Ion Channels, Carriers and Pumps

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Ion Channels, Carriers and Pumps Aug 28,
2007 Overview of Molecular vs Electrical
Analyses Membranes Pumps, Carriers and
Channels Properties of Ion Channels    Ways to
study Ion Channels   Properties of Voltage-Gated
Ion Channels   Voltage-Sensitive
Gating Mechanism of Ion Selectivity Inactivation
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Smith fig 6.1
Principal membrane lipids glycerophospholipids
A schematic B phosphatidyl choline C
phosphatidyl ethanolamine D phosphatidyl
serine E phosphatidyl inositol
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Artificial lipid bilayer membrane model of Müller
Rudin
phospholipids in solvent
phospholipid bilayer formed at pin-hole in a
partition separating 2 aqueous solutions
black lipid bilayer named for its black
interference color
solvent diffusion
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Physical properties of membranes (based on
Müller Rudin black lipid bilayer model
membrane) cell membrane lipid
bilayer capacitance 1 µF/cm2 1
µF/cm2 resistance 103 O cm2 106109 O
cm2 H2O permeability 90400 µm/sec 17104
µm/sec surface tension 0.31 dyne/cm 0.52
dyne/cm
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Cooper fig 2.48
Fluid mosaic model of membrane structure
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MCB 7-2
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MCB 7-9
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Ways to look at ion channels.
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Fig. 2-4
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Fig 6-9
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(No Transcript)
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gtgi12830376embAJ310479.1HSA310479 Homo
sapiens mRNA for potassium voltage-gated channel,
shaker-related subfamily, member 7 (KCNA7 gene)
  AAACTTGGAGAGACGCAGGACAGGATCCCGGCGGCAGAAGGACGGAGA
GAAAGGGGACCCCGGGACGGGAAAGGCGCAGAGCAGGCGCGGGCGGCGGC
GGCGGCGGGGCAGGGCAGGGCGGGCGTCCCGGCAGAGGGCGCGCGGTCGC
CCTGTCGCCCTCCGCCCCGCCGGGGTCACAGTGCCCCCTCCCTCGCGCCC
TAGCCGCCCTGCCGGGCTATTTTTACGCGCGGACACCGGACACCGGACAC
CGGGCTGGGGCGGCGGCGGCGGCGGCCGAGGCGGCCGAGGCGGGGCCGCA
CCGGGGCCGGGCGTCGGGGCCACACGTCGGTTCGCGGGTCGCCGGGGCTG
CGCGCGCCATGGAGCCGCGGTGCCCGCCGCCGTGCGGCTGCTGCGAGCGG
CTGGTGCTCAACGTGGCCGGGCTGCGCTTCGAGACGCGGGCGCGCACGCT
GGGCCGCTTCCCGGACACTCTGCTAGGGGACCCAGCGCGCCGCGGCCGCT
TCTACGACGACGCGCGCCGCGAGTATTTCTTCGACCGGCACCGGCCCAGC
TTCGACGCCGTGCTCTACTACTACCAGTCCGGTGGGCGGCTGCGGCGGCC
GGCGCACGTGCCGCTCGACGTCTTCCTGGAAGAGGTGGCCTTCTACGGGC
TGGGCGCGGCGGCCCTGGCACGCCTGCGCGAGGACGAGGGCTGCCCGGTG
CCGCCCGAGCGCCCCCTGCCCCGCCGCGCCTTCGCCCGCCAGCTGTGGCT
GCTTTTCGAGTTTCCCGAGAGCTCTCAGGCCGCGCGCGTGCTCGCCGTAG
TCTCCGTGCTGGTCATCCTCGTCTCCATCGTCGTCTTCTGCCTCGAGACG
CTGCCTGACTTCCGCGACGACCGCGACGGCACGGGGCTTGCTGCTGCAGC
CGCAGCCGGCCCGTTCCCCGCTCCGCTGAATGGCTCCAGCCAAATGCCTG
GAAATCCACCCCGCCTGCCCTTCAATGACCCGTTCTTCGTGGTGGAGACG
CTGTGTATTTGTTGGTTCTCCTTTGAGCTGCTGGTACGCCTCCTGGTCTG
TCCAAGCAAGGCTATCTTCTTCAAGAACGTGATGAACCTCATCGATTTTG
TGGCTATCCTTCCCTACTTTGTGGCACTGGGCACCGAGCTGGCCCGGCAG
CGAGGGGTGGGCCAGCAGGCCATGTCACTGGCCATCCTGAGAGTCATCCG
ATTGGTGCGTGTCTTCCGCATCTTCAAGCTGTCCCGGCACTCAAAGGGCC
TGCAAATCTTGGGCCAGACGCTTCGGGCCTCCATGCGTGAGCTGGGCCTC
CTCATCTTTTTCCTCTTCATCGGTGTGGTCCTCTTTTCTAGCGCCGTCTA
CTTTGCCGAAGTTGACCGGGTGGACTCCCATTTCACTAGCATCCCTGAGT
CCTTCTGGTGGGCGGTAGTCACCATGACTACAGTTGGCTATGGAGACATG
GCACCCGTCACTGTGGGTGGCAAGATAGTGGGCTCTCTGTGTGCCATTGC
GGGCGTGCTGACTATTTCCCTGCCAGTGCCCGTCATTGTCTCCAATTTCA
GCTACTTTTATCACCGGGAGACAGAGGGCGAAGAGGCTGGGATGTTCAGC
CATGTGGACACGCAGCCTTGTGGCCCACTGGAGGGCAAGGCCAATGGGGG
GCTGGTGGACGGGGAGGTACCTGAGCTACCACCTCCACTCTGGGCACCCC
CAGGGAAACACCTGGTCACCGAAGTGTGAGGAACAGTTGAGGTCTGCAGG
ACCTCACACCTCCCTAGAGGGAGGGAGGGAGGGCAGGGTGGAGGGCAAGG
CTGGGGGGAGGGGATTGGGTTTAGGAAGAGCTAGGTTAAGTCATAACGAG
TGGGGAAACACTGAGTCTTGTTGGGTCTTGGGTTGTGTGGTTTGGTAGCT
CCTGTGGGTACCTCCTGAAGCAGCAGCGAATGGCAATGGGTTGTGTTGTG
TTAATGAAGACTCAATTGGTTCATATTACTCTGAGTTGTGCAAAGCTCAT
GGAGCCTTTTGGGGTAGTGTTGAGATAGGTTTGGTCGTATCATTTTGTGA
GTTTCCTAGGTCAGTGTTGGGTTTGGTTGGGTTGTGAGTCTGGGATAGTG
TGGTCCAGCTGCATTGTGTAGGATTCTGTGGTTTGGTGGGTCCCCTAGGG
CCATGTTGGGTCAAGTTAGATGGTCCCCCATGGCATTGTTGAGATCGAAT
GTGTGTGGTGTTAAGTTTCGTTGAGACATGGTGGAAATTGTGTAGCTCTG
TGATTCTTCCAGGGGCATGTTATTTTAGGTTCTGTGAACTTGCGAGTCAT
GTAGAAATGTGAAGAGTCCAGTGGTAGAATTTGAGCTTTCTAGGTCACAT
TGGGTTAAGTTTGTATGACCAAATGAATCTTGTAGGGTTCTGTTGGGCTT
AACTGTGTAGAGGTGTGTGGCTGGACATTTTTCGTGGCCACAGCGAGTTG
AGTTGTGTTGAATTGTACAACCATATGAGCCTTGTAAGGCCAGTTCAGTT
GGGTCATGCCACTGTTTGAGTCTCATAGGGCCATGCTGAATTGAGTTCCA
TTGAGTTGTGTCACTATGTGAGTCCTACAGGAAGTTGGGTTGAGTTGGAC
TGTGCGAACGAGTTCCATAGGGCCACATCGGGCTGTTTTGCATTTAGTGG
TAGCACCAGGACCCAAAGGAAATAGCAGTGGGGAAGCATCATGTATCTGG
GAGCATGCAGTGGCGAGGGCTCTGGGAGGTGTGCCGAGCTGGCTCCCCAG
CTCGCTGTAGGGGGCGGGACTGGATTCTGTATCCATGGGATTGGGTGTTC
ATCCAGAGGCGACTGGGTAAATTAGGAAGAGGTGGATGCTCCTCCTGTTT
ACCCCACATCCACTTCATTGTGCTGTTCACTCCCATTCTCCCCTACAGTT
TTATGCTCAGACATGGAGGTCAGAGCCACAAGGGAAAGGGGAGAGGGGGA
GAAAACTGTACTCTGTCCAGACATGATAGAGGGACAGAGCCAAAAGGATA
GAGAAAGAGACCCAGAAAAAGGAAGAGGTGGAAACCCAGAGAGACAGAGA
CCCAAAGGGAGAGAAACAGAGACTCAGGGAGAGGGAGACAATGACCTGGA
GGGTGGGGTATGGCAGAGACGCAGAAGAGAGGAACAGAAATCCAGAGTGG
GGAGACAGAGACCAAGAGCAGGGGATAGAAGCCGGGCGAAGTGGCCCATG
CCTGTAATCTCAGCACTCTGGGAGACCGAGGAAGGGGGATTGATTGAGGC
CAGGAGTTCAAGACCAGCCTGGGCAACATGGTGAGACCCCATCTCTACAA
AAAATACAAAAATTAGCTGAGTGTGGTGGCACATGCCTGTGATCCCAGCT
ACTCAGGAAGCTGAGGCAGAAAGATCCCTTGACCCTGAGAGGTAGAGGCT
GCATTGAGCCATGATTGCACCACTGCACTCCAGCCTGGGCAACAGAGGGA
GCCCCCGTCTCAACAAACAAACAAAAAGAGCCAGTGGGGGAGGGAGGGAC
AGAGACCCAGAGGGCAGCGTCAGACACCCAGAGTTGGAGACAGAACAACA
GAGTCTCAGGGAAAGAGAACCACAATAGAAAAAGGCAGAAAAGGCCGGGC
GCGGTGGCTCATGCCTGTAACCCCAGCACTTTGGGAGGCCGAGGTGGGCA
AATTACGAGGTCAGGAGATCCAGACCATCCTGGCTAACACGGTGAAACCC
CGTCTCTACTAAAAATACAAAAAAATTAGCCGGGTGCGGTGGCGGGCACC
TGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCATGAACCTG
GGAGGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCACTCCAGCCTG
GGCAGCAGAGCAACACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAA
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What are the Functional Properties Of Ion
Channels?
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Ways to study Ion Channels   Sequence
analysis Cloning and Mutation (Expression
Analysis) Structural Studies Biochemical
Studies Antibodies X-ray Crystallography
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gtgi14485555gbAAK63002.1AF315818_1
voltage-gated potassium channel KCNA7 Homo
sapiens MEPRCPPPCGCCERLVLNVAGLRFETRARTLGRFPDTLLGD
PARRGRFYDDARREYFFDRHRPSFDAVLY YYQSGGRLRRPAHVPLDVFL
EEVAFYGLGAAALARLREDEGCPVPPERPLPRRAFARQLWLLFEFPESSQ
AARVLAVVSVLVILVSIVVFCLETLPDFRDDRDGTGLAAAAAAGPFPAP
LNGSSQMPGNPPRLPFNDPFF VVETLCICWFSFELLVRLLVCPSKAIFF
KNVMNLIDFVAILPYFVALGTELARQRGVGQQAMSLAILRVI RLVRVFR
IFKLSRHSKGLQILGQTLRASMRELGLLIFFLFIGVVLFSSAVYFAEVDR
VDSHFTSIPESFW WAVVTMTTVGYGDMAPVTVGGKIVGSLCAIAGVLTI
SLPVPVIVSNFSYFYHRETEGEEAGMFSHVDMQP CGPLEGKANGGLVDG
EVPELPPPLWAPPGKHLVTEV
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Fig 6-10
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Fig 6-11
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Potassium Channel Amino Acid Comparison
130 140nn 150
160 170 180

RatKxx1 QLKTLAQFPNTLLGNPKKRMRYFDPLRNEYFFDR
NRPSFDAILYYYQSGGRLRRPVNVPL MouseK
QLKTLAQFPNTLLGNPKKRMRYFDPLRNEYFFDRNRPSFDAILYYYQSGG
RLRRPVNVPL XenopusK QLKTLAQFPSTLLGNPKKRMRYFDP
LRNEYFFDRNRPSFDAILYYYQSGGRLRRPVNVPL AplysiaK
QLKTLNQFPDTLLGNPQKRNRYYDPLRNEYFFDRNRPSFDAILYFYQSGG
RLRRPVNVPL DrosophilaK QLRTLNQFPDTLLGDPARRLRYFDP
LRNEYFFDRSRPSFDAILYYYQSGGRLRRPVNVPL HumanK
QLRTLSQFPETLLGDREKRMQFFDSMRNEYFFDRNRPSFDGILYYYQSGG
KIRRPANVPI .
.... Prim.cons
. QLKTLAQFP2TLLGNPKKRMRYFDPLRNEYFFDRNRPSFDAILYY
YQSGGRLRRPVNVPL   190
200 210 220 230 240

RatKxx1
DMFSEEIKFYELGEEAMEKFREDEGFIKEEERPLPEKEYQRQVWLLFEYP
ESSGPARVIA MouseK DMFSEEIKFYELGEEAMEKFREDEG
FIKEEERPLPEKEYQRQVWLLFEYPESSGPARVIA XenopusK
DMFSEEIKFYELGEEAMEKFREDEGFVKEEERPLPDKEFQRQVWLLFEFP
ESSGPARIIA AplysiaK DVFSEEIKFYELGENAFERYREDEG
FIKEEEKPLPQNEFQRRVWLLFEYPESSAAARLCA DrosophilaK
DVFSEEIKFYELGDQAINKFREDEGFIKEEERPLPDNEKQRKVWLLFEYP
ESSQAARVVA HumanK DIFADEISFYELGSEAMDQFREDEG
FIKDPETLLPTNDIHRQFWLLFEYPESSSAARAVA
..
. . Prim.cons.
DMFSEEIKFYELGEEAMEKFREDEGFIKEEERPLP22E2QRQVWLLFEYP
ESSG2ARVIA   250 260
270 280 290 300

RatKxx1 IVSVMVILISIVIFCLETLPELK
DDKDFTGTIH-RIDNTTVIYTSNIFTDPFFIVETLCI MouseK
IVSVMVILISIVIFCLETLPELKDDKDFTGTIH-RIDNTTVIYTSNIF
TDPFFIVETLCI XenopusK IISVMVILISIVIFCLETLPELK
DERIFS--R--RVNNSTVFYKSNIFTDPFFVVETLCI AplysiaK
IFSVVIILLSIVIFCLETLPQFKHYRVVNSTAN-DSKESIEEDDIPKF
NEPFFIIETCCI DrosophilaK IISVFVILLSIVIFCLETLPEFK
HYKVFNTTTN-GTK--IEEDEVPDITDPFFLIETLCI HumanK
VVSVLVVVISITIFCLETLPEFREDRELKVVRDPNLNMSKTVLSQTMF
TDPFFMVESTCI ...
. .. . . Prim.cons.
IVSVMVILISIVIFCLETLPE2KDD22F2GT22PRI3NSTV2YTSNIF
TDPFFIVETLCI
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Box 3.1
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Box 3.1
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Box. 3.3
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Fig 6-3
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Fig 6-3
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X-Ray Crystallography
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In-class Exercise
You have identified a new cDNA clone from the
human genome Project. You think it might code for
an ion channel. Describe the steps you would
take, and the characteristics you would look for
to determine if it was a voltage-gated potassium
channel using just a computer. How would you
test your hypothesis in the laboratory? What
would the data look like that would prove your
hypothesis
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Voltage Gated Ion Channels How are they
Gated? How are they Inactivated? How is their
specificity regulated?
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Fig 6-6
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Fig. 3.6
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S4 Domain Comparison
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Kandel Essentials of Neural Science and Behavior
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Fig. 6.11
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How would you test to see if S4 domains really
exist and work as described?
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How Is Ion Specificity Achieved?
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Effect of hydration on size and mobility of
cations
ion atomic weight crystal radius hydrated
radius mobility Li 6.9
0.60 Å 4.5 Å
4.0 Na 23.0 0.95
3.4 5.2 K
39.0 1.33 2.2
7.6

in an electric field
Na
K
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Fig 6-1
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How Is Inactivation Achieved?
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Fig 6-5