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Protein Structure Prediction
Why do we want to know protein structure? Classification Functional Prediction
What is protein structure? Primary - chains of amino acids Secondary - interaction between groups
of amino acids Tertiary - the organization in three
dimensions of all the atoms in a polypeptide
Quaternary - the conformation assumed by a multimeric protein
Proteins are chains of amino acids joined by peptide bonds
The N-C-C sequence is repeated throughout the protein, forming the backbone
The bonds on each side of the C atom are free to rotate within spatial constrains,the angles of these bonds determine the conformation of the protein backbone
The R side chains also play an important structural role
Polypeptide chain
The structure of two amid acids
Primary Structure
Interactions that occur between the C=O and N-H groups on amino acids
Much of the protein core comprises helices and sheets, folded into a three-dimensional configuration:
- regular patterns of H bonds are formed between neighboring amino acids- the amino acids have similar angles- the formation of these structures neutralizes the polar groups on each amino acid- the secondary structures are tightly packed in a hydrophobic environment- Each R side group has a limited volume to occupy and a limited number of interactions with other R side groups
helix sheet
Secondary Structure
helix
sheet
Secondary Structure
Other Secondary structure elements(no standardized classification)
- loop
- random coil
- others (e.g. 310 helix, -hairpin, paperclip)
Super-secondary structure
- In addition to secondary structure elements that apply to all proteins (e.g. helix, sheet) there are some simple structural motifs in some proteins
- These super-secondary structures (e.g. transmembrane domains, coiled coils, helix-turn-helix, signal peptides) can give important hints about protein function
Secondary Structure
Structural classification of proteins (SCOP)
Class 1: mainly alpha
Class 4: few secondary structures
Class 2: mainly beta
Class 3: alpha/beta
Classification
Alternative SCOP
Class : only helices Class : antiparallel sheets Class / : mainly sheetswith intervening helices
Class + : mainlysegregated helices withantiparallel sheets
Membrane structure:hydrophobic helices withmembrane bilayers
Multidomain: containmore than one class
More Classification
Q: If we have all the Psi and Phi angles in a protein, do we then have enough information to describe the 3-D structure?
Tertiary structure
A: No, because the detailed packing of the amino acid side chains is not revealed from this information. However, the Psi and Phi angles do determine the entire secondary structure of a protein
Protein Structure Review
Secondary-Structure Prediction Programs * PSI-pred * JPRED Consensus prediction (includes many of the
methods given below) * DSC * PREDATOR * PHD * ZPRED * nnPredict * BMERC PSA * SSP
The tertiary structure describes the organization in three dimensions of all the atoms in the polypeptide
The tertiary structure is determined by a combination of different types of bonding (covalent bonds, ionic bonds, h-bonding, hydrophobic interactions, Van der Waal’s forces) between the side chains
Many of these bonds are very week and easy to break, but hundreds or thousands working together give the protein structure great stability
If a protein consists of only one polypeptide chain, this level then describes the complete structure
Tertiary Structure
Proteins can be divided into two general classes based on their tertiary structure:
- Fibrous proteins have elongated structure with the polypeptide chains arranged in long strands. This class of proteins serves as major structural component of cells Examples: silk, keratin, collagen
- Globular proteins have more compact, often irregular structures. This class of proteins includes most enzymes and most proteins involved in gene expression and regulation
Tertiary Structure
The quaternary structure defines the conformation assumed by a multimeric protein.The individual polypeptide chains that make up a multimeric protein are often referred toas protein subunits. Subunits are joined by ionic, H and hydrophobic interactions
Example:Haemoglobin(4 subunits)
Quaternary Structures
Common displays are (among others) cartoon, spacefill, and backbone
cartoon spacefill backbone
Structure Displays
Software RasMol Cn3D Jmol (Chime)
Classic Approach to Determining Structure?
Determine biochemicaland cellularrole of protein
Purify protein
Experimentally determine3D structure
Clone cDNAencodingprotein
Obtain proteinBy expression
Infer function, mechanism of action
Structural Genomics Approach?
genomicDNA sequences
predictprotein-codinggenes
Obtain proteinby expression
Obtain proteinIn silico
Experimentallydetermine3D structure
Predict 3D structure
Determinebiochemical andcellular roleof protein
homology searches (PSI-BLAST)
3-D macromolecular structures stored in databases
The most important database: the Protein Data Bank (PDB)
The PDB is maintained by the Research Collaboratory for Structural Bioinformatics (RCSB) and can be accessed at three different sites (plus a number of mirror sites outside the USA):
- http://rcsb.rutgers.edu/pdb (Rutgers University)- http://www.rcsb.org/pdb/ (San Diego Supercomputer Center)- http://tcsb.nist.gov/pdb/ (National Institute for Standards and Technology)
It is the very first “bioinformatics” database ever build
Sources of Protein Structure Information?
Researches have been working for decades to develop procedures for predicting protein structure that are not so time consuming and not hindered by size and solubility constrains.
As protein sequences are encoded in DNA, in principle, it should therefore be possible to translate a gene sequence into an amino acid sequence, and topredict the three-dimensional structure of the resulting chain from this amino acid sequence
Computational Modeling
Structural Prediction
How to predict the protein structure?
Ab initio prediction of protein structure from sequence: not yet.
Problem: the information contained in protein structures lies essentially in theconformational torsion angles. Even if we only assume that every amino-acid residuehas three such torsion angles, and that each of these three can only assume oneof three "ideal" values (e.g., 60, 180 and -60 degrees), this still leaves us with 27possible conformations per residue.
For a typical 200-amino acid protein, this would give 27200 (roughly 1.87 x 10286)possible conformations!
If we were able to evaluate 109 conformations per second, this would still keep us busy 4 x 10259 times the current age of the universe
There are optimized ab initio prediction algorithms available as well as fold recognition algorithms that use threading (compares protein folds with know fold structures from databases), but the results are still very poor
Q: Can’t we just generate all these conformations, calculate their energy and see which conformation has the lowest energy?
Computational Modeling
Homology (comparative) modeling attempts to predict structure on
the strength of a protein’s sequence similarity to another protein of known
structure
Basic idea: a significant alignment of the query sequence with a target sequence from PDB is evidence that the query sequence has a similar 3-D structure (current threshold ~ 40% sequence identity). Then multiple sequence alignment and pattern analysis can be used to predict the structure of the protein
Homology Modeling
Computational modeling: summary
Partial or full sequencespredicted through gene
finding
Similarity searchagainst proteins
in PDB
Alignment can be used to position theamino acids of the query sequence inthe same approximate 3-D structure
Find structures that have a significantlevel of structural similarity (but not
necessarily significant sequence similarity)
If member of a family with a predicted structural fold,
multiple alignment can be used for structural modeling
Infer structural information (e.g. presence of smallamino acid motifs; spacing and arrangement of
amino acids; certain typical amino acid combinationsassociated with certain types of secondary structure)
can provide clues as to the presence of active sites andregions of secondary structure
Structural analyses in the lab(X-ray crystallography, NMR)
How do wedo this?
3D Comparative Modeling Profile Methods - match sequences to folds
by describing each fold in terms of the environment of each residue in the structure
Threading Methods - match sequences to structure by considering pairwise interactions for each residue, rather than averaging them into an environmental class
HMM Methods - the equivalent state corresponds to one structurally aligned position in a structural fold, including gaps
Structural HMM