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Secondary structure prediction from amino acid sequence
Homology: Paralogs and orthologs
a
a b
duplication
speciation
species 1 species 2
a b a b
Paralogs = gene families in same species
orthologs
Amino acid primary sequence
2. Homologue(s) with known 3D structure?
Homology modellingavailable
1. Search for sequence homologue(s) and construct an alignment
3. Motif recognition: Search secondary databases
Secondary structure prediction
Fold assignment
Physico-chemical properties
(e. g., using EMBOSS suite)
DNA sequence
Automatic translation
Primary db searches
FASTA, BLAST
Chou-Fasman Parameters
• Amino acid propensities
• Q3 score
Q3 = q+q+qcoil X 100%
total no. of residues
Accuracy of prediction
Recent improvements
• The availability of large families of homologous sequences has greatly enhanced secondary structure prediction.
• The combination of sequence data in multiple alignments with sophisticated computing techniques such as neural networks has lead to accuracies well in excess of 70 %.
• The limit of 70-80% may be a function of secondary structure variation within homologous proteins.
Stereochemical analysis
Patterns of residue conservation are indicative of particular secondary structure types.
Alpha helices have a periodicity of 3.6. Many alpha helices in proteins are amphipathic, meaning that one face is pointing towards the hydrophobic core and the other towards the solvent.
Patterns of hydrophobic residue conservation showing the i, i+3, i+4, i+7 pattern are highly indicative of an alpha helix.
XOOXXOOX
Stereochemical analysis
The geometry of beta strands means that adjacent residues have their side chains pointing in oppposite directions.
Beta strands that are half buried in the protein core will tend to have hydrophobic residues at positions i, i+2, i+4, i+8 etc, and polar residues at positions i+1, i+3, i+5, etc.
XOXOXOXOXO
Stereochemical analysis
Beta strands that are completely buried (as is often the case in proteins containing both alpha helices and beta strands) usually contain a run of hydrophobic residues.
XXXXXXXXXXXX
Helical transmembrane proteins
• Strong hydrophobicity signal from membrane spanning regions, each ~25 residues in length
• Predominance of positively charged amino acid residues on cytoplasmic side
•Prediction accuracy with multiple alignment = 95%
+
Helical transmembrane proteins• ~30% of top 100 drugs bind to membrane
proteins• Difficult to determine experimentally• But much easier to predict than globular
proteins!
• TMpred – based on statistical analysis of transmembrane proteins
• TMHMM – based on Hidden Markov Model
Protein Structure Classification
http://www.cathdb.info/latest/index.html
Class(C) secondary structure content – mainly alpha, mainly beta, alpha/beta, few secondary structures (type) Architecture(A) gross arrangement of sec. structure elements (type and number of SS elements)
Topology(T) shape and connectivity of SS (type, number and order of SS elements)
Homologous superfamily (H)
Topology
Class Architecture Topology H-level
Fold families
Homologous domains, share common ancestor
Class Architecture Topology H-level
Fold families
Homologous domains, share common ancestor
In CATH, the assignments of structures to fold groups and homologous superfamilies are made by sequence and structure comparisons.
Architecture: ‘Barrel’
9 Topologies : type of SS, number and order
Homologous domain family ?
Secondary structure prediction methods
• PSI-pred (PSI-BLAST profiles used for prediction; David Jones, Warwick)
• JPRED Consensus prediction (includes many of the methods given below; Cuff & Barton, EBI)
• DSC King & Sternberg• PREDATORFrischman & Argos (EMBL) • PHD home page Rost & Sander, EMBL, Germany • ZPRED server Zvelebil et al., Ludwig, U.K. • nnPredict Cohen et al., UCSF, USA. • BMERC PSA Server Boston University, USA • SSP (Nearest-neighbor) Solovyev and Salamov, Baylor
College, USA.
http://speedy.embl-heidelberg.de/gtsp/secstrucpred.html
Consensus prediction method
hydrophobic
highly conserved b= buried, e = exposed
Consensus prediction method -JPRED
hydrophobic
highly conserved b= buried, e = exposed
amphipathichydrophobic
Neural network prediction - PHD
Multiple alignment
of protein family
SS profile for window of adjacent residues
Hidden Markov Models-HMMSTR
amino acid
secondary structure element
structural context
Markov state
• Recurrent local features of protein sequences
• Accuracy of 74%
Bystroff et al., 2000