Analysis of rare variations reveals roles of amino acid residues in the N-terminal extracellular domain of nicotinic acetylcholine receptor (nAChR) alpha6 subunit in the functional expression of human alpha6*-nAChRs

Table 1 Characteristics of single nucleotide variants (SNVs) located in the N-terminal domain of nAChR hα6 subunit

rs ID #	Nucleotide position in chromosome 8	All [AA + EA] Allele #	Amino acid change	Change in electrical charge	Conservation in human nAChR α subunits	Conservation in α6 subunits of other species	NTD location
rs140930963	8:42620300	G = 37/A = 10721	S43P		No	-		α-helix
rs80342906	8:42620289	C = 6/G = 10752	N46K		No	N: yes		α-helix
rs149966755	8:42620258	T = 1/C = 10757	D57N	‘-‘ve to zero	D: weak	D: yes		α-helix
unknown	8:42614217	A = 2/G = 10756	R87C	‘+’ve to zero	R: strong	R: yes	Complementary face/inner β-sheet	Strand β2
rs146332801	8:42612169	C = 1/A = 10755	D92E		D: fully	D: yes		β2-β3 loop (loop D)
rs188620180	8:42612158	A/G	R96H		No	-		β2-β3 loop
rs200380236	8:42612144	T = 1/C = 10755	E101K	‘-‘ve to ‘+’ve	No	E: yes		β2-β3 loop/¹MIR
unknown	8:42611874	C = 1/A = 10757	S156R	neutral to ‘+’ve	S: fully	S: yes		Strand β6
unknown	8:42611747	A = 2/C = 10756	D199Y	‘-’ve to neutral	D: weak	D: weak		β8-β9 loop (loop F)
rs143385261	8:42611734	G = 3/T = 10755	N203T		N: weak	N: weak		β8-β9 loop (loop F)
rs141518931	8:42612110	A = 1/G = 10755	A112V		No	A: yes	Principal face/outer β-sheet	β3-β4 loop (Loop A)
rs79945499	8:42611829	G/C	N171K	neutral to ‘+’ve	N: strong	N: yes		β6-β7 (Cysteine loop)
rs200745568	8:42611791	T = 1/G = 10757	A184D	neutral to ‘-‘ve	No	A: yes		β7-β8 loop (loop B)
rs199987912	8:42611665	G = 2/A = 10756	I226T		No	I: yes		β9-β10 loop (loop C)
unknown	8:42611644	C = 1/G = 10757	S233C		No	S: yes		Strand β10

¹MIR: Main immunogenic region.
Pertinent information about the N-terminal variations in nAChR hα6 subunit such as their reference SNP (rs) identification (ID) number, location in the chromosome 8, combined frequency of nucleotide variations discovered in more than 10000 genomes of African Americans (AA) and European Americans (EA) (Exome Sequencing Project: ESP; https://esp.gs.washington.edu/), change in amino acids, change in electrical charges, conservation in the human nAChR α subunits (Figure 1), conservation in nAChR α6 subunit of other species and putative locations in the secondary structure of the nAChR hα6 subunits (Figure 2) are presented. The WT AAs with the exception of S43 are strongly conserved in nAChR α6 subunits studied from a limited number of other species (Figure 1). Please note that hα6 variations R87C, S156R, D199Y and S233C retrieved from ESP do not have an rs ID number yet. The N-terminal domain of a typical human nAChR subunit is presumed to contain an inner β-sheet (strand β1-β3, β5, β6 and β8) and outer β-sheet (strand β4, β7, β9 and β10) like those of seen in the crystal structure of Torpedo muscle nAChR subunits. ‘-‘ indicates lack of indicated information in these positions.

ISSN: 1756-6606