactions. Download full text (pdf) of Improved affinity at the cost of decreased specificity: a recurring theme in PDZ-peptide interactions.

Let There Be Light!

Raykova, Doroteya; Koos, Bjoern; Asplund, Anna; Gelleri, Marton et al.

Part of Proteomes, 2016.

DOI for Let There Be Light! Download full text (pdf) of Let There Be Light!

Pooled screening for antiproliferative inhibitors of protein-protein interactions.

Nim, Satra; Jeon, Jouhyun; Corbi-Verge, Carles; Seo, Moon-Hyeong et al.

Part of Nature Chemical Biology, p. 275-281, 2016.

DOI for Pooled screening for antiproliferative inhibitors of protein-protein interactions.

Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin

Garrido-Urbani, Sarah; Garg, Pankaj; Ghossoub, Rania; Arnold, Roland et al.

Part of FEBS Letters, p. 3-12, 2016.

DOI for Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin Download full text (pdf) of Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin

Uncovering novel substrates and functions for the calcineurin phosphatase in human cells.

Wigington, C. P.; Damle, N. P.; Roy, J.; Cho, S. E. et al.

Part of Molecular Biology of the Cell, 2016.

DOI for Uncovering novel substrates and functions for the calcineurin phosphatase in human cells.

High-throughput methods for identification of protein-protein interactions involving short linear motifs

Blikstad, Cecilia; Ivarsson, Ylva

Part of Cell Communication and Signaling, 2015.

DOI for High-throughput methods for identification of protein-protein interactions involving short linear motifs Download full text (pdf) of High-throughput methods for identification of protein-protein interactions involving short linear motifs

Selectivity of Aggregation-Determining Interactions

Ganesan, Ashok; Debulpaep, Maja; Wilkinson, Hannah; Van Durme, Joost et al.

Part of Journal of Molecular Biology, p. 236-247, 2015.

DOI for Selectivity of Aggregation-Determining Interactions

Structural basis of Sorcin-mediated calcium-dependent signal transduction

Ilari, Andrea; Fiorillo, Annarita; Poser, Elena; Lalioti, Vasiliki S. et al.

Part of Scientific Reports, 2015.

A Structural Portrait of the PDZ Domain Family

Ernst, Andreas; Appleton, Brent A; Ivarsson, Ylva; Zhang, Yingnan et al.

Part of Journal of Molecular Biology, p. 3509-3519, 2014.

DOI for A Structural Portrait of the PDZ Domain Family

Interaction Analysis through Proteomic Phage Display

Sundell, Gustav; Ivarsson, Ylva

Part of BioMed Research International, p. 176172-, 2014.

DOI for Interaction Analysis through Proteomic Phage Display Download full text (pdf) of Interaction Analysis through Proteomic Phage Display

Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes

Ivarsson, Ylva; Arnold, Roland; McLaughlin, Megan; Nim, Satra et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 2542-2547, 2014.

DOI for Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes

The Development and Characterization of a Peptide-Based Syntenin Inhibitor: Implacations for Cancer Metastasis

Haugaard-Kedstrom, L. M.; Albertsen, L.; Gil, F. Abalde; Ivarsson, Ylva et al.

Part of Journal of Peptide Science, p. S39-S39, 2014.

A ZO-1/α5β1-integrin complex regulates cytokinesis downstream of PKCε in NCI-H460 cells plated on fibronectin

Hämälistö, Saara; Pouwels, Jeroen; de Franceschi, Nicola; Saari, Markku et al.

Part of PLOS ONE, p. e70696-, 2013.

DOI for A ZO-1/α5β1-integrin complex regulates cytokinesis downstream of PKCε in NCI-H460 cells plated on fibronectin

Prevalence, specificity and determinants of lipid-interacting PDZ domains from an in-cell screen and in vitro binding experiments

Ivarsson, Ylva; Wawrzyniak, Anna Maria; Kashyap, Rudra; Polanowska, Jolanta et al.

Part of PloS one, p. e54581-, 2013.

DOI for Prevalence, specificity and determinants of lipid-interacting PDZ domains from an in-cell screen and in vitro binding experiments

Extensions of PSD-95/discs large/ZO-1 (PDZ) domains influence lipid binding and membrane targeting of syntenin-1

Wawrzyniak, Anna Maria; Vermeiren, Elke; Zimmermann, Pascale; Ivarsson, Ylva

Part of FEBS Letters, p. 1445-1451, 2012.

DOI for Extensions of PSD-95/discs large/ZO-1 (PDZ) domains influence lipid binding and membrane targeting of syntenin-1

Plasticity of PDZ domains in ligand recognition and signaling

Ivarsson, Ylva

Part of FEBS Letters, p. 2638-47, 2012.

DOI for Plasticity of PDZ domains in ligand recognition and signaling

Syndecan-syntenin-ALIX regulates the biogenesis of exosomes

Baietti, Maria Francesca; Zhang, Zhe; Mortier, Eva; Melchior, Aurélie et al.

Part of Nature cell biology, p. 677-685, 2012.

DOI for Syndecan-syntenin-ALIX regulates the biogenesis of exosomes

Syntenin, a syndecan adaptor and an Arf6 phosphatidylinositol 4,5-bisphosphate effector, is essential for epiboly and gastrulation cell movements in zebrafish

Lambaerts, Kathleen; Van Dyck, Stijn; Mortier, Eva; Ivarsson, Ylva et al.

Part of Journal of Cell Science, p. 1129-1140, 2012.

DOI for Syntenin, a syndecan adaptor and an Arf6 phosphatidylinositol 4,5-bisphosphate effector, is essential for epiboly and gastrulation cell movements in zebrafish

Cooperative phosphoinositide and peptide binding by PSD-95/discs large/ZO-1 (PDZ) domain of polychaetoid, Drosophila zonulin

Ivarsson, Ylva; Wawrzyniak, Anna Maria; Wuytens, Gunther; Kosloff, Mickey et al.

Part of Journal of Biological Chemistry, p. 44669-78, 2011.

DOI for Cooperative phosphoinositide and peptide binding by PSD-95/discs large/ZO-1 (PDZ) domain of polychaetoid, Drosophila zonulin

Misregulated alternative splicing of BIN1 is associated with T tubule alterations and muscle weakness in myotonic dystrophy

Fugier, Charlotte; Klein, Arnaud F; Hammer, Caroline; Vassilopoulos, Stéphane et al.

Part of Nature medicine, p. 720-725, 2011.

DOI for Misregulated alternative splicing of BIN1 is associated with T tubule alterations and muscle weakness in myotonic dystrophy

Structural characterization of a misfolded intermediate populated during the folding process of a PDZ domain

Gianni, Stefano; Ivarsson, Ylva; De Simone, Alfonso; Travaglini-Allocatelli, Carlo et al.

Part of Nature Structural & Molecular Biology, p. 1431-1437, 2010.

DOI for Structural characterization of a misfolded intermediate populated during the folding process of a PDZ domain

Structural diversity of PDZ-lipid interactions

Gallardo, Rodrigo; Ivarsson, Ylva; Schymkowitz, Joost; Rousseau, Frédéric et al.

Part of ChemBioChem (Print), p. 456-67, 2010.

DOI for Structural diversity of PDZ-lipid interactions

Engineered symmetric connectivity of secondary structure elements highlights malleability of protein folding pathways

Ivarsson, Ylva; Travaglini-Allocatelli, Carlo; Brunori, Maurizio; Gianni, Stefano

Part of Journal of the American Chemical Society, p. 11727-33, 2009.

DOI for Engineered symmetric connectivity of secondary structure elements highlights malleability of protein folding pathways

Folding and stability of globular proteins and implications for function

Travaglini-Allocatelli, Carlo; Ivarsson, Ylva; Jemth, Per; Gianni, Stefano

Part of Current opinion in structural biology, p. 3-7, 2009.

DOI for Folding and stability of globular proteins and implications for function

Folding and misfolding in a naturally occurring circularly permuted PDZ domain

Ivarsson, Ylva; Travaglini-Allocatelli, Carlo; Brunori, Maurizio; Gianni, Stefano

Part of Journal of Biological Chemistry, p. 8954-60, 2008.

DOI for Folding and misfolding in a naturally occurring circularly permuted PDZ domain

Mechanisms of protein folding

Ivarsson, Ylva; Travaglini-Allocatelli, Carlo; Brunori, Maurizio; Gianni, Stefano

Part of European Biophysics Journal, p. 721-728, 2008.

DOI for Mechanisms of protein folding

The folding pathway of an engineered circularly permuted PDZ domain

Ivarsson, Ylva; Travaglini-Allocatelli, Carlo; Morea, Veronica; Brunori, Maurizio et al.

Part of Protein Engineering Design & Selection, p. 155-160, 2008.

DOI for The folding pathway of an engineered circularly permuted PDZ domain

An on-pathway intermediate in the folding of a PDZ domain

Ivarsson, Ylva; Travaglini-Allocatelli, Carlo; Jemth, Per; Malatesta, Francesco et al.

Part of Journal of Biological Chemistry, p. 8568-8572, 2007.

DOI for An on-pathway intermediate in the folding of a PDZ domain

Engineering the enantioselectivity of glutathione transferase by combined active-site mutations and chemical modifications

Ivarsson, Ylva; Norrgård, Malena A.; Hellman, Ulf; Mannervik, Bengt

Part of Biochimica et Biophysica Acta - General Subjects, p. 1374-1381, 2007.

DOI for Engineering the enantioselectivity of glutathione transferase by combined active-site mutations and chemical modifications

Identification and characterization of protein folding intermediates

Gianni, Stefano; Ivarsson, Ylva; Jemth, Per; Brunori, Maurizio et al.

Part of Biophysical Chemistry, p. 105-113, 2007.

DOI for Identification and characterization of protein folding intermediates

Mechanism of Na(+) binding to thrombin resolved by ultra-rapid kinetics

Gianni, Stefano; Ivarsson, Ylva; Bah, Alaji; Bush-Pelc, Leslie A et al.

Part of Biophysical Chemistry, p. 111-114, 2007.

DOI for Mechanism of Na(+) binding to thrombin resolved by ultra-rapid kinetics

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Norrgård, Malena A.; Ivarsson, Ylva; Tars, Kaspars; Mannervik, Bengt

Part of Proceedings of the National Academy of Sciences of the USA, p. 4876-4881, 2006.

Alternative mutations of a positively selected residue elicit gain or loss of functionalities in enzyme evolution

Norrgård, Malena A; Ivarsson, Ylva; Tars, Kaspars; Mannervik, Bengt

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 4876-4881, 2006.

DOI for Alternative mutations of a positively selected residue elicit gain or loss of functionalities in enzyme evolution

Combinatorial protein chemistry in three dimensions: a paradigm for the evolution of glutathione transferases with novel activities

Ivarsson, Ylva; Mannervik, Bengt

Part of Toxicology of Glutathione Transferases, p. 47-69, 2006.

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Ivarsson, Ylva; Mannervik, Bengt

Part of Protein Engineering Design and Selection, p. 607-616, 2006.

Exploring the importance of an active site residue on the stereo and regio selectivity of Mu class glutathione transferases

Ivarsson, Ylva; Mannervik, Bengt

Part of FEBS Journal, p. 88 Suppl-, 2005.

Regio- and enantioselectivities in epoxide conjugations are modulated by residue 210 in Mu class glutathione transferases.

Ivarsson, Ylva; Mannervik, Bengt

Part of Protein Eng Des Sel, p. 607-16, 2005.

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Ivarsson, Ylva; Mackey, Aaron J.; Edalat, Maryam; Pearson, William R. et al.

Part of Journal of Biological Chemistry, p. 8733-8738, 2003.