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DNA/Protein%20structure-function%20analysis%20and%20prediction

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DNA/Protein structure-function analysis and prediction Protein-protein Interaction (PPI): Protein-protein Interaction Interfaces Solvation Energetics – PowerPoint PPT presentation

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Title: DNA/Protein%20structure-function%20analysis%20and%20prediction


1
DNA/Protein structure-function analysis and
prediction
  • Protein-protein Interaction (PPI)
  • Protein-protein Interaction
  • Interfaces
  • Solvation
  • Energetics
  • Conformational change
  • Allostery
  • Prediction
  • Gene Cluster
  • Phylogenetic Profile
  • Rosetta Stone
  • Sequence co-evolution
  • Random Decision forest
  • Docking
  • Examples

2
PPI Characteristics
  • Universal
  • Cell functionality based on protein-protein
    interactions
  • Cyto-skeleton
  • Ribosome
  • RNA polymerase
  • Numerous
  • Yeast
  • 6.000 proteins
  • at least 3 interactions each
  • 18.000 interactions
  • Human
  • estimated 100.000 interactions
  • Network
  • simplest homodimer (two)?
  • common hetero-oligomer (more)?
  • holistic protein network (all)?

3
Interface Area
  • Contact area
  • usually gt1100 Ã…2
  • each partner gt550 Ã…2
  • each partner loses 800 Ã…2 of solvent accessible
    surface area
  • 20 amino acids lose 40 Ã…2
  • 100-200 J per Ã…2
  • Average buried accessible surface area
  • 12 for dimers
  • 17 for trimers
  • 21 for tetramers
  • 83-84 of all interfaces are flat
  • Secondary structure
  • 50 ?-helix
  • 20 ?-sheet
  • 20 coil
  • 10 mixed
  • Less hydrophobic than core, more hydrophobic than
    exterior

4
Complexation Reaction
  • A B ? AB
  • Ka AB/AB ? association
  • Kd AB/AB ? dissociation
  • Free energy
  • DGd -RTln Kd
  • Kd exp(-DGd / RT)?
  • (R 8.3144 J mol-1 K-1 )?

5
Experimental Methods
  • 2D (poly-acrylamide) gel electrophoresis ? mass
    spectrometry
  • Liquid chromatography
  • e.g. gel permeation chromatography
  • Binding study with one immobilized partner
  • e.g. surface plasmon resonance
  • In vivo by two-hybrid systems or FRET
  • Binding constants by ultra-centrifugation,
    micro-calorimetry or competition
  • experiments with labelled ligand
  • e.g. fluorescence, radioactivity
  • Role of individual amino acids by site directed
    mutagenesis
  • Structural studies
  • e.g. NMR or X-ray

6
PPI Network
http//www.phy.auckland.ac.nz/staff/prw/biocomplex
ity/protein_network.htm
7
Protein-protein interactions
  • Complexity
  • Multibody interaction
  • Diversity
  • Various interaction types
  • Specificity
  • Complementarity in shape and binding properties

8
Binding vs. Localization
strong
Non-obligatetriggered transient e.g. GTPPO4-
Non-obligatepermanente.g. antibody-antigen
Obligateoligomers
Non-obligateco-localised e.g. in membrane
Non-obligateweak transient
weak
co-expressed
different places
9
Some terminology
  • Transient interactions
  • Associate and dissociate in vivo
  • Weak transient
  • dynamic oligomeric equilibrium
  • Strong transient
  • require a molecular trigger to shift the
    equilibrium
  • Obligate PPI
  • protomers not stable structures on their own
  • (functionally obligate)?

10
Strong medium weak
  • Nanomolar to sub-nanomolar
  • Kd lt 10-9
  • Micromolar to nanomolar
  • 10-6 gt Kd gt 10-9
  • Micromolar
  • 10-3 gt Kd gt 10-6
  • A B ? AB
  • Kd AB/AB ? dissociation

11
Analysis of 122 Homodimers
  • 70 interfaces single patched
  • 35 have two patches
  • 17 have three or more

12
Patches
  • Cluster in different domains
  • (structurally defined units often with specific
    function)?

two domains
anticodon-binding
catalytic
13
Interfaces
  • 30 polar
  • 70 non-polar

14
Interface
  • Rim is water accessible

rim
core
15
Interface composition
  • Composition of interface essentially the same as
    core
  • But surface area can be quite different!

16
Propensities
  • Interface vs. surface propensities
  • as ln(fint/fsurf)?

17
Conformational Change
  • Chaperones
  • extreme conformational changes upon complexation
  • ligand unfolds within the chaperone GroEL/GroES
  • Allosteric proteins
  • conformational change at 'active' site
  • ligand binds to 'regulating' site
  • Peptides
  • often adopt 'bound' conformation
  • different from the 'free' conformation

18
Allostery 1
  • Regulation by 'remote' modulation of binding
    affinity (complex strength)?

www.blc.arizona.edu/courses/181gh/rick/energy/allo
stery.html
19
Allostery 2
  • Substrate binding is cooperative
  • Binding of first substrate at first active site
  • stimulates active shape
  • promotes binding of second substrate

20
Allostery 3
  • Committed step of metabolic pathway
  • regulated by an allosteric enzyme
  • Pathway end product
  • can regulate the allosteric enzyme for the first
    committed step
  • Inhibitor binding favors inactive form

21
DNA/Protein structure-function analysis and
prediction
  • Protein-protein Interaction (PPI)
  • Protein-protein Interaction
  • Interfaces
  • Solvation
  • Energetics
  • Conformational change
  • Allostery
  • Prediction
  • Gene Cluster
  • Phylogenetic Profile
  • Rosetta Stone
  • Sequence co-evolution
  • Random Decision forest
  • Docking
  • Examples

22
Predicting Protein-Protein Interactions
  • Gene Cluster
  • Gene neighborhood
  • Phylogenetic Profile
  • Co-occurrence across species/genomes
  • Rosetta Stone
  • Occurrence of protein with domains linked
  • Sequence co-evolution
  • Tree correlation indicated functional relation
  • Random Decision forest
  • Using data on domain interactions
  • Shoemaker Panchenko, PLOS-CB 2007 3 e43

23
Gene Cluster / Neighborhood
24
Gene Cluster / Neighborhood
  • Genes with closely related functions encoding
    potentially interacting proteins
  • transcribed as a single unit (operon) in bacteria
  • co-regulated in eukaryotes
  • Operons can be predicted from intergenic distance
  • Neutral evolution tends to shuffle gene order
    between distantly related organisms
  • but gene clusters or operons that encode
    co-regulated genes are usually conserved
  • operons found by gene neighbor methods provide
    additional evidence about functional linkage

25
Phylogenetic Profile
26
Phylogenetic Profile
  • hypothesis that functionally linked and
    potentially interacting nonhomologous proteins
    co-evolve and have orthologs in the same subset
    of organisms
  • components of complexes and pathways should be
    present simultaneously in order to perform their
    functions.
  • phylogenetic profile is a vector of N elements
    (number of genomes)
  • presence/absence of protein in genome is 1 or
    0 at each position of a profile.
  • clustered using bit-distance measure
  • proteins in a cluster are considered functionally
    related.
  • also for protein domains instead of entire
    proteins

27
Rosetta Stone
28
Rosetta Stone
  • infer protein interactions from sequences in
    different genomes
  • some interacting proteins/domains have homologs
    that are fused into one protein
  • a so-called Rosetta Stone protein
  • Apparently, gene fusion can occur to optimize
    co-expression of genes encoding for interacting
    proteins.

29
Sequence co-evolution
30
Sequence co-evolution
  • interacting proteins often co-evolve so changes
    in one protein leading to the loss of function or
    interaction can be compensated by changes in the
    other
  • orthologs of coevolving proteins also tend to
    interact
  • infer unknown interactions in other genomes
  • similarity between phylogenetic trees of two
    non-homologous interacting protein families
  • correlation coefficient between the distance
    matrices
  • requires correspondence between the matrix
    elements / tree branches (i.e. ortholog
    relations)?
  • align distance matrices to minimize difference
  • predicted interactions correspond to aligned
    cols
  • max. 30 proteins in a family

31
Classification / Random Decision Forest
32
Random Forest Decision
  • Decision trees based on domains of interacting
    and non-interacting proteins
  • All possible combinations of interacting domains
  • vector of length N (different domain types or
    features)?
  • 2, 1, or 0 found in both, one, or no protein of
    pair
  • experimental training set of interacting protein
    pairs
  • decision tree (many trees)
  • defines the best splitting feature at each node
  • from a randomly selected feature subspace
  • best feature is selected based on goodness of
    fit,
  • can discriminate interacting and non-interacting
  • stops growing the tree when all pairs at a given
    node are well-separated
  • Traverse the tree to classify an unknown protein
    pair

33
DNA/Protein structure-function analysis and
prediction
  • Protein-protein Interaction (PPI) and Docking
  • Protein-protein Interaction
  • Interfaces
  • Solvation
  • Energetics
  • Conformational change
  • Allostery
  • Prediction
  • Docking
  • Search space
  • Docking methods
  • Examples

34
Docking - ZDOCK
  • Protein-protein docking
  • 3-dimensional (3D) structure of protein complex
  • starting from 3D structures of receptor and
    ligand
  • Rigid-body docking algorithm (ZDOCK)
  • pairwise shape complementarity function
  • all possible binding modes
  • using Fast Fourier Transform algorithm
  • Refinement algorithm (RDOCK)?
  • top 2000 predicted structures
  • three-stage energy minimization
  • electrostatic and desolvation energies
  • molecular mechanical software (CHARMM)?
  • statistical energy method (Atomic Contact
    Energy)?
  • 49 non-redundant unbound test cases
  • near-native structure (lt2.5Ã…) for 37 test cases
  • for 49 within top 4

35
Protein-protein docking
  • Finding correct surface match
  • Systematic search
  • 2 times 3D space!
  • Define functions
  • 1 on surface
  • ? or ? inside
  • 0 outside

?
?
36
Protein-protein docking
  • Correlation function
  • C????? 1/N3 ?o ?p ?q exp2?i(o? p? q?)/N
    Co,p,q

37
Docking Programs
  • ZDOCK, RDOCK
  • AutoDock
  • Bielefeld Protein Docking
  • DOCK
  • DOT
  • FTDock, RPScore and MultiDock
  • GRAMM
  • Hex 3.0
  • ICM Protein-Protein docking
  • KORDO
  • MolFit
  • MPI Protein Docking
  • Nussinov-Wolfson Structural Bioinformatics Group
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