Protein structure determination cb1 3dexp lecture: Protein ... · Experiments determine protein...

© Burkhard Rost (TUM Munich) /701

title: Protein structure determinationshort title: cb1_3dexp

lecture: Protein Prediction 1 - Protein structure Computational Biology 1 TUM summer 2014

Monday May 19, 2014


Announcements

Videos: YouTube / www.rostlab.orgTHANKS : Tim Karl + Jonas ReebSpecial lectures:• Apr 15 - Andrea Schafferhans

No lecture:• Apr 17/22 Easter• May 01 Thu May day• May 06 Tue Student assembly• May 29 Thu Ascension day• Jun 03 Tue no room• Jun 10 Tue Whitsun holidays• Jun 19 Thu Corpus Christi

LAST lecture: July 1Examen: July 8 • Makeup: Oct 21 - morning

CONTACT: Lothar Richter [email protected]

2

TimKarl

LotharRichter

JonasReeb

Monday May 19, 2014

http://www.rostlab.org

http://www.rostlab.org

mailto:[email protected]

mailto:[email protected]


Recap: 3D prediction by

comparative modeling

3Monday May 19, 2014


Zones

4

Day

light

Zon

e

Twili

ght Z

one

Mid

nigh

t Zon

eprofile - profile

sequence - profilesequence - sequence

sequ

ence

sim

ilar

->st

ruct

ure s

imila

r

B Rost (1997) Fold Des 2:S19-24B Rost (1999) Protein Eng 12:85-94

Monday May 19, 2014


human - fly - bacteria

5

3gft: Y Tong et al. & H Park (unpublished) / 4IW3: JS Scotti (unpublished)3lbn: G Buhrman et al. & C Mattos (2010) PNAS 107:4931-6.2y8e: M Walden, HT Jenkins, TA Edwards (2011) Acta Crystallogr F 67:744

green: 3gft K-Ras - humanlime: 3lbn Rash - humanorange: 2y8e Rab6 - flypurple: 2y8e hydroxylase P putida

AndreaSchaffer-

hans

Slide from:

PIDE: pairwise identical residues

19%

Monday May 19, 2014


Comparative modeling methods

6

MODELLERlots of whistles and bells, downloadable, very accurate

SWISS-MODELautomated, increasingly comprehensive and flexible

Monday May 19, 2014


Comparative modeling applicable to about 1/3 of all proteins



Comparative modeling 2



Goal of structure prediction

Epstein & Anfinsen, 1961: sequence uniquely determines structure

• INPUT: sequence

3D structureand function

• OUTPUT:

Monday May 19, 2014


protein folding from first principles should then be

possible10

Monday May 19, 2014


Protein structure prediction problem solved!

60s - Washington Post

70s - New York Times

90s - Washington Post

11

Problem: predict the 3D structure of a protein from sequence alone

Monday May 19, 2014


How would you assess prediction performance?



??

???

How to get those into the prediction?

Monday May 19, 2014


CASP

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Critical Assessment of Structure PredictionApril-May (Organizers): collect experimental structures (since 2004 from structural genomics)June-August: Prediction seasondeadline: predictions in before experimental structures are publishedSeptember-November: Assessors divineDecember: Meeting to discuss results

Monday May 19, 2014


CASP

Protein Structure Prediction

© Burkhard Rost (Columbia New York)

Monday May 19, 2014


CASP


Only homology modeling good


Monday May 19, 2014


CASP


Only homology modeling goodNo general prediction of 3D from sequence, yet


Monday May 19, 2014


CASP


Only homology modeling goodNo general prediction of 3D from sequence, yetImportant improvements in many fields!


Monday May 19, 2014


Servers, META-servers, META-META, …

Monday May 19, 2014


CASP 9 results

TBM • overall good

17A Kryshtafovych et al. 2011 Proteins, 79 Suppl 10:196-207

Monday May 19, 2014


Problems with CASP



Problems of CASP

Comparisons based on apples and orangesAnalysis of irrelevant types of test casesInappropriate rankingConclusions based on insignificant differencesDifferent categories evaluated differentlytoo few targets



Ranking not stable!

29 different worse than 11 identical

VA Eyrich, IYY Koh, D Przybylski, O Graña, F Pazos, A Valencia and B Rost (2003) Proteins 53 Suppl 6 548-60


Monday May 19, 2014


Pairwise comparison matrix


Monday May 19, 2014


Conclusion: Comparative modeling

Comparative modeling/homology modeling most accurate way to predict structureas good and as complete as the templateè depends on quality and similarity of templatemostly driven by accuracy of alignmentè driven by alignment qualityloop modeling: still not fully there, yetside chain modeling: unclear how well we do

Monday May 19, 2014


3D from experiment 2 co-ordinates



3D details - 3D cartoon

Monday May 19, 2014


Structure by experiment



Experiments determine protein structure

26

Number Percentage

PDB 84,413 1Xray 75,068 89NMR 8,723 10EMElectronMicroscopy 428 1

PDB (Protein Data Bank) Helen Berman (Rutgers Univ, New Brunswick) &

Phil Bourne (UCSD San Diego)

Monday May 19, 2014


Protein structure by X-ray crystallography

27

Number Percentage

PDB 84,413 1

Xray 75,068 89

NMR 8,723 10

EMElectronMicroscopy

428 1

© Wikipedia

Myoglobin structure * JC Kendrew, G Bodo, HM Dintzis, RG Parrish, H Wyckoff & DC Phillips (1958) Nature 181:662-6* THIS 1mbo: SE Philips JMB 142:531-54(image Wikipedia Aza Toth)(Hemoglobin: Max Perutz 1959)

Monday May 19, 2014


Protein structure by NMR* spectroscopy

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© Wikipedia

Number Percentage

PDB 84,413 1

Xray 75,068 89

NMR 8,723 10


428 1

* NMR: Nuclear Magnetic Resonance

NMR tube

Monday May 19, 2014


Protein structure by NMR* spectroscopy

29

© Wikipedia

900 MHz NMR machine

1ssu: Y Kamikubo et al. & HJ Dyson (2004) Biochemistry 43:6519-34

Number Percentage

PDB 84,413 1

Xray 75,068 89

NMR 8,723 10


428 1

* NMR: Nuclear Magnetic Resonance

NYSBC - City College New

York City

Monday May 19, 2014


Protein structure by cryo-EM

30

© Wikipedia

Number Percentage

PDB 84,413 1

Xray 75,068 89

NMR 8,723 10


428 1

* EM: Cryo-Electron Microscopy

4 Ångstrøm 8Å 16Å 32ÅGroEL - J Wang & DC Bosvert (2004) 1j4zImages: Vossman 2007 - Wikipedia

Monday May 19, 2014


Protein structure by cryo-EM

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Number Percentage

PDB 84,413 1

Xray 75,068 89

NMR 8,723 10


428 1

* EM: Cryo-Electron Microscopy

T Ju, M Baker, W Chiu (2006) Computer-Aided Design 39:352-60

Monday May 19, 2014


Structure resolution

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© PDB

Monday May 19, 2014


Notation: protein structure 1D, 2D, 3DPQITLWQRPLVTIKIGGQLKEALLDTGADDTVL

PP PQQQYFFQVISSIVRLLSTLWWQEDRKQAKRRRPQPPPPPVVTKFVVLIITTKEKAALIVHYKKFIILVIEENGGGGGTGQQKRRPPLWWVVFKVEESKKVVGLGLLILLLLLVVDDDDDTTTTTGGGGGAAAAADDDDDDDAKESSTTVIIVIVVVIVL

1281757077

120238169200247114740

904

466268

11831

1241

292449726217

102691

140

1109760691481976248590

690

730

415371597395000

5851300

79586900

EEEEE

EEEEEE

EEEEEEE

EE

EEEEE

EEEEEE

EE

kcal/mol0 -1 -2 -3 -4 -5

1 10 20 30 40 50 60 70 80 90

1

10

20

30

40

50

60

70

80

90

1D1D 2D2D 3D3D



Secondary structure stabilized by

hydrogen bonds

Monday May 19, 2014


Linus Pauling: introduce conceptL Pauling and RB Corey (1951) Configurations of Polypeptide Chains with Favored Orientations Around Single Bonds: Two New Pleated Sheets PNAS 37: 729-40L Pauling, RB Corey and HR Branson (1951) The Structure of Proteins: Two Hydrogen-bonded Helical Configurations of the Polypeptide Chain PNAS 37: 205-34L Pauling, RB Corey and HR Branson (1951) Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain PNAS 37: 205-11L Pauling and RB Corey (1953) Two Rippled-sheet Configurations of Polypeptide Chains, and a Note About the Pleated Sheets PNAS 39: 253-6L Pauling and RB Corey (1953) Two Pleated-sheet Configurations of Polypeptide Chains Involving Both cis and trans Amide Groups PNAS 39: 247-52

35

Linus Pauling

Nobel Foundation: The Nobel Prize in Chemistry 1954 was awarded to Linus Pauling "for his research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances”.http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1954/

Monday May 19, 2014

http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1954/

http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1954/


Hydrogen-bond formation

36© Wikipedia

http://www.ausetute.com.au/proteins.html

strandhelix

Monday May 19, 2014





Monday May 19, 2014


Pauling Nobel Prize 1954 -

first protein structure when?



First protein structures

40

John Kendrew Max Perutz

myoglobin

JC Kendrew et al. & DC Phillips (Mar 1958) Nature 181: 662–6.

hemoglobin

MF Perutz et al. & AC North (1960) Nature 185: 416-22.

Monday May 19, 2014


Secondary structure assignment

Different evaluation criteria applied:

Assignment coverage: DEFINEGeometry (fitting ideal sec str segments)FM Richards & CE Kundrot (1988) Proteins 3:71-84

Enthalpic energy: DSSPW Kabsch & C Sander (1983) Biopolymers 22:2577-637

Monday May 19, 2014


DSSPDictionary of

Secondary Structure of Proteins



Secondary Structure Assignment: DSSP

Dictionary of protein Secondary Structure for Proteins

43

Wolfgang Kabsch & Chris Sander (1983) Biopolymers 22:2577-637

Wolfgang KabschChris Sander

Monday May 19, 2014


DSSP: W Kabsch & C Sander (1983) Biopolymers 22: 2577-2637

DSSP: Coulomb



L Pauling & RB Corey (1953) PNAS 39:247-252L Pauling, RB Corey & HR Branson (1951) PNAS 37:205-234W Kabsch & C Sander (1983) Biopolymers 22:2577-2637

DSSP

Pauling’s H-bond pattern used in DSSP




DSSP




DSSP assigns 7 “states”

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H -> helix (i,i+4) helix HG -> 310 helix (i,i+3) helix HT -> turn of helix other LE -> extended/strand strand EB -> beta-bulge strand ES -> bend (no H-bond) other L“ “ -> loop other L

7 DSSP states 3 state map

Monday May 19, 2014


Secondary structure assignment

Different evaluation criteria applied:

Assignment coverage: DEFINEGeometry (fitting ideal sec str segments)FM Richards & CE Kundrot (1988) Proteins 3:71-84

Enthalpic energy: DSSPW Kabsch & C Sander (1983) Biopolymers 22:2577-637 Expert assignment: STRIDED Frishman & P Argos (1995) Proteins 23:566-79

Predictability: NNass

Monday May 19, 2014


1D: secondarystructureprediction



Notation: protein structure 1D, 2D, 3DPQITLWQRPLVTIKIGGQLKEALLDTGADDTVL

PP PQQQYFFQVISSIVRLLSTLWWQEDRKQAKRRRPQPPPPPVVTKFVVLIITTKEKAALIVHYKKFIILVIEENGGGGGTGQQKRRPPLWWVVFKVEESKKVVGLGLLILLLLLVVDDDDDTTTTTGGGGGAAAAADDDDDDDAKESSTTVIIVIVVVIVL

1281757077

120238169200247114740

904

466268

11831

1241

292449726217

102691

140

1109760691481976248590

690

730

415371597395000

5851300

79586900

EEEEE

EEEEEE

EEEEEEE

EE

EEEEE

EEEEEE

EE

kcal/mol0 -1 -2 -3 -4 -5

1 10 20 30 40 50 60 70 80 90

1

10

20

30

40

50

60

70

80

90

1D1D 2D2D 3D3D



Words

52

Secondary structure prediction2ndary structure prediction2D prediction

Monday May 19, 2014


Close Homology (Sequence Id. > 60% Psi-Blast Eval < 10-20)

Distant Homology (Domain, Motif)

Machine Learning (NN, SVM)

Protein Space:

X=Positive Y=Negative

Protein function classification

© Kaz Wrzeszczynski: Thesis

W

Monday May 19, 2014


Coverage of structure space

Monday May 19, 2014


Secondary structure prediction

55

DSSP secondary assignment has 8 “states”

H = HelixG = 310 helixI = Pi helixE = Extended (strand)B = beta-bridge, single strand residueT = Turn, i.e. one turn of helixS = bent“ “ = loop

Monday May 19, 2014


Goal of secondary structure prediction

LEDKSPDHNPTGID

AKGKPMDRNFTGRNHPPKDSS

AAQVKDALTK

LEQWGTLAQLRAIWEQELTDFPEFLTMMARQETWLGWLTI

helix strand

loop

LAVIGVLMKW

FVFLMIEKIYHKLT

DIRVGLTYYIAQ

VNTFVGTFAAVAHAL

56W Kabsch & C Sander (1985) Identical pentapetides with different backbones. Nature 317:207

Monday May 19, 2014


??

???

How pentapeptides occur in 2 states?

Monday May 19, 2014


Secondary structure prediction methods

58

L Pauling, RB Corey and HR Branson (1951) Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain. PNAS 37:205-211.L Pauling, RB Corey and HR Branson (1951) The Structure of Proteins: Two Hydrogen-bonded Helical Configurations of the Polypeptide Chain. PNAS 37:205-234.AG Szent-Györgyi & C Cohen (1957) Role of proline in polypeptide chain configuration of proteins. Science 126:697.some are more equal than others ...

Monday May 19, 2014


Sec str pred methods: single residues

59

Pauling, RB Corey and HR Branson (1951) Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain. PNAS 37:205-211.L Pauling, RB Corey and HR Branson (1951) The Structure of Proteins: Two Hydrogen-bonded Helical Configurations of the Polypeptide Chain. PNAS 37:205-234.AG Szent-Györgyi & C Cohen (1957) Role of proline in polypeptide chain configuration of proteins. Science 126:697.MF Perutz, MG Rossmann, AF Cullis, G Muirhead, G Will and AT North (1960) Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5 Å resolution, obtained by X-ray analysis. Nature 185:416-422.JC Kendrew, RE Dickerson, BE Strandberg, RJ Hart, DR Davies and DC Phillips (1960) Structure of myoglobin: a three-dimensional Fourier synthesis at 2 Å resolution. Nature 185:422-427.

Monday May 19, 2014


Simple prediction: frequency

First step (Szent-Györgyi)Proline breaks a helixHelices span several turns, i.e. >4 residues-> identify helices/non-helices

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Proline bends main chain

Monday May 19, 2014



First step (Szent-Györgyi)Proline breaks a helixHelices span several turns, i.e. >4 residues-> identify helices/non-helices

from Proline to odds for all ....




from Proline to odds for all

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....,....1....,....2....QEKSPREVTMKKGDILTLLNSTNK E..E EEEEEE

AA D E G I K L M N P Q R S T V

E 1 1 3 1 1 1

L 1 1 1 4 1 1 1 1 2 1

Monday May 19, 2014



63

single residues (1. generation)• Chou-Fasman, GOR 1957-70/80

Robson B & Pain RH (1971) Analysis of the Code Relating Sequence to Conformation in Proteins: Possible Implications for the Mechanism of Formation of Helical Regions. J. Mol. Biol. 58:237-259.Chou PY & Fasman GD (1974) Prediction of protein conformation. Biochemistry 13:211-215.Garnier J, Osguthorpe DJ and Robson B (1978) Analysis of the accuracy and Implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 120:97-120.

Monday May 19, 2014


how to assess performance?

problem 1: where to get secondary structure from?



how to assess performance?

problem 2: how to measure?



Secondary structure prediction accuracy

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• Q3 : three-state per-residue accuracy

number of correctly predicted residues in states helix, strand, otherQ3= ---------------------------------------------------------------------------- number of residues in protein

Schulz GE & Schirmer RH (1979) Prediction of secondary structure from the amino acid sequence. In: (eds). Principles of protein structure. Berlin: Springer-Verlag, pp 108-130.

Monday May 19, 2014



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published: 63% accuracy


Monday May 19, 2014


Secondary Structure Assignment: DSSP

Dictionary of protein Secondary Structure for ProteinsASSESSING secondary structure prediction

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Wolfgang Kabsch & Chris Sander (1983) Biopolymers 22:2577-637

Wolfgang KabschChris Sander

Monday May 19, 2014



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50-55% accuracy (assessed in 1994)


Monday May 19, 2014


Lecture plan (CB1: Structure)-generic01: 2014/04/08 Tue: sorry02: 2014/04/10 Thu: welcome: who we are03: 2014/04/15 Tue: Intro I - acids/structure (Andrea Schafferhans)04: 2014/04/17 Thu: SKIP: Easter vacation05: 2014/04/22 Tue: SKIP: Easter vacation06: 2014/04/24 Thu: Intro 2 - domains07: 2014/04/29 Tue: Intro 3 - 3D comparisons08: 2014/05/01 Thu: SKIP: “May day” - (NOT to be confused with “m’aidez”)09: 2014/05/06 Tue: SKIP: student assembly (SVV)10: 2014/05/08 Thu: Alignment 111: 2014/05/13 Tue: Alignment 2 12: 2014/05/15 Thu: Comparative modeling 113: 2014/05/20 Tue: CM2 + Experimental structure determination + Secondary structure prediction 114: 2014/05/22 Thu: Secondary structure prediction 215: 2014/05/27 Tue: 1D: Secondary structure prediction 116: 2014/05/29 Thu: SKIP: holiday (Ascension Day)17: 2014/06/03 Tue: SKIP: no room 18: 2014/06/05 Thu: 1D: Secondary structure prediction 219: 2014/06/10 Tue: SKIP: Whitsun holidays20: 2014/06/12 Thu: 1D: Transmembrane helix prediction21: 2014/06/17 Tue: Nobel prize symposium22: 2014/06/19 Thu: SKIP: Corpus Christi (Fronleichnam)23: 2014/06/24 Tue: 1D: Transmembrane strand prediction, solvent accessibility24: 2014/06/26 Thu: 2D prediction25: 2014/07/01 Tue: 3D prediction/wrap up26: 2014/07/03 Thu: wrap up again27: 2014/07/08 Tue: examen, no lecture28: 2014/07/10 Thu: no lecture


Protein structure determination cb1 3dexp lecture: Protein ... · Experiments determine protein...

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