Comparative modelling of cytochromes P450

Advanced Drug Delivery Reviews

Volumn 54, Issue 3, 2002, Pages 385-406

  Kirton, Stewart B ^a   Baxter, Carol A ^a   Sutcliffe, Michael J ^a  

^a UNIVERSITY OF LEICESTER   (United Kingdom)

Author keywords

Model validation; Protein modelling; Sequence alignment; Structure prediction

Indexed keywords

CRYSTAL STRUCTURE; ENZYMES; HORMONES; METABOLISM; PROTEINS; STEREOCHEMISTRY;

CYTOCHROMES;

DRUG DOSAGE;

BACTERIAL ENZYME; CYTOCHROME P450; CYTOCHROME P450 ISOENZYME;

AMINO ACID SEQUENCE; COMPARATIVE STUDY; CRYSTAL STRUCTURE; DNA TEMPLATE; ENZYME ANALYSIS; ENZYME STRUCTURE; EVALUATION; MOLECULAR MODEL; NONHUMAN; PREDICTION; PRIORITY JOURNAL; QUALITY CONTROL; REVIEW; SEQUENCE ALIGNMENT; STEREOCHEMISTRY;

AMINO ACID SEQUENCE; ANIMALS; CYTOCHROME P-450 ENZYME SYSTEM; HUMANS; INFANT, NEWBORN; ISOENZYMES; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; TEMPLATES, GENETIC;

EID: 0037204550     PISSN: 0169409X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0169-409X(02)00010-8     Document Type: Article

References (71)

1. The relation between the divergence of sequence and structure in proteins
2. Crystal structure of hemoprotein domain of P450BM-3, a prototype for microsomal P450s
3. Molecular modelling of CYP3A4 from an alignment with CYP102: Identification of key interactions between putative active site residues and CYP3A-specific chemicals
4. The CYP2 family: Models, mutants and interactions
5. Complete cDNA and protein sequence of a pregnenolone 16 alpha-carbonitrile-induced cytochrome P-450. A representative of a new gene family
6. The protein data bank
7. Molecular modelling of CYP1A subfamily members based on an alignment with CYP102: Rationalization of CYP1A substrate specificity in terms of active site amino acid residues
8. Molecular modelling of members of the P4502A subfamily: Application to studies of enzyme specificity
9. Application of 3-dimensional homology modeling of cytochrome P450 2B1 for interpretation of site-directed mutagenesis results
10. Molecular modelling of mammalian CYP2B isoforms and their interaction with substrates, inhibitors and redox partners
11. Molecular modelling of CYP2B6, the human CYP2B isoform, by homology with the substrate-bound CYP102 crystal structure: Evaluation of CYP2B6 substrate characteristics, the cytochrome b5 binding site and comparisons with CYP2B1 and CYP2B4
12. Molecular modelling of human CYP2C subfamily enzymes CYP2C9 and CYP2C19: Rationalization of substrate specificity and site-directed mutagenesis experiments in the CYP2C subfamily
13. Molecular modelling of cytochrome P4502D6 (CYP2D6) based on an alignment with CYP102: Structural studies on specific CYP2D6 substrate metabolism
14. Homology modelling of human cytochromes P450 involved in xenobiotic metabolism and rationalization of substrate selectivity
15. A hypothetical model for the active site of human cytochrome P4502E1
16. Microsomal cytochrome P450 2C5: Comparison to microbial P450s and unique features
17. Molecular modeling of cytochrome P450 2B1: Mode of membrane insertion and substrate specificity
18. Construction of a 3D model of cytochrome P450 2B4
19. Homology modeling and substrate binding study of human CYP2C9 enzyme
20. Homology modeling and substrate binding study of human CYP2C18 and CYP2C19 enzymes
21. A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of substrate binding
22. A three-dimensional protein model for human cytochrome P450 2D6 based on the crystal structures of P450 101, P450 102, and P450 108
23. Molecular modeling of cytochrome P450 3A4
24. Homology modeling and substrate binding study of human CYP4A11 enzyme
25. Alignment of the amino acid sequences of distantly related proteins using variable gap penalties
26. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
27. Assessment of comparative modeling in CASP2
28. Structure of a cytochrome P450-redox partner electron-transfer complex
29. Crystal structure and refinement of cytochrome P450terp at 2.3 Å resolution
30. Crystal structures of ligand complexes of P450eryF exhibiting homotropic cooperativity
31. Crystal structure of substrate-free Pseudomonas putida cytochrome P-450
32. Crystal structure of nitric oxide reductase from denitrifying fungus Fusarium oxysporum
33. Arginines 97 and 108 in CYP2C9 are important determinants of the catalytic function
34. Structure and function of cytochromes P450: A comparative analysis of three crystal structures
35. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
36. Comparative protein modelling by satisfaction of spatial restraints
37. The FSSP database: Fold classification based on structure-structure alignment of proteins
38. Physical methods in the study of the active site geometry of cytochromes P-450
39. A predictive model for substrates of cytochrome P450-debrisoquine (2D6)
40. Determinants of the substrate specificity of human cytochrome P-450 CYP2D6: Design and construction of a mutant with testosterone hydroxylase activity
41. The structure of the cytochrome p450BM-3 haem domain complexed with the fatty acid substrate, palmitoleic acid
42. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
43. Protein secondary structure prediction based on position-specific scoring matrices
44. Knowledge based modelling of homologous proteins. Part II: Rules for the conformations of substituted sidechains
45. Knowledge based modelling of homologous proteins. Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures
46. An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies
47. Main-chain bond lengths and bond angles in protein structures
48. Deviations from standard atomic volumes as a quality measure for protein crystal structures
49. Homology modeling, model and software evaluation: Three related resources
50. Assessment of protein models with three-dimensional profiles
51. Verification of protein structures: Patterns of nonbonded atomic interactions
52. Criteria that discriminate between native proteins and incorrectly folded models
53. Criteria for evaluating protein structures derived from comparative modeling
54. CASP3 comparative modeling evaluation
55. Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences
56. Structures of eukaryotic cytochrome P450 enzymes
57. Stereochemical quality of protein structure coordinates