Persistently conserved positions in structurally similar, sequence dissimilar proteins: Roles in preserving protein fold and function

Protein Science

Volumn 11, Issue 2, 2002, Pages 350-360

  Friedberg, Iddo ^a   Margalit, Hanah ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

Bioinformatics; Molecular evolution; Protein folding; Protein structure; Sequence conservation

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

AMINO ACID MOTIFS; ANIMALS; DATABASES, FACTUAL; HUMANS; HYDROLASES; LIPASE; PEPTIDES; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SEQUENCE ALIGNMENT; SOLVENTS; XANTHOBACTER;

EID: 0036145469     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.18602     Document Type: Article

References (43)

1. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
2. Helix capping
3. The protein data bank
4. Pairwise sequence alignment below the twilight zone
5. Deciphering the message in protein sequences: Tolerance to amino acid substitutions
6. Expectations from structural genomics
7. Identification of kinetically hot residues in proteins
8. Stabilization centers in proteins: Identification, characterization and predictions
9. Glimmers in the midnight zone: Characterization of aligned identical residues in sequence-dissimilar proteins sharing a common fold
10. Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments
11. Amino acid substitution matrices from protein blocks
12. Enlarged representative set of protein structures
13. The FSSP database: Fold classification based on structure-structure alignment of proteins
14. Search for a new description of protein topology and local structure
15. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
16. Identification of side-chain clusters in protein structures by a graph spectral method
17. Replacement of tryptophan residues in haloalkane dehalogenase reduces halide binding and catalytic activity
18. Structure-based conformational preferences of amino acids
19. Characterization of novel proteins based on known protein structures
20. Dissecting α-helices: Position-specific analysis of α-helices in globular proteins
21. Alternative packing arrangements in the hydrophobic core of lambda repressor
22. Divergence measures based on the Shannon entropy
23. Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as "spacers" which do not require a specific sequence
24. Protein stability effects of a complete set of alanine substitutions in Arc repressor
25. Interior and surface of monomeric proteins
26. Evolutionary conservation of the folding nucleus
27. Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function
28. How evolution makes proteins fold quickly
29. SCOP: A structural classification of proteins database for the investigation of sequences and structures
30. Amino acid pair interchanges at spatially conserved locations
31. SSAP: Sequential structure alignment program for protein structure comparison
32. Protein superfamilies and domain superfolds
33. CATH - A hierarchic classification of protein domain structures
34. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
35. Structure-derived substitution matrices for alignment of distantly related sequences
36. Non-functional conserved residues in globins and their possible role as a folding nucleus
37. Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins
38. Systematic mutation of bacteriophage T4 lysozyme
39. A graph-theoretic algorithm for comparative modeling of protein structure
40. Identification of common molecular subsequences
41. Genetic studies of the Lac repressor. XV: 4000 Single amino acid substitutions and analysis of the resulting phenotypes on the basis of the protein structure
42. The sequence, crystal structure determination and refinement of two crystal forms of lipase B from Candida antarctica
43. Refined x-ray structures of haloalkane dehalogenase at pH 6.2 and pH 8.2 and implications for the reaction mechanism