Alignment of herg potassium channel with known structures of potassium channel Name: Prachi Sharma Superviser: Prof. Gert Vriend introduction

1.1.4 POTASSIUM CHANNEL 6TM

The alpha subunit is formed from 6 transmembrane segments (Fig6).

Fig6 :Shows six transmembrane helices.A pore is formed between helix 5 and helix 6

Source:http://www.nature.com/nrn/journal/v3/n2/images/nrn727-f1.gif

Types of potassium channel with 6 transmembrane helices are given below.

1.1.4.1 Voltage-gated potassium channel

Voltage-gated potassium (Kv) channels are ubiquitous transmembrane proteins involved in electric signaling of excitable tissues. Voltage-gated potassium (Kv) channels play a key role in setting the resting membrane potential and shaping action potential repolarization Kv channels in nervous and cardiovascular systems, skeletal muscle, gastrointestinal tract and uterus (17). The structure of the this type of potassium channel has four homologous transmembrane domains which contains six transmembrane domains, which includes the voltage sensor and the ion conducting pore. Voltage driven confirmation changes causes activation of these ion channels which opens the transmembrane pore. Depolarization of the membrane causes an electrical force on voltage sensors which contain the gating charges of the channel located within the transmembrane electric field (18). Each alpha subunit comprises six hydrophobic TM domains with a P-domain between the fifth and sixth, which partially resides in the membrane. The fourth TM domain has positively charged residues at every third residue and acts as a voltage sensor, which triggers the conformational change that opens the channel pore in

response to a displacement in membrane potential. The Kv family can be divided into several subfamilies.

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Fig7: a | A plan view of the voltage-dependent potassium channel (K_vAP). The tetrameric ion channel is viewed from the inside of the cell looking towards the extracellular side. The -helical structures represent the S1–S6 elements, including the channel P domain. b | The classical (pre-crystallization) transmembrane view of a single voltage-gated ion channel subunit. This diagram is based largely on hydropathy plot analyses. A complete channel would comprise four of these subunits.

Source: http://www.nature.com/nrd/journal/v3/n3/images/nrd1361-f1.jpg
1.1.4.1.1 hERG (Kv11.1)

hERG is a protein which is encoded by a gene KCNH2. HERG is most highly expressed in heart, but it is also found in other tissues and cell type like neuronal, smooth muscle and tumor cells.

Cardiac cycle of human heart involves different phases. Activation of inward Na ion current triggers a rapid depolarization of the membrane (phase 0). Repolarization is much slower. During first phase of repolarization, repolarization proceeds rapidly which is followed by much slower rate of repolarization (Phase 2) called the plateau. The third phase of repolarization terminates the action potential and returns the membrane potentials to its resting level. The most important component of phase 3 repolarization is the rapid delayed rectifier potassium current (Ikr) conducted by hERG channels (19) .

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1.1.4.1.1.1Structure of hERG channel

Fig8: hERG channel: for clarity only S5 and S6 segments are show. There is a Drug docked (in white) to hERG potassium channel.

Source http://www.cvrti.utah.edu/ms-lab/images/mk499-360.gif

Mutations that disrupt normal biosynthesis and function of HERG have been associated with three cardiac arrhythmias: Short QT syndrome (SQTS) , atrial fibrillation and Long QT syndrome (LQTS). Blockade of hERG K⁺ channels in the heart is an unintentional side effect of many drugs and cardiac arrhythmia and sudden death can also be induced by this blocking. For this reason, most pharmaceutical companies screen compounds for hERG channel activity early in the drug discovery/development process.

LQTS

QT interval is the time required for ventricular repolarization during a single cardiac cycle. LQTS is defined by prolongation of the QT interval which greatly increases the risk of ventricular fibrillation.

This arrhythmia, which affects an estimated 1 in 5000–10000 people worldwide, is characterized by a prolongation of the QT interval on an electrocardiogram and can lead to Torsade de Pointes (TdP), ventricular fibrillation and sudden cardiac death . More recently, the progression from LQTS into TdP has been proposed as a cause of sudden infant death syndrome (SIDS) and sudden unexplained death
syndrome (SUDS) (20). LQTS is most often caused by a dominant mutation in the alpha subunit of potassium channel that conducts the slow delayed rectifier potassium current. Some times it can also occurs due to mutation in the beta subunit which coassembles alpha subunit.
SQTS

The substitution of one of the lysine for asparagines in KCNH2, was found to cause a loss of the normal

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rectification of the current at plateau voltages, thus resulting in a large increase of IKr during the action potential plateau, leading to marked abbreviation of the action potential. The short QT syndrome is the first disease to be linked to a gain of function of IKr (21).

1.1.4.1.1.2 Blocking of hERG by Drugs

hERG channels are blocked by chemicals with diverse structures that encompass several therapeutic drug classes, including antiarrhythmic, psychiatric, antimicrobial and antihistamine. This unpredictability has frustrated conventional drug-design approaches as it increases arrythmia side effect. The hERG channel is unusually more susceptible to blockage by drugs in comparison with other Kv channels, suggesting that it has a unique binding site. Mutation of two polar residues (Thr and Ser located at the base of the pore helix) and two aromatic residues (Tyr and Phe ) located in the S6 domain of the hERG subunit decreased the affinity of MK-499, a potent antiarrhythmic drug (Fig9).

Fig9:Homology model of the hERG-channel pore module (S5, S6 and pore helix of two subunits) based on the crystal structure of KvAP (ref. 6). The key residues that interact with structurally diverse drugs are highlighted, including Thr (orange) and Ser (white) located at the base of the pore helix, and Tyr (yellow) and Phe (magenta) located on the S6 domain.

Source: http://www.nature.com/nature/journal/v440/n7083/fig_tab/nature04710_F5.html
The same residues were found to be important for binding of cisapride, terfenadine and several other drugs from diverse chemical and therapeutic classes. The side chains of all four residues are orientated towards the large central cavity of the channel, which is consistent with the observation that hERG channels are only blocked by these drugs after the channel has opened (22).
1.1.4.1.2 Shaker related KCNA (Kv1)

Shaker potassium channel from Drosophila melanogaster open, or activate, when the membrane potential becomes sufficiently positive. Once activated channel enter a long-lived nonconducting state, the inactivated state. The inactivation process has little intrinsic voltage dependence and that it is fast and coupled to the activation process similar to the gating of vertebrate neuronal sodium channels.
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1.1.4.1.3 Shab related KCNB (Kv2)

Carry a delayed-rectifier current, and their subunits have only five positively charged residues in S4, they would be expected to have smaller gating-charge movements and voltage sensitivities.

1.1.4.1.4 Shaw

Shaw is expressed mainly in excitable cells of the CNS and PNS of late embryos.