Stem-loop SL4 of the HIV-1 Ψ RNA packaging signal exhibits weak affinity for the nucleocapsid protein. Structural studies and implications for genome recognition

Journal of Molecular Biology

Volumn 314, Issue 5, 2001, Pages 961-970

  Amarasinghe, Gaya K ^a   Zhou, Jing ^a   Miskimon, Matthew ^a   Chancellor, Kalola J ^a   McDonald, Jasmine A ^a   Matthews, Akida G ^a   Miller, Robyn R ^a   Rouse, Michael D ^a   Summers, Michael F ^a  

^a UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

Author keywords

Human immunodeficiency virus; NMR; Nucleocapsid protein; Psi site; RNA

Indexed keywords

GAG PROTEIN; NUCLEOCAPSID PROTEIN; STEM LOOP 2 PROTEIN; STEM LOOP 3 PROTEIN; STEM LOOP 4 PROTEIN; UNCLASSIFIED DRUG; VIRUS PROTEIN; VIRUS RNA;

ARTICLE; BINDING AFFINITY; CALORIMETRY; CONTROLLED STUDY; DISSOCIATION CONSTANT; DNA PACKAGING; ENCAPSULATION; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR RECOGNITION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN RNA BINDING; RNA STABILITY; RNA STRUCTURE; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; TITRIMETRY; VIRUS ASSEMBLY;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; UNIDENTIFIED RETROVIRUS;

EID: 0035861980     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2000.5182     Document Type: Article

References (62)

1. Identification of a sequence required for efficient packaging of human immunodeficiency virus type 1 RNA into virions
2. Mutations of RNA and protein sequences involved in human immunodeficiency virus type 1 packaging result in production of noninfectious virus
3. A mutant of human immunodeficiency virus with reduced RNA packing and abnormal particle morphology
4. Gene transfer into human lymphocytes by a defective human immunodeficiency virus type 1 vector
5. Mass determination of Rous sarcoma virus virions by scaning transmission electron microscopy
6. The human immunodeficiency virus type 1 packaging signal and major splice donor region have a conserved stable secondary structure
7. Specific binding of human immunodeficiency virus type 1 gag polyprotein and nucleocapsid protein to viral RNAs detected by RNA mobility shift assays
8. Analysis of binding elements in the human immunodeficiency virus type 1 genomic RNA and nucleocapsid protein
9. Functional sites in the 5′ region of human immunodeficiency virus type 1 RNA form defined structural domains
10. RNA secondary structure and binding sites for gag gene products in the 5′ packaging signal of human immunodeficiency virus type 1
11. Mutant human immunodeficiency virus type 1 genomes with defects in RNA dimerization or encapsidation
12. Idenification of a binding site for the human immunodeficiency virus type 1 nucleocapsid protein
13. The human immunodeficiency virus type 1 encapsidation site is a multipartite RNA element composed of functional hairpin structures
14. Position dependence of functional hairpins important for human immunodeficiency virus type 1 RNA encapsidation in vivo
15. A heterologous, high-affinity RNA ligand for human immunodeficiency virus Gag protein has RNA packaging activity
16. RNA packaging
17. Retroviral RNA packaging: A review
18. Varying the position of a retrovirus packaging sequence results in the encapsidation of both unspliced and spliced RNA
19. NMR structure of stem loop SL2 of the HIV-1 Y-RNA packaging signal reveals a novel A-U-A base triple platform
20. RNA packaging signal of human immunodeficiency virus type 1
21. Functional analysis of the core human immunodeficiency virus type 1 packaging signal in a permissive cell line
22. NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the Y-RNA packaging signal
23. Structure of the HIV-1 nucleocapsid protein bound to the SL3 Y-RNA recognition element
24. Dynamical behavior of the HIV-1 nucleocapsid protein
25. Advanced 5′-silyl-2′-orthoester approach to RNA oligonucleotide synthesis
26. Synthesis of small RNAs using T7 RNA polymerase
27. Synthesis and purification of large amounts of RNA oligonucleotides
28. Binding of human immunodeficiency virus type-1 nucleocapsid protein to psi RNA SL3
29. A network of heterogeneous hydrogen bonds in GNRA tetraloops
30. The conformation of the sarcin/ricin loop from 28 S ribosomal RNA
31. The sarcin/ricin loop, a modular RNA
32. High-resolution NMR study of a synthetic oligonucleotide with a tetranucleotide GAGA loop that is a substrate for the cytotoxic protein, ricin
33. High resolution NMR study of GdAGA tetranucleotide loop that is an improved substrate for ricin, a cytotoxic plant protein
34. Crystal structure of the ribosomal RNA domain essential for binding elongation factors
35. Structural studies on site-directed mutants of domain 3 of Xenopus laevis oocyte 5 S ribosomal RNA
36. Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: Solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing
37. Investigation of the structural basis for thermodynamic stabilities of tandem GU wobble pairs: NMR structures of (rGGAGUUCC)2 and (rGGAUGUCC)2
38. Three-dimensional folding of an RNA hairpin required for packaging HIV-1
39. Modeling of the three-dimensional architecture of group I catralytic introns based on comparative sequence analysis
40. Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin
41. Remarkable morphological variability of a common RNA folding motif: The GNRA tetraloop-receptor interaction
42. RNA tertiary structure mediation by adenosine platforms
43. Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: Comparison with in vivo evolution
44. Involvement of a GNRA tetraloop in long-range RNA tertiary interactions
45. GAAA tetraloop and conserved bulge stabilize tertiary structure of a group-I intron domain
46. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix
47. Three-dimensional structure of a hammerhead ribozyme
48. Preparation of isotopically enriched RNAs for heteronuclear NMR
49. Investigation of exchange processes by two-dimensional NMR spectroscopy
50. Elucidation of cross relaxation in liquids by two-dimensional NMR spectroscopy
51. Separation of chemical exchange and cross relaxation effects in two-dimensional NMR spectroscopy
52. Coherence transfer by isotropic mixing: Application to proton correlation spectroscopy
53. 1H spin system identification in macromolecules
54. 13C assignments from sensitivity enhanced detection of heteronuclear multiple bond connectivity by 2D multiple quantum NMR
55. NMRPipe: A multidimensional spectral processing system based on UNIX pipes
56. NMRview: A computer program for the visualization and analysis for NMR data
57. 2O in protein NMR. Application to sensitivity enhancement and NOE measurement
58. Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions
59. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
60. Raster3D: Photo-realistic molecular graphics
61. Characterization of the Hantaan nucleocapsid protein-ribonucleic acid interaction