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Article ; Online: SnoN Stabilizes the SMAD3/SMAD4 Protein Complex.

Walldén, Karin / Nyman, Tomas / Hällberg, B Martin

2017 Volume 7, Page(s) 46370

Abstract: TGF-β signaling regulates cellular processes such as proliferation, differentiation and apoptosis through activation of SMAD transcription factors that are in turn modulated by members of the Ski-SnoN family. In this process, Ski has been shown to ... ...

Abstract	TGF-β signaling regulates cellular processes such as proliferation, differentiation and apoptosis through activation of SMAD transcription factors that are in turn modulated by members of the Ski-SnoN family. In this process, Ski has been shown to negatively modulate TGF-β signaling by disrupting active R-SMAD/Co-SMAD heteromers. Here, we show that the related regulator SnoN forms a stable complex with the R-SMAD (SMAD3) and the Co-SMAD (SMAD4). To rationalize this stabilization at the molecular level, we determined the crystal structure of a complex between the SAND domain of SnoN and the MH2-domain of SMAD4. This structure shows a binding mode that is compatible with simultaneous coordination of R-SMADs. Our results show that SnoN, and SMAD heteromers can form a joint structural core for the binding of other transcription modulators. The results are of fundamental importance for our understanding of the molecular mechanisms behind the modulation of TGF-β signaling.
MeSH term(s)	Humans ; Intracellular Signaling Peptides and Proteins/metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; Proto-Oncogene Proteins/metabolism ; Signal Transduction/physiology ; Smad3 Protein/metabolism ; Smad4 Protein/metabolism
Chemical Substances	Intracellular Signaling Peptides and Proteins ; Proto-Oncogene Proteins ; SKIL protein, human ; SMAD3 protein, human ; SMAD4 protein, human ; Smad3 Protein ; Smad4 Protein
Language	English
Publishing date	2017-04-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/srep46370
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Article ; Online: Design, synthesis, and evaluation of peptide-imidazo[1,2-a]pyrazine bioconjugates as potential bivalent inhibitors of the VirB11 ATPase HP0525.

Sayer, James R / Walldén, Karin / Koss, Hans / Allan, Helen / Daviter, Tina / Gane, Paul J / Waksman, Gabriel / Tabor, Alethea B

Journal of peptide science : an official publication of the European Peptide Society

2021 Volume 27, Issue 10, Page(s) e3353

Abstract: Helicobacter pylori (H. pylori) infections have been implicated in the development of gastric ulcers and various cancers: however, the success of current therapies is compromised by rising antibiotic resistance. The virulence and pathogenicity of H. ... ...

Abstract	Helicobacter pylori (H. pylori) infections have been implicated in the development of gastric ulcers and various cancers: however, the success of current therapies is compromised by rising antibiotic resistance. The virulence and pathogenicity of H. pylori is mediated by the type IV secretion system (T4SS), a multiprotein macromolecular nanomachine that transfers toxic bacterial factors and plasmid DNA between bacterial cells, thus contributing to the spread of antibiotic resistance. A key component of the T4SS is the VirB11 ATPase HP0525, which is a hexameric protein assembly. We have previously reported the design and synthesis of a series of novel 8-amino imidazo[1,2-a]pyrazine derivatives as inhibitors of HP0525. In order to improve their selectivity, and potentially develop these compounds as tools for probing the assembly of the HP0525 hexamer, we have explored the design and synthesis of potential bivalent inhibitors. We used the structural details of the subunit-subunit interactions within the HP0525 hexamer to design peptide recognition moieties of the subunit interface. Different methods (cross metathesis, click chemistry, and cysteine-malemide) for bioconjugation to selected 8-amino imidazo[1,2-a]pyrazines were explored, as well as peptides spanning larger or smaller regions of the interface. The IC
MeSH term(s)	Adenosine Triphosphatases ; Bacterial Proteins ; Helicobacter pylori ; Peptides/pharmacology ; Pyrazines
Chemical Substances	Bacterial Proteins ; Peptides ; Pyrazines ; Adenosine Triphosphatases (EC 3.6.1.-)
Language	English
Publishing date	2021-06-17
Publishing country	England
Document type	Journal Article
ZDB-ID	1234416-3
ISSN	1099-1387 ; 1075-2617
ISSN (online)	1099-1387
ISSN	1075-2617
DOI	10.1002/psc.3353
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Article ; Online: Design, structure and plasma binding of ancestral β-CoV scaffold antigens.

Hueting, David / Schriever, Karen / Sun, Rui / Vlachiotis, Stelios / Zuo, Fanglei / Du, Likun / Persson, Helena / Hofström, Camilla / Ohlin, Mats / Walldén, Karin / Buggert, Marcus / Hammarström, Lennart / Marcotte, Harold / Pan-Hammarström, Qiang / Andréll, Juni / Syrén, Per-Olof

Nature communications

2023 Volume 14, Issue 1, Page(s) 6527

Abstract: We report the application of ancestral sequence reconstruction on coronavirus spike protein, resulting in stable and highly soluble ancestral scaffold antigens (AnSAs). The AnSAs interact with plasma of patients recovered from COVID-19 but do not bind to ...

Abstract	We report the application of ancestral sequence reconstruction on coronavirus spike protein, resulting in stable and highly soluble ancestral scaffold antigens (AnSAs). The AnSAs interact with plasma of patients recovered from COVID-19 but do not bind to the human angiotensin-converting enzyme 2 (ACE2) receptor. Cryo-EM analysis of the AnSAs yield high resolution structures (2.6-2.8 Å) indicating a closed pre-fusion conformation in which all three receptor-binding domains (RBDs) are facing downwards. The structures reveal an intricate hydrogen-bonding network mediated by well-resolved loops, both within and across monomers, tethering the N-terminal domain and RBD together. We show that AnSA-5 can induce and boost a broad-spectrum immune response against the wild-type RBD as well as circulating variants of concern in an immune organoid model derived from tonsils. Finally, we highlight how AnSAs are potent scaffolds by replacing the ancestral RBD with the wild-type sequence, which restores ACE2 binding and increases the interaction with convalescent plasma.
MeSH term(s)	Humans ; Angiotensin-Converting Enzyme 2 ; COVID-19 ; COVID-19 Serotherapy ; Hydrogen Bonding ; Organoids ; Spike Glycoprotein, Coronavirus/genetics ; Protein Binding
Chemical Substances	Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2023-10-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-42200-x
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Article ; Online: Structural basis for the allosteric regulation and substrate recognition of human cytosolic 5'-nucleotidase II.

Walldén, Karin / Nordlund, Pär

Journal of molecular biology

2011 Volume 408, Issue 4, Page(s) 684–696

Abstract: Cytosolic 5'-nucleotidase II (cN-II) catalyzes the dephosphorylation of 6-hydroxypurine nucleoside 5'-monophosphates and participates in the regulation of purine nucleotide pools within the cell. It interferes with the phosphorylation-dependent ... ...

Abstract	Cytosolic 5'-nucleotidase II (cN-II) catalyzes the dephosphorylation of 6-hydroxypurine nucleoside 5'-monophosphates and participates in the regulation of purine nucleotide pools within the cell. It interferes with the phosphorylation-dependent activation of nucleoside analogues used in the treatment of cancer and viral diseases. It is allosterically activated by a number of phosphate-containing cellular metabolites such as ATP, diadenosine polyphosphates, and 2,3-bisphosphoglycerate, which couple its activity with the metabolic state of the cell. We present seven high-resolution structures of human cN-II, including a ligand-free form and complexes with various substrates and effectors. These structures reveal the structural basis for the allosteric activation of cN-II, uncovering a mechanism where an effector-induced disorder-to-order transition generates rearrangements within the catalytic site and the subsequent coordination of the catalytically essential magnesium. Central to the activation is the large transition of the catalytically essential Asp356. This study also provides the structural basis for the substrate specificity of cN-II, where Arg202, Asp206, and Phe157 seem to be important residues for purine/pyrimidine selectivity. These structures provide a comprehensive structural basis for the design of cN-II inhibitors. They also contribute to the understanding of how the nucleotide salvage pathway is regulated at a molecular level.
MeSH term(s)	5'-Nucleotidase/chemistry ; Allosteric Regulation ; Amino Acid Sequence ; Asparagine/chemistry ; Catalytic Domain ; Humans ; Magnesium/chemistry ; Models, Molecular ; Molecular Sequence Data ; Substrate Specificity
Chemical Substances	Asparagine (7006-34-0) ; 5'-Nucleotidase (EC 3.1.3.5) ; NT5C2 protein, human (EC 3.1.3.5) ; Magnesium (I38ZP9992A)
Language	English
Publishing date	2011-05-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2011.02.059
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Article: Structural Basis for the Allosteric Regulation and Substrate Recognition of Human Cytosolic 5′-Nucleotidase II

Walldén, Karin / Nordlund, Pär

Journal of molecular biology. 2011 May 13, v. 408, no. 4

2011

Abstract: Cytosolic 5′-nucleotidase II (cN-II) catalyzes the dephosphorylation of 6-hydroxypurine nucleoside 5′-monophosphates and participates in the regulation of purine nucleotide pools within the cell. It interferes with the phosphorylation-dependent ... ...

Abstract	Cytosolic 5′-nucleotidase II (cN-II) catalyzes the dephosphorylation of 6-hydroxypurine nucleoside 5′-monophosphates and participates in the regulation of purine nucleotide pools within the cell. It interferes with the phosphorylation-dependent activation of nucleoside analogues used in the treatment of cancer and viral diseases. It is allosterically activated by a number of phosphate-containing cellular metabolites such as ATP, diadenosine polyphosphates, and 2,3-bisphosphoglycerate, which couple its activity with the metabolic state of the cell. We present seven high-resolution structures of human cN-II, including a ligand-free form and complexes with various substrates and effectors. These structures reveal the structural basis for the allosteric activation of cN-II, uncovering a mechanism where an effector-induced disorder-to-order transition generates rearrangements within the catalytic site and the subsequent coordination of the catalytically essential magnesium. Central to the activation is the large transition of the catalytically essential Asp356. This study also provides the structural basis for the substrate specificity of cN-II, where Arg202, Asp206, and Phe157 seem to be important residues for purine/pyrimidine selectivity. These structures provide a comprehensive structural basis for the design of cN-II inhibitors. They also contribute to the understanding of how the nucleotide salvage pathway is regulated at a molecular level.
Keywords	adenosine triphosphate ; dephosphorylation ; humans ; magnesium ; metabolites ; polyphosphates ; substrate specificity
Language	English
Dates of publication	2011-0513
Size	p. 684-696.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2011.02.059
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Article ; Online: Publisher Correction: Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor.

Perez Boerema, Annemarie / Aibara, Shintaro / Paul, Bijoya / Tobiasson, Victor / Kimanius, Dari / Forsberg, Björn O / Wallden, Karin / Lindahl, Erik / Amunts, A

Nature plants

2018 Volume 4, Issue 8, Page(s) 615

Abstract: In the version of this Article originally published, the name of co-author Annemarie Perez Boerema was coded wrongly, resulting in it being incorrect when exported to citation databases. This has been corrected, though no visible changes will be apparent. ...

Abstract	In the version of this Article originally published, the name of co-author Annemarie Perez Boerema was coded wrongly, resulting in it being incorrect when exported to citation databases. This has been corrected, though no visible changes will be apparent.
Language	English
Publishing date	2018-07-23
Publishing country	England
Document type	Journal Article ; Published Erratum
ISSN	2055-0278
ISSN (online)	2055-0278
DOI	10.1038/s41477-018-0203-0
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Article ; Online: Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor.

Perez Boerema, Annemarie / Aibara, Shintaro / Paul, Bijoya / Tobiasson, Victor / Kimanius, Dari / Forsberg, Björn O / Wallden, Karin / Lindahl, Erik / Amunts, A

Nature plants

2018 Volume 4, Issue 4, Page(s) 212–217

Abstract: Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions underpinning this process in plants take place in the ... ...

Abstract	Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions underpinning this process in plants take place in the chloroplast. Chloroplasts evolved ~1.2 billion years ago from an engulfed primordial diazotrophic cyanobacterium, and chlororibosomes are responsible for synthesis of the core proteins driving photochemical reactions. Chlororibosomal activity is spatiotemporally coupled to the synthesis and incorporation of functionally essential co-factors, implying the presence of chloroplast-specific regulatory mechanisms and structural adaptation of the chlororibosome
MeSH term(s)	Chloroplasts/chemistry ; Chloroplasts/metabolism ; Cryoelectron Microscopy ; Image Processing, Computer-Assisted ; Models, Molecular ; Plant Proteins/chemistry ; Plant Proteins/metabolism ; Protein Conformation ; Ribosomes/chemistry ; Ribosomes/metabolism ; Spinacia oleracea/cytology
Chemical Substances	Plant Proteins
Language	English
Publishing date	2018-04-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2055-0278
ISSN (online)	2055-0278
DOI	10.1038/s41477-018-0129-6
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Article ; Online: Type IV secretion systems: versatility and diversity in function.

Wallden, Karin / Rivera-Calzada, Angel / Waksman, Gabriel

Cellular microbiology

2010 Volume 12, Issue 9, Page(s) 1203–1212

Abstract: Type IV secretion systems (T4SSs) are large protein complexes which traverse the cell envelope of many bacteria. They contain a channel through which proteins or protein-DNA complexes can be translocated. This translocation is driven by a number of ... ...

Abstract	Type IV secretion systems (T4SSs) are large protein complexes which traverse the cell envelope of many bacteria. They contain a channel through which proteins or protein-DNA complexes can be translocated. This translocation is driven by a number of cytoplasmic ATPases which might energize large conformational changes in the translocation complex. The family of T4SSs is very versatile, shown by the great variety of functions among family members. Some T4SSs are used by pathogenic Gram-negative bacteria to translocate a wide variety of virulence factors into the host cell. Other T4SSs are utilized to mediate horizontal gene transfer, an event that greatly facilitates the adaptation to environmental changes and is the basis for the spread of antibiotic resistance among bacteria. Here we review the recent advances in the characterization of the architecture and mechanism of substrate transfer in a few representative T4SSs with a particular focus on their diversity of structure and function.
MeSH term(s)	Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Bacterial Secretion Systems ; Biological Transport ; Conjugation, Genetic ; DNA, Bacterial/metabolism ; Gram-Negative Bacteria/genetics ; Gram-Negative Bacteria/metabolism ; Gram-Negative Bacteria/pathogenicity ; Gram-Positive Bacteria/genetics ; Gram-Positive Bacteria/metabolism ; Gram-Positive Bacteria/pathogenicity ; Humans ; Virulence Factors/genetics ; Virulence Factors/metabolism
Chemical Substances	Bacterial Proteins ; Bacterial Secretion Systems ; DNA, Bacterial ; T-DNA ; Virulence Factors
Language	English
Publishing date	2010-07-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1468320-9
ISSN	1462-5822 ; 1462-5814
ISSN (online)	1462-5822
ISSN	1462-5814
DOI	10.1111/j.1462-5822.2010.01499.x
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Article: Type IV secretion systems: versatility and diversity in function

Wallden, Karin / Rivera-Calzada, Angel / Waksman, Gabriel

Cellular microbiology. 2010 Sept., v. 12, no. 9

2010

Abstract	Type IV secretion systems (T4SSs) are large protein complexes which traverse the cell envelope of many bacteria. They contain a channel through which proteins or protein-DNA complexes can be translocated. This translocation is driven by a number of cytoplasmic ATPases which might energize large conformational changes in the translocation complex. The family of T4SSs is very versatile, shown by the great variety of functions among family members. Some T4SSs are used by pathogenic Gram-negative bacteria to translocate a wide variety of virulence factors into the host cell. Other T4SSs are utilized to mediate horizontal gene transfer, an event that greatly facilitates the adaptation to environmental changes and is the basis for the spread of antibiotic resistance among bacteria. Here we review the recent advances in the characterization of the architecture and mechanism of substrate transfer in a few representative T4SSs with a particular focus on their diversity of structure and function.
Language	English
Dates of publication	2010-09
Size	p. 1203-1212.
Publisher	Blackwell Publishing Ltd
Publishing place	Oxford, UK
Document type	Article
ZDB-ID	1468320-9
ISSN	1462-5822 ; 1462-5814
ISSN (online)	1462-5822
ISSN	1462-5814
DOI	10.1111/j.1462-5822.2010.01499.x
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Article ; Online: Structure of the VirB4 ATPase, alone and bound to the core complex of a type IV secretion system.

Walldén, Karin / Williams, Robert / Yan, Jun / Lian, Pei W / Wang, Luchun / Thalassinos, Konstantinos / Orlova, Elena V / Waksman, Gabriel

Proceedings of the National Academy of Sciences of the United States of America

2012 Volume 109, Issue 28, Page(s) 11348–11353

Abstract: Type IV secretion (T4S) systems mediate the transfer of proteins and DNA across the cell envelope of bacteria. These systems play important roles in bacterial pathogenesis and in horizontal transfer of antibiotic resistance. The VirB4 ATPase of the T4S ... ...

Abstract	Type IV secretion (T4S) systems mediate the transfer of proteins and DNA across the cell envelope of bacteria. These systems play important roles in bacterial pathogenesis and in horizontal transfer of antibiotic resistance. The VirB4 ATPase of the T4S system is essential for both the assembly of the system and substrate transfer. In this article, we present the crystal structure of the C-terminal domain of Thermoanaerobacter pseudethanolicus VirB4. This structure is strikingly similar to that of another T4S ATPase, VirD4, a protein that shares only 12% sequence identity with VirB4. The VirB4 domain purifies as a monomer, but the full-length protein is observed in a monomer-dimer equilibrium, even in the presence of nucleotides and DNAs. We also report the negative stain electron microscopy structure of the core complex of the T4S system of the Escherichia coli pKM101 plasmid, with VirB4 bound. In this structure, VirB4 is also monomeric and bound through its N-terminal domain to the core's VirB9 protein. Remarkably, VirB4 is observed bound to the side of the complex where it is ideally placed to play its known regulatory role in substrate transfer.
MeSH term(s)	Adenosine Triphosphatases/chemistry ; Adenosine Triphosphatases/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray/methods ; DNA, Bacterial/genetics ; Escherichia coli/metabolism ; Macromolecular Substances/metabolism ; Magnesium/chemistry ; Mass Spectrometry/methods ; Microscopy, Electron/methods ; Models, Biological ; Nucleotides/chemistry ; Plasmids ; Protein Binding ; Protein Conformation ; Virulence Factors/genetics
Chemical Substances	Bacterial Proteins ; DNA, Bacterial ; Macromolecular Substances ; Nucleotides ; Virulence Factors ; Adenosine Triphosphatases (EC 3.6.1.-) ; Magnesium (I38ZP9992A)
Language	English
Publishing date	2012-06-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1201428109
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