Pearl Tsang

The Binding of a Glycoprotein 120 V3 Loop Peptide to HIV-1 Neutralizing Antibodies STRUCTURAL IMPLICATIONS

The structural and antigenic properties of a peptide (“CRK”) derived from the V3 loop of HIV-1 gp120 protein were studied using NMR and SPR techniques. The sequence of CRK corresponds to the central portion of the V3 loop containing the highly conserved “GPGR” residue sequence. Although the biological significance of this conserved sequence is unknown, the adoption of conserved secondary structure (type II β-turn) in this region has been proposed. The tendency of CRK (while free or conjugated to protein), to adopt such structure and the influence of such structure upon CRK antigenicity were investigated by NMR and SPR, respectively. Regardless of conjugation, CRK is conformationally averaged in solution but a weak tendency of the CRK “GPGR” residues to adopt a β-turn conformation was observed after conjugation. The influence of GPGR structure upon CRK antigenicity was investigated by measuring the affinities of two cognate antibodies: “5023A” and “5025A,” for CRK, protein-conjugated CRK and gp120 protein. Each antibody bound to all the antigens with nearly the same affinity. From these data, it appears that: (a) antibody binding most likely involves an induced fit of the peptide and (b) the gp120 V3 loop is probably conformationally heterogeneous. Since 5023A and 5025A are HIV-1 neutralizing antibodies, neutralization in these cases appears to be independent of adopted GPGR β-turn structure.

Observing selected domains in multi-domain proteins via sortase-mediated ligation and NMR spectroscopy

NMR spectroscopy has distinct advantages for providing insight into protein structures, but faces significant resolution challenges as protein size increases. To alleviate such resonance overlap issues, the ability to produce segmentally labeled proteins is beneficial. Here we show that the S. aureus transpeptidase sortase A can be used to catalyze the ligation of two separately expressed domains of the same protein, MecA (B. subtilis). The yield of purified, segmentally labeled MecA protein conjugate is ~40%. The resultant HSQC spectrum obtained from this domain-labeled conjugate demonstrates successful application of sortase A for segmental labeling of multi-domain proteins for solution NMR study.

Antigen-antibody interactions: an NMR approach.

With recent advances in methodology, it now appears that NMR can be used at an unprecedented level of sophistication to obtain new insights into the solution structure and dynamics of the antibody combining site, both free and in its complex with antigen. Most promising in this regard is the Fv fragment (molecular weight approximately 25 kD) which can be produced by genetic engineering in a form suitable for NMR studies. Isotopic labeling is required to make specific resonance assignments. NMR can also provide information on the conformational preferences of immunogenic peptides and can be used to probe the conformation and dynamics of peptides (appropriately labeled with 13C or 15N) bound to the Fab fragment (molecular weight approximately 50 kD) of antipeptide antibodies.

The binding of a gp120 V3 loop peptide to HIV-1 neutralizing antibodies: structural implications

The structural and antigenic properties of a peptide (“CRK”) derived from the V3 loop of HIV-1 gp120 protein were studied using NMR and SPR techniques. The sequence of CRK corresponds to the central portion of the V3 loop containing the highly conserved “GPGR” residue sequence. Although the biological significance of this conserved sequence is unknown, the adoption of conserved secondary structure (type II β-turn) in this region has been proposed. The tendency of CRK (while free or conjugated to protein), to adopt such structure and the influence of such structure upon CRK antigenicity were investigated by NMR and SPR, respectively. Regardless of conjugation, CRK is conformationally averaged in solution but a weak tendency of the CRK “GPGR” residues to adopt a β-turn conformation was observed after conjugation. The influence of GPGR structure upon CRK antigenicity was investigated by measuring the affinities of two cognate antibodies: “5023A” and “5025A,” for CRK, protein-conjugated CRK and gp120 protein. Each antibody bound to all the antigens with nearly the same affinity. From these data, it appears that: (a) antibody binding most likely involves an induced fit of the peptide and (b) the gp120 V3 loop is probably conformationally heterogeneous. Since 5023A and 5025A are HIV-1 neutralizing antibodies, neutralization in these cases appears to be independent of adopted GPGR β-turn structure.

Isotope-edited nuclear magnetic resonance studies of Fab-peptide complexes.

Publisher Summary This chapter describes the application of nuclear magnetic resonance (NMR) spectroscopy to studies of higher molecular weight systems such as Fab-antigen or Fab-antigen complexes through the development of isotope-edited techniques. It focuses on the approach involving selective labeling of the peptide. NMR studies of high-molecular-weight systems stand to benefit considerably from spectral editing techniques. Isotope editing allows monitoring selectively not only a chosen component of a biomolecular complex—e.g., the peptide in a peptide-receptor complex—but also individual residues at the level of atomic resolution. An example of the effects of isotope-editing techniques applied to a Fab-peptide complex in which the peptide is 15N-labeled at two residues. Isotope-edited NMR techniques offer new possibilities for detailed studies of the structure and dynamics of peptide-Fab complexes and promise to provide important new insights into the molecular basis for antibody–antigen recognition. The specificity of these methods allows to distinguish residues of the antigen that interact directly at the antibody combining site.

A peptide from the extension of Lys-tRNA synthetase binds to transfer RNA and DNA.

Eukaryotic aminoacyl-tRNA synthetases have dispensable extensions appended at the amino- or carboxyl-terminus as compared to their bacterial counterparts. While a synthetic peptide corresponding to the basic amino-terminal extension in yeast Asp-tRNA synthetase binds to DNA, the extension in the intact protein evidently binds to tRNA and enhances the tRNA specificity of Asp-tRNA synthetase. On the other hand, the amino-terminal extension in human Asp-tRNA synthetase, both within the intact protein and as a synthetic peptide, binds to tRNA. Here, the tRNA binding of a synthetic peptide, hKRS(Arg(25)-Glu(42)), corresponding to the amino-terminal extension of human Lys-tRNA synthetase (hKRS) was analyzed. This basic peptide bound to tRNA(Phe) and the apparent-binding constant increased with increasing concentrations of Mg(2+). The hKRS peptide also bound to DNA and polyphosphate; however, the apparent DNA-binding constants decreased at increasing concentrations of Mg(2+). The ability of the hKRS peptide to adopt alpha-helical conformation was demonstrated by NMR and circular dichroism. A Lys-rich peptide derived from the elongation factor 1alpha was also examined and bound to DNA but not to tRNA.

1H, 13C and 15N resonance assignment of the N-terminal domain of human lysyl aminoacyl tRNA synthetase

Human lysyl aminoacyl tRNA synthetase (hLysRS) is integral to a variety of different functions ranging from protein biosynthesis, initiation of a proinflammatory response as well as signal transduction. Another important, non-canonical function of hLysRS is that it chaperones tRNALys,3, the HIV-1 reverse transcription primer molecule into new HIV-1 particles. Since the N-terminal domain of hLysRS has been shown to be essential for such primer uptake, NMR studies of this domain are being conducted to obtain a better understanding of how hLysRS interacts with the primer tRNA. In order to study the RNA binding behavior of this domain, we are studying its complex with a fragment of the cognate tRNA corresponding to the tRNA anticodon loop. We report herein the backbone and side chain NMR resonance assignments of uniformly 15N-, 13C-labeled hLysRS N-terminal domain alone, as well as complexed to RNA.

1H, 13C and 15N resonance assignment of the anticodon binding domain of human lysyl aminoacyl tRNA synthetase

Human lysyl aminoacyl tRNA synthetase (hLysRS) is a multi-functional aminoacyl tRNA synthetase which is primarily involved in protein biosynthesis as well as crucial processes ranging from proinflammatory response to signal transduction. One important, non-canonical function of hLysRS is to target tRNALys,3, the HIV-1 reverse transcription primer molecule, for uptake and packaging into new HIV-1 particles. Since the anticodon binding (ACB) domain of hLysRS is required for proper recognition of its cognate tRNA, NMR studies of the ACB domain are being conducted to enhance our understanding of how hLysRS interacts with these RNAs during protein biosysnthesis as well as HIV-1 viral packaging. Here, we report the backbone and side chain NMR resonance assignments of the uniformly 15N-, 13C-labeled ACB domain of hLysRS.

NMR study and comparison of the antigenic properties of a peptide recognized by two HIV-1 neutralizing antibodies

Fab–peptide complexes formed between a 15 residue peptide derived from the HIV‐1 gp120 V3 loop and two of its cognate monoclonal antibodies, 5023A and 5025A, were studied using isotope‐edited solution nuclear magnetic resonance (NMR) techniques. Since these antibodies neutralize HIV‐1 virus with different strain specificities, this study was conducted to better understand the nature of these differences. The amide proton and nitrogen NMR resonances of specific residues were used to monitor the backbone of this peptide in these complexes. Three central residues of this peptide (‘RAF’) were found to be strongly affected by binding to both antibodies. Several other peptide residues were affected by binding to antibody 5023A but not 5025A. The antibody epitopes mapped by NMR are similar to those obtained previously via PEPSCAN at higher pH. One main difference between the PEPSCAN and NMR determined epitopes for 5023A involved two glycine residues of the peptide. By NMR, one of these glycines was more dramatically affected by antibody binding than predicted by PEPSCAN, while the other was much less so.