Research Article
Metal ion effects on ion channel gating
- Fredrik Elinder, Peter Århem
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- Published online by Cambridge University Press:
- 04 June 2004, pp. 373-427
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1. Introduction 374
2. Metals in biology 378
3. The targets: structure and function of ion channels 380
4. General effects of metal ions on channels 382
4.1 Three types of general effect 382
4.2 The main regulators 383
5. Effects on gating: mechanisms and models 384
5.1 Screening surface charges (Mechanism A) 387
5.1.1 The classical approach 387
5.1.1.1 Applying the Grahame equation 388
5.1.2 A one-site approach 391
5.2 Binding and electrostatically modifying the voltage sensor (Mechanism B) 391
5.2.1 The classical model 391
5.2.1.1 The classical model as state diagram – introducing basic channel kinetics 392
5.2.2 A one-site approach 395
5.2.2.1 Explaining state-dependent binding – a simple electrostatic mechanism 395
5.2.2.2 The relation between models assuming binding to smeared and to discrete charges 396
5.2.2.3 The special case of Zn2+ – no binding in the open state 396
5.2.2.4 Opposing effects of Cd2+ on hyperpolarization-activated channels 398
5.3 Binding and interacting non-electrostatically with the voltage sensor (Mechanism C) 398
5.3.1 Combining mechanical slowing of opening and closing with electrostatic modification of voltage sensor 400
5.4 Binding to the pore – a special case of one-site binding models (Mechanism D) 400
5.4.1 Voltage-dependent pore-block – adding extra gating 401
5.4.2 Coupling pore block to gating 402
5.4.2.1 The basic model again 402
5.4.2.2 A special case – Ca2+ as necessary cofactor for closing 403
5.4.2.3 Expanding the basic model – Ca2+ affecting a voltage-independent step 404
5.5 Summing up 405
6. Quantifying the action: comparing the metal ions 407
6.1 Steady-state parameters are equally shifted 407
6.2 Different metal ions cause different shifts 408
6.3 Different metal ions slow gating differently 410
6.4 Block of ion channels 412
7. Locating the sites of action 412
7.1 Fixed surface charges involved in screening 413
7.2 Binding sites 413
7.2.1 Group 2 ions 414
7.2.2 Group 12 ions 414
8. Conclusions and perspectives 415
9. Appendix 416
10. Acknowledgements 418
11. References 418
Metal ions affect ion channels either by blocking the current or by modifying the gating. In the present review we analyse the effects on the gating of voltage-gated channels. We show that the effects can be understood in terms of three main mechanisms. Mechanism A assumes screening of fixed surface charges. Mechanism B assumes binding to fixed charges and an associated electrostatic modification of the voltage sensor. Mechanism C assumes binding and an associated non-electrostatic modification of the gating. To quantify the non-electrostatic effect we introduced a slowing factor, A. A fourth mechanism (D) is binding to the pore with a consequent pore block, and could be a special case of Mechanisms B or C. A further classification considers whether the metal ion affects a single site or multiple sites. Analysing the properties of these mechanisms and the vast number of studies of metal ion effects on different voltage-gated ion channels we conclude that group 2 ions mainly affect channels by classical screening (a version of Mechanism A). The transition metals and the Zn group ions mainly bind to the channel and electrostatically modify the gating (Mechanism B), causing larger shifts of the steady-state parameters than the group 2 ions, but also different shifts of activation and deactivation curves. The lanthanides mainly bind to the channel and both electrostatically and non-electrostatically modify the gating (Mechanisms B and C). With the exception of the ether-à-go-go-like channels, most channel types show remarkably similar ion-specific sensitivities.
Geometry of the DNA strands within the RecA nucleofilament: role in homologous recombination
- Chantal Prévost, Masayuki Takahashi
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- Published online by Cambridge University Press:
- 04 June 2004, pp. 429-453
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1. Introduction 430
2. Transformations of the RecA filament 431
2.1 The different forms of the RecA filament 431
2.2 Orientation and position of the RecA monomers in the active filament 433
2.3 Transmission of structural information along the filament 433
3. RecA-induced DNA deformations 435
3.1 Characteristics of RecA-bound DNA 435
3.2 Stretching properties of double-stranded DNA 436
3.3 DNA bound to architectural proteins 437
3.4 Implications for RecA-induced DNA deformations 438
3.5 Axial distribution of the DNA stretching deformation 438
4. Contacts between RecA and the DNA strands 440
4.1 The DNA-binding sites 440
4.2 Possible arrangement of loops L1 and L2 and the three bound strands of DNA 442
5. Strand arrangement during pairing reorganization 444
5.1 Hypotheses for DNA strand association 444
5.2 Association via major or minor grooves 446
5.3 Post-strand exchange geometries 446
6. Conclusion 447
7. Acknowledgments 448
8. References 448
Homologous recombination consists of exchanging DNA strands of identical or almost identical sequence. This process is important for both DNA repair and DNA segregation. In prokaryotes, it involves the formation of long helical filaments of the RecA protein on DNA. These filaments incorporate double-stranded DNA from the cell's genetic material, recognize sequence homology and promote strand exchange between the two DNA segments. DNA processing by these nucleofilaments is characterized by large amplitude deformations of the double helix, which is stretched by 50% and unwound by 40% with respect to B-DNA. In this article, information concerning the structure and interactions of the RecA, DNA and ATP molecules involved in DNA strand exchange is gathered and analyzed to present a view of their possible arrangement within the filament, their behavior during strand exchange and during ATP hydrolysis, the mechanism of RecA-promoted DNA deformation and the role of DNA deformation in the process of homologous recombination. In particular, the unusual characteristics of DNA within the RecA filament are compared to the DNA deformations locally induced by architectural proteins which bind in the DNA minor groove. The possible role and location of two flexible loops of RecA are discussed.