experimental structure determination pp1 exp3d · assignment coverage: define geometry (fitting...
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title: Experimental structure determinationshort title: pp1_exp3D
lecture: Computational Biology 1 - Protein structure (for Informatics) - TUM summer semester
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Videos: YouTube / www.rostlab.org THANKS :. EXERCISES: Special lectures:
• 05/24 Predrag Radivojac - Indiana University • TBD - Thomas Hopf • TBD - Jonas Reeb No lecture:
• 05/05 Ascension day • 05/10 Student assembly (SVV) • 05/17 Whitsun holiday • 06/26 Corpus Christi LAST lecture: June 28 (followed by 2 wrap-up sessions) Examen: June 30, 2016: lecture time room TBD
• Makeup: TBC: Oct 18 & 20, 2016 - lecture time
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CONTACT: Lothar Richter [email protected]
Dmitrij Nechaev
Lothar Richter
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Recap: 3D prediction by
comparative modeling
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Zones
Day
light
Zon
e
Twili
ght Z
one
Mid
nigh
t Zon
eprofile - profile
sequence - profilesequence - sequence
sequ
ence
sim
ilar
->
stru
ctur
e sim
ilar
B Rost (1997) Fold Des 2:S19-24B Rost (1999) Protein Eng 12:85-94
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human - fly - bacteria
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 & H Park (unpublished) / 4IW3: JS Scotti (unpublished)3lbn: G Buhrman et al.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 - human lime: 3lbn Rash - human orange: 2y8e Rab6 - fly purple: 2y8e hydroxylase P putida
Andrea Schaffer-
hans
Slide from:
PIDE: pairwise identical residues
19%
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MODELLERlots of whistles and bells, downloadable, very accurate
SWISS-MODELautomated, increasingly comprehensive and flexible
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Comparative modeling methods
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Comparative modeling/homology modeling most accurate way to predict structure as good and as complete as the templateè depends on quality and similarity of template mostly driven by accuracy of alignmentè driven by alignment quality loop modeling: still not fully there, yet side chain modeling: unclear how well we do
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Conclusion: Comparative modeling
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Comparative modeling applicable to about 50% of all proteins
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3D prediction from first principles?
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Goal of structure prediction
Epstein & Anfinsen, 1961:sequence uniquely determines structure
• INPUT: sequence
3D structureand function
• OUTPUT:
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protein folding from first principles should then be
possible
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60s - Washington Post 70s - New York Times 90s - Washington Post
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Protein structure prediction problem* solved!
*Problem: “predict the 3D structure of a protein from sequence alone”
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How would you assess prediction
performance?
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Critical Assessment of Structure Prediction April-May (Organizers): collect experimental structures (since 2004 from structural genomics) June-August: Prediction seasondeadline: predictions in before experimental structures are published September-November: Assessors divine December: Meeting to discuss results
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CASP: how it works
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CASPOnly homology modeling good
No general prediction of 3D from sequence, yet Important improvements in many fields!
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Protein Structure Prediction
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Servers, META-servers, META-META, …
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3D from experimental co-ordinates
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3D details - 3D cartoon
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Structure by experiment
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Experiments determine protein structure
Number Percentage
PDB 84,413 1Xray 75,068 89NMR 8,723 10
EM ElectronMicroscopy 428 1
PDB (Protein Data Bank) Helen Berman (Rutgers Univ, New Brunswick) &
Phil Bourne (UCSD San Diego)
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Protein structure by X-ray crystallography
© 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)
Number Percentage
PDB 84,413 1
Xray 75,068 89
NMR 8,723 10
EM ElectronMicroscopy
428 1
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Protein structure by NMR* spectroscopy
© Wikipedia
Number PercentagePDB 84,413 1
Xray 75,068 89
NMR 8,723 10
EM ElectronMic
428 1
* NMR: Nuclear Magnetic Resonance
NMR tube
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Protein structure by NMR* spectroscopy
© Wikipedia
900 MHz NMR machine
1ssu: Y Kamikubo et al. & HJ Dyson (2004) Biochemistry 43:6519-34
Number PercentagePDB 84,413 1
Xray 75,068 89
NMR 8,723 10
EM ElectronMic
428 1
* NMR: Nuclear Magnetic Resonance
NYSBC - City College New
York City
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Protein structure by cryo-EM
© Wikipedia
Number PercentagePDB 84,413 1
Xray 75,068 89
NMR 8,723 10
EM ElectronMic
428 1
* EM: Cryo-Electron Microscopy
4 Ångstrøm 8Å 16Å 32Å GroEL - J Wang & DC Bosvert (2004) 1j4z Images: Vossman 2007 - Wikipedia
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Protein structure by cryo-EMNumber Percentage
PDB 84,413 1
Xray 75,068 89
NMR 8,723 10
EM ElectronMic
428 1
* EM: Cryo-Electron Microscopy
T Ju, M Baker, W Chiu (2006) Computer-Aided Design 39:352-60
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Structure resolution
© PDB
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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
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Secondary structure stabilized by
hydrogen bonds
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1951 e.g. :L Pauling and RB Corey (1951) Configurations of Polypeptide Chains with Favored Orientations Around Single Bonds: Two New Pleated Sheets PNAS 37: 729-40 1953 e.g.: L Pauling and RB Corey (1953) Two Rippled-sheet Configurations of Polypeptide Chains, and a Note About the Pleated Sheets PNAS 39: 253-6
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Linus Pauling: introduce concept
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/
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Hydrogen-bond formation
© Wikipediahttp://www.ausetute.com.au/proteins.html
strandhelix
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3D details - 3D cartoon
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3D details - 3D cartoon
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Pauling Nobel Prize 1954 -
first protein structure when?
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First protein structures
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.
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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
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Secondary structure assignment
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Secondary structure from 3D structure
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3D details - 3D cartoon
HHHHHHHLLL
EEEEE
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How to “annotate” 1D-secondary
structure from 3D co-ordinates?
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Answer the question in groups
??
???
© Wikipedia
How to assign secondary structure from 3D structure?
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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
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Secondary structure assignment
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DSSP: Coulomb
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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
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Pauling’s H-bond pattern used in DSSP
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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
Continuous: DSSPcontC Andersen, AG Palmer, S Brunak & B Rost (2002) Structure 10:175-84
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Other ideas to assign secondary structure
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3 methods (DSSP, DEFINE, P-Curve)
agree in 30% of HEL
assignments completely
44N Colloc’h et al & JP Mornon (1993) Prot Engng 6:377-82
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01: 04/11 Tue: no lecture 02: 04/13 Thu: no lecture 03: 04/19 Tue: Organization of lecture: intro into cells & biology 04: 04/21 Thu: Intro I - acids/structure - domains 05: 04/26 Tue: Alignment 1 06: 04/28 Thu: Alignment 2 07: 05/03 Tue: Alignment 3 08: 05/05 Thu: SKIP: Ascension Day 09: 05/10 Tue: SKIP: student assembly (SVV) 10: 05/12 Thu: & experimental structure determination & secondary structure assignment 11: 05/17 Tue: SKIP: Whitsun holiday (05/15-17) 12: 05/19 Thu: 1D: Secondary structure prediction 1 13: 05/24 Tue: Predrag Radivojac: Protein disorder 14: 05/26 Thu: SKIP: Corpus Christi 15: 06/31 Tue: 1D: Secondary structure prediction 2 16: 06/02 Thu: 1D: Transmembrane structure prediction 1 17: 06/07 Tue: 1D: Transmembrane structure prediction 2 / Solvent accessibility prediction 18: 06/09 Thu: 2D prediction 1 19: 06/14 Tue: 2D prediction 2 - Thomas Hopf 20: 06/16 Thu: 3D prediction / Nobel prize symposium 21: 06/21 Tue: 1D: Disorder prediction 22: 06/23 Thu: recap 1 23: 06/28 Tue: recap 2 24: 06/30 Thu: examen, no lecture 25: 07/05 Tue: examen alternative, no lecture 26: 07/07 Thu: examen, no lecture 27: 07/12 Tue: wrap up exercises - no lecture 28: 07/14 Thu: wrap up exercises - no lecture
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Lecture plan (CB1 structure)