Protein structure

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Protein structure
Anne Mølgaard, Center for Biological Sequence
Analysis
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Could the search for ultimate truth
really have revealed so hideous and
visceral-looking an object?
Max Perutz, 1964 on protein structure
John Kendrew, 1959 with myoglobin model
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Holdings of the Protein Data Bank (PDB)
Sep. 2001 Feb. 2005 X-ray 13116 25350 NMR
2451 4383 theoretical 338 0 total 15905
29733
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Methods for structure determination

• X-ray crystallography
• Nuclear Magnetic Resonance (NMR)
• Modelling techniques

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X-ray crystallography

• No size limitation
• Protein molecules are stuck in a crystal
  lattice
  
• Some proteins seem to be uncrystallizable
• Slow

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X-rays
Fourier transform
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NMR spectroscopy

• Upper limit for structure determination currently
  50 kDa
  
• Protein molecules are in solution
• Dynamics, protein folding
• Slow

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Modeling

• Need structure of a 30 id homolog
• Only applicable to 50 of sequences
• Fast
• Accuracy poor for low sequence id.
• There is still need for experimental structure
  determination!
  

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Amino acids

• Amino group and acid group
• Side chain at Ca
• Chiral, only one enantiomer found in proteins
• (L-amino acids)

Ca
C
N
O
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http//www.ch.cam.ac.uk/magnus/molecules/amino/
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Amino acids
A Ala C Cys D Asp E Glu F Phe G G
ly H His I Ile K Lys L Leu M Met N
Asn P Pro Q Gln R Arg S Ser T Th
r V Val W Trp Y - Tyr
Livingstone Barton, CABIOS, 9, 745-756, 1993
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• Levels of protein structure
• Primary
• Secondary
• Tertiary
• Quarternary

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Primary structure
MKTAALAPLFFLPSALATTVYLA GDSTMAKNGGGSGTNGWGEYL AS
YLSATVVNDAVAGRSAR(etc)
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Ramachandran plot
left-handed ?-helix
?-sheet
?-helix
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Hydrophobic core

• Hydrophobic side chains go into the core of the
  molecule but the main chain is highly polar
  
• The polar groups (CO and NH) are neutralized
  through formation of H-bonds

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Secondary structure
?-helix CO(n)HN(n4)
?-sheet
(anti-parallel)
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and all the rest

• 310 helices (CO(n)HN(n3)), p-helices
  (CO(n)HN(n5))
  
• b-turns and loops (in old textbooks sometimes
  referred to as random coil)

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The ?-helix has a dipole moment
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Two types of ?-sheet
parallel
anti-parallel
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Tertiary structure (domains, modules)
Rhamnogalacturonan acetylesterase (1k7c)
Rhamnogalacturonan lyase (1nkg)
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Quarternary structure
B.caldolyticus UPRTase (1i5e)
B.subtilis PRPP synthase (1dkr)
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Protein structure and water
A. aculeatus RG acetylesterase
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Classification schemes

• SCOP
• Manual classification (A. Murzin)
• CATH
• Semi manual classification (C. Orengo)
• FSSP
• Automatic classification (L. Holm)

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Levels in SCOP

• Class Folds Superfamilies Families
• All alpha proteins 202 342 550
• All beta proteins 141 280 529
• Alpha and beta proteins (a/b) 130 213 593
• Alpha and beta proteins (ab) 260 386 650
• Multi-domain proteins 40 40 55
• Membrane and cell surface
• proteins 42 82 91
• Small proteins 72 104 162
• Total 887 1447 2630

http//scop.berkeley.edu/count.htmlscop-1.67
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Major classes in SCOP

• Classes
• All alpha proteins
• Alpha and beta proteins (a/b)
• Alpha and beta proteins (ab)
• Multi-domain proteins
• Membrane and cell surface proteins
• Small proteins

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All a Hemoglobin (1bab)
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All b Immunoglobulin (8fab)
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a/b Triose phosphate isomerase (1hti)
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ab Lysozyme (1jsf)
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Folds

• Proteins which have 50 of their secondary
  structure elements arranged the in the same order
  in the protein chain and in three dimensions are
  classified as having the same fold
• No evolutionary relation between proteins
• confusingly also called fold classes

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Superfamilies

• Proteins which are (remote) evolutionarily
  related
  
• Sequence similarity low
• Share function
• Share special structural features
• Relationships between members of a superfamily
  may not be readily recognizable from the sequence
  alone

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Families

• Proteins whose evolutionarily relationship is
  readily recognizable from the sequence (25
  sequence identity)
  
• Families are further subdivided into Proteins
• Proteins are divided into Species
• The same protein may be found in several species

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Links

• PDB (protein structure database)
• www.rcsb.org/pdb/
• SCOP (protein classification database)
• scop.berkeley.edu
• CATH (protein classification database)
• www.biochem.ucl.ac.uk/bsm/cath
• FSSP (protein classification database)
• www.ebi.ac.uk/dali/fssp/fssp.html

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Why are protein structures so interesting?
They provide a detailed picture of interesting
biological features, such as active site,
substrate
specificity, allosteric regulation etc.
They aid in rational drug design and protein
engineering
They can elucidate evolutionary relationships
undetectable by sequence comparisons
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Inferring biological features from the structur
e
1deo
Topological switchpoint
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Inferring biological features from the structure
Active site
Triose phosephate isomerase (1ag1)
(Verlinde et al. (1991) Eur.J.Biochem. 198, 53)
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Engineering thermostability in serpins

• Overpacking
• Buried polar groups
• Cavities

Im, Ryu Yu (2004) Engineering thermostability
in serine protease inhibitors
PEDS, 17, 325-331.
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Evolution...
Structure is conserved longer than
both sequence and function
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Rhamnogalacturonan acetylesterase (A. aculeatus)
(1k7c)
Platelet activating factor acetylhydrolase
(Bos Taurus) (1wab)
Serine esterase (S. scabies) (1esc)
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Rhamnogalacturonan acetylesterase
Serine esterase
Platelet activating factor acetylhydrolase
Mølgaard, Kauppinen Larsen (2000) Structure, 8,
373-383.
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• "We wish to suggest a structure for the salt of
  deoxyribose nucleic acid (D.N.A.). This structure
  has novel features which are of considerable
  biological interest.
• It has not escaped our notice that the specific
  pairing we have postulated immediately suggests a
  possible copying mechanism for the genetic
  material."
• J.D. Watson F.H.C. Crick (1953) Nature, 171,
  737.

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