The objective of the proposed studies is to solve the three-dimensional structure of the intact psi-site of Human Immunodeficiency Virus type 1 (HIV-1), the approximately 120 nt segment of RNA responsible for genome recognition, packaging, and virus assembly. The complete psi-complex includes two copies of psi-RNA and an undetermined number of units of nucleocapsid protein p7 (NC) and is too large to be structurally characterized by NMR. Its apparent flexibility has thus far prevented crystallization for structural studies by X-ray diffraction. The 3D structures of the 4 individual RNA stem-loops believed to form the psi-site and those of their complexes with NC have been solved by NMR and could be used as starting data for the molecular modeling of the intact complex. Distance constraints, spatial orientation, and points of contact between the stem-loops will be obtained by a novel strategy based on chemical and biochemical probes in combination with electrospray ionization-ion cyclotron resonance (ESI-ICR) mass spectrometry. In particular, we will apply ESI-ICR to obtain the stoichiometry of binding between psi-RNA and NC in the intact psi-complex and to characterize the products of nucleic acid and proteic nature (or both for crosslinked species) provided by probing psi-RNA and its complex with NC. Mass mapping and MS/MS sequencing techniques will be employed to identify the location of the points of attack of each probe. The distance constraints obtained experimentally will be used in restrained structural calculations to determine the global fold of psi-RNA in presence and absence of NC. The use of electrospray ionization mass spectrometry as the detection method for classical probes offers the possibility of detecting in parallel a large number of molecular contacts with no need for labor-intensive separation procedures or radioactive tracers. Based on the large choice of available probes and the capability of handling large size RNAs, which are beyond the detection limit of NMR spectroscopy, this approach promises to have a major impact on the investigation of RNA-RNA and RNA-protein interactions. The long-term goal is to understand the molecular basis for the recognition and packaging of the retroviral genome mediated by the psi-site. A full understanding of this mechanism is crucial to elucidate at the molecular level the process of assembly and maturation of HIV-1 and similar retro-viruses and should facilitate the design of new therapeutic strategies for AIDS and cancer.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM064328-05
Application #
6928658
Study Section
Special Emphasis Panel (ZRG1-AARR-1 (01))
Program Officer
Edmonds, Charles G
Project Start
2001-08-01
Project End
2006-08-31
Budget Start
2005-08-01
Budget End
2006-08-31
Support Year
5
Fiscal Year
2005
Total Cost
$249,263
Indirect Cost
Name
University of Maryland Balt CO Campus
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
061364808
City
Baltimore
State
MD
Country
United States
Zip Code
21250
Lippens, Jennifer L; Mangrum, J B; McIntyre, William et al. (2016) A simple heated-capillary modification improves the analysis of non-covalent complexes by Z-spray electrospray ionization. Rapid Commun Mass Spectrom 30:773-83
Rose, Rebecca E; Pazos 2nd, Manuel A; Curcio, M Joan et al. (2016) Global Epitranscriptomics Profiling of RNA Post-Transcriptional Modifications as an Effective Tool for Investigating the Epitranscriptomics of Stress Response. Mol Cell Proteomics 15:932-44
Lippens, Jennifer L; Ranganathan, Srivathsan V; D'Esposito, Rebecca J et al. (2016) Modular calibrant sets for the structural analysis of nucleic acids by ion mobility spectrometry mass spectrometry. Analyst 141:4084-99
Spell, Sarah R; Mangrum, John B; Peterson, Erica J et al. (2016) Au(iii) compounds as HIV nucleocapsid protein (NCp7)-nucleic acid antagonists. Chem Commun (Camb) 53:91-94
Rose, Rebecca E; Quinn, Ryan; Sayre, Jackie L et al. (2015) Profiling ribonucleotide modifications at full-transcriptome level: a step toward MS-based epitranscriptomics. RNA 21:1361-74
Tosoni, Elena; Frasson, Ilaria; Scalabrin, Matteo et al. (2015) Nucleolin stabilizes G-quadruplex structures folded by the LTR promoter and silences HIV-1 viral transcription. Nucleic Acids Res 43:8884-97
Welch, Joshua D; Slevin, Michael K; Tatomer, Deirdre C et al. (2015) EnD-Seq and AppEnD: sequencing 3' ends to identify nontemplated tails and degradation intermediates. RNA 21:1375-89
Scalabrin, Matteo; Siu, Yik; Asare-Okai, Papa Nii et al. (2014) Structure-specific ribonucleases for MS-based elucidation of higher-order RNA structure. J Am Soc Mass Spectrom 25:1136-45
Doria, Filippo; Nadai, Matteo; Folini, Marco et al. (2013) Targeting loop adenines in G-quadruplex by a selective oxirane. Chemistry 19:78-81
Quinn, Ryan; Basanta-Sanchez, Maria; Rose, Rebecca E et al. (2013) Direct infusion analysis of nucleotide mixtures of very similar or identical elemental composition. J Mass Spectrom 48:703-12

Showing the most recent 10 out of 19 publications