2024-03-28T13:55:40Zhttp://repository.helmholtz-hzi.de/oai/requestoai:repository.helmholtz-hzi.de:10033/2719922019-08-30T11:26:42Zcom_10033_271853com_10033_6832col_10033_271872
Myllykoski, Matti
Raasakka, Arne
Han, Huijong
Kursula, Petri
2013-03-13T08:07:51Z
2013-03-13T08:07:51Z
2012
Myelin 2',3'-cyclic nucleotide 3'-phosphodiesterase: active-site ligand binding and molecular conformation. 2012, 7 (2):e32336 PLoS ONE
1932-6203
22393399
10.1371/journal.pone.0032336
http://hdl.handle.net/10033/271992
PloS one
The 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) is a highly abundant membrane-associated enzyme in the myelin sheath of the vertebrate nervous system. CNPase is a member of the 2H phosphoesterase family and catalyzes the formation of 2'-nucleotide products from 2',3'-cyclic substrates; however, its physiological substrate and function remain unknown. It is likely that CNPase participates in RNA metabolism in the myelinating cell. We solved crystal structures of the phosphodiesterase domain of mouse CNPase, showing the binding mode of nucleotide ligands in the active site. The binding mode of the product 2'-AMP provides a detailed view of the reaction mechanism. Comparisons of CNPase crystal structures highlight flexible loops, which could play roles in substrate recognition; large differences in the active-site vicinity are observed when comparing more distant members of the 2H family. We also studied the full-length CNPase, showing its N-terminal domain is involved in RNA binding and dimerization. Our results provide a detailed picture of the CNPase active site during its catalytic cycle, and suggest a specific function for the previously uncharacterized N-terminal domain.
en
Archived with thanks to PloS one
openAccess
Myelin 2',3'-cyclic nucleotide 3'-phosphodiesterase: active-site ligand binding and molecular conformation.
Article
oai:repository.helmholtz-hzi.de:10033/3160362019-08-30T11:26:42Zcom_10033_271853com_10033_6832col_10033_271872
Vahokoski, Juha
Bhargav, Saligram Prabhakar
Desfosses, Ambroise
Andreadaki, Maria
Kumpula, Esa-Pekka
Martinez, Silvia Muñico
Ignatev, Alexander
Lepper, Simone
Frischknecht, Friedrich
Sidén-Kiamos, Inga
Sachse, Carsten
Kursula, Inari
2014-04-22T12:36:37Z
2014-04-22T12:36:37Z
2014-04
Structural differences explain diverse functions of Plasmodium actins. 2014, 10 (4):e1004091 PLoS Pathog.
1553-7374
24743229
10.1371/journal.ppat.1004091
http://hdl.handle.net/10033/316036
PLoS pathogens
Actins are highly conserved proteins and key players in central processes in all eukaryotic cells. The two actins of the malaria parasite are among the most divergent eukaryotic actins and also differ from each other more than isoforms in any other species. Microfilaments have not been directly observed in Plasmodium and are presumed to be short and highly dynamic. We show that actin I cannot complement actin II in male gametogenesis, suggesting critical structural differences. Cryo-EM reveals that Plasmodium actin I has a unique filament structure, whereas actin II filaments resemble canonical F-actin. Both Plasmodium actins hydrolyze ATP more efficiently than α-actin, and unlike any other actin, both parasite actins rapidly form short oligomers induced by ADP. Crystal structures of both isoforms pinpoint several structural changes in the monomers causing the unique polymerization properties. Inserting the canonical D-loop to Plasmodium actin I leads to the formation of long filaments in vitro. In vivo, this chimera restores gametogenesis in parasites lacking actin II, suggesting that stable filaments are required for exflagellation. Together, these data underline the divergence of eukaryotic actins and demonstrate how structural differences in the monomers translate into filaments with different properties, implying that even eukaryotic actins have faced different evolutionary pressures and followed different paths for developing their polymerization properties.
en
Archived with thanks to PLoS pathogens
Structural differences explain diverse functions of Plasmodium actins.
Article
oai:repository.helmholtz-hzi.de:10033/3164572019-08-30T11:26:42Zcom_10033_271853com_10033_6832col_10033_271872
Han, Huijong
Kursula, Petri
2014-05-02T14:10:50Z
2014-05-02T14:10:50Z
2013-07
Preliminary crystallographic analysis of the N-terminal PDZ-like domain of periaxin, an abundant peripheral nerve protein linked to human neuropathies. 2013, 69 (Pt 7):804-8 Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
1744-3091
23832213
10.1107/S1744309113016266
http://hdl.handle.net/10033/316457
Acta crystallographica. Section F, Structural biology and crystallization communications
Periaxin (PRX) is an abundant protein in peripheral nerves and contains a predicted PDZ-like domain at its N-terminus. The large isoform, L-PRX, is required for the maintenance of myelin in the peripheral nervous system and its defects cause neurological disease. Here, the human periaxin PDZ-like domain was crystallized and X-ray diffraction data were collected to 2.85 Å resolution using synchrotron radiation. The crystal belonged to the primitive hexagonal space group P3121 or P3221, with unit-cell parameters a = b = 80.6, c = 81.0 Å, γ = 120° and either two or three molecules in the asymmetric unit. The structure of PRX will shed light on its poorly characterized function in the nervous system.
en
Archived with thanks to Acta crystallographica. Section F, Structural biology and crystallization communications
Preliminary crystallographic analysis of the N-terminal PDZ-like domain of periaxin, an abundant peripheral nerve protein linked to human neuropathies.
Article
oai:repository.helmholtz-hzi.de:10033/3207952019-08-30T11:31:23Zcom_10033_271853com_10033_6832col_10033_271872
Lehtimäki, Mari
Laulumaa, Saara
Ruskamo, Salla
Kursula, Petri
2014-06-11T13:22:33Z
2014-06-11T13:22:33Z
2012-11-01
Production and crystallization of a panel of structure-based mutants of the human myelin peripheral membrane protein P2. 2012, 68 (Pt 11):1359-62 Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
1744-3091
23143249
10.1107/S1744309112039036
http://hdl.handle.net/10033/320795
Acta crystallographica. Section F, Structural biology and crystallization communications
The myelin sheath is a multilayered membrane that surrounds and insulates axons in the nervous system. One of the proteins specific to the peripheral nerve myelin is P2, a protein that is able to stack lipid bilayers. With the goal of obtaining detailed information on the structure-function relationship of P2, 14 structure-based mutated variants of human P2 were generated and produced. The mutants were designed to potentially affect the binding of lipid bilayers by P2. All mutated variants were also crystallized and preliminary crystallographic data are presented. The structural data from the mutants will be combined with diverse functional assays in order to elucidate the fine details of P2 function at the molecular level.
en
Archived with thanks to Acta crystallographica. Section F, Structural biology and crystallization communications
Production and crystallization of a panel of structure-based mutants of the human myelin peripheral membrane protein P2.
Article
oai:repository.helmholtz-hzi.de:10033/3234342019-08-30T11:35:39Zcom_10033_271853com_10033_6832col_10033_271872
Ruskamo, Salla
Chukhlieb, Maryna
Vahokoski, Juha
Bhargav, Saligram Prabhakar
Liang, Fengyi
Kursula, Inari
Kursula, Petri
2014-07-18T14:30:54Z
2014-07-18T14:30:54Z
2012
Juxtanodin is an intrinsically disordered F-actin-binding protein. 2012, 2:899 Sci Rep
2045-2322
23198089
10.1038/srep00899
http://hdl.handle.net/10033/323434
Scientific reports
Juxtanodin, also called ermin, is an F-actin-binding protein expressed by oligodendrocytes, the myelin-forming cells of the central nervous system. While juxtanodin carries a short conserved F-actin-binding segment at its C terminus, it otherwise shares no similarity with known protein sequences. We carried out a structural characterization of recombinant juxtanodin in solution. Juxtanodin turned out to be intrinsically disordered, as evidenced by conventional and synchrotron radiation CD spectroscopy. Small-angle X-ray scattering indicated that juxtanodin is a monomeric, highly elongated, unfolded molecule. Ensemble optimization analysis of the data suggested also the presence of more compact forms of juxtanodin. The C terminus was a strict requirement for co-sedimentation of juxtanodin with microfilaments, but juxtanodin had only mild effects on actin polymerization. The disordered nature of juxtanodin may predict functions as a protein interaction hub, although F-actin is its only currently known binding partner.
en
Archived with thanks to Scientific reports
Juxtanodin is an intrinsically disordered F-actin-binding protein.
Article
oai:repository.helmholtz-hzi.de:10033/3244832019-08-30T11:36:05Zcom_10033_271853com_10033_6832col_10033_271872
Patel, Ashok K
Singh, Vijay K
Bergmann, Ulrich
Jagannadham, Medicherla V
Kursula, Petri
2014-08-08T10:42:32Z
2014-08-08T10:42:32Z
2011-05-01
Purification, crystallization and preliminary X-ray crystallographic analysis of MIL, a glycosylated jacalin-related lectin from mulberry (Morus indica) latex. 2011, 67 (Pt 5):608-12 Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
1744-3091
21543873
10.1107/S174430911101013X
http://hdl.handle.net/10033/324483
Acta crystallographica. Section F, Structural biology and crystallization communications
A quantitatively major protein has been purified from the latex of Morus indica. The purified previously uncharacterized protein, M. indica lectin (MIL), was further shown to be a glycosylated tetramer and belongs to the family of jacalin-related lectins. Crystallization of MIL was also accomplished and the tetragonal crystals diffracted synchrotron X-rays to a resolution of 2.8 Å.
en
Archived with thanks to Acta crystallographica. Section F, Structural biology and crystallization communications
Purification, crystallization and preliminary X-ray crystallographic analysis of MIL, a glycosylated jacalin-related lectin from mulberry (Morus indica) latex.
Article
oai:repository.helmholtz-hzi.de:10033/3328422019-08-30T11:27:46Zcom_10033_271853com_10033_6832col_10033_271872
Myllykoski, Matti
Kursula, Petri
2014-10-16T13:46:51Z
2014-10-16T13:46:51Z
2010
Expression, purification, and initial characterization of different domains of recombinant mouse 2',3'-cyclic nucleotide 3'-phosphodiesterase, an enigmatic enzyme from the myelin sheath. 2010, 3:12 BMC Res Notes
1756-0500
20180985
10.1186/1756-0500-3-12
http://hdl.handle.net/10033/332842
BMC research notes
2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) is an enigmatic enzyme specifically expressed at high levels in the vertebrate myelin sheath, whose function and physiological substrates are unknown. The protein consists of two domains: an uncharacterized N-terminal domain with little homology to other proteins, and a C-terminal phosphodiesterase domain.
en
Archived with thanks to BMC research notes
Expression, purification, and initial characterization of different domains of recombinant mouse 2',3'-cyclic nucleotide 3'-phosphodiesterase, an enigmatic enzyme from the myelin sheath.
Article
oai:repository.helmholtz-hzi.de:10033/3443852019-08-30T11:37:23Zcom_10033_271853com_10033_6832col_10033_271872
Singh, Bishal K
Sattler, Julia M
Chatterjee, Moon
Huttu, Jani
Schüler, Herwig
Kursula, Inari
2015-02-12T13:11:48Z
2015-02-12T13:11:48Z
2011-08-12
Crystal structures explain functional differences in the two actin depolymerization factors of the malaria parasite. 2011, 286 (32):28256-64 J. Biol. Chem.
1083-351X
21832095
10.1074/jbc.M111.211730
http://hdl.handle.net/10033/344385
The Journal of biological chemistry
Apicomplexan parasites, such as the malaria-causing Plasmodium, utilize an actin-based motor for motility and host cell invasion. The actin filaments of these parasites are unusually short, and actin polymerization is under strict control of a small set of regulatory proteins, which are poorly conserved with their mammalian orthologs. Actin depolymerization factors (ADFs) are among the most important actin regulators, affecting the rates of filament turnover in a multifaceted manner. Plasmodium has two ADFs that display low sequence homology with each other and with the higher eukaryotic family members. Here, we show that ADF2, like canonical ADF proteins but unlike ADF1, binds to both globular and filamentous actin, severing filaments and inducing nucleotide exchange on the actin monomer. The crystal structure of Plasmodium ADF1 shows major differences from the ADF consensus, explaining the lack of F-actin binding. Plasmodium ADF2 structurally resembles the canonical members of the ADF/cofilin family.
en
Crystal structures explain functional differences in the two actin depolymerization factors of the malaria parasite.
Article
oai:repository.helmholtz-hzi.de:10033/3444102019-08-30T11:25:43Zcom_10033_271853com_10033_6832col_10033_271872
Patel, Ashok K
Yadav, Ravi P
Majava, Viivi
Kursula, Inari
Kursula, Petri
2015-02-12T12:38:59Z
2015-02-12T12:38:59Z
2011-06-10
Structure of the dimeric autoinhibited conformation of DAPK2, a pro-apoptotic protein kinase. 2011, 409 (3):369-83 J. Mol. Biol.
1089-8638
21497605
10.1016/j.jmb.2011.03.065
http://hdl.handle.net/10033/344410
Journal of molecular biology
The death-associated protein kinase (DAPK) family has been characterized as a group of pro-apoptotic serine/threonine kinases that share specific structural features in their catalytic kinase domain. Two of the DAPK family members, DAPK1 and DAPK2, are calmodulin-dependent protein kinases that are regulated by oligomerization, calmodulin binding, and autophosphorylation. In this study, we have determined the crystal and solution structures of murine DAPK2 in the presence of the autoinhibitory domain, with and without bound nucleotides in the active site. The crystal structure shows dimers of DAPK2 in a conformation that is not permissible for protein substrate binding. Two different conformations were seen in the active site upon the introduction of nucleotide ligands. The monomeric and dimeric forms of DAPK2 were further analyzed for solution structure, and the results indicate that the dimers of DAPK2 are indeed formed through the association of two apposed catalytic domains, as seen in the crystal structure. The structures can be further used to build a model for DAPK2 autophosphorylation and to compare with closely related kinases, of which especially DAPK1 is an actively studied drug target. Our structures also provide a model for both homodimerization and heterodimerization of the catalytic domain between members of the DAPK family. The fingerprint of the DAPK family, the basic loop, plays a central role in the dimerization of the kinase domain.
en
Structure of the dimeric autoinhibited conformation of DAPK2, a pro-apoptotic protein kinase.
Article
oai:repository.helmholtz-hzi.de:10033/6040342019-08-30T11:37:44Zcom_10033_271853com_10033_6832col_10033_271872
Tarr, Alexander W
Khera, Tanvi
Hueging, Kathrin
Sheldon, Julie
Steinmann, Eike
Pietschmann, Thomas
Brown, Richard J P
2016-03-30T14:15:08Z
2016-03-30T14:15:08Z
2015-07
Genetic Diversity Underlying the Envelope Glycoproteins of Hepatitis C Virus: Structural and Functional Consequences and the Implications for Vaccine Design. 2015, 7 (7):3995-4046 Viruses
1999-4915
26193307
10.3390/v7072809
http://hdl.handle.net/10033/604034
Viruses
In the 26 years since the discovery of Hepatitis C virus (HCV) a major global research effort has illuminated many aspects of the viral life cycle, facilitating the development of targeted antivirals. Recently, effective direct-acting antiviral (DAA) regimens with >90% cure rates have become available for treatment of chronic HCV infection in developed nations, representing a significant advance towards global eradication. However, the high cost of these treatments results in highly restricted access in developing nations, where the disease burden is greatest. Additionally, the largely asymptomatic nature of infection facilitates continued transmission in at risk groups and resource constrained settings due to limited surveillance. Consequently a prophylactic vaccine is much needed. The HCV envelope glycoproteins E1 and E2 are located on the surface of viral lipid envelope, facilitate viral entry and are the targets for host immunity, in addition to other functions. Unfortunately, the extreme global genetic and antigenic diversity exhibited by the HCV glycoproteins represents a significant obstacle to vaccine development. Here we review current knowledge of HCV envelope protein structure, integrating knowledge of genetic, antigenic and functional diversity to inform rational immunogen design.
en
Genetic Diversity Underlying the Envelope Glycoproteins of Hepatitis C Virus: Structural and Functional Consequences and the Implications for Vaccine Design.
Article
oai:repository.helmholtz-hzi.de:10033/6036042019-08-30T11:37:44Zcom_10033_271853com_10033_6832col_10033_271872
Ignatev, Alexander
Bhargav, Saligram Prabhakar
Vahokoski, Juha
Kursula, Petri
Kursula, Inari
2016-03-24T12:01:45Z
2016-03-24T12:01:45Z
2012
The lasso segment is required for functional dimerization of the Plasmodium formin 1 FH2 domain. 2012, 7 (3):e33586 PLoS ONE
1932-6203
22428073
10.1371/journal.pone.0033586
http://hdl.handle.net/10033/603604
PloS one
Apicomplexan parasites, such as the malaria-causing Plasmodium species, utilize a unique way of locomotion and host cell invasion. This substrate-dependent gliding motility requires rapid cycling of actin between the monomeric state and very short, unbranched filaments. Despite the crucial role of actin polymerization for the survival of the malaria parasite, the majority of Plasmodium cellular actin is present in the monomeric form. Plasmodium lacks most of the canonical actin nucleators, and formins are essentially the only candidates for this function in all Apicomplexa. The malaria parasite has two formins, containing conserved formin homology (FH) 2 and rudimentary FH1 domains. Here, we show that Plasmodium falciparum formin 1 associates with and nucleates both mammalian and Plasmodium actin filaments. Although Plasmodium profilin alone sequesters actin monomers, thus inhibiting polymerization, its monomer-sequestering activity does not compete with the nucleating activity of formin 1 at an equimolar profilin-actin ratio. We have determined solution structures of P. falciparum formin 1 FH2 domain both in the presence and absence of the lasso segment and the FH1 domain, and show that the lasso is required for the assembly of functional dimers.
en
openAccess
The lasso segment is required for functional dimerization of the Plasmodium formin 1 FH2 domain.
Article
oai:repository.helmholtz-hzi.de:10033/6159852019-08-30T11:31:23Zcom_10033_271853com_10033_6832col_10033_271872
Raasakka, Arne
Myllykoski, Matti
Laulumaa, Saara
Lehtimäki, Mari
Härtlein, Michael
Moulin, Martine
Kursula, Inari
Kursula, Petri
2016-07-12T14:06:57Z
2016-07-12T14:06:57Z
2015
Determinants of ligand binding and catalytic activity in the myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase. 2015, 5:16520 Sci Rep
2045-2322
26563764
10.1038/srep16520
http://hdl.handle.net/10033/615985
Scientific reports
2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) is an enzyme highly abundant in the central nervous system myelin of terrestrial vertebrates. The catalytic domain of CNPase belongs to the 2H phosphoesterase superfamily and catalyzes the hydrolysis of nucleoside 2',3'-cyclic monophosphates to nucleoside 2'-monophosphates. The detailed reaction mechanism and the essential catalytic amino acids involved have been described earlier, but the roles of many amino acids in the vicinity of the active site have remained unknown. Here, several CNPase catalytic domain mutants were studied using enzyme kinetics assays, thermal stability experiments, and X-ray crystallography. Additionally, the crystal structure of a perdeuterated CNPase catalytic domain was refined at atomic resolution to obtain a detailed view of the active site and the catalytic mechanism. The results specify determinants of ligand binding and novel essential residues required for CNPase catalysis. For example, the aromatic side chains of Phe235 and Tyr168 are crucial for substrate binding, and Arg307 may affect active site electrostatics and regulate loop dynamics. The β5-α7 loop, unique for CNPase in the 2H phosphoesterase family, appears to have various functions in the CNPase reaction mechanism, from coordinating the nucleophilic water molecule to providing a binding pocket for the product and being involved in product release.
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Determinants of ligand binding and catalytic activity in the myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase.
Article