membrane structure prediction 1 cb1 tmh1 - rostlab · • makeup: oct 13, 2015 - morning/noon 2...

/00© Burkhard Rost

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title: Computational Biology 1 - Protein structure: Membrane structure prediction 1short title: cb1_tmh1

lecture: Protein Prediction 1 - Protein structure Computational Biology 1 - TUM Summer 2015

/00© Burkhard Rost

Videos: YouTube / www.rostlab.org THANKS : Tim Karl + Carlo Di Domenico Special lectures:

• TBA No lecture:

• 05/12 Student assembly (SVV) • 05/14 Ascension day • 05/26 Whitsun holiday • 06/04 Corpus Christi LAST lecture: Jul 7 Examen: Jul 9

• Makeup: Oct 13, 2015 - morning/noon

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CONTACT: Inga Weise [email protected]

Tim Karl

Tatyana Goldberg

Edda Kloppmann

Andrea Schaffer-

hans

Jonas Reeb

Carlo Di [email protected]

http://www.rostlab.org

mailto:[email protected]

mailto:[email protected]

/00© Burkhard Rost

1D: TM

transmembrane helix

prediction3

/00© Burkhard Rost

What to put around a cell?

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Roshni Nelson: Cell Membranes

© Roshni Nelson UT Southwestern Dallas http://www.roshninelson.com

http://utsouthwestern.edu/STARS - vimeo.com/31412291

http://www.roshninelson.com

http://gregs-educational.info

/00© Burkhard Rost

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Roshni Nelson: Phospholipids

© Roshni Nelson UT Southwestern Dallas http://www.roshninelson.com

http://utsouthwestern.edu/STARS - vimeo.com/31412291

http://www.roshninelson.com

http://gregs-educational.info

/00© Burkhard Rost K Rogers (2011) Britannica

Prokaryotic Cell Eukaryotic Cell (bacillus type)

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Cellular compartments

© Tatyana Goldberg (TUM Munich)

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Localization for drug targets

TM Bakheet and AJ Doig (2008) Bioinforma)cs

Membrane 57%

Cytoplasm 13%

Extra-cellular 13%

ER 7%

Nucleus 3%

Mito 2%

Other 2%

Microsome 2%

Pero 1%

Drug targets tend to be found in membranes, cytoplasm or are

extra-cellular!© Tatyana Goldberg (TUM Munich)

/00© Burkhard Rost

TMH (Transmembrane

helix) background

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1JB0Cyanobacterial Photosystem I

Jordan P, Krauss N

1E7PFumarate ReductaseLancaster CD, Michel

H

periplasm

cytoplasmCytoplasm (stromal side)

?

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1KFYQuinol Fumarate Reductase

Iverson TM, Rees DC1MSL

Mechanosensitive Ion ChannelMscL Homolog

Chang G, Rees DC

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2BCC Cytochrome bc1 Zhang Z, Kim S

1QCR Cytochrome bc1 complex from Bovine Heart Mitochondria Xia D, Diesenhofer J

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Transmembrane vs. membrane anchored/associated

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Membrane prediction

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HTM prediction wait for db growth ...

1993

1999

1996

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Topology for membrane helical proteins.

exex tratra -cy-cy toto pp ll aa smsm ii cc

ii nn tt rr aa -- cc yy tt oo pp ll aa ss mm ii ccin

protein Aprotein C

C-term

out

in

protein B

C-term

C-term

lipid membranebilayer

inside cytoplasm

outside cytoplasm

/00© Burkhard Rost

TMH prediction

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PHDsec “success” on Poly-Valine

HEADER LIPOPROTEIN(SURFACE FILM)COMPND PULMONARY SURFACTANT-ASSOCIATED POLYPEPTIDE C(SP-C)SOURCE PIG (SUS SCROFA)AUTHOR J.JOHANSSON,T.SZYPERSKI,T.CURSTEDT,K.WUTHRICH

AA LRIPCCPVNLKRLLVVVVVVVLVVVVTVGALLMGLOBS sec HHHHHHHHHHHHHHHHHHHHHHHHHPHD sec EEEEEEEEEEEEEEEEEEEEEEE

/00© Burkhard Rost

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How 2 separate outside/inside?

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Lipid bilayer

Wikipedia © http://en.wikipedia.org/wiki/Lipid_bilayer

https://www.uclaaccess.ucla.edu/uploads/image/faculty/134.jpg

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Example 1: GPCR*: signaling

* G-Protein Coupled Receptor


40% of all drugs target GPCRs


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Example 2: pumps and channels

Wikipedia © http://en.wikipedia.org/wiki/Potassium_channel

Shaker: voltage gated potassium channel

SB Long, EB Campbell & R Mackinnon (2005) Science 309: 897–903


/00© Burkhard Rost

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Example 3: cell fusion

J Rizo & TC Südhof (2002) Snares and munc18 in synaptic vesicle fusion. Nature Reviews Neuroscience 3, 641-653

http://www.nature.com/nrn/journal/v3/n8/full/nrn898.html

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Lipid bilayer: hydrophobic in inside



/00© Burkhard Rost

-+-

+ +++

-

-

--

----

- ++

++

+

+

HHHHH

H HH

HHH H H

H-

+

solvent

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Hydrophobic core of a protein

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protein Aprotein C

C-term

out

in

protein B

C-term

C-term


inside cytoplasm

outside cytoplasm

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Hydrophobic side chains

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Eisenberg hydrophobicity indexAA-3 AA-1 Eisenberg

Ile I 1.38Phe F 1.19Val V 1.08Leu L 1.06Trp W 0.81Met M 0.64Ala A 0.62Gly G 0.48Cys C 0.29Tyr Y 0.26Pro P 0.12Thr T -0.05Ser S -0.18His H -0.4Glu E -0.74Asn N -0.78Gln Q -0.85Asp D -0.9Lys K -1.5Arg R -2.53

David Eisenberg, UCLA © https://www.uclaaccess.ucla.edu/

uploads/image/faculty/134.jpg

D Eisenberg et al. (1984) J Mol Biol 179:125-42


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Pure hydrophobicity scaleshydrophobicity scales

-6.75

-4.50

-2.25

0.00

2.25

4.50

6.75

9.00

A R N D C Q E G H I L K M F P S T W Y VGES EISEN KYDO

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5 Hydrophobicity/tm/occupancy scaleshydrophobicity scales

0.00

0.25

0.50

0.75

1.00

A R N D C Q E G H I L K M F P S T W Y VGES EISEN KYDO OOI HEIJNE

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Many indices exist

K Tomii and M Kanehisa (1996) Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng 9:27-36: Fig. 2 (402 indices)

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PHDsec success on Poly-Valine



NLKRLLVVVVVVVLVVVVTVGALL h hhhhhhhhhhhhhh h hhhh: hydrophobic

/00© Burkhard Rost

Gunnar von Heijne • G von Heijne (1981) On the hydrophobic nature of signal sequences. Eur J

Biochem 116: 419-22. • G von Heijne (1981) Membrane proteins: the amino acid composition of

membrane-penetrating segments. Eur J Biochem 120: 275-8. • G von Heijne (1992) Membrane protein structure prediction. Hydrophobicity

analysis and the positive-inside rule. J Mol Biol 225: 487-94.

• I Nilsson & G von Heijne (1990) Fine-tuning the topology of a polytopic membrane protein: role of positively and negatively charged amino acids. Cell 62: 1135-41.

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Membrane protein prediction

Gunnar von HeijneStockholm Univ

Royal Swedish Academy of Sciences

©http://www.abo.fi/public/fi/media/6765/

heijne_von_gunnar_2.jpg

http://www.abo.fi/public/fi/media/6765/heijne_von_gunnar_2.jpg

/00© Burkhard Rost

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Identify hydrophobic regions

G von Heijne (1992) Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J Mol Biol 225: 487-94: Fig. 4

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protein Aprotein C

C-term

out

in

protein B

C-term

C-term


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G von Heijne (1986) The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology. EMBO J 5:3021-7Fig. 2

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Positive-inside rule

cytosolic loops

periplasmic loops

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protein Aprotein C

C-term

out

in

protein B

C-term

C-term


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Heijne rule: positive inside out

0.920.95

0.93

0.91 0.900.92

0.870.89

N-term C-term

5 30 6 5

outout

Eight bestHTM's

µ=0: 0 HTM

µ=2: 2 HTMµ=3: 3 HTM

µ=1: 1 HTM

Loop lengths

Charge:Number of R+Kin loops 1-4

final prediction:∆ =(5+1) - (2+3)>0=> first loop out lipid membrane bilayer

extra-cytoplasmic

intra-cytoplasmic

R+KΣ=2

R+KΣ =5

R+KΣ =3

R+KΣ=1

/00© Burkhard Rost

1. predict <H> 2. assign positive inside-out 3. choose threshold to optimize inside-out difference

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S Jayasinghe, K Hristova, SH White (2001) Energetics, stability, and prediction of transmembrane helices. J Mol Biol 12:927-34idea: optimize hydrophobicity scale for prediction

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Hydrophobicity-based

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PHDsec success on Poly-Valine



/00© Burkhard Rost

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HTM

nonHTM

outputlayer

inputlayer

hiddenlayer

20444

21+3""""""

percentage of each amino acid in proteinlength of protein (≤60, ≤120, ≤240, >240)distance: centre, N-term (≤40,≤30,≤20,≤10)distance: centre, C-term (≤40,≤30,≤20,≤10)

input global in sequence

input local in sequence

localalign-ment13

adjacentresidues

:::

AAA

AA.

LLL

LII

AAG

CCS

GVV

:::

globalstatist.wholeprotein

%AALength∆ N-term∆ C-term

A C L I G S V ins del cons

100 0 0 0 0 0 0 0 0 1.17

100 0 0 0 0 0 0 33 0 0.42

0 0 100 0 0 0 0 0 33 0.92

0 0 33 66 0 0 0 0 0 0.74

66 0 0 0 33 0 0 0 0 1.17

0 66 0 0 0 33 0 0 0 0.74

0 0 0 33 0 0 66 0 0 0.48

HTM

nonHTM

3+1""""""

20444

first levelsequence-to- structure

second levelstructure-to- structure

P H D ht m

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Dynamic programming on NN ‘energy’

1

01

0residue number

T

N

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PHDhtm

refine

0.920.95

0.93

0.91 0.900.92

0.870.89

N-term C-term

5 30 6 5

outout

Eight bestHTM's

µ=0: 0 HTM

µ=2: 2 HTMµ=3: 3 HTM

µ=1: 1 HTM

Loop lengths

Charge:Number of R+Kin loops 1-4

final prediction:∆ =(5+1) - (2+3)>0=> first loop out lipid membrane bilayer

extra-cytoplasmic

intra-cytoplasmic

R+KΣ=2

R+KΣ =5

R+KΣ =3

R+KΣ=1

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PHDhtm on Poly-Valine


AA LRIPCCPVNLKRLLVVVVVVVLVVVVTVGALLMGLOBS htm TTTTTTTTTTTTTTTTTTTTTTTTTPHD htm TTTTTTTTTTTTTTTTTTTTTTTT

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Membrane helix prediction: TMHMM

TMHMM: sketch

details: inside/outside loop

details: TM core

A Krogh, B Larsson, G von Heijne, EL Sonnhammer (2001) 305:567-80, Fig. 1

/00© Burkhard Rost

Gabor E Tusnady & Istvan Simon (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics 17:849-850.

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Membrane helix prediction: HMMTOP

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Prediction of membrane helicesQo

k: %

of p

rote

in w

ith al

l TM

H rig

ht

J Reeb & E Kloppmann unpublished

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Other problems unravelled by recent

structures

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Inventory of life: membrane proteins

0 5 10 15 20 25 30

A pernixA fulgidus

M jannaschiiM thermoautotrophicu

P abyssiP horikoshii

A aeolicusB subtilis

B burgdorferiC jejuni

C pneumoniaeC trachomatisD radiodurans

E coliH influenzae

H pyloriM genitalium

M pneumoniaeM tuberculosisN meningitidis

R prowazekiiS PCC6803T maritimaT pallidum

U urealyticum

S cerevisiaeC elegans

D melanogasterH sapiens (SP/TrEmbl

H sapiens(chr 22)

%mem

eukaryotes

bacteria

archaea

J Liu. & B Rost (2001) Prot. Sci. 10, 1970-1979.

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Kingdoms similar in length

J Liu. & B Rost (2001) Prot. Sci. 10, 1970-1979.B Rost (2002) Curr Op Struct Biol, 12, 409-416

eukaryotesbacteriaarchaea

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Kingdoms similar in amino acids usage

J Liu. & B Rost (2001) Prot Sci 10, 1970-1979.B Rost (2002) Curr Op Struct Biol, 12, 409-416

eukaryotes

bacteria

archaea

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010203040506070

0 20 40 60 80 100

yeastcaeeldromehumanhs22

01020304050607080

0 20 40 60 80 100

aerpearcfumetjamettmpyrabpyrho

0 20 40 60 80 100

Number of proteins in familyJ Liu & B Rost 2001 Prot Science 10, 1970-79 55

Family sizes similar

01020304050607080

0 20 40 60 80 100

aquaebacsuborbucamjechlpnchltrdeiraecolihaeinhelpymycgemycpnmyctuneimericprsyny3thematrepaureur

0 20 40 60 80 100

eukaryotes

Cum

ulat

ive

perc

enta

ge o

f pro

tein

s

bacteria

archaea

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Inventory of life: membrane proteins

0 5 10 15 20 25 30

A pernixA fulgidus






E coliH influenzae




U urealyticum

S cerevisiaeC elegans

D melanogasterH sapiens (SP/TrEmbl

H sapiens(chr 22)

%mem

eukaryotes

bacteria

archaea


2013 note: some issues with data (incomplete sequences?)e.g. human has more than 18%

/00© Burkhard Rost

Number of transmembrane helices

Cum

ulat

ive

perc

enta

ge o

f mem

bran

e pr

otei

ns

0

20

40

60

80

100

0 5 10 15 20

ArchaeaProkaryoteEukaryote

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More TM -> more complexity?


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Membraneproteins:

0

10

20

30

40 aerpe bacsu yeast

0

10

20

30

40 arcfu camje caeel

0

10

20

30

40 metja ecoli drome

0

10

20

30

40

1 3 5 7 9 11 13 15 17

pyrho haein human

inout

1 3 5 7 9 11 13 15 17 1 3 5 7 9 11 13 15 17


/00© Burkhard Rost

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Length of globular regions in membrane proteins

IntracellularExtracellular

Length of globular regions in membrane proteins

Perc

enta

ge o

f glo

bula

r reg

ions

10

20

30

40

50

10

20

30

40

50

0

10

20

30

40

50

100 200 300 400 500 600 100 200 300 400 500 600 700

Aeropyrum pernix K1

Caenorhabditiselegans

Bacillussubtilis

Drosophilamelangoster

Archaeoglobus fulgidus

Escherichiacoli


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Inventory of life: coiled-coil proteins

0 5 10 15 20 25 30

A pernixA fulgidus






E coliH influenzae




U urealyticumS cerevisiae

C elegansD melanogaster

H sapiens (SP/TrEmblH sapiens(chr 22)

%mem

0 2 4 6 8 10 12

%coils


eukaryotes

bacteria

archaea

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Inventory of life: compartments

5 10 15 20 25

% extra-cellular

0 5 10 15 20 25 30

A pernixA fulgidus






E coliH influenzae




U urealyticumS cerevisiae

C elegansD melanogaster

H sapiens (SP/TrEmblH sapiens(chr 22)

% membrane

5 10 15 20

% nuclear

J Liu. & B Rost (2001) Prot. Sci. 10, 1970-1979.B Rost (2002) Curr Op Struct Biol, 12, 409-416

euka

ry

otes

bact

eria

arch

aea

/00© Burkhard Rost

statistics for PDB in June 2010:67,086 structures in PDB (June 2010) 1,197 transmembrane 1,014 alpha helical 179 beta barrel

-> < 2% BUT: >20% of all proteins!

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TMH proteins: reminders

GE Tusnady, ZS Dosztanyi & I Simon (2005) Bioinformatics 21:1276-7

/00© Burkhard Rost

statistics for PDB in June 2010:67,086 structures in PDB (June 2010) 246 unique* transmembrane

-> < way less than 2% BUT: >20% of all proteins!

• * unique=non-identical sequence (can have PIDE>99.5%!)

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S Jayasinghe, K Hristova, SH White (2001) Protein Sci 10:455-8

/00© Burkhard Rost

Edda Kloppmann & Marco Punta: 1,035 PDB unique TM structures (Jan 2012)-> 107 Pfam families

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E Kloppmann, M Punta & B Rost (2012) Curr Op Struct Biol 22:326-32

/00© Burkhard Rost

78 interface helices ~50% of chains contain interface helix Average length ~ 9 aa Longest is 19 aa Most frequent in photosynthetic reaction center

E Granseth, G von Heijne & A Elofsson (2005) J Mol Biol 346:377-85

© Arne Elofsson (Stockholm Univ) 67

Interface helices (Granseth, JMB 2005)

/00© Burkhard Rost

36 reentrant helices • 20 in new classification 24% contain reentry 72% on the outside Length 3-32 residues Loops 11-117 residues

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Reentry regions

H Viklund, E Granseth & A Elofsson (2006) J Mol Biol 361:591-603

© Arne Elofsson (Stockholm Univ)

/00© Burkhard Rost

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36 reentry regions in 3 classes

Helix-coil/Coil-helix

Helix-coil-helix Coil

H Viklund, E Granseth & A Elofsson (2006) J Mol Biol 361:591-603© Arne Elofsson (Stockholm Univ)

/00© Burkhard Rost

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Predict re-entry regions

H Viklund, E Granseth & A Elofsson (2006) J Mol Biol 361:591-603: Fig. 5

/00© Burkhard Rost

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Rentry predicted in entire genomes



0.280.720.24079Observed in dataset

0.520.480.167773E. coli0.400.600.10757S. cerevisiae

0.540.460.154181H. sapiens

Reentrants in

Reentrants out

Reentrant fraction

ProteinsGenome

0.310.220.110.07FractionChannels

Active transporters

Electron transporters

Signal receptors

/00© Burkhard Rost

Membrane protein structures are complex • TM-helices ends at different locations • Different angles • Neighboring helices often interact • Interface helices • reentrant regions No sheets close to the membrane

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The not so simple TM proteins



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More complex structures need new prediction methods

Nout

Cin

C

N

cytoplasm

periplasm

Membrane



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The Z-coordinate

Z-coordinate: distance residue 2 membrane center

Z

0

15

-15

Periplasm

Cytoplasm

H Viklund, E Granseth & A Elofsson (2006) J Mol Biol 361:591-603 © Arne Elofsson (Stockholm Univ)

/00© Burkhard Rost

01: 04/14 Tue: no lecture 02: 04/16 Thu: no lecture 03: 04/21 Tue: Organization of lecture: intro into cells & biology 04: 04/23 Thu: Intro I - acids/structure 05: 04/28 Tue: Intro 2 - domains/3D comparisons 06: 04/30 Thu: Alignment 1 07: 05/05 Tue: Alignment 2 08: 05/07 Thu: Comparative modeling 1 09: 05/12 Tue: SKIP: student assembly (SVV) 10: 05/14 Thu: SKIP: Ascension Day 11: 05/19 Tue: Experimental structure determination/Secondary structure assignment 12: 05/21 Thu: 1D: Secondary structure prediction 1 13: 05/26 Tue: SKIP: Whitsun holiday (05/23-26) 14: 05/28 Thu: 1D: Secondary structure prediction 2 15: 06/02 Tue: 1D: Secondary structure prediction 3 / Transmembrane structure prediction 1 16: 06/04 Thu: SKIP: Corpus Christi 17: 06/09 Tue: 1D: Transmembrane structure prediction 2 18: 06/11 Thu: 1D: Transmembrane structure prediction 3 - Jonas 19: 06/16 Tue: 1D: Solvent accessibility prediction 20: 06/18 Thu: 1D: Disorder prediction 21: 06/23 Tue: 2D prediction 1 22: 06/25 Thu: 2D prediction 2 23: 06/30 Tue: 3D prediction 1 24: 07/02 Thu: Nobel prize symposium 25: 07/07 Tue: wrap up 26: 07/09 Thu: examen, no lecture 27: 07/14 Tue: examen, no lecture 28: 07/16 Thu: examen alternative, no lecture

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Lecture plan (CB1 structure)

membrane structure prediction 1 cb1 tmh1 - rostlab · • makeup: oct 13, 2015 - morning/noon 2...

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