title: Specificity of RSG-1.2 peptide binding to RRE-IIB RNA element of HIV-1 over Rev peptide is mainly enthalpic in origin.
abstract: Rev is an essential HIV-1 regulatory protein which binds to the Rev responsive element (RRE) present within the env gene of HIV-1 RNA genome. This binding facilitates the transport of the RNA to the cytoplasm, which in turn triggers the switch between viral latency and active viral replication. Essential components of this complex have been localized to a minimal arginine rich Rev peptide and stem IIB region of RRE. A synthetic peptide known as RSG-1.2 binds with high binding affinity and specificity to the RRE-IIB than the Rev peptide, however the thermodynamic basis of this specificity has not yet been addressed. The present study aims to probe the thermodynamic origin of this specificity of RSG-1.2 over Rev Peptide for RRE-IIB. The temperature dependent melting studies show that RSG-1.2 binding stabilizes the RRE structure significantly (ΔT(m) = 4.3°C), in contrast to Rev binding. Interestingly the thermodynamic signatures of the binding have also been found to be different for both the peptides. At pH 7.5, RSG-1.2 binds RRE-IIB with a K(a) = 16.2±0.6×10(7) M(-1) where enthalpic change ΔH = -13.9±0.1 kcal/mol is the main driving force with limited unfavorable contribution from entropic change TΔS = -2.8±0.1 kcal/mol. A large part of ΔH may be due to specific stacking between U72 and Arg15. In contrast binding of Rev (K(a) = 3.1±0.4×10(7) M(-1)) is driven mainly by entropy (ΔH = 0 kcal/mol and TΔS = 10.2±0.2 kcal/mol) which arises from major conformational changes in the RNA upon binding.
authors.affiliation: Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi, India.
authors.forename: Santosh
authors.initials: S
authors.lastname: Kumar
authors.forename: Debojit
authors.initials: D
authors.lastname: Bose
authors.forename: Hemant
authors.initials: H
authors.lastname: Suryawanshi
authors.forename: Harshana
authors.initials: H
authors.lastname: Sabharwal
authors.forename: Koyeli
authors.initials: K
authors.lastname: Mapa
authors.forename: Souvik
authors.initials: S
authors.lastname: Maiti
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002151:Calorimetry; D002942:Circular Dichroism; D019277:Entropy; D005453:Fluorescence; D015752:Genes, env / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics*; D006358:Hot Temperature; D008969:Molecular Sequence Data; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D009690:Nucleic Acid Conformation / Q000528:radiation effects; D009691:Nucleic Acid Denaturation / Q000528:radiation effects; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding / Q000528:radiation effects; D055550:Protein Stability / Q000528:radiation effects; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics*; D017186:Titrimetry; D014466:Ultraviolet Rays
chemical_list: D050505:Mutant Proteins; D010455:Peptides; D012367:RNA, Viral; C568602:RSG-1.2 peptide; C503402:Rev peptide