The reduced form of the antibody CH2 domain.

Among the immunoglobulin domains, the CH2 domain has the lowest thermal stability, which also depends on amino acid sequence and buffer conditions. To further identify factors that influence CH2 folding and stability, we characterized the domain in the reduced form using differential scanning fluorimetry and nuclear magnetic resonance. We show that the CH2 domain can fold, similarly to the disulfide-bridged form, without forming a disulfide-bridge, even though the protein contains two Cys residues. Although the reduced form exhibits thermal stability more than 15°C lower than the disulfide-bridged form, it does not undergo immediate full oxidization. To explain this phenomenon, we compared CH2 oxidization at different conditions and demonstrate a need for significant fluctuation of the folded conformation to enhance CH2 disulfide-bridge formation. We conclude that, since CH2 can be purified as a folded, semi-stable, reduced protein that can coexist with the oxidized form, verification of the level of oxidization at each step is critical in CH2 engineering studies.

A synergy of activity, stability, and inhibitor-interaction of HIV-1 protease mutants evolved under drug-pressure.

A clinically-relevant, drug-resistant mutant of HIV-1 protease (PR), termed Flap+(I54V) and containing L10I, G48V, I54V and V82A mutations, is known to produce significant changes in the entropy and enthalpy balance of drug-PR interactions, compared to wild-type PR. A similar mutant, Flap+(I54A) , which evolves from Flap+(I54V) and contains the single change at residue 54 relative to Flap+(I54V) , does not. Yet, how Flap+(I54A) behaves in solution is not known. To understand the molecular basis of V54A evolution, we compared nuclear magnetic resonance (NMR) spectroscopy, fluorescence spectroscopy, isothermal titration calorimetry, and enzymatic assay data from four PR proteins: PR (pWT), Flap+(I54V) , Flap+(I54A) , and Flap+(I54) , a control mutant that contains only L10I, G48V and V82A mutations. Our data consistently show that selection to the smaller side chain at residue 54, not only decreases inhibitor affinity, but also restores the catalytic activity.

An NMR strategy to detect conformational differences in a protein complexed with highly analogous inhibitors in solution.

This manuscript presents an NMR strategy to investigate conformational differences in protein-inhibitor complexes, when the inhibitors tightly bind to a protein at sub-nanomolar dissociation constants and are highly analogous to each other. Using HIV-1 protease (PR), we previously evaluated amide chemical shift differences, ΔCSPs, of PR bound to darunavir (DRV) compared to PR bound to several DRV analogue inhibitors, to investigate subtle but significant long-distance conformation changes caused by the inhibitor's chemical moiety variation [Khan, S. N., Persons, J. D. Paulsen, J. L., Guerrero, M., Schiffer, C. A., Kurt-Yilmaz, N., and Ishima, R., Biochemistry, (2018), 57, 1652-1662]. However, ΔCSPs are not ideal for investigating subtle PR-inhibitor interface differences because intrinsic differences in the electron shielding of the inhibitors affect protein ΔCSPs. NMR relaxation is also not suitable as it is not sensitive enough to detect small conformational differences in rigid regions among similar PR-inhibitor complexes. Thus, to gain insight into conformational differences at the inhibitor-protein interface, we recorded 15N-half filtered NOESY spectra of PR bound to two highly analogous inhibitors and assessed NOEs between PR amide protons and inhibitor protons, between PR amide protons and hydroxyl side chains, and between PR amide protons and water protons. We also verified the PR amide-water NOEs using 2D water-NOE/ROE experiments. Differences in water-amide proton NOE peaks, possibly due to amide-protein hydrogen bonds, were observed between subunit A and subunit B, and between the DRV-bound form and an analogous inhibitor-bound form, which may contribute to remote conformational changes.

Probing Structural Changes among Analogous Inhibitor-Bound Forms of HIV-1 Protease and a Drug-Resistant Mutant in Solution by Nuclear Magnetic Resonance.

In the era of state-of-the-art inhibitor design and high-resolution structural studies, detection of significant but small protein structural differences in the inhibitor-bound forms is critical to further developing the inhibitor. Here, we probed differences in HIV-1 protease (PR) conformation among darunavir and four analogous inhibitor-bound forms and compared them with a drug-resistant mutant using nuclear magnetic resonance chemical shifts. Changes in amide chemical shifts of wild-type (WT) PR among these inhibitor-bound forms, ΔCSP, were subtle but detectable and extended >10 Å from the inhibitor-binding site, asymmetrically between the two subunits of PR. Molecular dynamics simulations revealed differential local hydrogen bonding as the molecular basis of this remote asymmetric change. Inhibitor-bound forms of the drug-resistant mutant also showed a similar long-range ΔCSP pattern. Differences in ΔCSP values of the WT and the mutant (ΔΔCSPs) were observed at the inhibitor-binding site and in the surrounding region. Comparing chemical shift changes among highly analogous inhibitors and ΔΔCSPs effectively eliminated local environmental effects stemming from different chemical groups and enabled exploitation of these sensitive parameters to detect subtle protein conformational changes and to elucidate asymmetric and remote conformational effects upon inhibitor interaction.

Gas-Phase Infrared and NMR Investigation of the Conformers of Diacetone Diperoxide (DADP).

Gas-phase infrared measurements of diacetone diperoxide (DADP) indicate a chair conformation with less than 5% of the predicted twist conformer. Vibrational frequencies are very similar to those previously measured in the solid state. Solution NMR measurements using 2D exchange spectroscopy (EXSY) also set a very low maximum limit on the equilibrium population of the twist conformer, with a room-temperature free-energy difference in excess of 14.5 kJ/mol. These experimental results are in accord with high-level quantum calculations incorporating full thermochemistry and solvation effects, which indicate a free-energy difference in the range of 14.7-17.5 kJ/mol in polar solvents.

The (14)N quadrupole coupling in hexamethylene triperoxide diamine (HMTD).

Using high-field NMR, we have determined the magnitude of the nuclear quadrupole interaction in hexamethylene triperoxide diamine (HMTD), the explosive allegedly used in the London bombings of July 2005. The experimental quadrupolar coupling constant, 5.334 MHz, is in good agreement with quantum chemical calculations. The predicted single zero-field transition frequency should lie in a relatively empty part of the (14)N nuclear quadrupole resonance (NQR) spectrum; the spin relaxation rate is reasonably fast.

Slow turning reveals enormous quadrupolar interactions (STREAQI).

We introduce a new solid-state NMR method, which uses very slow sample rotation to visualize NMR spectra whose width exceeds feasible spectrometer bandwidths. It is based on the idea that if we reorient a tensor by a known angle about a known axis, the shifts in the NMR frequencies observed across the spectral width allow us to reconstruct the entire tensor. Called STREAQI (Slow Turning Reveals Enormous Anisotropic Quadrupolar Interactions), this method allows us to probe NMR nuclei that are intractable to current methods. To prove the concept and demonstrate its promise we have implemented the method for several 79Br containing samples with quadrupolar coupling constants in the range of 10-50 MHz.

Helical chirality in hexamethylene triperoxide diamine.

The primary explosive hexamethylenetriperoxide diamine has previously been found to exist in the solid state as a racemic mixture of helically chiral, threefold symmetric enantiomers; another enantiomeric pair of low-energy conformers has been predicted, but has never been observed. We show by solution 2D NMR at 14 T, in achiral solution and by addition of chiral shift reagents, that all four optically isomeric conformers coexist at slow equilibrium on the NMR timescale at room temperature, and can be observed. Calculations of the 1H and 13C NMR chemical shifts using gauge-including atomic orbital methods are in excellent agreement with experiment; thermochemical calculation of the free energies in solution are in somewhat worse agreement, but correctly predict the relative stability of the conformers. Analysis of the effects of chiral shift reagents on the NMR spectra suggests that discrimination between chiral isomers is primarily around the molecular equator, around which the enantiomeric gauche O--O linkages are arrayed.