CRNA Investigators and Technologies
Hashim M. Al-Hashimi, PI
RNA Dynamics and Inhibitors
ha2639@cumc.columbia.edu
RNA-targeted high-throughput screening
Structure-based lead compound optimization
Visualization of transient RNA structure
Dynamics support in RNA molecular/structural biology
Paul Bieniasz, PI
RNA protein interactions in HIV-1 replication
Structure and function of Zinc finger antiviral proteins and cofactors
Identification of antiviral proteins
Regulation of HIV-1 gene expression, splicing and latency
HIV-1 assembly and HIV-1 RNA packaging
Charles Bou-Nader, Collaborative Development Awardee
Structural biochemistry of R-loops and ribonucleoprotein complexes
charles.bou.nader@emory.edu
Defining viral nucleic acid sensing by the host
Determining the molecular basis of ribonucleoprotein complex assembly using cryo-EM and X-ray crystallography
Uncovering the role of secondary messengers in innate immunity during HIV infection
Mechanistic basis of gene regulation during viral infection
Shi-Jie Chen, Collaborative Development Awardee
Computational Structural Biology
chenshi@missouri.edu
RNA structure prediction
Computational modeling of cotranscriptional folding
RNA-ligand docking and virtual screening
David Case, PI
Computational Methods: Force fields & refinement
david.case@rutgers.edu
Molecular dynamics simulations (with explicit or implicit solvent) of RNA or RNA/protein complexes
Structure refinement based on experimental restraints derived from NMR, X-ray or cryo-EM measurements
The "inverse folding" problem for RNA: design of sequences to match secondary structure motifs
Victoria D'Souza, PI
Ribosomal frame shifting
Understand how programmed ribosomal frameshfiting is used to precisely maintain the Gag to Gag-Pol protein ratio
Understand the structure and dynamics of the RNA regulatory signal that regulates frameshifting
Understand the interactions between the RNA regulatory signal and the ribosome
Kwaku Dayie, PI
RNA Labeling: Enzymatic Methods
Chemo-enzymatic synthesis of atom specifically labeled nucleotides
Biomass synthesis of labeled nucleotides
Site alternate labeled nucleotides in support of NMR structure and dynamic studies
Stephen Goff, PI
Regulation of HIV-1 RNA synthesis and trafficking
spg1@cumc.columbia.edu
Silencing of unintegrated HIV-1 DNA; Histones and histone modifications associated with silencing; Host factors required for silencing.
Mechanisms of reactivation of latent proviruses to initiate RNA synthesis. Post-transcriptional regulation of escape from latency.
Mechanism of action of the host restriction factor ZAP in targeting and degrading viral RNAs. We will identify and characterize new host cofactors involved in stimulating ZAP activity.
Exploring the mechanisms for translational frameshifting at the Gag-Pol junction.
Probing the host regulation of viral mRNA export from the nucleus.
Amanda Hargrove, PI
Small Molecule: RNA Recognition
amanda.hargrove@duke.edu
RNA ligand design and synthesis
Analysis of small molecule:RNA binding interactions
Synthetic incorporation of modified nucleobases
Small molecule: RNA screening
Theodora Hatziioannou, PI
Interactions of host antiviral proteins with viral RNA and viral antagonists
thatziio@mail.rockefeller.edu
Structure and function of viral and antiviral proteins
Interactions of antiviral factors with viral RNA
Species-specific evolution of viral and host factors
Molecular virology techniques
Sun Hur, PI
RNA sensing and TRIM E3 ligases
sun.hur@crystal.harvard.edu
defining HIV-1 RNA selectivity of TRIM56
determining the structure of TRIM56 in complex with HIV-1 RNA
defining the downstream consequence of TRIM56-RNA recognition
Bruce A. Johnson, PI
Computational Methods: NMR data analysis
RNA chemical shift prediction
Chemical shift assignment tools
RNA structure calculation
Signal Processing and Machine Learning as applied to RNA NMR data
Deepak Koirala, Collaborative Development Awardee
3D structures and functions of viral RNAs
dkoirala@umbc.edu
Fab-assisted RNA crystallography
Strategies of genome replication and translation in RNA viruses
Protein-RNA interactions
RNA structure-function relationship
Sebla Kutluay, PI
Regulation of HIV-1 replication by RNA binding proteins, NGS methodologies
kutluay@wustl.edu
HIV-1 integrase:RNA interactions
Selective genome packaging
Recognition of HIV-1 RNAs by cellular proteins
CLIP-seq, ribo-seq, RNA-seq and related NGS methodologies
Jan Marchant, PI
Nuclear export: RNA structure and protein interactions
Structural studies of HIV-1 nuclear export and packaging
RNA structure and dynamics by NMR
Biophysical characterization of RNA-protein interactions
Development of NMR and computational methods for large RNAs
Melanie Ohi, PI
Cryo-EM analysis of dynamic complexes
Negative stain EM
Single particle Cryo-EM Analysis
Cryo-Electron Tomography
RNA-protein complexes
Biochemical purification of heterogenous complexes
Owen Pornillos, PI
Protein-RNA interactions, Crystallography, CryoEM
reconstitution of protein-RNA complexes and assembly mechanisms
biochemical and biophysical characterization
structure determination by X-ray crystallography and cryoEM
Nathan Sherer, PI
HIV RNA post-transcriptional regulation and live cell imaging
Roles for the 5’ leader in regulating HIV-1 RNA localization, translation, and genome packaging
Studies of host RNA binding proteins regulating HIV-1 RNA stability and host detection
Defining links between HIV-1 RNA nuclear history and cytoplasmic fate
Differential detection of individual HIV-1 RNA species in cells using high resolution light microscopy and live cell imaging
Identification of HIV-1 RNA-associated host factors using RNA capture coupled to mass spectrometry (HyPR-MS)
Janet Smith, PI
X-ray crystallography and protein production
Methods for production of protein and RNA-protein complexes
Zn-finger antiviral protein
APOBEC3H restriction factor
Redmond Smyth, Collaborative Development Awardee
Structure and function of HIV-1 RNAs
redmond.smyth@helmholtz-hiri.de
RNA structure determination by chemical probing
HIV-1 packaging and translation
RNA structural switches
RNA-protein and RNA-RNA interactions
Jeanne Stuckey, PI
Protein Expression and Crystallization
Lab website
Michael F. Summers, PI
NMR studies of HIV-1 genome packaging
RNA structure and dynamics
NMR methods
Nucleocapsid-RNA interactions
Gag assembly
Aussie Suzuki, Collaborative Development Awardee
Spatiotemporal dynamics of HIV RNA
aussie.suzuki@wisc.edu
Utilizing super-resolution microscopy to enhance visualization and tracking of HIV RNA dynamics within host cells
HIV-1 RNA nuclear entry, nuclear exit, and packaging
HIV-1 entry and mitosis
Ronald Swanstrom, PI
HIV-1 Splicing Regulation
Next gen sequencing assays for splicing quantification
Regulation of HIV-1 splicing
Mechanisms of splicing suppression
Screening small molecule inhibitors of splicing
Harry Taylor, Collaborative Development Awardee
TaylorHa@upstate.edu
Metabolic regulation of HIV-1 latency reversal
Post-transcriptional regulation of HIV-1 expression
Metabolite-mediated control of HIV-1 RNA splicing and translation
Alice Telesnitsky, PI
Quantitative Virology
Viral molecular genetics in support of biophysical studies
Molecular biology support
Viral RNA quantification and characterization
Generation and analysis of viral mutants and their replication and biochemical properties
Blanton Tolbert, PI
Mechanisms of transcriptional control and splicing
RNA structure
RNA binding protein conformational dynamics
RNA-protein interactions
RNA-small molecule interactions
Kevin Tsai, PI
Regulation of viral RNA metabolism by epitranscriptomic RNA modifications
Viral genomic RNA & mRNA modifications
RNA-induced innate immune responses
RNA metabolism
CLIP-seq-based RNA modification mapping
RNA-protein interaction probing through CLIP-seq
Jinwei Zhang, PI
Noncoding RNA Structure, Dynamics, and Recognition
Co-transcriptional RNA folding, complex assembly, and native purification
Structural analyses of large noncoding and viral RNAs using X-ray Crystallography, Cryo-EM, and SAXS
Biophysical analyses of RNA-RNA and RNA-protein interactions
Modulation of innate immunity by structured viral and host RNAs