Calculation of interaction energy between voltage-gated potassium channel Kv1.2 and

Calculation of interaction energy between voltage-gated potassium channel Kv1.2 and

blocker agitoxin

Valery N. Novoseletsky Maria A. Bolshakova Konstantin V. Shaitan

Moscow 2013

Molecular modeling groupBioengineering departmentBiology Faculty M.V.Lomonosov Moscow State University

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Pore-forming membrane proteins that open or close in response to changes in the transmembrane voltage.

Potassium channels are the most widely distributed type of ion channel and are found in virtually all living organisms.

Voltage-Dependent Potassium Channels

Action potential is a short-lasting event in which the electrical membrane potential of a cell rapidly rises and falls, following a consistent trajectory.

During action potentials, voltage-dependent potassium channels play a crucial role in returning the depolarized cell to a resting state.

3(Long, Campbell, MacKinnon, 2005)

Crystal Structure of a Mammalian Voltage-Dependent K+ Channel

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Transmembrane domain scheme: helices S1-S4 form the voltage-sensing domain, helices S5 and S6 take place in the ions conduction.

Crystal Structure of a Mammalian Voltage-Dependent K+ Channel

5Side view: voltage-sensing domain , pore domain and selective filter.

Crystal Structure of a Mammalian Voltage-Dependent K+ Channel

Scorpion venom toxin – agitoxin

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Agitoxin structure was determined by NMR (Kresel, Kasibhatha, 1995). Structure has highly conserved motif consisting of- 3 antiparallel β-sheets- α-helix - 3 disulfide bridges Agitoxin specifically blocks Kv1.2 channel with high affinity (Kd < 1 nmol/L)

Extracellular and membrane view. Highly conserved residues involved in binding are marked (pdb-codes 1AGT for agitoxin, 2A79 for channel).

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Kv1.2 channel complex with agitoxin

Molecular system preparation

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Potential of mean force with umbrella sampling1. Pulling the toxin away from the channel using steered molecular dynamics

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Toxin-channel distance increases with time from 2.5 nm at 0 ps to 7 nm at 500 ps.

2. Frame selection 3. Configuration space sampling

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Potential of mean force with umbrella sampling

Dependence of PMF on toxin-channel distance in 0.1 M NaCl solution.

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Potential of mean force with umbrella sampling4. PMF extraction and ΔG calculation

Dependence of PMF on toxin-channel distance in 0.1 M NaCl solution.

Binding energy is equal to the max PMF value and consists 22 ± 2 kcal/mol.12

Potential of mean force with umbrella sampling

22 ± 2 kcal/mol

5. Error estimation

Effect of ionic strength on the free energy of binding

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Binding energy drops with the increase of ionic strength.

0, 025M 0, 05M

0,1M 0,2M

0,4M

z (nm)

25

20

15

10

5

0

E (k

cal/m

ol)

Comparison of the results

* Zachariae et al, 2008** Our data*** Khabiri et al, 2011

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Complex Experiment CalculationKv 1.2 - agitoxin

∆G = 10,3 ± 0,2 kcal/mol*(160 мМ NaCl, 4.5 мМ KCl, 2 мМ CaCl₂, 1 мМ MgCl₂)

∆G = 22 ± 2 kcal/mol**(100 мМ NaCl)

Kv 1.3 - charibdotoxin

∆G = 10,6 ± 0,2 kcal/mol***(164.5 мМ KCl, 2 мМ CaCl₂, 1 мМ MgCl₂)

∆G = 27 ± 1 kcal/mol***(160 мМ KCl)

Kv 1.3 - charibdotoxin

∆G = 11,4 ± 0,2 kcal/mol***(160 мМ NaCl, 4.5 мМ KCl, 2 мМ CaCl₂, 1мМ MgCl₂)

∆G = 26 ± 1 kcal/mol***(4.5 мМ KCl)

Conclusion

1. Structural model of agitoxin-channel complex was constructed

2. Free energy binding was calculated using potential of mean force and umbrella sampling

3. Obtained results differ from experimental data. Probable reason is in the mistake of system preparation

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Thank you for attention!

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