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

1.1.4.1.5 Shal related KCND (Kv4)

Shal-related subfamily form voltage-activated A-type potassium ion channels and are prominent in the repolarization phase of the action potential.

1.1.4.2 Calcium-activated potassium channel

The other major group of six/seven transmembrane potassium selective channels consist of Calcium activated potassium channel. They regulate neuronal excitability. A change in the concentration of calcium concentration coupled with changes in the membrane potential causes activation of the Calcium-activated potassium channel. They are found to play a very important role in some of the physiological functions like neurosecretion, smooth muscle tone, action potential shape and spike frequency adaptation.
Calcium activated potassium channels are of three types (23).

1. 
   Large conductance calcium-activated potassium channels (BK) which have a very high single channel conductance(~250pS in symmetric 0.1M KCL)
   
2. 
   Small conductance calcium-activated potassium channels (SK). Their activation cause membrane hyperpolarization which inhibit cell firing which causes SK channel to generate a long-lasting hyperpolarization called after hyperpolarization (sAHP)
   
3. 
   Intermediate Small conductance calcium-activated potassium channels (SK) which exhibit unit conductance value of 20-80pS.
   

1.1.5 POTASSIUM CHANNEL 7TM

These are Calcium activated potassium channel. Alpha subunit has 7 transmembrane helices (Fig 10).

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Fig10:bk channel structure

Source: http://images.google.nl/imgres?

Alpha subunit of BK channels in addition to the S1-S6 transmembrane (TM) helices conserved in all voltage-gated potassium channels, contains a unique seventh TM helix, S0, N-terminal to S1-S6 (24). Calcium activated potassium channel is already explained under Potassium channel 6TM.

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1.2 SEQUENCE OVERVIEW

1.2.1 Potassium channel with One transmembrane helix (1TM)

TM 1 has only one transmembrane helix. These proteins are encoded by KCNE family of gene. The specificity of KCNE1 (minK) and KCNE3 control of activation of the potassium channel KvLQT1 is due to a triplet of amino acids within the KCNE transmembrane domain. These triplets are FTL for minK and TVG for KCNE3 (7). Thr-58 of minK and Val-72 See under multiple sequence alignment both of these residues are residue numbers 950.(http://www.cmbi.ru.nl/~psharma/FILE.mview_tm1.html) of KCNE3 is essential for the specific control of voltage- dependent channel activation characteristics of both minK and KCNE3 It was found that a hydroxylated central amino acid is necessary for the slow sigmoidal activation produced by minK. Precise spacing of this hydroxyl group is required for the mink like activity (25)

1.2.2 Potassium channel with two transmembrane helices (2TM)

Transmembrane helix before pore is called M1 and after pore is called M2. M1 has a highly conserved residues Phe542, trp546, Phe549, G550 and Ala557 (http://www.cmbi.ru.nl/~psharma/FILE.mview_tm2.html). M2 has a highly conserved Gly at position 663.This Gly has potential to induce flexibility in the transmembrane as they induce kink in the transmembrane. Kinked helix plays a role of swivel in an ion channel protein. As the confirmation of M2 helix differs between closed and open confirmation with the central kink acting as a swivel (26). Near the mid region of M2 a Glu (at position 658) is present. This negative residue is involved in the blockade of some Kir's by Mg ions (27).

1.2.3 Potassium channel with 2pore and 4Transmembrane helices (4TM)

Interestingly, the GYG K -selectivity motif is preserved in the first pore domain of most 4Tm–2P subunits, but replaced by GFG or GLG in the second pore (http://www.cmbi.ru.nl/~psharma/FILE.mview_tm4.html). Thus, the fourfold symmetry of homomeric Kv and Kir channels is reduced to a twofold symmetry in the channels with tandem pore subunits (28).

1.2.4 Potassium channel with six transmembrane helices (6TM)

Voltage gated potassium channels have six transmembrane segments (S1-S6). S1-S4 are voltage sensors and S5-S6 are pore domain. S1 segment has positive charge (R130) at the starting and negative charge (E150) towards the end of helix (http://www.cmbi.ru.nl/~psharma/FILE.mview_tm6.html). S1 also has extremely well conserved Thr residue at position 151, suggesting that it has some important role (25). S2 has a negatively charged residue Glu at position 260. This Glu residue play an important role in gating charges in voltage sensing domain. In S3 segment Glu 360 is a potential voltage sensing residue.The gating process is initiated by a cluster of positively charged residues on the fourth transmembrane segment. We found seven Arg (at positions 444, 447, 450, 453, 456, 459 and 462) at an interval of two residues in S4 segment (http://www.cmbi.ru.nl/~psharma/FILE.mview_tm6.html).

S5 has conserved residues Lys547, Gly550 and Phe554 pointing towards S6. Gly550 interact with side

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chain of S6.

Pore segment has a conserved sequence SMTTVGYG (http://www.cmbi.ru.nl/~psharma/FILE.mview_tm6.html).

In the center of the S6 segment of channel there is a highly conserved Pro-Val-Pro motif. The presence of proline in the middle of a helix causes a kink in the helix. Proline induced kinks are accommodated by alteration in the backbone dihedral angles for the residues in the turn N-terminal to the kink site, while residues C-terminal to the proline retain standard alpha-helical geometry. Like Glycine in M2 proline in S6 acts as molecular swivels within the intact protein. This flexibility caused due to kink plays a functional role in the intact protein (29).

1.2.5 Potassium channel with seven transmembrane helices (7TM)

Large conductance voltage- and Ca²⁺-dependent K⁺ (MaxiK) channels show sequence similarities to voltage-gated ion channels. They have a homologous S1-S6 region, but are unique at the N and C termini. 7TM potassium channel has extra transmembrane helix S0 which is N-terminal to S1-S6. S0 helix starts with conserved sequences RGQR (http://www.cmbi.ru.nl/~psharma/FILE.mview_tm7.html).

1.3 ALIGNMENT OVERVIEW

In this project we are trying to align different families of potassium channel together so that with these alignments homology modelling can be done. But aligning these sequences are not easy as they are not identical or similar, but we have to align them anyways to obtain a homology model. So sequences were aligned using our knowledge about different families of potassium channel.

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