Structural alphabets, from protein structure description

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Structural alphabets, from protein structure
description to comparison
Manoj Tyagi LBGM Université de la Réunion
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Synopsis

• Classical method of protein structure analysis
• Structural alphabets protein blocks
• Reduction of protein space
• Generation of PB substitution matrix
• Applications of PB matrix
• Structure comparison and mining
• Identification of rigid body movement or local
  conformation changes
• Conclusion

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Analysis of protein structures
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Secondary structures 3 states
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Structural Alphabets / Protein Blocks

• A structural alphabet is a set (or library) of
  small structural motifs/prototypes which
  approximate every part of the protein structures.
  
• They are composed by a limited number of
  recurrent structural elements of proteins. i.e.
  are recurring in protein space.
• Protein blocks are set of 16 short structural
  motifs of 5 consecutive residues/amino acids.
• Each motif is represented by vector/set of 8
  dihedral angles (f,y).
• Denoted by letter a, b, ,p.

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Structural Alphabets / Protein Blocks

• PBs can be characterized by their secondary
  structure composition. e.g.PB m forms the central
  part of helix and PB d is ideal for sheet
• PBs from a to c and d to f are mainly concerned
  with N and C caps of sheet
• Similarly PBs k, l and n, o, p form N and C
  caps of helix.
• PBs labelled from g to j are mainly concerned
  with coils.

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yn-2 , fn-1 (41.14,75.53) yn-1 , fn
(13.92,99.80) yn , fn1 (131.88,96.27) yn1 ,
fn2 (122.08,99.68)
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Encoding 3D structure as 1D PB sequence
PB sequence
KBCCDDDDFBFKLMMMMMMMMMMNOPABDCDDFBFKL MMMMMMNGOIAB
DCDDFBDGHILMLMMMMMMMMPMKL MMPCCDDDDFBDCFKLMMMMMMNO
PABDCDDDDDFKL MMMMMMMMMMMNO
What we found ? PBs when combined together gives
back regular structures of a protein and also
highlight variable regions present between
regular structure elements
3D structure
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What can we do with PB sequence ?

• PB sequence comparison to identify equivalent
  regions
• Structure comparison based on sequence alignment
  algorithm
• Identification of conformational change or rigid
  body displacement/shift in proteins
• Extension of above to study active inactive
  states of enzymes

What do we need now? A substitution matrix !
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Generation of PBs substitution matrix

• Required large number of structurally aligned
  proteins
• PALI database was used
• Structure alignments encoded into PB sequence
  alignments
• Calculations of substitution frequency of each
  PB in conservered regions
• Conversation to log odds score

Balaji S, Sujatha S, Kumar SS, Srinivasan N.
PALI-a database of Phylogeny and ALIgnment of
homologous protein structures. Nucleic Acids Res
200129(1)61-65.
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Substitution table calculation
PALI aa alignment
PB alignment
Substitution count
Log odd score
PB matrix (16x16)
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PB substitution matrix
Tyagi M, Venkataraman SG, Srinivasan N, de
Brevern AG, Offmann B A substitution matrix for
structural alphabet based on structural alignment
of homologous proteins and its applications.
Proteins in press.
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Potential applications of PB substitution table

• Use of classical sequence alignment methods (DP)
  to align and compare two PBs sequences to
  identify structurally equivalent and non
  equivalent regions
• Extension of above to structure mining in large
  database
• Combination of substitution table with rigid body
  superimposition to identify conformational
  changes or rigid body displacment in homologous
  proteins
• Extension of above approach to study enzymes
  active/inactive form

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Structure comparison
3chy
2fox
?
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Structure comparison
3chy_ KBCCDDDDFBF--KLMMMMMMMMMMNOPABDCDDFBFKLMMMM
MMNGOIABDCDDFBDGHI 2fox_ ---DDDDFKOMMMMMMMMMMMMMM
MNOPACDDDD--FKLPCFKLMMM-PFBDCDDDDDEHJ 3chy_
LM--LMMMMMMMMPMKLMMPCCDDDDFBDCFKL-----MM-MMM-M-NOP
A--BDCDDDD- 2fox_ LPACFKLMMMMMMMMMMMMGHIACDDEHIAF
KLNOMMMMMMMMMMMMNOPACFBACDDDEH 3chy_
-DFKLMMMMMMMMMMMNO 2fox_ JACKLMMMMMMMMMMMMM
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Contd

• Metallohydrolase superfamily members 1qh5a and
  1smla of equivalent length

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Contd

• 1bnka 1fmtb from all beta class FMT
  C-terminal domain like superfamily

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Structure mining
Score based ranking

• 98.2 89 of success rate in finding true
  class and fold resp. within top 10 hits

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Structure mining
Based on 7259 x 7259 pairwise PB alignments
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Protein Block Expert (PBE)

• Pair wise PB sequence alignment to compare two
  protein structure
• Mining of structurally similar proteins from SCOP
  at 95 database
• Preprocessed pair wise PB alignments at family
  and superfamily level
• Provides both local and global alignment
  algorithm falvors
• Available at http//bioinformatics.univ-reunion.fr
  /PBE/

Tyagi M, Sharma P, Swamy CS, Cadet F, Srinivasan
N, Brevern AG, Offmann B Protein Block Expert
(PBE) A web-based protein structure analysis
server using a structural alphabet. Nucl Acids
Res in press.
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Identification of conformational changes

• Rigid body superimposition methods e.g. STAMP
  report sequence alignment based on structurally
  equivalent and variable regions
• A cutoff/threshold residue residue rmsd value is
  used to define variable regions
• Are these high rmsd values, due to difference in
  conformations or rigid body displacment of
  equivalent regions ?
• We dont know from simple rigid body structure
  alignment

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Rigid body superimposition
Corresponding sequence alignment
Two proteins
Study substitution scores in variable regions
PB alignment
-ve
ve
Rigid body displacment
Conformation change
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• Analysis of two distantly related tRNA synthetase
  1eiy and 1set

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• Example of two zinc metallo proteinases 1hov and
  1fbl

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Cyclic AMP dependent protein kinase
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(No Transcript)
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Conclusion

• Use of simple PB sequence representation of 3D
  structure enables us to align and compare protein
  structures in simple and intuitive way
• PB alignment enables us to identify structurally
  equivalent regions and highlights subtle
  differences
• Efficient and fast mining process gt structural
  genomics
• Methodology is simple and can be used in other
  applications e.g. realignment of variable regions
  from rigid body superimposition alignment

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Thank you