Protein structure

Anne Mølgaard, Center for Biological Sequence Analysis

“Could the search for ultimate truth really have revealed so hideous and visceral-looking an object?”

Max Perutz, 1964on protein structure

John Kendrew, 1959with myoglobin model

Sep. 2001 Feb. 2005X-ray 13116 25350NMR 2451 4383 theoretical 338 0total 15905 29733

Holdings of the Protein Data Bank (PDB):

Methods for structure determination

X-ray crystallography

Nuclear Magnetic Resonance (NMR)

Modeling techniques

Modeling

Only applicable to ~50% of sequences

FastAccuracy poor for low sequence id.

• There is still need for experimental structure determination!

Structual genomics consortium (SGC)• The SGC deposited its 275th structure into the Protein Data Bank in August 2006 • currently operating at a pace of 170 structures per year

• at a cost of USD$125,000 per structure. • Scientific highlights include:

• several (> 1!!) novel structures of protein kinases

• completing the structural descriptions of the human 14-3-3

• adenylate kinase and cytosolic sulfotransferase protein families

• human chromatin modifying enzymes; human inositol phosphate signaling

• and a significant number of structures from human parasites.

http://www.ch.cam.ac.uk/magnus/molecules/amino/

Amino acids

Amino acids

Livingstone & Barton, CABIOS, 9, 745-756, 1993

A – AlaC – CysD – AspE – GluF – PheG – GlyH – HisI – IleK – LysL – LeuM – MetN – AsnP – ProQ – GlnR – ArgS – SerT – ThrV – ValW – TrpY - Tyr

•Primary

•Secondary

•Tertiary

•Quarternary

Levels of protein structure

Primary structure

MKTAALAPLFFLPSALATTVYLAGDSTMAKNGGGSGTNGWGEYLASYLSATVVNDAVAGRSAR…(etc)

-helix

-sheetleft-handed -helix

Ramachandran plot

Hydrophobic core

Hydrophobic side chains go into the core of the molecule – but the main chain is highly polar

The polar groups (C=O and NH) are neutralized through formation of H-bonds

Secondary structure

-helix C=O(n)…HN(n+4)

-sheet(anti-parallel)

… and all the rest

310 helices (C=O(n)…HN(n+3)), -helices

(C=O(n)…HN(n+5))

-turns and loops (in old textbooks sometimes referred to as random coil)

The -helix has a dipole moment

+-C

N

Two types of -sheet:

anti-parallel parallel

Tertiary structure (domains, modules)

Rhamnogalacturonan lyase (1nkg) Rhamnogalacturonan acetylesterase (1k7c)

Quaternary structure

B.caldolyticus UPRTase (1i5e) B.subtilis PRPP synthase (1dkr)

Classification schemes

SCOP– Manual classification (A. Murzin)

CATH– Semi manual classification (C. Orengo)

FSSP– Automatic classification (L. Holm)

Levels in SCOP

Class # Folds # Superfamilies # FamiliesAll alpha proteins 202 342 550All beta proteins 141 280 529Alpha and beta proteins (a/b) 130 213 593Alpha and beta proteins (a+b) 260 386 650Multi-domain proteins 40 40 55Membrane and cell surface

proteins 42 82 91Small proteins 72 104 162Total 887 1447 2630

http://scop.berkeley.edu/count.html#scop-1.67

Major classes in SCOP

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

All : Hemoglobin (1bab)

All : Immunoglobulin (8fab)

Triose phosphate isomerase (1hti)

a+b: Lysozyme (1jsf)

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

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

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

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

Why are protein structures so interesting?

They provide a detailed picture of interestingbiological features, such as active site, substratespecificity, allosteric regulation etc.

They aid in rational drug design and protein engineering

They can elucidate evolutionary relationshipsundetectable by sequence comparisons

COOH

NH2

Asp His Ser Topological switchpoint

Inferring biologicalfeatures from the structure

1deo

Inferring biological features from the structure

Active site

Triose phosephate isomerase (1ag1) (Verlinde et al. (1991) Eur.J.Biochem. 198, 53)

Engineering thermostability in serpins

OverpackingBuried polar groupsCavities

Im, Ryu & Yu (2004) Engineering thermostability in serine protease inhibitorsPEDS, 17, 325-331.

Evolution...

Structure is conserved longer thanboth sequence and function

Rhamnogalacturonanacetylesterase(A. aculeatus) (1k7c)

Platelet activating factor acetylhydrolase(Bos Taurus) (1wab)

Serine esterase (S. scabies)(1esc)

Platelet activatingfactor acetylhydrolase

Serine esterase

Rhamnogalacturonanacetylesterase

Mølgaard, Kauppinen & Larsen (2000) Structure, 8, 373-383.

"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.