Protein Structure Prediction

1
Protein Structure Prediction
2
Historical Perspective

• Protein Folding From the Levinthal Paradox to
  Structure Prediction, Barry Honig, 1999
• A personal perspective on advances and
  developments in protein folding over the last 40
  years

3
Levinthal Paradox

• Cyrus Levinthal, Columbia University, 1968
• Observed that there is insufficient time to
  randomly search the entire conformational space
  of a protein
• Resolution Proteins have to fold through some
  directed process
• Goal is to understand the dynamics of this process

4
Old vs. New Views

• Old
• Heirarchical view of protein folding
• Secondary structures form, then interact to form
  tertiary structures
• General order of events
• New
• Statistical ensembles of states
• Potential energy landscape
• Folding Funnel
• Not all that different most important ideas were
  theorized many years ago

5
Secondary Structures

• Consensus view is that secondary structure
  formation is the earliest part of the folding
  process
• Numerous studies indicate that local sequence
  codes for local structures
• Helical sequences in a folded protein tend to be
  helical in isolation
• Current SSE prediction algorithms about 70
  correct (1993). Failure indicates some tertiary
  interactions in stabilizing SSEs

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However

• Not clear what sequence elements code for overall
  topology
• One factor is the existence of hydrophobic faces
  on the surface of SSEs
• Still challenges in predicting topology of SSEs,
  even when protein class is known

7
Atomic level calculations

• Molecular calculations have made great impact in
  our understanding of protein folding
• Harold Scheraga, 1968
• Shneior Lifson, 1969
• Martin Karpluss laboratory, 1979
• Early calculations had trouble dealing with
  solvent effects

8
Secondary Structure

• Many of the essential elements of protein
  energetics can be derived from looking at SSE
  formation
• Early experimental work Ingwall et all, 1968
• Baldwin et all, 1989, Worked on stabilizing
  shorter helices
• Dyson, Wright, 1991, demonstrated that even short
  peptides in solution can be partially structured

9
Results

• Yang and Honig, 1995
• Alpha-helices stabilized by hydrophobic
  interactions and close packing hydrogen bonding
  has little effect
• Beta-sheets stabilized by non-polar interactions
  between residues on adjacent strands
• Work supports idea that SSEs coded for locally in
  the sequence

10
Folding Pathways

• SSEs can change conformation in the presence of a
  relatively small number of tertiary interactions
• Free-energy difference between alpha-helix,
  beta-sheet, and coil is not great
• Individual helices can be changed into
  beta-sheets by changing just a few amino acids
• This suggests that proteins have a structural
  plasticity which allows for changes in
  conformation

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Folding Pathways

• Early in folding processes, many different
  combinations of SSEs have very similar
  stabilities
• In the end, it is the tertiary interactions which
  drive towards the native topology
• Early in folding, flickering of SSEs,
  eventually stabilized by tertiary interactions
  and converge to native state
• Suggests that multiple folding pathways exist,
  which can all lead to the same end result once
  stabilized

12
Structure Prediction

• Recently, a split has been seen
• Protein prediction problem
• Trying to predict the end result of folding,
  using a large amount of comparison between known
  and unknown structures
• Protein folding problem
• Trying to understand the folding path which leads
  to the end result of folding, typically by MD
  simulations or energy calculation
• Authors contention that both areas will need to
  be used together to fully understand protein
  folding

13
PrISM

• Yang and Honig, 1999
• Software suite which integrates prediction based
  on simulations and known information about
  structures
• Sequence analysis
• Structure based sequence alignment
• Fast structure-structure superposition using a
  structural domain database
• Multiple Structure alignment
• Fold recognition and homology model building
• Used to make predictions for all 43 targets of
  CASP3 conference (more on CASP later)

14
Conclusions

• Much of the current understanding of protein
  folding was theorized long ago
• Vague and speculative ideas have been replaced by
  carefully defined theoretical concepts and
  rigorous experimental observations

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Conclusions

• Polypeptide backbone is the most important
  determinant of structure
• SSEs are meta-stable statement that sequence
  determines structure not wholly accurate
• More accurate statement is that sequence chooses
  from a limited set of available SSEs and
  determines how they are ordered in space

16
Conclusions

• Free-energy differences between alternate
  conformations is not large may provide a bases
  for rapid evolutionary change

17
CASP

• A decade of CASP progress, bottlenecks and
  prognosis in protein structure prediction, John
  Moult
• CASP Critical Assessment of Structure
  Prediction
• First held in 1994, every 2 years afterwards
• Teams make structure predictions from sequences
  alone

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CASP

• Two categories of predictors
• Automated
• Automatic Servers, must complete analysis within
  48 hours
• Shows what is possible through computer analysis
  alone
• Non-automated
• Groups spend considerable time and effort on each
  target
• Utilize computer techniques and human analysis
  techniques

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CASP

• CASP6, 1994
• 200 prediction teams from 24 countries
• Over 30,000 predictions for 64 protein targets
  collected and evaluated
• Conference held after to discuss results, with
  many teams presenting individual results and
  methodologies
• Helps to steer future work

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Modeling classes

• Comparative modeling based on a clear sequence
  relationship
• Modeling based on more distant evolutionary
  relationships
• Modeling based on non-homologous fold
  relationships
• Template free modeling

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Comparative modeling based on a clear sequence
relationship

• Easily detectable sequence relationship between
  the target protein and one or more known protein
  structures, typically through BLAST
• Copy from template, however
• Must align target and template sequences
• In general, reliably building regions not present
  in the template is still a challenge
• Sidechain accuracy is poor
• Refinement remains a challenge

22
Comparative modeling based on a clear sequence
relationship

• Progress in MD needed for refinement
• Models useful for identifying which members of a
  protein family have similar functionalities, and
  which are different

23
Modeling based on more distant evolutionary
relationships

• Makes use of PSI-BLAST and hidden Markov models
• Compile a profile for the sequence, compare this
  profile to other known profiles
• Allows for prediction of structures, even when
  sequence is not close
• Use of metaservers to find consensus structures
  between CASP4 and CASP5 has led to improved
  accuracy

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Modeling based on more distant evolutionary
relationships

• Limitations
• Correct template may not be identified
• Alignment of target sequence to template is not
  trivial
• Significant fraction of residues will have no
  structural equivalent in the template modeling
  of these regions is hit or miss
• Although regions are similar, they are not
  identical, and the greater the difference, the
  higher the error
• Details are thus not accurate, but overall
  structure can be useful
• For improvements, must work together with
  template-free methodologies

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Modeling based on more distant evolutionary
relationships
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Modeling based on non-homologous fold
relationships

• Protein threading
• In recent CASP experiments, these methods have
  not been competitive with template free models

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Template-free Modeling

• For sequences where no template is available
• Historically physics based approaches were used
• Newer methods focus on substructures
• While we have not seen all folds, we have
  probably seen nearly all substructures
• Make use of substructure relationships
• From a few residues through SSEs to
  super-secondary structures

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Template-free Modeling

• Range of possible conformations and considered
• Most successful package has been ROSETTA
• For proteins less than 100 residues, produce one
  or several approximately correct structures (4-6
  A rmsd for C-alpha atoms)
• Selecting the most accurate structures from all
  possibilities is still to be solved, typically
  make use of clustering currently
• Development of atomic models is crucial to
  further progress

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Template-free Modeling
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CASP Progress