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

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Alignment of hERG Potassium channel with known structures of potassium channel

Name: Prachi Sharma

Superviser: Prof. Gert Vriend


All living cells are enclosed by membrane which acts as a barrier between the cells internal environment and outer environment. Potassium channels are signaling elements. Potassium channels are tetrameric integral membrane proteins. They are found in virtually all organisms. They are very vital to vertebrate and involved in couple of physiological functions like neurotransmission, and cardiac and renal function(1). The genomes of humans, Drosophila, and Caenorhabditis elegans contain 30-100 K+ channel genes each (2). Potassium channels form aqueous pores through which K+ can flow. Potassium channels consist of a Selectivity Filter which selects and allows conduction of potassium ion and the gate consisting of four subunit which shuts down or open based on different environmental signals like voltage or the presence of key signaling molecules etc. Potassium ions are generally surrounded by eight water molecules the dimensions of the channel are designed to mimic this shell of water. The selectivity filter is so narrow that potassium ion has to shed its water molecules. The internal wall of the pore and the cavity is hydrophobic but the main chain atoms from the signature sequence lining the selectivity filter are polar (3). Oxygen atoms of protein lining the pore are oriented toward the center of the channel. Eight of these oxygen atoms surround each potassium ion acts as a perfect replacement for the normal layer of water molecules. Sodium ions, are slightly smaller in size, so they fail to interact with the oxygen atoms lining the pore wall (4).
Fig1: (A) Ribbon representation of the transmembrane section of two opposing KirBac1.1 monomers. The residues forming the selectivity filter, displayed as ball-and-stick, interact with four K+ ions, colored green (Sext), indigo (S1), cyan (S2), and indigo (S3). The inner helices are colored purple, whereas the side chains of the Phe blocking residues are colored red.(B) Relative positions of the pore helices are depicted in red in the crystal structure of KirBac1.1 and KcsA.This view is from the extracellular side of the channel looking directly down the central ion-conduction pathway. 20
All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the K+ selectivity sequence (T/SxxTxGxG) (5) (Fig2). In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits.

Fig2:Potassium ions bind at four locations in the selectivity filter ― at positions 1 and 3, or 2 and 4 ― before being shunted through by other ions entering the channel. G, T, V and Y indicate the key amino acids forming the filter.


In this project we are trying to find important residues involved in the transfer of potassium ion through the selectivity filter and obtain an alignment for the sequences from different families of potassium channel. To achieve this goal we are trying to generate a system that gives all information about the sequences from different potassium channel with a focus on hERG channel found in heart and how these sequences from different species are related to each other. Our system should be able to transfer interspecific information from one sequence to other even when these sequences or their structures are not aligned. This system should give information about most conserved sequences and effect of mutations on neighboring part of sequences can be analyzed from our sequence.

Potassium channels are related to many pathologies. Potassium channels play a key role in the regulation of membrane excitability. So any abnormality in potassium channel protein either genetic or acquired results in altered functioning of neurons, smooth muscle, and cardiac cells.

Cardiac diseases

Potassium channels play a fundamental role in repolarization of the action potential in heart thus it is very important for cardiac excitability. Various classes of potassium channels with different time and voltage dependencies and pharmacological properties functions together to regulate the heart rate by setting the resting membrane potential, amplitude, and duration of action potential. Any malfunctioning in the potassium channels present in heart can cause severe defects in excitation-contraction process of heart (6). Potassium channel related cardiac diseases are elaborately explained


under hERG potassium channel. Cardiac diseases are explained more elaborately under heading hERG.

Neuronal Diseases

Potassium channel are very important for neurotransmission in the nervous system. Any alteration in the function of these channels can cause remarkable perturbation in membrane excitability and neuronal function. Altered function of a type of potassium channel (Kv1.1) can impair the capacity of the affected neurons to repolarize effectively following an action potential. From gene knock down studies it has been found that the diminished function of KCNA1 leads to ataxia.

Benign Family Neonatal Convulsions which is a idiopathic form of epilepsy beginning within the first six months after birth is also caused by mutations in KCNQ2/KCNQ3 potassium channel.

A small conductance calcium activated potassium channel, hKCa3, mapped to chromosome 1q21 has been reported to be associated with schizophrenia (6).
Hearing and vestibular Diseases: Nonsyndromic Dominant Deafness and KCNQ4

Gene for one of the potassium channel called KCNQ is the locus of hereditary hearing impairment (6).
Renal Diseases: Bartter’s Syndrome and Kir1.1

Bartter’s syndrome is an autosomal recessive inherited renal tubular disorder characterized by hypokalemia, metabolic alkalosis, hyper-re-ninism and hyperaldosteronism. It has been proved from genetic analysis that Bartter’s syndrome is caused by dysfunction of an inward rectifier potassium channel Kir1.1 (6).
Metabolic Diseases: Family Persistent Hyperinsulinemic Hypoglycemia of Infancy and Sulfonylurea Receptor 1

PHHI is an autosomal disorder characterized by increased irregularity in insulin secretion leading to hypoglycemia, coma, and severe brain damage in children. Opening of ATP-sensitive potassium channel results in membrane hyperpolarization and consequently supression of insulin secretion thus resulting in PHHI (6).




These kind of potassium channels have one subunit. 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. KCNE1 (mink)
Fig3:A mink protein (red) associate with a voltage gated channel to control gating mechanism.

The minK gene encodes a protein of 130 amino acids that has a single transmembrane segment and is
expressed in many tissues including heart, uterus, and kidney (8). MinK co-assemble with another subunit (KvLQT1) to form the KV(s) delayed-rectifier K+ channel (9) (Fig 3). Mutation in this gene are
associated with both Jervell and Lange-Nielsen and Romano-Ward forms of long-QT syndrome. KCNE1, however, has neither the P region nor signature sequence that characterizes the pore-forming subunits of all known K+ channel proteins. KCNE3
Diverse functions of these proteins include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. These are type I membrane protein, and a beta subunit that assembles with a potassium channel alpha-subunit to modulate the gating kinetics and enhance stability of the multimeric complex.
A missense mutation in their gene can cause hypokalemic periodic paralysis. Unlike KCNE1 it
assembles with KvLQT1 and yields a more rapidly activating current with a distinct constitutively active component (8).


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