Amphiphilicity index index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces

Bioinformatics

Volumn 18, Issue 4, 2002, Pages 608-616

  Mitaku, Shigeki ^a   Hirokawa, Takatsugu ^a,b   Tsuji, Toshiyuki ^a  

^a TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; AMINO ACID; ARGININE; ASPARAGINASE; ASPARTIC ACID; CARBON; CYSTEINE; GLUTAMIC ACID; GLUTAMINE; GLYCINE; HISTIDINE; HYDROCARBON; ISOLEUCINE; LEUCINE; LYSINE; MEMBRANE PROTEIN; METHIONINE; PHENYLALANINE; PROLINE; SERINE; THREONINE; TRYPTOPHAN; TYROSINE; VALINE; WATER;

AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; ARTICLE; COMPUTER SYSTEM; CONTROLLED STUDY; ENERGY TRANSFER; HYDROPHOBICITY; MEMBRANE COMPONENT; PRIORITY JOURNAL; PROTEIN STRUCTURE; SURFACE PROPERTY; CHEMICAL MODEL; CHEMISTRY; CLASSIFICATION; MOLECULAR GENETICS; OPEN READING FRAME; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN FOLDING; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY;

AMINO ACID SEQUENCE; AMINO ACIDS; DATABASES, PROTEIN; MEMBRANE PROTEINS; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PROTEIN CONFORMATION; PROTEIN FOLDING; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; WATER;

EID: 0035999985     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.4.608     Document Type: Article

References (41)

1. The aromatic residues Trp and Phe have different effects on the positioning of a transmembrane helix in the microsomal membrane
2. Structure of the MscL homolog from Mycobacteria tuberculosis: A gated mechanosensitive ion channel
3. Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3A resolution
4. Composition of proteins
5. The structure of the potassium channel: Molecular basis of K+ conduction and selectivity
6. Solvation energy in protein folding and binding
7. The hydrophobic moment detects periodicity in protein hydrophobicity
8. The identification of helical segments in the polypeptide chain of bacteriorhodopsin
9. Solution structure of the transmembrane H+-transporting subunit c of the F1F0 ATP synthase
10. SOSUI: Classification and secondary structure prediction system for membrane proteins
11. Selection of a representative set of structures from the Brookhaven protein data bank
12. Structure of the Escherichia coli fumarate reductase respiratory complex
13. Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex
14. How proteins adapt to a membrane-water interface?
15. Surface of bacteriorhodopsin revealed by high-resolution electron crystallography
16. Structure of the light-driven chloride pump halorhodopsin at 1.8 A resolution
17. The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianum
18. A simple method for displaying the hydropathic character of a protein
19. Structure of fumarate reductase from Wolinella succinogenes at 2.2 A resolution
20. Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria
21. The role of hydrophobic interaction in phase transition and structure formation of lipid membrane and proteins
22. Physicochemical factors for discriminating between soluble and membrane proteins: Hydrophobicity of helical segments and length of proteins
23. Spectral analysis of amino acid sequence. II. Characterization of α-helices by local periodicity
24. Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by a prediction system SOSUI
25. A collection of well characterized integral membrane proteins
26. Cluster analysis of amino acid indices for prediction of protein structure and function
27. Crystal structure of rhodopsin: A G protein-coupled receptor
28. Characterization and modeling of membrane proteins using sequence analysis
29. Analysis of the role of interfacial tryptophan residues in controlling the topology of membrane proteins
30. The functions of tryptophan residues in membrane proteins
31. Amphipathic helix motif: Classes and properties
32. Structure and mechanism of the aberrant ba(3)-cytochrome c oxidase from Thermusthermophilus
33. The Hydrophobic Effect; Formation of Micelles and Biological Membrane
34. Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution
35. The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A
36. Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins
37. Membrane protein structure prediction hydrophobicity analysis and the positive-inside rule
38. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
39. Architecture of helix bundle membrane proteins: An analysis of cytochrome c oxidase from bovine mitochondria