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Register a new userUltraviolet Photostability Improvement for Autofluorescence Correlation Spectroscopy on Label-Free Proteins
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The poor photostability and low brightness of protein autofluorescence have been major limitations preventing the detection of label-free proteins at the single molecule level. Overcoming these issues, we report here a strategy to promote the photostability of proteins and use their natural tryptophan autofluorescence in the ultraviolet (UV) for fluorescence correlation spectroscopy (FCS). Combining enzymatic oxygen scavengers with antioxidants and triplet state quenchers greatly promotes the protein photostability, reduces the photobleaching probability and improves the net autofluorescence detection rate. Our results show that the underlying photochemical concepts initially derived for organic visible fluorescent dyes are quite general. Using this approach, we achieved UV fluorescence correlation spectroscopy on label-free streptavidin proteins containing only 24 tryptophan residues, 6.5x less than the current state-of-the-art. This strategy greatly extends the possibility to detect single label-free proteins with the versatility of single molecule fluorescence without requiring the presence of a potentially disturbing external fluorescent marker. It also opens new perspectives to improve the UV durability of organic devices.
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Recent literatures reported blue-green emission from amyloid fibril as exclusive signature of fibril formation. This unusual visible luminescence is regularly used to monitor fibril growth. Blue-green emission has also been observed in crystalline protein and in solution. However, the origin of this emission is not known exactly. Our spectroscopic study of serum proteins reveals that the blue-green emission is a property of protein monomer. Evidences suggest that semiconductor-like band structure of proteins with the optical band-gap in the visible region is possibly the origin of this phenomenon. We show here that the band structure of proteins is primarily the result of electron delocalization through the peptide chain, rather than through the hydrogen bond network in secondary structure.
Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have reduced the cost of high-accuracy models. Trade-offs between sampling and accuracy have motivated modeling with molecular mechanics (MM) in a multi-scale QM/MM or iterative approach. Limitations to both conventional density functional theory (DFT) and classical MM force fields remain for describing non-covalent interactions in comparison to experiment or wavefunction theory. Because predictions of enzyme action (i.e., electrostatics), free energy barriers, and mechanisms are sensitive to the protocol and embedding method in QM/MM, convergence tests and systematic methods for quantifying QM-level interactions are a needed, active area of development.
The development of spectroscopic techniques able to detect and verify quantum coherence is a goal of increasing importance given the rapid progress of new quantum technologies, the advances in the field of quantum thermodynamics, and the emergence of new questions in chemistry and biology regarding the possible relevance of quantum coherence in biochemical processes. Ideally, these tools should be able to detect and verify the presence of quantum coherence in both the transient dynamics and the steady state of driven-dissipative systems, such as light-harvesting complexes driven by thermal photons in natural conditions. This requirement poses a challenge for standard laser spectroscopy methods. Here, we propose photon correlation measurements as a new tool to analyse quantum dynamics in molecular aggregates in driven-dissipative situations. We show that the photon correlation statistics on the light emitted by a molecular dimer model can signal the presence of coherent dynamics. Deviations from the counting statistics of independent emitters constitute a direct fingerprint of quantum coherence in the steady state. Furthermore, the analysis of frequency resolved photon correlations can signal the presence of coherent dynamics even in the absence of steady state coherence, providing direct spectroscopic access to the much sought-after site energies in molecular aggregates.
The recently proposed Hamiltonian Adaptive Resolution Scheme (H-AdResS) allows to perform molecular simulations in an open boundary framework. It allows to change on the fly the resolution of specific subset of molecules (usually the solvent), which are free to diffuse between the atomistic region and the coarse-grained reservoir. So far, the method has been successfully applied to pure liquids. Coupling the H-AdResS methodology to hybrid models of proteins, such as the Molecular Mechanics/Coarse-Grained (MM/CG) scheme, is a promising approach for rigorous calculations of ligand binding free energies in low-resolution protein models. Towards this goal, here we apply for the first time H-AdResS to two atomistic proteins in dual-resolution solvent, proving its ability to reproduce structural and dynamic properties of both the proteins and the solvent, as obtained from atomistic simulations.
Nuclear inelastic scattering in conjunction with density functional theory (DFT) calculations has been applied for the identification of vibrational modes of the high-spin ferric and the high-spin ferrous iron-sulfur center of a rubredoxin-type protein from the thermophylic bacterium Pyrococcus abysii.
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