membrane structure prediction 1 cb1 tmh1 - rostlab€¦ · /78 © burkhard rost phdsec h l e 4+1...

/77© Burkhard Rost

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title: Membrane structure prediction 1short title: cb1_tmh1

lecture: Computational Biology 1 - Protein structure (for Informatics) - TUM summer semester

/00© Burkhard Rost

Videos: YouTube / www.rostlab.org/talks THANKS :. EXERCISES: Special lectures: • Mikal Boden UQ Brisbane No lecture: • 04/26 Security check Rostlab (exercise WILL be) • 05/01 May Day (also no exercise) • 05/08 Student representation (SVV) - exercise WILL happen • 05/10 Ascension Day (also no exercise) • 05/22 Whitsun holiday (also no exercise) • 05/31 Corpus Christi (also no exercise) • 06/19 no lecture (but exercise) • 06/21 no lecture (but exercise) LAST lecture: bef: Jul 12 Examen: Jul 12 18-20:00 (room TBA) • Makeup: no makeup (sorry due to overload)

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Announcements

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Your Name

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CONTACT: [email protected]© Michael Leunig

http://www.rostlab.org

mailto:[email protected]

© Burkhard Rost

1D: TM

transmembrane helix

prediction�3

© Burkhard Rost

Intro: membranes

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© Burkhard Rost /77

What to put around a cell?

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/78© Burkhard Rost

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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

/78© 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

/78© Burkhard Rost K Rogers (2011) Britannica

Prokaryotic Cell Eukaryotic Cell(bacillus type)

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Cellular compartments

© Tatyana Goldberg (TUM Munich)

/78© Burkhard Rost

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How 2 separate outside/inside?

/78© Burkhard Rost

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Lipid bilayer

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

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

/78© Burkhard Rost

-+-

+ +++

-

-

--

----

- ++

++

+

+

HHHHH

H HH

HHH H H

H-

+

solvent

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Hydrophobic core of a protein

/78© Burkhard Rost

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Lipid bilayer: hydrophobic in inside

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

/78© Burkhard Rost

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Lipid bilayer: hydrophobic in insideeasy to pull aroundhorizontally


/78© Burkhard Rost

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Lipid bilayer: hydrophobic in insidehard to enter


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Bacterial injection needles

Model of type VI secretion system (TSS6) in gram-negative bacteria

Marek Basler Biozentrum Basel

/78© Burkhard Rost

�16Borenstein DB, Ringel P, Basler M, Wingreen NS (2015) Established Microbial Colonies Can Survive Type VI Secretion Assault. PLoS Comput Biol 11(10): e1004520. doi:10.1371/

Shot through two membranes

Marek Basler

Biozentrum Basel

/78© Burkhard Rost

�17Marek Basler, BT Ho, JJ Mekalanos (2013) Cell 152:884-894

Tit-for-tat: type 6 secretion system counter-attack

Marek Basler

Biozentrum Basel

/78© Burkhard Rost

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Localization for drug targets

TMBakheetandAJDoig(2008)Bioinforma)cs

Membrane57 %

Cytoplasm13 %

Extra-cellular13 %

ER7 %

Nucleus3 %

Mito2 %

Other2 %

Microsome2 %

Pero1 %

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

extra-cellular!© Tatyana Goldberg (TUM Munich)

© Burkhard Rost

TMH (Transmembrane

helix) background

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/77© Burkhard Rost

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/77© Burkhard Rost

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1JB0Cyanobacterial Photosystem I

Jordan P, Krauss N

1E7PFumarate ReductaseLancaster CD, Michel

H

periplasm

cytoplasmCytoplasm (stromal side)

?

/78© Burkhard Rost

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Membrane prediction

/78© Burkhard Rost

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TM prediction wait for db growth ...

1993

1999

1996

/78© Burkhard Rost

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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

© Burkhard Rost

TMH prediction

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/78© Burkhard Rost

P H D s e c

H

L

E

4+1""""""

20444

outputlayer

inputlayer

hiddenlayer

20444

21+3""""""

H

L

E

0.5

0.1

0.4percentage 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

:::AAAAA.LLLLIIAAGCCSGVV:::

globalstatist.wholeprotein

%AALength∆ N-term∆ C-term

A C L I G S V ins del cons100 0 0 0 0 0 0 0 0 1.17100 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

first levelsequence-to- structure

second levelstructure-to- structure

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Membrane helices are helices, right?

B Rost (1996) Methods Enzymol 266:525-39

/78© Burkhard Rost

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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

/78© Burkhard Rost

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Goes wrong because swap: outside/inside

Protein

Membrane

H=hydrophobic

LIPID

H

HHHH

H

HH H H

H

HProtein

non-membrane(globular water-soluble)

H=hydrophobicL= hydrophilic

Water

H

LL

HL L

HH

HL L L

L

LL

/78© Burkhard Rost

-+-

+ +++

-

-

--

----

- ++

++

+

+

HHHHH

H HH

HHH H H

H-

+

solvent

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Hydrophobic core of a protein

/78© Burkhard Rost

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protein Aprotein C

C-term

out

in

protein B

C-term

C-term


inside cytoplasm

outside cytoplasm

/78© Burkhard Rost

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Hydrophobic side chains

/78© Burkhard Rost

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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



/78© Burkhard Rost

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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

/78© Burkhard Rost

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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

/78© Burkhard Rost

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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)

/78© Burkhard Rost

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PHDsec success on Poly-Valine



NLKRLLVVVVVVVLVVVVTVGALL h hhhhhhhhhhhhhh h hhhh: hydrophobic

/78© 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

/78© Burkhard Rost

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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 5:3021-7 Fig. 2

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Positive-inside rule

cytosolic loops

periplasmic loops

/78© Burkhard Rost

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protein Aprotein C

C-term

out

in

protein B

C-term

C-term


/78© Burkhard Rost

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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

/77© Burkhard Rost

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

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

Identify hydrophobic regions

/77© Burkhard Rost

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

/78© Burkhard Rost

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PHDsec success on Poly-Valine



/77© 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

:::AAAAA.LLLLIIAAGCCSGVV:::

globalstatist.wholeprotein

%AALength∆ N-term∆ C-term

A C L I G S V ins del cons100 0 0 0 0 0 0 0 0 1.17100 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

/78© Burkhard Rost

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Dynamic programming on NN ‘energy’

1

01

0residue number

T

N

/78© Burkhard Rost

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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

/78© Burkhard Rost

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PHDhtm on Poly-Valine


AA LRIPCCPVNLKRLLVVVVVVVLVVVVTVGALLMGLOBS htm TTTTTTTTTTTTTTTTTTTTTTTTTPHD htm TTTTTTTTTTTTTTTTTTTTTTTT

/78© Burkhard Rost

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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

/77© 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

/78© Burkhard Rost

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TMHs (helices) correctly predicted?

C-P Chen, A Kernytsky & B Rost 2002 Protein Science 11, 2774-91

Observed Helix 1 (O1) O2 O3

Predicted Helix 1 (P1) P2 P3

/78© Burkhard Rost

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TMHs (helices) correctly predicted: if at most ±5 residues overlap

C-P Chen, A Kernytsky & B Rost 2002 Protein Science 11, 2774-91

Observed Helix 1 (O1) O2 O3

Predicted Helix 1 (P1) P2 P3

here=0

/78© Burkhard Rost

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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, M Bernhofer & B Rost (2015) Proteins 83:473-84

/78© Burkhard Rost

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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

/78© Burkhard Rost

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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

/78© Burkhard Rost

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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.

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

/78© Burkhard Rost

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Inventory of life: coiled-coil 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 urealyticumS cerevisiae

C elegansD melanogaster

H sapiens (SP/TrEmblH sapiens(chr 22)

%mem

0 2 4 6 8 10 12

%coils

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

eukaryotes

bacteria

archaea

/77© 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

/77© 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

/77© 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

/77© 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) �63

Interface helices (Granseth, JMB 2005)

/77© 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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Re-entry regions

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

© Arne Elofsson (Stockholm Univ)

/78© 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)

/78© 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

/78© Burkhard Rost

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Re-entry 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

/77© 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



/78© Burkhard Rost

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More complex structures need new prediction methodsNout

Cin

C

N

cytoplasm

periplasm

Membrane



/78© Burkhard Rost

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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: 04/10 Tue: No lecture 02: 04/12 Thu: No lecture 03: 04/17 Tue: No lecture 04: 04/19 Thu: Intro 1: organization of lecture: intro into cells & biology 05: 04/24 Tue: Intro 2: amino acids, protein structure (comparison), domains 06: 04/26 Thu: No lecture 07: 05/01 Tue: SKIP: May Day 08: 05/03 Thu: Alignment 1 09: 05/08 Tue: SKIP: Student Representation (SVV) 10: 05/10 Thu: SKIP: Ascension Day 11: 05/15 Tue: Alignment 2 12: 05/17 Thu: Comparative modeling & exp structure determination & secondary structure assignment 13: 05/22 Tue: SKIP: Whitsun holiday 14: 05/24 Thu: Comparative modeling 2 & 1D: Secondary structure prediction 1 15: 05/29 Tue: 1D: Secondary structure prediction 2 16: 05/31 Thu: SKIP: Corpus Christi 17: 06/05 Tue: 1D: Secondary structure prediction 3 18: 06/07 Thu: 1D: Transmembrane structure prediction 1 19: 06/12 Tue: 1D: Transmembrane structure prediction 2 / Solvent accessibility prediction 20: 06/14 Thu: 1D: Disorder prediction; 2D prediction / 3D prediction 21: 06/19 Tue: No lecture (but exercises) 22: 06/21 Thu: No lecture (but exercises) 23: 06/26 Tue: recap 1 24: 06/28 Thu: recap 2 25: 07/03 Tue: TBA 26: 07/05 Thu: TBA 27: 07/10 Tue: TBA 28: 07/12 Thu: TBA

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Lecture plan (CB1 structure: INF)

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membrane structure prediction 1 cb1 tmh1 - rostlab€¦ · /78 © burkhard rost phdsec h l e 4+1...

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