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Literature DB >> 8939745

A structural explanation for the twilight zone of protein sequence homology.

Abstract

Homology modeling of protein structures as a function of sequence breaks down at the twilight zone limit of sequence identity between the template and target proteins. Our results suggest that protein sequences that have diverged from a common ancestor beyond the twilight zone may adopt side-chain interactions that are very different from those endowed by the ancestral sequence.

Mesh：

Substances：
Proteins

Year: 1996 PMID： 8939745 DOI： 10.1016/s0969-2126(96)00119-0

Source DB: PubMed Journal: Structure ISSN： 0969-2126 Impact factor: 5.006

Keyword Cloud
Cited

29 in total

1. Modeling of loops in protein structures.

Authors: A Fiser; R K Do; A Sali
Journal: Protein Sci Date: 2000-09 Impact factor: 6.725

2. Targeting of Ikaros to pericentromeric heterochromatin by direct DNA binding.

Authors: B S Cobb; S Morales-Alcelay; G Kleiger; K E Brown; A G Fisher; S T Smale
Journal: Genes Dev Date: 2000-09-01 Impact factor: 11.361

3. Sequence variations within protein families are linearly related to structural variations.

Authors: Patrice Koehl; Michael Levitt
Journal: J Mol Biol Date: 2002-10-25 Impact factor: 5.469

Review 4. Structural genomics: computational methods for structure analysis.

Authors: Sharon Goldsmith-Fischman; Barry Honig
Journal: Protein Sci Date: 2003-09 Impact factor: 6.725

5. The evolutionary origins and catalytic importance of conserved electrostatic networks within TIM-barrel proteins.

Authors: Dennis R Livesay; David La
Journal: Protein Sci Date: 2005-05 Impact factor: 6.725

6. Comparative mitochondrial genomics of freshwater mussels (Bivalvia: Unionoida) with doubly uniparental inheritance of mtDNA: gender-specific open reading frames and putative origins of replication.

Authors: Sophie Breton; Hélène Doucet Beaupré; Donald T Stewart; Helen Piontkivska; Moumita Karmakar; Arthur E Bogan; Pierre U Blier; Walter R Hoeh
Journal: Genetics Date: 2009-10-12 Impact factor: 4.562

A structural explanation for the twilight zone of protein sequence homology.

1. Modeling of loops in protein structures.

2. Targeting of Ikaros to pericentromeric heterochromatin by direct DNA binding.

3. Sequence variations within protein families are linearly related to structural variations.

Review 4. Structural genomics: computational methods for structure analysis.

5. The evolutionary origins and catalytic importance of conserved electrostatic networks within TIM-barrel proteins.

6. Comparative mitochondrial genomics of freshwater mussels (Bivalvia: Unionoida) with doubly uniparental inheritance of mtDNA: gender-specific open reading frames and putative origins of replication.

Review 7. Bioinformatics in support of molecular medicine.

8. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships.

9. Atomic interaction networks in the core of protein domains and their native folds.

10. Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be.