PMID- 19646998
OWN - NLM
STAT- MEDLINE
DCOM- 20091020
LR  - 20211020
IS  - 1089-8638 (Electronic)
IS  - 0022-2836 (Print)
IS  - 0022-2836 (Linking)
VI  - 393
IP  - 2
DP  - 2009 Oct 23
TI  - Thermodynamic profiling of HIV RREIIB RNA-zinc finger interactions.
PG  - 369-82
LID - 10.1016/j.jmb.2009.07.066 [doi]
AB  - The interactions between the HIV Rev-responsive element (RRE) RNA and the HIV 
      regulatory protein Rev, are crucial for the HIV life-cycle. Earlier, we showed 
      that single C(2)H(2) zinc fingers (znfs) have the same binding site as the Rev 
      peptide and exhibit nanomolar affinity. In this study, the specific role of amino 
      acid side chains and molecular processes involved with complex formation were 
      investigated by perturbation of the binding energetics via changes in 
      temperature, pH, buffers, and salt concentrations, as well as znf and RNA 
      mutations, by isothermal titration calorimetry. Interestingly, despite the large 
      cationic charge on the znfs, the number of interactions with the RNA phosphate 
      backbone was lower than intuitively expected. The presence of binding induced 
      protonation was established by ITC and localized by NMR to a histidine on the znf 
      beta-sheet. The DeltaC(p) of znf-RNA binding was observed to be substantially 
      negative and could not be accounted for by conventional solvent-accessible 
      surface area models. An alternative model, based on the extent of hydrogen bond 
      changes as a result of differences in ligand-induced water displacement at the 
      binding site, provided reasonable explanation of the trends in DeltaC(p), as well 
      as DeltaH and DeltaS. Our studies show that incorporation of favorable 
      interactions at the solvent-excluded binding interface can be used to alleviate 
      the unfavorable enthalpic penalties of displacing water molecules from the 
      hydrated RNA surface.
FAU - Mishra, Subrata H
AU  - Mishra SH
AD  - Departments of Chemistry and Biology, Georgia State University, Atlanta, 30303, 
      USA.
FAU - Spring, Alexander M
AU  - Spring AM
FAU - Germann, Markus W
AU  - Germann MW
LA  - eng
GR  - R01 AI047459/AI/NIAID NIH HHS/United States
GR  - R01 AI047459-06/AI/NIAID NIH HHS/United States
GR  - AI/GM47459/AI/NIAID NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20090730
PL  - Netherlands
TA  - J Mol Biol
JT  - Journal of molecular biology
JID - 2985088R
RN  - 0 (Gene Products, rev)
RN  - 0 (RNA, Viral)
SB  - IM
MH  - Amino Acid Sequence
MH  - Calorimetry
MH  - Circular Dichroism
MH  - Gene Products, rev/chemistry/genetics/*metabolism
MH  - Genes, env/*genetics
MH  - Hydrogen-Ion Concentration
MH  - Magnetic Resonance Spectroscopy
MH  - Molecular Sequence Data
MH  - Protein Binding/genetics
MH  - Protein Structure, Secondary
MH  - RNA, Viral/genetics/*metabolism
MH  - Sequence Homology, Amino Acid
MH  - Temperature
MH  - Thermodynamics
MH  - Zinc Fingers/*genetics
PMC - PMC2757539
MID - NIHMS136180
EDAT- 2009/08/04 09:00
MHDA- 2009/10/21 06:00
PMCR- 2010/10/23
CRDT- 2009/08/04 09:00
PHST- 2009/03/25 00:00 [received]
PHST- 2009/07/20 00:00 [revised]
PHST- 2009/07/23 00:00 [accepted]
PHST- 2009/08/04 09:00 [entrez]
PHST- 2009/08/04 09:00 [pubmed]
PHST- 2009/10/21 06:00 [medline]
PHST- 2010/10/23 00:00 [pmc-release]
AID - S0022-2836(09)00933-4 [pii]
AID - 10.1016/j.jmb.2009.07.066 [doi]
PST - ppublish
SO  - J Mol Biol. 2009 Oct 23;393(2):369-82. doi: 10.1016/j.jmb.2009.07.066. Epub 2009 
      Jul 30.