Efficient aminoacylation of the tRNAAla acceptor stem: Dependence on the 2:71 base pair

RNA

Volumn 8, Issue 5, 2002, Pages 659-670

  Beuning, Penny J ^a   Nagan, Maria C ^a   Cramer, Christopher J ^a   Musier Forsyth, Karin ^a   Gelpí, Josep Lluis ^a   Bashford, Donald ^a  

^a University of Minnesota   (United States)

Author keywords

Atomic group mutagenesis; Electrostatic potential; Molecular dynamics; Molecular interaction potential; RNA recognition; TRNA acceptor stem

Indexed keywords

ALANINE; AMINO ACID TRANSFER RNA LIGASE; PURINE; PYRIMIDINE; TRANSFER RNA;

AMINOACYLATION; ARTICLE; BASE PAIRING; CALCULATION; DIELECTRIC CONSTANT; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; MUTAGENESIS; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL;

ACYLATION; ALANINE-TRNA LIGASE; BASE PAIRING; BASE SEQUENCE; ELECTROSTATICS; ESCHERICHIA COLI; HYDROGEN BONDING; MUTAGENESIS, SITE-DIRECTED; NUCLEIC ACID CONFORMATION; RNA, BACTERIAL; RNA, TRANSFER, ALA; THERMODYNAMICS;

EID: 0036247311     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838202020277     Document Type: Article

References (71)

1. Water and ion binding around RNA and DNA (C,G) oligomers
2. An object-oriented programming suite for electrostatic effects in biological molecules
3. a values of ionizable groups in bacteriorhodopsin
4. Molecular dynamics with coupling to an external bath
5. Atomic group "mutagensis" reveals major groove fine interactions of a tRNA synthetase with an RNA helix
6. Transfer RNA recognition by aminoacyl-tRNA synthetases
7. Specific atomic groups and RNA helix geometry in acceptor stem recognition by a tRNA synthetase
8. Metal-binding sites in the major groove of a large ribozyme domain
9. Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes
10. Calculating the electrostatic properties of RNA provides new insights into molecular interactions and functions
11. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
12. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain
13. Ser and a seryl-adenylate analogue reveals a conformational switch in the active site
14. Self-consistent molecular-orbital methods. IX. An extended Gaussian-type basis for molecular-orbital studies of organic molecules
15. Active site titration and aminoacyl adenylate binding stolchiometry of aminoacyl-tRNA synthetases
16. Identification of discriminator base atomic groups that modulate the alanine aminoacylation reaction
17. Aminoacylation of RNA minihelices with alanine
18. Overlapping nucleotide determinants for specific aminoacylation of RNA microhelices
19. Improved free-energy parameters for predictions of RNA duplex stability
20. Classical molecular interaction potentials. Improved setup procedure in molecular dynamics simulations of proteins
21. Universal rules and idiosyncratic features in tRNA identity
22. Calculation of total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
23. The effects of d-functions on molecular orbital energies for hydrocarbons
24. Self-consistent molecular orbital methods. XII. Further extensions of Gaussian-type basis sets for use in molecular orbital studies of organic molecules
25. A simple structural feature is a major determinant of the identity of a transfer RNA
26. VMD: Visual molecular dynamics
27. Aminoacyl-tRNA synthesis
28. Comparison of simple potential functions for simulating liquid water
29. Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt(III) hexamine
30. The electrostatic field of DNA: The role of nucleic acid conformation
31. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
32. Defining the structure of irregular nucleic acids: Conventions and principles
33. Ion-RNA interactions in the RNA pseudoknot of a ribosomal frameshifting site: Molecular modeling studies
34. Single atomic group in RNA helix needed for positive and negative tRNA synthetase discrimination
35. Changing the identity of a tRNA by introducing a G-U wobble pair near the 3′ acceptor end
36. Ala determine the molecule's acceptor identity
37. Salt effects on protein-DNA interactions. The lambda cI repressor and EcoRI endonuclease
38. Crystal structure of acceptor stem of tRNA(Ala) from Escherichia coli shows unique G.U wobble base pair at 1.16 Å resolution
39. Transfer RNA acceptor stem determinants for specific aminoacylation by class II aminoacyl-tRNA synthetases
40. Functional contacts of a transfer RNA synthetase with 2′-hydroxyl groups in the RNA minor groove
41. Atomic determinants for aminoacylation of RNA minihelices and relationship to genetic code
42. Base analog-induced aminoacylation of an RNA helix by a tRNA synthetase
43. Specificity for aminoacylation of an RNA helix: An unpaired, exocyclic amino group in the minor groove
44. AIa variants
45. AIa and 3:70 variants: Molecular dynamics analysis of local helical structure and tightly bound water
46. Molecular interaction potential: A new tool for the theoretical study of molecular reactivity
47. Proton NMR studies of manganese ion binding to tRNA-derived acceptor stem duplexes
48. Evidence for interaction of an aminoacyl transfer RNA synthetase with a region important for the identity of its cognate transfer RNA
49. Ala: Role of the G3:U70 base pair in synthetase recognition
50. Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
51. Ser acceptor stem by E. coli seryl-tRNA synthetase
52. Thr complex enlightens its repressor activity and reveals an essential zinc ion in the active site
53. Reduced surface: An efficient way to compute molecular surfaces
54. Chemical synthesis of biologically active oligoribonucleotides using β-cyanoethyl protected ribonucleoside phosphoramidites
55. Multiple structures for the 2-aminopurine-cytosine mispair
56. An efficient method for the isolation and purification of oligoribonucleotides
57. Unusual metal ion catalysis in an acyl-transferase ribozyme
58. RNA structure prediction
59. Structural alignment of ferredoxin and flavodoxin based on electrostatic potentials: Implications for their interactions with photosystem I and ferredoxin-NADP reductase
60. Structural and dynamic helix geometry alterations induced by mismatch base pairs in double-helical RNA
61. Major groove accessibility of RNA
62. Synthesis and pairing properties of oligoribo-nucleotide analogues containing a metal-binding site attached to β-D-allofuranosyl cytosine
63. The effects of long-range electrostatic interactions in simulations of macromolecular crystals: Comparison of the Ewald and truncated list methods
64. Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets