Computational Analysis of Protein-DNA Interactions

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Computational Analysis of Protein-DNA Interactions

• Changhui (Charles) Yan
• Department of Computer Science
• Utah State University

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Problem I

• Identifying amino acid residues involved in
  protein-DNA interactions from sequence

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Materials And Methods

• 56 double-stranded DNA binding proteins
  previously used in the study of Jones et al.
  (2003)
• Encoding

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Materials And Methods
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Naïve Bayes Classifier

• Leave-one-out cross-validation

Naïve Bayes
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Naïve Bayes Classifier

• Leave-one-out cross-validation

Naïve Bayes
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Leave-One-Out Cross-Validations
Sequence-based Sequence-based Sequence/structure-based Sequence/structure-based
Identities (ID) ID entropy ID rASA ID rASA entropy
Correlation coefficient 0.25 0.29 0.28 0.30
Accuracy() 77 75 76 77
Specificity() 37 37 36 39
Sensitivity() 43 53 51 52
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Predictions in The Context of 3-D Structures
Actual
Predicted

• Pit-1, PDB 1au7
• TP30
• FP 16
• TN 86
• FN14
• CC 0.51 (2nd)
• Accuracy 79

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Predictions in The Context of 3-D Structures
Predicted
Actual

• ?-Cro, PDB 6cro
• TP10
• FP 5
• TN 34
• FN10
• CC 0.37 (19th)
• Accuracy 73

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Predictions Compared With PROSITE Motifs

• Predicted binding sites substantially overlap
  with 34 of the 37 DNA-binding PROSITE motifs
• In 52 of the 56 proteins, the predictor
  identifies at least 20 of the DNA-binding
  residues
• 28 of the 56 proteins contain no PROSITE motifs
  that are annotated as DNA-binding

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Comparison With Previous Study
Method Naïve Bayes classifier Ahmad and Sarai method
Correlation Coefficient 0.26 0.23
Accuracy () 80 66
Specificity() 29 21
Sensitivity() 48 68
Ahmad, S. and Sarai, A. (2005) PSSM-based
prediction of DNA binding sites in proteins. BMC
Bioinformatics, 6, 33.
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Summary

• A simple sequence-based Naive Bayes classifier
  predicts interface residues in DNA-binding
  proteins with 75 accuracy, 37 specificity, 53
  sensitivity and correlation coefficient of 0.29
• Predicted binding sites
• correctly indicate the locations of actual
  binding sites
• substantially overlap with known PROSITE motifs

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Problem II

• Identification of Helix-Turn-Helix (HTH)
  DNA-binding motifs

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HTH Motifs

• Sequences sharing low similarities can fold into
  a similar HTH structure
• Identifying HTH motifs from sequence is extremely
  challenging

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Trick 1

• Including more information
• Amino acid sequence
• Secondary structure

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Hidden Markov Model (HMM)
LQQITHIANQL-GLE----KDVVRVWF
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Hidden Markov Model (HMM_AA_SS)
LQQITHIANQL-GLE----KDVVRVWF
HHHEEHEEEHMHE----HHEEMMEH
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Trick 2

• There are similarities among the 20 naturally
  occurred amino acids
• Reduced alphabets

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Reduced Alphabets

• Schemes for reducing amino acid alphabet based on
  the BLOSUM50 matrix by Henikoff and Henikoff
  (1992) derived by grouping and averaging the
  similarity matrix elements as described in the
  text. (Murphy et al. 2000)

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Cross-Families Evaluations
True Positive 1 False Positive 2
HMM_AA 3 0
HMM_AA_SS (20 letters) 3 227 0
HMM_AA_SS (Murphy_15) 3 474 0
HMM_AA_SS (Murphy_10) 3 470 3
HMM_AA_SS (Murphy_8) 3 431 5

1. True positive HTH motifs that are correctly
   identified as such.
2. False positive Non-HTH motifs that are
   identified as HTH motifs.
3. The alphabet used to encode amino acid sequences.

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Questions
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Within-family Three-Fold Cross-Validations
Family (number of HTH motifs in the family) HMM_AA HMM_AA_SS (Murphy_15)
PF00126 (1635) 1594 1622
PF00165 (90) 63 80
PF00196 (30) 26 30
PF04545 (164) 137 164
PF01022 (42) 39 39
PF00046 (189) 176 188
PF03965 (48) 48 48
.
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Comparisons of HMM_AA_SS with FFAS03 in
Cross-Family Evaluations
Total HTH motifs Recognized by both FFAS03 and HMM_AA_SS Recognized by FFAS03 only Recognized by HMM_AA_SS only
563 135 24 71
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Putative HTH motifs in Ureaplasma parvum
Protein Location Annotation from Uniprot
spQ9PQE5SCPB_UREPA 176-214 Participates to chromosomal partition during cell division
spQ9PQV6RPOB_UREPA 540-587 DNA-directed RNA polymerase
spQ9PR27SYY_UREPA 340-380 Tyrosyl-tRNA synthetase
spQ9PQC2SYA_UREPA 217-265 Alanyl-tRNA synthetase
spQ9PQ74DPO3A_UREPA 365-400 DNA polymerase III subunit alpha
spQ9PQX7Y166_UREPA 507-553 Hypothetical protein