Disruption of Spatial Proximities among Charged Groups in Equilibrium-Denatured States of Proteins Tracked Using Protein Charge Transfer Spectra

Simulation of absorption spectra of native and unfolded proteins

Protein concentrations are routinely determined using the absorbance measured at 280 nm and Beer-Lambert's law. However, traditional single-wavelength approaches may be inferior to a multi-wavelength analysis of complete spectra given the larger amount of data that can be processed. Hence, the current study was aimed at simulating protein UV spectra (from 250 to 350 nm) with a view to more accurately estimate protein concentrations. We demonstrate that the spectra of unfolded proteins are well-simulated using primary sequence data and the wavelength-dependent molar absorption coefficients of l-cystine, l-phenylalanine, N-acetyl-l-tyrosinamide and N-acetyl-l-tryptophanamide (the latter two serving as L-Tyr and L-Trp model compounds). Alternatively, simulations can be performed with the coefficients of the Tyr and Trp mimics replaced by a pseudo-Voigt (pV) function, which mathematically fully describes the spectra of these model compounds. Furthermore, a pV function, generated from the analysis of the spectra of 14 proteins, can be utilized to simulate the spectral contributions of Tyr and Trp in native proteins with a reasonable degree of accuracy. A Microsoft Excel-based multi-wavelength fitting routine can be employed to simulate the spectra of proteins and compare them with those experimentally recorded, thereby facilitating the determination of protein concentrations.

Label-Free Tracking of Hepatitis B Virus Core Protein Capsid Assembly in Real-Time Using Protein Charge Transfer Spectra

Hepatitis B virions are double-shelled particles, with a diameter of 40-42 nm, consisting of a nucleocapsid called the HBV core protein (HBV Cp). It is an ordered assembly of 90-120 homodimers arranged in an icosahedral symmetry. Both the full-length HBV Cp and the first-149 residue domain, HBV Cp149, can spontaneously assemble in vitro into capsids with 120 Cp dimers (T = 4) or 90 Cp dimers (T = 3), triggered by high ionic strength of 0.25-0.5 M NaCl. The assembly disassembly of HBV Cp149 capsids are generally studied by light scattering, size-exclusion chromatography, atomic force microscopy, transmission electron microscopy, and other high-end expensive techniques. Here, we report a simple, yet robust, label-free technique exploiting protein charge transfer spectra (ProCharTS) to monitor the capsid assembly in real-time. ProCharTS absorption in the near UV-visible region (250-800 nm) arises when photoinduced electron transfer occurs from HOMO of COO- in glutamate (donor) to LUMO of NH3+ in lysine or polypeptide backbone (acceptor) of the protein. Alternatively, it can also occur from polypeptide backbone (donor) to acceptor in arginine, histidine, or lysine cation. ProCharTS is observed profusely among proximal charge clusters in folded proteins. Here, we show that, ProCharTS absorption among growing HBV capsids is amplified when HBV Cp homodimers assemble, generating new contacts among charged residues in the dimer-dimer interface. We notice a time-dependent sigmoidal increase in ProCharTS absorbance and luminescence during capsid formation in comparison to pure dimers. Additionally, a combined approach of anisotropy-based fluorescence assay is reported, where an increased fluorescence anisotropy was observed in capsids as compared to native and unfolded dimers. We conclude that ProCharTS can serve as a sensitive label-free tool for rapid tracking of capsid assembly in real-time and characterize the assembled capsids from dimers.

Monitoring Binding of Protamine with DNA Using Protein Charge Transfer Spectra

In this work, novel intrinsic electronic absorption (250-400 nm) with a molar extinction coefficient of 752 M-1cm-1 at 250 nm, arising from photoinduced electron transfer involving charged amino acid side chains and the polypeptide backbone, along with luminescence (300-500 nm) with quantum yield of 0.011 from subsequent charge recombination, was observed in salmon sperm Protamine (PRM). The absorption of PRM was attributed to the previously identified Peptide Backbone-to-Side chain Charge Transfer (PBS-CT) from the polypeptide backbone to the abundant cationic headgroups of Arginine in PRM, while the luminescence was believed to originate from charge recombination within the charge-separated excited states of PRM. Remarkably, since Arg is the only charged residue in the PRM sequence, the PRM Protein Charge Transfer Spectra (ProCharTS) is both totally and uniquely Arg specific. Interestingly, the peak of PRM luminescence emission spectrum was independent of the excitation wavelength, unlike other proteins such as human serum albumin, displaying unconventional luminescence. Aggregation-induced effects on PRM absorbance and luminescence were ruled out, as both PRM absorbance and luminescence increase maintained linearity with increasing concentration in the 25-150 μM range. Nucleoprotamine complex formation, resulting from the binding of PRM with calf-thymus genomic DNA (gDNA), was monitored through increased scattering by the nucleoprotamine complex, a decrease in gDNA/PRM absorbance, a decrease in gDNA/PRM ellipticity, and shifts of nucleoprotamine complex band upon agarose gel electrophoresis. Upon binding with gDNA (700 μM base pair concentration), PRM ProCharTS absorbance at 260 nm decreased by 72%. This decrease was attributed to the formation and subsequent precipitation of nucleoprotamine complex upon PRM-gDNA binding. The application of ProCharTS absorbance to indirectly monitor DNA-protein binding in a label-free approach was thus demonstrated.

Early events during the aggregation of Aβ16-22-derived switch-peptides tracked using Protein Charge Transfer Spectra

BACKGROUND

Understanding Aβ aggregation and inhibiting it at early stages is of utmost importance in treating Alzheimer's and other related amyloidogenic diseases. However, majority of the techniques to study Aβ aggregation mainly target the late stages; while those used to monitor early stages are either expensive, use extrinsic dyes, or do not provide information on molecular level interactions. Here, we investigate the early events of Aβ16-22(KLVFFAE) aggregation using Aβ16-22 derived switch-peptides (SwPs) through a novel label-free approach employing Protein Charge Transfer Spectra (ProCharTS).

RESULTS

When pH is increased from 2 to 7.2, the Aβ-derived switch peptides undergo controlled self-assembly, where the initial random coil peptides convert into β-sheet. We leveraged the intrinsic absorbance/luminescence arising from ProCharTS among growing peptide oligomers to observe the aggregation kinetics in real-time. In comparison to monomer, the lysine and glutamate headgroups in the peptide oligomer are expected to come in proximity enhancing ProCharTS intensity due to photoinduced electron transfer. With a combination of Aβ-derived switch-peptides and ProCharTS, we obtained structural insights on the early stages of Aβ-derived SwP aggregation in four unique peptides. Increase in scatter corrected ProCharTS absorbance (250-500 nm) and luminescence (320-720 nm) along with decreased mean luminescence lifetime (2.3-0.8 ns) characterize the initial stages of aggregation monitored for 1-96 h depending on the peptide. We correlated the results with Circular Dichroism (CD), 8-anilino-1-naphthalenesulfonic acid (ANS) and Thioflavin T (ThT) measurements.

SIGNIFICANCE

We demonstrate ProCharTS as an intrinsic analytical probe with following advantages over other conventional methods to track aggregation: it is a label-free probe; it's intensity can be measured using a UV-Vis spectrophotometer; it is more sensitive in detecting the early molecular events in aggregation compared to ANS and ThT; and it can provide information on specific contacts made between charged headgroups of Lysine/Glutamate in the oligomer.

An Excel fitting routine for correcting protein absorption spectra for scatter

Protein concentrations are often determined in a non-destructive manner by measuring the absorbance at 280 nm. However, light scattering in protein samples can complicate such assessment. We here describe a simple Excel Solver-based fitting routine to correct full protein UV absorption spectra for both Rayleigh and Mie scattering. Using samples displaying various degrees of natural and artificially induced scattering, we show that our multi-wavelength fitting method is not only capable of aiding in the determination of protein concentrations but can also be employed in the spectral analysis of protein structural changes that are accompanied by alterations in scatter intensity.