Millisecond Time-Resolved Solid-State NMR Initiated by Rapid Inverse Temperature Jumps

Efficient synthesis, stability-guided optimization and anticancer evaluation of bee venom peptide Melittin

Natural cytotoxic peptides (NCPs) are emerging sources of novel anticancer chemotherapeutics. Especially, Melittin, which is the major component of bee venom and the first-in-class NCP, has been considered as a promising anticancer scaffold. Nevertheless, as a classical linear, cationic, amphipathic, and membrane-lytic peptide, Melittin may be easily degraded by proteases, suffering from poor stability, moderate anticancer durability, and severe hemolysis. In this study, applying the terminal modification and hybridization strategies, ten Melittin-based derivatives were designed, synthesized, and investigated for their anticancer potential. The robust and economic synthetic method, in vitro anticancer efficiency, time-kill kinetics, serum stability, anti-migration activity, hemolysis effects, and anticancer mechanism were explored. As expected, the Melittin-based derivatives exhibited highly potent cytotoxicity against all six tested cancer cell lines. In particular, compared with natural Melittin, the derived peptides LJ-5 containing both N-terminal acetylation and C-terminal hydrazidation, and LJ-6, the methotrexate MTX-GFLG-Melittin conjugate exhibited significantly improved proteolytic stability, more durable anticancer efficiency, higher anti-migration activity, as well as reduced hemolysis effects. Besides, it was further verified that LJ-5 and LJ-6 could efficiently disrupt the integrity of cancer cell membrane, localize to the mitochondria and rapidly reduce the mitochondrial membrane potential of cancer cells. Collectively, the economic synthetic method and stability-guided optimization were conducted on Melittin, affording hydrolysis-resistant LJ-5 and LJ-6 that may serve as anticancer candidates and useful references for further optimizations of cytotoxic peptides.

Quantification of Rapid Cooling of Glycerol/Water Solutions Based on Photoluminescence from Thioflavin T

Rapid cooling to a solid state allows intermediates in chemical and biomolecular processes that occur in solution near room temperature to be trapped for subsequent measurements by magnetic resonance spectroscopies, electron microscopy, or other techniques. In time-resolved solid state nuclear magnetic resonance and rapid freeze-quench electron paramagnetic resonance studies, solutions are typically frozen by spraying into a cold bath or onto a cold metal surface. Although simulations suggest freezing on millisecond or submillisecond time scales, direct experimental measurements of cooling rates have been elusive. Here, we describe a method for quantification of rapid cooling rates based on measurements of temperature-dependent photoluminescence from thioflavin T (ThT). In our experiments, a jet of ThT solution in glycerol/water, with 10.8 m/s jet velocity and 30 μm diameter, freezes on a cold, rotating copper surface. Images of ThT photoluminescence on the copper surface indicate that the cooling rate of the solution increases linearly with the surface velocity over the 0.45-6.2 m/s range. At surface velocities greater than 3.8 m/s, the time to cool from 300 to 260 K or from 300 to 230 K is less than 100 μs or less than 700 μs. The experimental results do not agree quantitatively with calculations in which a layer of glycerol/water cools by thermal conduction when suddenly brought in contact with a cold copper surface. Discrepancies between experimental results and simplistic calculations illustrate the importance of direct measurements of cooling rates.

Conformations of a low-complexity protein in homogeneous and phase-separated frozen solutions

Solutions of the intrinsically disordered, low-complexity domain of the FUS protein (FUS-LC) undergo liquid-liquid phase separation (LLPS) below a temperature TLLPS. To investigate whether local conformational distributions are detectably different in the homogeneous (i.e., single-phase) and phase-separated states of FUS-LC, we performed solid-state NMR (ssNMR) measurements on solutions that were frozen on submillisecond timescales after equilibration at temperatures well above (50°C) or well below (4°C) TLLPS. Measurements were performed at 25 K with signal enhancements from dynamic nuclear polarization. Crosspeak patterns in two-dimensional ssNMR spectra of rapidly frozen solutions in which FUS-LC was uniformly 15N,13C labeled were found to be nearly identical for the two states. Similar results were obtained for solutions in which FUS-LC was labeled only at Thr, Tyr, and Gly residues, as well as solutions of a FUS construct in which five specific residues were labeled by ligation of synthetic and recombinant fragments. These experiments show that local conformational distributions are nearly the same in the homogeneous and phase-separated solutions, despite the much greater protein concentrations and more abundant intermolecular interactions within phase-separated, protein-rich "droplets." Comparison of the experimental results with simulations of the sensitivity of two-dimensional ssNMR crosspeaks to changes in populations of β strand-like conformations suggests that changes in conformational distributions are no larger than 5-10%.

Optimization of 15N-13C double-resonance NMR experiments under low temperature magic angle spinning dynamic nuclear polarization conditions

Dynamic nuclear polarization (DNP) enhanced magic angle spinning (MAS) solid-state NMR carried out at 25 K enables rapid acquisition of multi-dimensional 13C-15N correlation spectra for protein structure studies and resonance assignment. Under commonly used DNP conditions, solvent deuteration reduces 1H-15N cross polarization (CP) efficiencies, necessitates more careful optimization, and requires longer high-power 15N radio-frequency pulses. The sensitivity of 2D heteronuclear correlation experiments is potentially impaired. Here we show that 2D 15N-13C experiments based on 13C-15N transferred echo double resonance (TEDOR) methods outperform 2D experiments based on CP transfers in a fully deuterated solvent, and are competitive with CP-based experiments when the solvent is only partially deuterated. Additionally, we show that optimization of TEDOR-based 2D experiments is simpler than optimization of CP-based experiments under 25 K MAS conditions.

Conformations of a Low-Complexity Protein in Homogeneous and Phase-Separated Frozen Solutions

Solutions of the intrinsically disordered, low-complexity domain of the FUS protein (FUS-LC) undergo liquid-liquid phase separation (LLPS) below temperatures TLLPS in the 20-40° C range. To investigate whether local conformational distributions are detectably different in the homogeneous and phase-separated states of FUS-LC, we performed solid state nuclear magnetic resonance (ssNMR) measurements on solutions that were frozen on sub-millisecond time scales after equilibration at temperatures well above (50° C) or well below (4° C) TLLPS. Measurements were performed at 25 K with signal enhancements from dynamic nuclear polarization. Crosspeak patterns in two-dimensional (2D) ssNMR spectra of rapidly frozen solutions in which FUS-LC was uniformly 15N,13C-labeled were found to be nearly identical for the two states. Similar results were obtained for solutions in which FUS-LC was labeled only at Thr, Tyr, and Gly residues, as well as solutions of a FUS construct in which five specific residues were labeled by ligation of synthetic and recombinant fragments. These experiments show that local conformational distributions are nearly the same in the homogeneous and phase-separated solutions, despite the much greater protein concentrations and more abundant intermolecular interactions within phase-separated, protein-rich "droplets". Comparison of the experimental results with simulations of the sensitivity of 2D crosspeak patterns to an enhanced population of β-strand-like conformations suggests that changes in conformational distributions are no larger than 5-10%.

Statement of Significance

Liquid-liquid phase separation (LLPS) in solutions of proteins with intrinsically disordered domains has attracted recent attention because of its relevance to multiple biological processes and its inherent interest from the standpoint of protein biophysics. The high protein concentrations and abundant intermolecular interactions within protein-rich, phase-separated "droplets" suggests that conformational distributions of intrinsically disordered proteins may differ in homogeneous and phase-separated solutions. To investigate whether detectable differences exist, we performed experiments on the low-complexity domain of the FUS protein (FUS-LC) in which FUS-LC solutions were first equilibrated at temperatures well above or well below their LLPS transition temperatures, then rapidly frozen and examined at very low temperatures by solid state nuclear magnetic resonance (ssNMR) spectroscopy. The ssNMR data for homogeneous and phase-separated frozen solutions of FUS-LC were found to be nearly identical, showing that LLPS is not accompanied by substantial changes in the local conformational distributions of this intrinsically disordered protein.

Dynamic Nuclear Polarization Enhanced Multiple-Quantum Spin Counting of Molecular Assemblies in Vitrified Solutions

Crystallization pathways are essential to various industrial, geological, and biological processes. In nonclassical nucleation theory, prenucleation clusters (PNCs) form, aggregate, and crystallize to produce higher order assemblies. Microscopy and X-ray techniques have limited utility for PNC analysis due to the small size (0.5-3 nm) and time stability constraints. We present a new approach for analyzing PNC formation based on 31P nuclear magnetic resonance (NMR) spin counting of vitrified molecular assemblies. The use of glassing agents ensures that vitrification generates amorphous aqueous samples and offers conditions for performing dynamic nuclear polarization (DNP)-amplified NMR spectroscopy. We demonstrate that molecular adenosine triphosphate along with crystalline, amorphous, and clustered calcium phosphate materials formed via a nonclassical growth pathway can be differentiated from one another by the number of dipolar coupled 31P spins. We also present an innovative approach for examining spin counting data, demonstrating that a knowledge-based fitting of integer multiples of cosine wave functions, instead of the traditional Fourier transform, provides a more physically meaningful retrieval of the existing frequencies. This is the first report of multiquantum spin counting of assemblies formed in solution as captured under vitrified DNP conditions, which can be useful for future analysis of PNCs and other aqueous molecular clusters.

From Milliseconds to Minutes: Melittin Self-Assembly from Concerted Non-Equilibrium Pressure-Jump and Equilibrium Relaxation Nuclear Magnetic Resonance

Non-equilibrium kinetics techniques like pressure-jump nuclear magnetic resonance (NMR) are powerful in tracking changes in oligomeric populations and are not limited by relaxation rates for the time scales of exchange that can be probed. However, these techniques are less sensitive to minor, transient populations than are Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments. We integrated non-equilibrium pressure-jump and equilibrium CPMG relaxation dispersion data to fully map the kinetic landscape of melittin tetramerization. While monomeric peptides weakly form dimers (Kd,D/M ≈ 26 mM) whose population never exceeds 1.6% at 288 K, dimers associate tightly to form stable tetrameric species (Kd,T/D ≈ 740 nM). Exchange between the monomer and dimer, along with exchange between the dimer and tetramer, occurs on the millisecond time scale. The NMR approach developed herein can be readily applied to studying the folding and misfolding of a wide range of oligomeric assemblies.

Experimental Evidence for Millisecond-Timescale Structural Evolution Following the Microsecond-Timescale Folding of a Small Protein

Prior work has shown that small proteins can fold (i.e., convert from unstructured to structured states) within 10  μs. Here we use time-resolved solid state nuclear magnetic resonance (ssNMR) methods to show that full folding of the 35-residue villin headpiece subdomain (HP35) requires a slow annealing process that has not been previously detected. ^{13}C ssNMR spectra of frozen HP35 solutions, acquired with a variable time τ_{e} at 30 °C after rapid cooling from 95 °C and before rapid freezing, show changes on the 3-10 ms timescale, attributable to slow rearrangements of protein sidechains during τ_{e}.

Early events in amyloid-β self-assembly probed by time-resolved solid state NMR and light scattering

Self-assembly of amyloid-β peptides leads to oligomers, protofibrils, and fibrils that are likely instigators of neurodegeneration in Alzheimer's disease. We report results of time-resolved solid state nuclear magnetic resonance (ssNMR) and light scattering experiments on 40-residue amyloid-β (Aβ40) that provide structural information for oligomers that form on time scales from 0.7 ms to 1.0 h after initiation of self-assembly by a rapid pH drop. Low-temperature ssNMR spectra of freeze-trapped intermediates indicate that β-strand conformations within and contacts between the two main hydrophobic segments of Aβ40 develop within 1 ms, while light scattering data imply a primarily monomeric state up to 5 ms. Intermolecular contacts involving residues 18 and 33 develop within 0.5 s, at which time Aβ40 is approximately octameric. These contacts argue against β-sheet organizations resembling those found previously in protofibrils and fibrils. Only minor changes in the Aβ40 conformational distribution are detected as larger assemblies develop.

Recombinant Expression and Chemical Amidation of Isotopically Labeled Native Melittin

Post-translational modifications are ubiquitous in the eukaryotic proteome. However, these modifications are rarely incorporated in NMR studies of eukaryotic proteins, which are typically produced through recombinant expression in E. coli. Melittin is the primary peptide in honey bee venom. Its native C-terminal amide significantly affects its equilibrium structure and dynamics in solution and is thus a prerequisite for studying its native structure and function. Here, we present a method for producing triply isotopically labeled (2H, 13C, and 15N) native melittin through recombinant expression followed by chemical amidation. We then show that structural models produced with AlphaFold-Multimer are in even better agreement with experimental residual dipolar couplings than the 2.0 Å resolution X-ray crystal structure for residues G3-K23.

Time-resolved solid state NMR of biomolecular processes with millisecond time resolution

We review recent efforts to develop and apply an experimental approach to the structural characterization of transient intermediate states in biomolecular processes that involve large changes in molecular conformation or assembly state. This approach depends on solid state nuclear magnetic resonance (ssNMR) measurements that are performed at very low temperatures, typically 25-30 K, with signal enhancements from dynamic nuclear polarization (DNP). This approach also involves novel technology for initiating the process of interest, either by rapid mixing of two solutions or by a rapid inverse temperature jump, and for rapid freezing to trap intermediate states. Initiation by rapid mixing or an inverse temperature jump can be accomplished in approximately-one millisecond. Freezing can be accomplished in approximately 100 microseconds. Thus, millisecond time resolution can be achieved. Recent applications to the process by which the biologically essential calcium sensor protein calmodulin forms a complex with one of its target proteins and the process by which the bee venom peptide melittin converts from an unstructured monomeric state to a helical, tetrameric state after a rapid change in pH or temperature are described briefly. Future applications of millisecond time-resolved ssNMR are also discussed briefly.