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Protein Structure

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Protein Structure & Modeling Biology 224 Instructor: Tom Peavy Nov 15 & 17, 2010 – PowerPoint PPT presentation

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Title: Protein Structure


1
Protein Structure Modeling
  • Biology 224
  • Instructor Tom Peavy
  • Nov 15 17, 2010

ltImages adapted from Bioinformatics and
Functional Genomics by Jonathan Pevsnergt
2
Classical structural biology
Determine biochemical activity
Purify protein
Determine structure
Understand mechanism, function
3
Structural genomics
Determine genomic DNA sequence
Predict protein
Determine structure or analyze in silico
Understand mechanism, function
4
Protein function and structure
Function is often assigned based on homology.
However, homology based on sequence identity may
be subtle. Consider RBP and OBP these are true
homologs (they are both lipocalins, sharing the
GXW motif). But they are distant relatives, and
do not share significant amino acid identity in a
pairwise alignment. Protein structure evolves
more slowly than primary amino acid sequence. RBP
and OBP share highly similar three dimensional
structures.
5
Principles of protein structure
Primary amino acid sequence
Secondary structure a helices, b sheets
Tertiary structure from X-ray, NMR
Quaternary structure multiple subunits
6
Protein secondary structure
Protein secondary structure is determined by the
amino acid side chains. Myoglobin is an example
of a protein having many a-helices. These are
formed by amino acid stretches 4-40 residues in
length. Thioredoxin from E. coli is an example
of a protein with many b sheets, formed from b
strands composed of 5-10 residues. They are
arranged in parallel or antiparallel
orientations.
7
Myoglobin (John Kendrew, 1958)
8
Thioredoxin
9
Secondary structure prediction
Chou and Fasman (1974) developed an
algorithm based on the frequencies of amino acids
found in a helices, b-sheets, and
turns. Proline occurs at turns, but not in a
helices. GOR (Garnier, Osguthorpe, Robson)
related algorithm Modern algorithms use
multiple sequence alignments and achieve higher
success rate (about 70-75)
10
Secondary structure prediction
Web servers GOR4 Jpred NNPREDICT PHD Predator Pr
edictProtein PSIPRED SAM-T99sec
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Tertiary protein structure protein folding
Three main approaches 1 experimental
determination (X-ray crystallography,
NMR) 2 Comparative modeling (based on
homology) 3 Ab initio (de novo) prediction
14
Experimental approaches to protein structure
1 X-ray crystallography -- Used to determine
80 of structures -- Requires high protein
concentration -- Requires crystals -- Able to
trace amino acid side chains -- Earliest
structure solved was myoglobin 2 NMR --
Magnetic field applied to proteins in
solution -- Largest structures 350 amino acids
(40 kD) -- Does not require crystallization
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Access to PDB through NCBI
Molecular Modeling DataBase (MMDB) Cn3D (see in
3D or three dimensions) structure visualization
software Vector Alignment Search Tool
(VAST) view multiple structures
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Additional web-based sites to visualize
structures
Swiss-PDB Viewer Chime RasMol MICE VRML
27
Structural Classification of Proteins (SCOP)
SCOP describes protein structures using a
hierarchical classification scheme Classes Fold
s Superfamilies (likely evolutionary
relationship) Families Domains Individual PDB
entries http//scop.mrc.lmb.cam.ac.uk/scop/
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Approaches to predicting protein structures
There are about gt20,000 structures in PDB,
and about 1 million protein sequences in
SwissProt/ TrEMBL. For most proteins, structural
models derive from computational biology
approaches, rather than experimental
methods. The most reliable method of modeling
and evaluating new structures is by comparison to
previously known structures. This is comparative
modeling. An alternative is ab initio modeling.
30
Approaches to predicting protein structures
obtain sequence (target)
fold assignment
comparative modeling
ab initio modeling
build, assess model
31
Comparative modeling of protein structures
1 Perform fold assignment (e.g. BLAST, CATH,
SCOP) identify structurally conserved
regions 2 Align the target (unknown protein)
with the template. This is performed for gt30
amino acid identity over a sufficient
length 3 Build a model 4 Evaluate the model
32
Errors in comparative modeling
Errors may occur for many reasons 1 Errors in
side-chain packing 2 Distortions within
correctly aligned regions 3 Errors in regions
of target that do not match template 4 errors
in sequence alignment 5 use of incorrect
templates
33
Comparative modeling
Many web servers offer comparative modeling
services. Examples are SWISS-MODEL
(ExPASy) Predict Protein server (Columbia) WHAT
IF (CMBI, Netherlands)
34
Ab initio protein structure prediction
Ab initio prediction can be performed when a
protein has no detectable homologs. Protein
folding is modeled based on global
free-energy minimum estimates. The Rosetta
Stone methods was applied to sequence families
lacking known structures. For 80 of 131
proteins, one of the top five ranked models
successfully predicted the structure within 6.0 Å
RMSD (Bonneau et al., 2002).
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