| 1. |
- Arheimer, Berit, et al.
(författare)
-
The IAHS Science for Solutions decade, with Hydrology Engaging Local People IN a Global world (HELPING)
- 2024
-
Ingår i: Hydrological Sciences Journal. - 0262-6667 .- 2150-3435.
-
Tidskriftsartikel (refereegranskat)abstract
- The new scientific decade (2023-2032) of the International Association of Hydrological Sciences (IAHS) aims at searching for sustainable solutions to undesired water conditions - may it be too little, too much or too polluted. Many of the current issues originate from global change, while solutions to problems must embrace local understanding and context. The decade will explore the current water crises by searching for actionable knowledge within three themes: global and local interactions, sustainable solutions and innovative cross-cutting methods. We capitalise on previous IAHS Scientific Decades shaping a trilogy; from Hydrological Predictions (PUB) to Change and Interdisciplinarity (Panta Rhei) to Solutions (HELPING). The vision is to solve fundamental water-related environmental and societal problems by engaging with other disciplines and local stakeholders. The decade endorses mutual learning and co-creation to progress towards UN sustainable development goals. Hence, HELPING is a vehicle for putting science in action, driven by scientists working on local hydrology in coordination with local, regional, and global processes.
|
|
| 2. |
- Ellouze, C., et al.
(författare)
-
Difference between active and inactive nucleotide cofactors in the effect of DNA binding and the helical structure of RecA filament
- 1999
-
Ingår i: European Journal of Biochemistry. - : Wiley. - 0014-2956 .- 1432-1033. ; 262:1, s. 88-94
-
Tidskriftsartikel (refereegranskat)abstract
- The RecA protein requires ATP or dATP for its coprotease and strand exchange activities. Other natural nucleotides, such as ADP, CTP, GTP, UTP and TTP, have little or no activation effect on RecA for these activities. We have investigated the activation mechanism, and the selectivity for ATP, by studying the effect of various nucleotides on the DNA binding and the helical structure of the RecA filament. The interaction with DNA was investigated via fluorescence measurements with a fluorescent DNA analog and fluorescein-labeled oligonucleotides, assisted by linear dichroism. Filament structure was investigated via small-angle neutron scattering. There is no simple correlation between filament elongation, DNA binding affinity of RecA, and DNA structure in the RecA complex. There may be multiple conformations of RecA, Both coprotease and strand exchange activities require formation of a rigid and well organized complex. The triphosphate nucleotides which do not activate RecA, destabilize the RecA-DNA complex, indicating that the chemical nature of the nucleotide nucleobase is very important for the stability of RecA-DNA complex. Higher stability of the RecA-DNA complex in the presence of adenosine 5'-O-3-thiotriphosphate or guanosine 5'-O-3-thiotriphosphate than ATP or GTP indicates that contact between the protein and the chemical group at the gamma position of the nucleotide also affects the stability of the RecA-DNA complex. This contact appears also important for the rigid organization of DNA because ADP strongly decreases the rigidity of the complex.
|
|
| 3. |
- Ellouze, C., et al.
(författare)
-
Dissociation of non-complementary second DNA strand from RecA filament without ATP hydrolysis: mechanism of the search for homologous DNA
- 1997
-
Ingår i: Journal of Biochemistry. - 0021-924X. ; 121:6, s. 1070-1075
-
Tidskriftsartikel (refereegranskat)abstract
- RecA protein catalyzes the DNA annealing and mimics the DNA strand exchange reaction in vitro in the presence of ATP or its non-hydrolyzable analog, adenosine 5'-O-3-thiotriphosphate (ATP gamma S). For these activities RecA coordinates two DNA molecules [Takahashi, M. and Norden, B. (1994) Adv. Biophys, 30, 1-35]. In order to get a better understanding of how RecA performs the search for sequence complementarity or homology between two DNA molecules, the association and dissociation kinetics oa second DNA molecule to and from RecA in the presence of ATP gamma S have been investigated, The kinetics were monitored by fluorescence measurements of partly etheno-modified poly(dA) assisted by linear dichroism measurements of the flow-oriented complex. The association of the second DNA is fast;, regardless of whether the sequence is complementary or not. Bg contrast, the dissociation kinetics is strongly dependent on sequence complementarity, If the second DNA is complementary to the first, dissociation is extremely slow, whilst that of non-complementary second DNA is fast, In no case does the first DNA leave the RecA fiber, Our findings indicate that the dissociation step is important in the search for homology by RecA.
|
|
| 4. |
- Ellouze, C., et al.
(författare)
-
Evidence for Elongation of the Helical Pitch of the RecA Filament Upon ATP and ADP Binding Using Small-Angle Neutron Scattering
- 1995
-
Ingår i: European Journal of Biochemistry. - : Wiley. - 0014-2956 .- 1432-1033. ; 233:2, s. 579-583
-
Tidskriftsartikel (refereegranskat)abstract
- Structural changes of the RecA filament upon binding of cofactors have been investigated by small-angle neutron scattering. Both ATP and ADP increased the helical pitch of the RecA homopolymer, which is observed to be 7 nm in the absence of any cofactor. The binding of ATP altered the pitch to 9 nm, whereas the binding of ADP only produced a pitch of 8.2 nm. The pitch determined for the RecA complex with the ATP analog adenosine 5'-[gamma-thio]triphosphate was similar to that found with ATP. Thus, at least three, somewhat different, RecA helical filamentous structures may form in solution. The binding of DNA to RecA did not alter the pitch significantly, indicating that the cofactor binding is the determining factor for the size of the helical pitch of the RecA filament. We also found that elongation of the helical pitch is a necessary, but not a sufficient condition, for the coprotease activity of RecA. The presence of acetate or glutamate ions is also required. The pitch of the ADP . RecA filament is in agreement with that found in the crystal structure. This correlation indicates that this structure corresponds to that of the ADP . RecA filament in solution, although this is not the species active in recombination.
|
|
| 5. |
- Ellouze, C., et al.
(författare)
-
Nucleotide Cofactor-Dependent Structural Change of Xenopus laevis Rad51 Protein Filament Detected by Small-Angle Neutron Scattering Measurements in Solution
- 1997
-
Ingår i: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 36:44, s. 13524-13529
-
Tidskriftsartikel (refereegranskat)abstract
- Rad51 protein, a eukaryotic homologue of RecA protein, forms a filamentous complex with DNA and catalyzes homologous recombination. We have analyzed the structure of Xenopus Rad51 protein (XRad51.1) in solution by small-angle neutron scattering (SANS). The measurements showed that XRad51.1 forms a helical filament independently of DNA. The sizes of the cross-sectional and helical pitch of the filament could be determined, respectively, from a Guinier plot and the position of the subsidiary maximum of SANS data. We observed that the helical structure is modified by nucleotide binding as in the case of RecA. Upon ATP binding under high-salt conditions (600 mM NaCl), the helical pitch of XRad51.1 filament was increased from 8 to 10 nm and the cross-sectional diameter decreased from 7 to 6 nm. The pitch sizes of XRad51.1 are similar to, though slightly larger than, those of RecA filament under corresponding conditions. A similar helical pitch size was observed by electron microscopy for budding yeast Rad51 [Ogawa, T., et al. (1993) Science 259, 1896-1899]. In contrast to the RecA filament, the structure of XRad51.1 filament with ADP is not significantly different from that with ATP. Thus, the hydrolysis of ATP to ADP does not modify the helical filament of XRad51.1. Together with our recent observation that ADP does not weaken the XRad51.1/DNA interaction, the effect of ATP hydrolysis on XRad51.1 nucleofilament should be very different from that on RecA.
|
|
| 6. |
- Nordén, Bengt, 1945, et al.
(författare)
-
Base Orientation of Second DNA in RecA-DNA Filaments. Analysis by combination of linear dichroism and small angle neutron scattering in flow-oriented solution
- 1998
-
Ingår i: Journal of Biological Chemistry. - : Elsevier BV. - 0021-9258 .- 1083-351X. ; 273:25, s. 15682-15686
-
Tidskriftsartikel (refereegranskat)abstract
- To gain insight into the mechanism of pairing two complementary DNA strands by the RecA protein, we have determined the nucleobase orientation of the first and the second bound DNA strands in the RecA DNA filament by combined measurements of linear dichroism and small angle neutron scattering on flow-oriented samples. An etheno-modified DNA, poly(d epsilon A) was adapted as the first DNA and an oligo(dT) as the second DNA, making it possible to distinguish between the linear dichroism signals of the two DNA strands, The results indicate that binding of the second DNA does not alter the nucleobase orientation of the first bound strand and that the bases of the second DNA are almost coplanar to the bases of the first strand although somewhat more tilted (60 degrees relative to the fiber axis compared with 70 degrees for the first DNA strand). Similar results were obtained for the RecA DNA complex formed with unmodified poly(dA) and oligo(dT). An almost coplanar orientation of nucleobases of two DNA strands in a RecA-DNA filament would facilitate scanning for, and recognition of, complementary base sequences. The slight deviation from co-planarity could increase the free energy of the duplex to facilitate dissociation in case of mismatching base sequences.
|
|
| 7. |
- Wittung, Pernilla, 1968, et al.
(författare)
-
Thermochemical and kinetic evidence for nucleotide-sequence-dependent RecA-DNA interactions
- 1997
-
Ingår i: European Journal of Biochemistry. - : Wiley. - 0014-2956 .- 1432-1033. ; 245:3, s. 715-719
-
Tidskriftsartikel (refereegranskat)abstract
- RecA catalyses homologous recombination in Escherichia coli by promoting pairing of homologous DNA molecules after formation of a helical nucleoprotein filament with single-stranded DNA. The primary reaction of RecA with DNA is generally assumed to be unspecific. We show here, by direct measurement of the interaction enthalpy by means of isothermal titration calorimetry, that the polymerisation of RecA on single-stranded DNA depends on the DNA sequence, with a high exothermic preference for thymine bases. This enthalpic sequence preference of thymines by RecA correlates with faster binding kinetics of RecA to thymine DNA. Furthermore, the enthalpy of interaction between the RecA.DNA filament and a second DNA strand is large only when the added DNA is complementary to the bound DNA in RecA. This result suggests a possibility for a rapid search mechanism by RecA.DNA filaments for homologous DNA molecules.
|
|
