| 1. |
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| 2. |
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| 3. |
- Persson, Daniel, 1972, et al.
(författare)
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Vesicle size-dependent translocation of penetratin analogs across lipid membranes
- 2004
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Ingår i: Biochimica et Biophysica Acta - Biomembranes. - : Elsevier BV. - 1879-2642 .- 0005-2736. ; 1665:1-2, s. 142-155
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Tidskriftsartikel (refereegranskat)abstract
- The recent discoveries of serious artifacts associated with the use of cell fixation in studies of the cellular uptake of cell-penetrating peptides (CPPs) have prompted a reevaluation of the current understanding of peptide-mediated cellular delivery. Following a report on the differential cellular uptake of a number of penetratin analogs in unfixed cells, we here investigate their membrane translocation abilities in large and giant unilamellar vesicles (LUVs and GUVs, respectively). Surprisingly, in contrast to the behavior in living cells, all peptides readily entered the giant vesicles ( > 1 μm) as proved by confocal microscopy, while none of them could cross the membranes of LUVs (100 nm). For determination of the location of the peptides in the LUVs, a new concept was introduced, based on sensitive resonance energy transfer (RET) measurements of the enhanced fluorescence of acceptor fluorophores present solely in the inner leaflet. An easily adopted method to prepare such asymmetrically labeled liposomes is described. The membrane insertion depths of the tryptophan moieties of the peptides were determined by use of brominated lipids and found to be very similar for all of the peptides studied. We also demonstrate that infrared spectroscopy on the lipid carbonyl stretch vibration peak is a convenient technique to determine phospholipid concentration. © 2004 Elsevier B.V. All rights reserved.
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| 4. |
- Thoren, Per, 1972, et al.
(författare)
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Membrane binding and translocation of cell-penetrating peptides
- 2004
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 43:12, s. 3471-3489
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Tidskriftsartikel (refereegranskat)abstract
- Cell-penetrating peptides (CPPs) have been extensively studied during the past decade, because of their ability to promote the cellular uptake of various cargo molecules, e.g., oligonucleotides and proteins. In a recent study of the uptake of several analogues of penetratin, Tat(48-60) and oligoarginine in live (unfixed) cells [Thorén et al. (2003) Biochem. Biophys. Res. Commun. 307, 100-107], it was found that both endocytotic and nonendocytotic uptake pathways are involved in the internalization of these CPPs. In the present study, the membrane interactions of some of these novel peptides, all containing a tryptophan residue to facilitate spectroscopic studies, are investigated. The peptides exhibit a strong affinity for large unilamellar vesicles (LUVs) containing zwitterionic and anionic lipids, with binding constants decreasing in the order penetratin > R 7 W > TatP59W > TatLysP59W. Quenching studies using the aqueous quencher acrylamide and brominated lipids indicate that the tryptophan residues of the peptides are buried to a similar extent into the membrane, with an average insertion depth of ∼10-11 Å from the bilayer center. The membrane topology of the peptides was investigated using an assay based on resonance energy transfer between tryptophan and a fluorescently labeled lysophospholipid, lysoMC, distributed asymmetrically in the membranes of LUVs. By determination of the energy transfer efficiency when peptide was added to vesicles with lysoMC present exclusively in the inner leaflet, it was shown that none of the peptides investigated is able to translocate across the lipid membranes of LUVs. By contrast, confocal laser scanning microscopy studies on carboxyfluorescein-labeled peptides showed that all of the peptides rapidly traverse the membranes of giant unilamellar vesicles (GUVs). The choice of model system is thus crucial for the conclusions about the ability of CPPs to translocate across lipid membranes. Under the conditions used in the present study, peptide-lipid interactions alone cannot explain the different cellular uptake characteristics exhibited by these peptides.
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| 5. |
- Thoren, Per, 1972, et al.
(författare)
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Membrane destabilizing properties of cell-penetrating peptides
- 2005
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Ingår i: Biophysical Chemistry. - : Elsevier BV. - 1873-4200 .- 0301-4622. ; 114:2-3, s. 169-179
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Tidskriftsartikel (refereegranskat)abstract
- Although cell-penetrating peptides (CPPs), also denoted protein transduction domains (PTDs), have been widely used for intracellular delivery of large and hydrophilic molecules, the mechanism of uptake is still poorly understood. In a recent live cell study of the uptake of penetratin and tryptophan-containing analogues of Tat(48-60) and oligoarginine, denoted TatP59W, TatLysP59W and R7W, respectively, it was found that both endocytotic and non-endocytotic uptake pathways are involved [Thorén et al., Biochem. Biophys. Res. Commun. 307 (2003) 100-107]. Non-endocytotic uptake was only observed for the arginine-rich peptides TatP59W and R7W. In this paper, the interactions of penetratin, R7W, TatP59W and TatLysP59W with phospholipid vesicles are compared in the search for an understanding of the mechanisms for cellular uptake. While R7W, TatP59W and TatLysP59W are found to promote vesicle fusion, indicated by mixing of membrane components, penetratin merely induces vesicle aggregation. Studies of the leakage from dye-loaded vesicles indicate that none of the peptides forms membrane pores and that vesicle fusion is not accompanied by leakage of the aqueous contents of the vesicles. These observations are important for a proper interpretation of future experiments on the interactions of these peptides with model membranes. We suggest that the discovered variations in propensity to destabilize phospholipid bilayers between the peptides investigated, in some cases sufficient to induce fusion, may be related to their different cellular uptake properties.
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| 6. |
- Almaqwashi, A. A., et al.
(författare)
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Dissecting the Dynamic Pathways of Stereoselective DNA Threading Intercalation
- 2016
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 110:6, s. 1255-1263
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Tidskriftsartikel (refereegranskat)abstract
- DNA intercalators that have high affinity and slow kinetics are developed for potential DNA-targeted therapeutics. Although many natural intercalators contain multiple chiral subunits, only intercalators with a single chiral unit have been quantitatively probed. Dumbbell-shaped DNA threading intercalators represent the next order of structural complexity relative to simple intercalators, and can provide significant insights into the stereoselectivity of DNA-ligand intercalation. We investigated DNA threading intercalation by binuclear ruthenium complex [mu-dppzip(phen)(4)Ru-2](4+) (Piz). Four Piz stereoisomers are defined by the chirality of the intercalating subunit (Ru(phen)(2)dppz) and the distal subunit (Ru(phen)(2)ip), respectively, each of which can be either right-handed (Delta) or left-handed (Lambda). We used optical tweezers to measure single DNA molecule elongation due to threading intercalation, revealing force-dependent DNA intercalation rates and equilibrium dissociation constants. The force spectroscopy analysis provided the zero-force DNA binding affinity, the equilibrium DNA-ligand elongation Delta x(eq), and the dynamic DNA structural deformations during ligand association x(on) and dissociation x(off). We found that Piz stereoisomers exhibit over 20-fold differences in DNA binding affinity, from a K-d of 27 +/- 3 nM for (Delta,Lambda)-Piz to a K-d of 622 +/- 55 nM for (Lambda,Delta)-Piz. The striking affinity decrease is correlated with increasing Delta x(eq) from 0.30 +/- 0.02 to 0.48 +/- 0.02 nm and x(on) from 0.25 +/- 0.01 to 0.46 +/- 0.02 nm, but limited x(off) changes. Notably, the affinity and threading kinetics is 10-fold enhanced for right-handed intercalating subunits, and 2- to 5-fold enhanced for left-handed distal subunits. These findings demonstrate sterically dispersed transition pathways and robust DNA structural recognition of chiral intercalators, which are critical for optimizing DNA binding affinity and kinetics.
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| 7. |
- Almaqwashi, A. A., et al.
(författare)
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DNA intercalation optimized by two-step molecular lock mechanism
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 6, s. 37993-
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Tidskriftsartikel (refereegranskat)abstract
- The diverse properties of DNA intercalators, varying in affinity and kinetics over several orders of magnitude, provide a wide range of applications for DNA-ligand assemblies. Unconventional intercalation mechanisms may exhibit high affinity and slow kinetics, properties desired for potential therapeutics. We used single-molecule force spectroscopy to probe the free energy landscape for an unconventional intercalator that binds DNA through a novel two-step mechanism in which the intermediate and final states bind DNA through the same mono-intercalating moiety. During this process, DNA undergoes significant structural rearrangements, first lengthening before relaxing to a shorter DNA-ligand complex in the intermediate state to form a molecular lock. To reach the final bound state, the molecular length must increase again as the ligand threads between disrupted DNA base pairs. This unusual binding mechanism results in an unprecedented optimized combination of high DNA binding affinity and slow kinetics, suggesting a new paradigm for rational design of DNA intercalators.
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| 8. |
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| 9. |
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| 10. |
- Almaqwashi, A. A., et al.
(författare)
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Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex
- 2014
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 42:18, s. 11634-11641
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Tidskriftsartikel (refereegranskat)abstract
- DNA intercalation by threading is expected to yield high affinity and slow dissociation, properties desirable for DNA-targeted therapeutics. To measure these properties, we utilize single molecule DNA stretching to quantify both the binding affinity and the force-dependent threading intercalation kinetics of the binuclear ruthenium complex Delta, Delta-[mu-bidppz-(phen)(4)Ru-2]4(+) (Delta, Delta-P). We measure the DNA elongation at a range of constant stretching forces using optical tweezers, allowing direct characterization of the intercalation kinetics as well as the amount intercalated at equilibrium. Higher forces exponentially facilitate the intercalative binding, leading to a profound decrease in the binding site size that results in one ligand intercalated at almost every DNA base stack. The zero force Delta, Delta-P intercalation K-d is 44 nM, 25-fold stronger than the analogous mono-nuclear ligand (Delta-P). The force-dependent kinetics analysis reveals a mechanism that requires DNA elongation of 0.33 nm for association, relaxation to an equilibrium elongation of 0.19 nm, and an additional elongation of 0.14 nm from the equilibrium state for dissociation. In cells, a molecule with binding properties similar to Delta, Delta-P may rapidly bind DNA destabilized by enzymes during replication or transcription, but upon enzyme dissociation it is predicted to remain intercalated for several hours, thereby interfering with essential biological processes.
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| 11. |
- Andersson, Johanna, 1983, et al.
(författare)
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AT-Specific DNA Binding of Binuclear Ruthenium Complexes at the Border of Threading Intercalation
- 2010
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Ingår i: Chemistry - A European Journal. - : Wiley. - 1521-3765 .- 0947-6539. ; 16:36, s. 11037-11046
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Tidskriftsartikel (refereegranskat)abstract
- The binuclear ruthenium complex [mu-bidppz(phen)(4)Ru-2](4+) has been extensively studied since the discover}, of its unusual threading intercalation interaction with DNA, a binding mode with extremely slow binding and dissociation kinetics. The complex has been shown to be selective towards long stretches of alternating AT base pairs, which makes it interesting, for example, as a model compound for anti-malaria drugs due to the high AT content of the genome of the malaria parasite P falciparum. We have investigated the effect of bridging ligand structure on threading intercalation ability and found that length and rigidity as well as the size of the intercalated ring system are all factors that affect the rate and selectivity of the threading intercalation. In particular, we discovered a new DNA-threading compound, [mu-dppzip(phen)(4)Ru-2](4+) which appears to be just at the border of being capable of threading intercalation and displays even greater selectivity for AT-DNA than the parent compound, [mu-bidppz(phen)(4)Ru-2](4+).
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| 12. |
- Andersson, Johanna, 1983, et al.
(författare)
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Lifetime Heterogeneity of DNA-Bound dppz Complexes Originates from Distinct Intercalation Geometries Determined by Complex-Complex Interactions
- 2013
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 52:2, s. 1151-1159
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Tidskriftsartikel (refereegranskat)abstract
- Despite the extensive interest in structurally explaining the photophysics of DNA-bound [Ru(phen)(2)dppz](2+) and [Ru(bpy)(2)dppz](2+), the origin of the two distinct emission lifetimes of the pure enantiomers when intercalated into DNA has remained elusive. In this report, we have combined a photophysical characterization with a detailed isothermal titration calorimetry study to investigate the binding of the pure Delta and Lambda enantiomers of both complexes with [poly(dAdT)](2). We find that a binding model with two different binding geometries, proposed to be symmetric and canted intercalation from the minor groove, as recently reported in high-resolution X-ray structures, is required to appropriately explain the data. By assigning the long emission lifetime to the canted binding geometry, we can simultaneously fit both calorimetric data and the binding-density-dependent changes in the relative abundance of the two emission lifetimes using the same binding model. We find that all complex complex interactions are slightly unfavorable for Delta-[Ru(bpy)(2)dppz](2+), whereas interactions involving a complex canted away from a neighbor are favorable for the other three complexes. We also conclude that Delta-[Ru(bpy)(2)dppz](2+) preferably binds isolated, Delta-[Ru(phen)(2)dppz](2+) preferably binds as duplets of canted complexes, and that all complexes are reluctant to form longer consecutive sequences than triplets. We propose that this is due to an interplay of repulsive complex complex and attractive complex-DNA interactions modulated by allosteric DNA conformation changes that are largely affected by the nature of the ancillary ligands.
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| 13. |
- Andersson, Johanna, 1983, et al.
(författare)
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Photoswitched DNA-binding of a photochromic spiropyran
- 2008
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 130:36, s. 11836-11837
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Tidskriftsartikel (refereegranskat)abstract
- The dramatically different DNA-binding properties of the two isomeric forms of a photochromic spiropyran have been demonstrated, enabling photoswitched DNA binding. The closed, UV-absorbing form shows no signs of interaction with DNA. Upon UV exposure the spiropyran is isomerized to the open form that binds to DNA by intercalation. The process is fully reversible as the corresponding dissociation process is induced by visible light. Copyright © 2008 American Chemical Society.
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| 14. |
- Andersson, Johanna, 1983, et al.
(författare)
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Stereoselectivity for DNA Threading Intercalation of Short Binuclear Ruthenium Complexes
- 2011
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 115:49, s. 14768-14775
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Tidskriftsartikel (refereegranskat)abstract
- Threading intercalation is an unusual DNA binding mode with significantly slower association and dissociation rates compared with classical intercalation. The latter has been shown to correlate well with cytotoxicity, and therefore, threading intercalating compounds are of great interest in the search for new DNA binding drugs. Thus, there is a need for better understanding of the mechanisms behind this type of binding. In this work, we have investigated the threading intercalation ability, of the four stereoisomers of the AT-specific binuclear ruthenium complex [mu-dppzip(phen)(4)Ru(2)](4+) using different spectroscopic techniques. This complex contains an unsymmetrical bridging ligand consisting of a dipyridophenazine and an imidazophenanthroline ring system, in which the photophysical properties of the Ru-dipyridophenazine complex moiety make it possible to distinguish the intercalating part from the nonintercalating part We have found that Delta geometry around the ruthenium on the intercalating dipyridophenazine moiety and Lambda geometry on the nonintercalating imidazophenanthroline moiety is the optimal configuration for threading intercalation Of this complex and that the chirality on the ruthenium of the nonintercalating half dominates the stereospecificity in the threaded state. This is the cause of the reversed enantioselectivity compared with the parent threading intercalating complex [mu-bidppz(phen)(4)Ru(2)](4+), in which the enantioselectivity is controlled by the chirality on the intercalating half. The differences in the interactions with DNA between the two, complexes are most likely due to the fact that [mu-dppzip(phen)(4)Ru(2)](4+) has a slightly shorter bridging ligand than the parent complex.
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| 15. |
- Ardhammar, Malin, 1970, et al.
(författare)
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Absolute configuration and electronic state properties of light-switch complex [Ru(phen)2dppz]2+ deduced from oriented circular dichroism in a lamellar liquid crystal host
- 2002
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Ingår i: Chemical Physics Letters. - 0009-2614. ; 354:1-2, s. 44-50
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Tidskriftsartikel (refereegranskat)abstract
- Circular dichroism (CD) of enantiomers of [Ru(phen)(2)dppz](2+) oriented in a octanoate-decanol-water lamellar liquid crystal has been measured parallel to the orientation axis. where the sample does not exhibit linear dichroism (LD). At an inclined incidence, the emerging LD shows that the chromophores have an along-chain orientation in the liquid crystal. The changes in the CD spectrum compared to an isotropic sample, in conjunction with CD calculations, allow us to assess the absolute configuration of the enantiomers and assign the CD bands to specific electronic transitions.
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| 16. |
- Bahira, M., et al.
(författare)
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A ruthenium dimer complex with a flexible linker slowly threads between DNA bases in two distinct steps
- 2015
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 43:18, s. 8856-8867
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Tidskriftsartikel (refereegranskat)abstract
- Several multi-component DNA intercalating small molecules have been designed around ruthenium-based intercalating monomers to optimize DNA binding properties for therapeutic use. Here we probe the DNA binding ligand [mu-C-4(cpdppz)(2)(phen)(4)Ru-2](4+), which consists of two Ru(phen)(2)dppz(2+) moieties joined by a flexible linker. To quantify ligand binding, double-stranded DNA is stretched with optical tweezers and exposed to ligand under constant applied force. In contrast to other bis-intercalators, we find that ligand association is described by a two-step process, which consists of fast bimolecular intercalation of the first dppz moiety followed by similar to 10-fold slower intercalation of the second dppz moiety. The second step is rate-limited by the requirement for a DNA-ligand conformational change that allows the flexible linker to pass through the DNA duplex. Based on our measured force-dependent binding rates and ligand-induced DNA elongation measurements, we are able to map out the energy landscape and structural dynamics for both ligand binding steps. In addition, we find that at zero force the overall binding process involves fast association (similar to 10 s), slow dissociation (similar to 300 s), and very high affinity (K-d similar to 10 nM). The methodology developed in this work will be useful for studying the mechanism of DNA binding by other multi-step intercalating ligands and proteins.
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| 17. |
- Beke-Somfai, Tamas, 1977, et al.
(författare)
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Double-lock ratchet mechanism revealing the role of alpha SER-344 in FoF1 ATP synthase
- 2011
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 108:12, s. 4828-4833
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Tidskriftsartikel (refereegranskat)abstract
- In a majority of living organisms, FoF1 ATP synthase performs the fundamental process of ATP synthesis. Despite the simple net reaction formula, ADP + Pi. ATP + H2O, the detailed step-by-step mechanism of the reaction yet remains to be resolved owing to the complexity of this multisubunit enzyme. Based on quantum mechanical computations using recent high resolution X-ray structures, we propose that during ATP synthesis the enzyme first prepares the inorganic phosphate for the gamma P-O-ADP bond-forming step via a double-proton transfer. At this step, the highly conserved alpha S344 side chain plays a catalytic role. The reaction thereafter progresses through another transition state (TS) having a planar PO3- ion configuration to finally form ATP. These two TSs are concluded crucial for ATP synthesis. Using stepwise scans and several models of the nucleotide-bound active site, some of the most important conformational changes were traced toward direction of synthesis. Interestingly, as the active site geometry progresses toward the ATP-favoring tight binding site, at both of these TSs, a dramatic increase in barrier heights is observed for the reverse direction, i.e., hydrolysis of ATP. This change could indicate a "ratchet" mechanism for the enzyme to ensure efficacy of ATP synthesis by shifting residue conformation and thus locking access to the crucial TSs.
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| 18. |
- Beke-Somfai, Tamas, 1977, et al.
(författare)
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Mechanical Control of ATP Synthase Function: Activation Energy Difference between Tight and Loose Binding Sites
- 2010
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 49:3, s. 401-403
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Tidskriftsartikel (refereegranskat)abstract
- Despite exhaustive chemical and crystal structure studies, the mechanistic details of how F o F 1 -ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations using a recent highresolution X-ray structure, we conclude that formation of the P-O bond may be achieved through a transition state (TS) with a planar PO 3 - ion. Surprisingly, there is a more than 40 kJ/mol difference between barrier heights of the loose and tight binding sites of the enzyme. This indicates that even a relatively small change in active site conformation, induced by the γ-subunit rotation, may effectively block the back reaction in β TP and, thus, promote ATP. © 2009 American Chemical Society.
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| 19. |
- Beke-Somfai, Tamas, 1977, et al.
(författare)
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Rate of hydrolysis in ATP synthase is fine-tuned by alpha-subunit motif controlling active site conformation
- 2013
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 110:6, s. 2117-2122
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Tidskriftsartikel (refereegranskat)abstract
- Computer-designed artificial enzymes will require precise understanding of how conformation of active sites may control barrier heights of key transition states, including dependence on structure and dynamics at larger molecular scale. FoF1 ATP synthase is interesting as a model system: a delicate molecular machine synthesizing or hydrolyzing ATP using a rotary motor. Isolated F-1 performs hydrolysis with a rate very sensitive to ATP concentration. Experimental and theoretical results show that, at low ATP concentrations, ATP is slowly hydrolyzed in the so-called tight binding site, whereas at higher concentrations, the binding of additional ATP molecules induces rotation of the central gamma-subunit, thereby forcing the site to transform through subtle conformational changes into a loose binding site in which hydrolysis occurs faster. How the 1-angstrom-scale rearrangements are controlled is not yet fully understood. By a combination of theoretical approaches, we address how large macromolecular rearrangements may manipulate the active site and how the reaction rate changes with active site conformation. Simulations reveal that, in response to.-subunit position, the active site conformation is fine-tuned mainly by small alpha-subunit changes. Quantum mechanics-based results confirm that the sub-Angstrom gradual changes between tight and loose binding site structures dramatically alter the hydrolysis rate.
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| 20. |
- Choi, S. D., et al.
(författare)
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Binding Mode of [Ruthenium(II) (1,10-Phenanthroline)2L]2+ with Poly(dT*dA-dT) Triplex. Ligand Size Effect on Third-Strand Stabilization
- 1997
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 36:1, s. 214-223
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Tidskriftsartikel (refereegranskat)abstract
- The binding of homochiral [Ru(II)(1,10-phenanthroline)(2)L](2+) complexes {where L = 1,10-phenanthroline (phen), dipyrido[3,2-a:2',3'-c]phenazine (DPPZ) or benzodipyrido[3,2-a:2',3'-c]phenazine (BDPPZ)} to poly(dT*dA-dT) triplex has been investigated by linear and circular dichroism and thermal denaturation. Analysis of the linear dichroism spectra indicates that the extended DPPZ and BDPPZ ligands lie approximately parallel to the base-pair and base-tripler planes consistent with intercalation which is also supported by strong hypochromism in the interligand absorption bands with either duplex or tripler. The spectral properties of any of the metal complex enantiomers were similar for binding to either duplex or tripler DNA, indicating that the third strand, which occupies the major groove of the template duplex, has little effect on the binding geometries and hence supports the hypothesis that the metal complexes all bind from the minor groove with the DPPZ and BDPPZ ligands intercalated but without intercalation in the case of [Ru(phen)(3)](2+). Third-strand stabilization depended on the nature of the third substituted phenanthroline chelate ligand but was not directly related to its size, with stabilizing power increasing in the order phen
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| 21. |
- Clark, Andrew G., et al.
(författare)
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Reshaping the Energy Landscape Transforms the Mechanism and Binding Kinetics of DNA Threading Intercalation
- 2018
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 57:5, s. 614-619
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Tidskriftsartikel (refereegranskat)abstract
- Molecules that bind DNA via threading intercalation show high binding affinity as well as slow dissociation kinetics, properties ideal for the development of anticancer drugs. To this end, it is critical to identify the specific molecular characteristics of threading intercalators that result in optimal DNA interactions. Using single-molecule techniques, we quantify the binding of a small metal-organic ruthenium threading intercalator (δ,δ-B) and compare its binding characteristics to a similar molecule with significantly larger threading moieties (δ,δ-P). The binding affinities of the two molecules are the same, while comparison of the binding kinetics reveals significantly faster kinetics for δ,δ-B. However, the kinetics is still much slower than that observed for conventional intercalators. Comparison of the two threading intercalators shows that the binding affinity is modulated independently by the intercalating section and the binding kinetics is modulated by the threading moiety. In order to thread DNA, δ,δ-P requires a "lock mechanism", in which a large length increase of the DNA duplex is required for both association and dissociation. In contrast, measurements of the force-dependent binding kinetics show that δ,δ-B requires a large DNA length increase for association but no length increase for dissociation from DNA. This contrasts strongly with conventional intercalators, for which almost no DNA length change is required for association but a large DNA length change must occur for dissociation. This result illustrates the fundamentally different mechanism of threading intercalation compared with conventional intercalation and will pave the way for the rational design of therapeutic drugs based on DNA threading intercalation.
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| 22. |
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| 23. |
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| 24. |
- Coates, C. G., et al.
(författare)
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Picosecond time-resolved resonance Raman probing of the light-switch states of Ru(Phen)(2)dppz (2+)
- 2001
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 105:50, s. 12653-12664
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Tidskriftsartikel (refereegranskat)abstract
- Picosecond time-resolved resonance Raman (picosecond-TR3) spectroscopy has been used to conduct an extensive photophysical characterization of the light- switch complex [Ru(phen)(2)dppz](2+) as a function of environment, in which studies have been carried out in aqueous and nonaqueous media and in DNA. The results are considered in rotation to a previous report describing environment-sensitive lowest triplet MLCT states. Vibrational marker features and enhancement patterns were used to determine the rapid progression (< 20 ps) between two triplet MLCT states in aqueous environment, followed by subnanosecond, nonradiative deactivation to the ground state. In nonaqueous environment, the long-lived, emissive triplet MLCT state is spectrally identified as the short-lived first triplet MLCT state observed in water, in agreement with the earlier proposed mechanism. The present data are shown to correlate well with previous nanosecond RR findings for the complex in each environment. Interestingly, a precursor state has been identified upon excitation in both nonaqueous solvent and in DNA, which precedes the triplet MLCT state, and the lifetime of which appears to be environment dependent. Observation of this state is discussed in relation to other recent femtosecond spectroscopic studies on this complex.
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| 25. |
- Dehkordi, Maryam Nejat, et al.
(författare)
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Another step toward understanding the binding mode of other derivatives of [Ru(phen)(2)L] complexes
- 2020
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Ingår i: Journal of Biomolecular Structure and Dynamics. - : Informa UK Limited. - 0739-1102 .- 1538-0254. ; 36:11, s. 3318-3326
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Tidskriftsartikel (refereegranskat)abstract
- Linear dichroism (LD), UV-Vis and fluorescence spectroscopy were used to investigate the interaction of the ?- and ?-enantiomers of the two complexes of [Ru(phen)(2) 2-phenylimidazophenanthroline](+2) (referred to as B-complex) and [Ru(phen)(2) 2-(1-pyrenyl)limidazophenanthroline](+2) (named as P-complex), with ct-DNA. Absorption titration experiments of the enantiomers showed significant hypochromism with red shift indicating a strong perturbation of the DNA on the intra-ligand (IL) and the metal-to-ligand charge transfer (MLCT) transitions of the complexes, and fluorescence titration curves indicate strong binding. LD spectra for the B-enantiomers bound to DNA were qualitatively similar to spectra for the well-studied intercalator [Ru(phen)(2)dppz](+2), indicating intercalation of the phenyl-imidazophenanthroline part of the complex. However, for ?-P, the LD-spectrum resembled ?-B, and ?-P resembled ?-B, indicating a mirror image relationship of the transition moment directions relative to the helix axis when going from B to P. For interpretation of the data, and clarifying the nature of the binding mode of the P-complexes, a model was proposed based on the crystal structure previously presented by the Cardin group. The reversed LD is suggested to be due to partial intercalation of the pyrene moiety, pushing the Ru(phen)(2)-moiety out from the opposite groove and allowing it to rotate anticlockwise around the pyrene-imidazole bond. Communicated by Ramaswamy H. Sarma
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