| 1. |
- Starikov, E. B., et al.
(författare)
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On mechanism of enhanced flourescence in green flourescent protein
- 2007
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Ingår i: Biophysical Reviews and Letters. - : World Scientific Pub Co Pte Lt. - 1793-0480 .- 1793-7035. ; 2:3-4, s. 221-227
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Tidskriftsartikel (refereegranskat)abstract
- In spite of the numerous experimental and theoretical studies on green fluorescent protein and its modifications, there is still no definitive answer to the central question: why such systems exhibit enhanced fluorescence. Based upon detailed quantum-chemical estimations, we advocate the following hypothesis. In the green fluorescent protein ground electronic state, the protein surrounding strains the chromophore with respect to its native intramolecular conformational preference in vacuo or in solution. Absorbing a photon of the proper wavelength not only causes a joint proton-electron transfer in and around the chromophore, but also increases the intrinsic strain of the latter. Since conformational relaxation of such a structure will not require any additional energy input, the energy gained by the chromophore cannot be dissipated into the chromophore's internal non-radiative degrees of freedom, and thus it returns as a fluorescence emission.
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| 2. |
- Starikov, Evgeni B., et al.
(författare)
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Protein folding as a result of 'self-regulated stochastic resonance': A new paradigm?
- 2008
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Ingår i: Biophysical Reviews and Letters. - 1793-0480. ; 3:3, s. 343-363
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Tidskriftsartikel (refereegranskat)abstract
- We scrutinize the available (seemingly disparate) theories of protein folding and propose a new concept which brings them under one roof. First, we single out dipole-dipole coupling within protein backbone as the main reason for intrinsic double-well nature of the protein potential. Then, protein folding as a whole ought to be (at least) a two-stage process, namely: (a) both amino-acid side chains and solvent enslave the dynamics of the backbone to reach the folding transition state with the help of stochastic resonance, and (b) the backbone funnels the whole protein into the global potential energy minimum by enslaving the dynamics of the amino-acid side chains plus solvent, and simultaneously arresting the stochastic resonance prerequisites to lock the protein in its folded state. The latter is accomplished owing to the concerted action of the protein compactization (enthalpic contribution) and thermal motion intensification (entropic contribution), which is, in fact, a physical hallmark of enthalpy-entropy compensation.
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| 3. |
- Starikov, Evgeni B., et al.
(författare)
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Screw motion of DNA duplex during translocation through pore. I. Introduction of the coarse-grained model
- 2009
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Ingår i: Biophysical Reviews and Letters. - 1793-0480. ; 4:3, s. 209-230
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Tidskriftsartikel (refereegranskat)abstract
- Based upon the structural properties of DNA duplexes and their counterion-water surrounding in solution, we have introduced here a screw model which may describe translocation of DNA duplexes through artificial nanopores of the proper diameter (where the DNA counterion-hydration shell can be intact) in a qualitatively correct way. This model represents DNA as a kind of "screw," whereas the counterion-hydration shell is a kind of "nut." Mathematical conditions for stable dynamics of the DNA screw model are investigated in detail. When an electrical potential is applied across an artificial membrane with a nanopore, the "screw" and "nut" begin to move with respect to each other, so that their mutual rotation is coupled with their mutual translation. As a result, there are peaks of electrical current connected with the mutual translocation of DNA and its counterion-hydration shell, if DNA is possessed of some non-regular base-pair sequence. The calculated peaks of current strongly resemble those observed in the pertinent experiments. An analogous model could in principle be applied to DNA translocation in natural DNA-protein complexes of biological interest, where the role of "nut" would be played by protein-tailored "channels." In such cases, the DNA screw model is capable of qualitatively explaining chemical-to-mechanical energy conversion in DNA-protein molecular machines via symmetry breaking in DNA-protein friction.
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| 4. |
- Zeller, Kathrin Stephanie, et al.
(författare)
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Common and diverging integrin signals downstream of adhesion and mechanical stimuli and their interplay with reactive oxygen species
- 2014
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Ingår i: Biophysical Reviews and Letters. - 1793-0480. ; 9:2, s. 159-171
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The integrin family of adhesion receptors regulates basic functions of cells, and the signals they induce are altered in tumor cells. In this review we discuss how different integrin-dependent signals are generated during cell adhesion and by physical forces acting on cells. We also describe how reactive oxygen species are integral parts of integrin signaling and highlight a few important questions in the field. Answers to those may improve our understanding of integrins and their role in the development of cancer.
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| 8. |
- Zhdanov, Vladimir, 1952
(författare)
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Kinetics of single-enzyme reactions on vesicles: Role of substrate aggregation
- 2015
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Ingår i: Biophysical Reviews and Letters. - 1793-0480. ; 10:2, s. 69-83
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Tidskriftsartikel (refereegranskat)abstract
- Enzymatic reactions occurring in vivo on lipid membranes can be influenced by various factors including macromolecular crowding in general and substrate aggregation in particular. In academic studies, the role of these factors can experimentally be clarified by tracking single-enzyme kinetics occurring on individual lipid vesicles. To extend the conceptual basis for such experiments, we analyze herein the corresponding kinetics mathematically with emphasis on the role of substrate aggregation. In general, the aggregation may occur on different length scales. Small aggregates may e.g. contain a few proteins or peptides while large aggregates may be mesoscopic as in the case of lipid domains which can be formed in the membranes composed of different lipids. We present a kinetic model describing comprehensively the effect of aggregation of the former type on the dependence of the reaction rate on substrate membrane concentration. The results obtained with physically reasonable parameters indicate that the aggregation-related deviations from the conventional Michaelis-Menten kinetics may be appreciable. Special Issue Comments: This theoretical article is focused on single-enzyme reactions occurring in parallel with substrate aggregation on individual vesicles. This subject is related to a few Special Issue articles concerning enzyme dynamics and function and mathematical aspects of stochastic kinetics.
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