Conformational Disorder and Dynamics of Proteins Sensed by Raman Optical Activity

Tidying up the conformational ensemble of a disordered peptide by computational prediction of spectroscopic fingerprints

The most advanced structure prediction methods are powerless in exploring the conformational ensemble of disordered peptides and proteins and for this reason the "protein folding problem" remains unsolved. We present a novel methodology that enables the accurate prediction of spectroscopic fingerprints (circular dichroism, infrared, Raman, and Raman optical activity), and by this allows for "tidying up" the conformational ensembles of disordered peptides and disordered regions in proteins. This concept is elaborated for and applied to a dodecapeptide, whose spectroscopic fingerprint is measured and theoretically predicted by means of enhanced-sampling molecular dynamics coupled with quantum mechanical calculations. Following this approach, we demonstrate that peptides lacking a clear propensity for ordered secondary-structure motifs are not randomly, but only conditionally disordered. This means that their conformational landscape, or phase-space, can be well represented by a basis-set of conformers including about 10 to 100 structures. The implications of this finding have profound consequences both for the interpretation of experimental electronic and vibrational spectral features of peptides in solution and for the theoretical prediction of these features using accurate and computationally expensive techniques. The here-derived methods and conclusions are expected to fundamentally impact the rationalization of so-far elusive structure-spectra relationships for disordered peptides and proteins, towards improved and versatile structure prediction methods.

Single-droplet surface-enhanced Raman scattering decodes the molecular determinants of liquid-liquid phase separation

Biomolecular condensates formed via liquid-liquid phase separation (LLPS) are involved in a myriad of critical cellular functions and debilitating neurodegenerative diseases. Elucidating the role of intrinsic disorder and conformational heterogeneity of intrinsically disordered proteins/regions (IDPs/IDRs) in these phase-separated membrane-less organelles is crucial to understanding the mechanism of formation and regulation of biomolecular condensates. Here we introduce a unique single-droplet surface-enhanced Raman scattering (SERS) methodology that utilizes surface-engineered, plasmonic, metal nanoparticles to unveil the inner workings of mesoscopic liquid droplets of Fused in Sarcoma (FUS) in the absence and presence of RNA. These highly sensitive measurements offer unprecedented sensitivity to capture the crucial interactions, conformational heterogeneity, and structural distributions within the condensed phase in a droplet-by-droplet manner. Such an ultra-sensitive single-droplet vibrational methodology can serve as a potent tool to decipher the key molecular drivers of biological phase transitions of a wide range of biomolecular condensates involved in physiology and disease.

The authors introduce a unique single-droplet surface-enhanced Raman scattering (SERS) methodology that illuminates a wealth of molecular information within the mesoscopic liquid condensed phase of Fused in Sarcoma in the absence and presence of RNA.

Structure analysis and non-invasive detection of cadmium-phytochelatin2 complexes in plant by deep learning Raman spectrum

Plants synthesize phytochelatins to chelate in vivo toxic heavy metal ions and produce nontoxic complexes for tolerating the stress. Detection of the complexes would simplify the identification of high phytoremediation cultivars, as well as assessment of plant food for safe consumption. Thus, a confocal Raman spectroscopy combined with density functional theory and deep learning was used for characterizing phytochelatin2 (PC₂), and Cd-PC₂ mixtures. Results showed the PC₂ chelate Cd²⁺ in a 2:1 ratio to produce Cd(PC₂)₂; Cd-S bonds of the Cd(PC₂)₂ have signature Raman vibrations at 305 and 610 cm^-1 which are the most distinctive spectral signatures for varieties of Cd-PCs complexes. The PC₂ was used as a natural probe to stabilize the chemical status of Cd, and to enrich and magnify Raman signature of the trace Cd for deep learning models which enabled condition of the Cd(PC₂)₂ in pak choi leaf to be visualized, quantified, and classified by directly using raw spectra of the leaf. This study provides a general protocol by using Raman information for structure analysis and non-invasive detection of heavy metal-PCs complexes in plants and provides a novel idea for simplifying identification of high phytoremediation cultivars, as well as assessment of heavy metal related food safeties.

Paving the way to conformationally unravel complex glycopeptide antibiotics by means of Raman optical activity

It is crucial for fundamental physical chemistry techniques to find their application in tackling real-world challenges. Hitherto, Raman optical activity (ROA) spectroscopy is one of the examples where a promising future within the pharmaceutical sector is foreseen, but has not yet been established. Namely, the technique is believed to be able to contribute in investigating the conformational behaviour of drug candidates. We, herein, strive towards the alignment of the ROA analysis outcome and the pharmaceutical expectations by proposing a fresh strategy that ensures a more complete, reliable, and transferable ROA study. The strategy consists of the treatment of the conformational space by means of a principal component analysis (PCA) and a clustering algorithm, succeeded by a thorough ROA spectral analysis and a novel way of estimating the contributions of the different chemical fragments to the total ROA spectral intensities. Here, vancomycin, an antibiotic glycopeptide, has been treated; it is the first antibiotic glycopeptide studied by means of ROA and is a challenging compound in ROA terms. By applying our approach we discover that ROA is capable of independently identifying the correct conformation of vancomycin in aqueous solution. In addition, we have a clear idea of what ROA can and cannot tell us regarding glycopeptides. Finally, the glycopeptide class turns out to be a spectroscopically curious case, as its spectral responses are unlike the typical ROA spectral responses of peptides and carbohydrates. This preludes future ROA studies of this intriguing molecular class.

Ultrasensitive Characterization of the Prion Protein by Surface-Enhanced Raman Scattering: Selective Enhancement via Electrostatic Tethering of the Intrinsically Disordered Domain with Functionalized Silver Nanoparticles

Surface-enhanced Raman scattering (SERS) circumvents the inherent insensitivity of Raman spectroscopy and offers a powerful tool for the ultrasensitive detection and characterization of biomolecules at low concentrations. Here we show that SERS via electrostatic tethering between surface-modified negatively charged silver nanoparticles and highly positively charged intrinsically disordered N-terminal domain of the prion protein allows highly sensitive and reproducible protein detection and characterization at as low as hundreds of nanomolar protein concentrations. These measurements preferentially illuminate a selective part of the protein due to a sharp dependence of the near-field intensity on the distance between the nanoparticle surface and the protein. We also demonstrate that by shortening the length of the disordered tail it is possible to achieve a domain-selective Raman enhancement to study the C-terminal globular domain. Our tether-length-dependent SERS methodology will serve as a potent, noninvasive, and label-free strategy to detect and characterize a wide range of proteins possessing disordered segments.

Employing complementary spectroscopies to study the conformations of an epimeric pair of side-chain stapled peptides in aqueous solution

Understanding the conformational preferences of free ligands in solution is often necessary to rationalize structure-activity relationships in drug discovery. Herein, we examine the conformational behavior of an epimeric pair of side-chain stapled peptides that inhibit the FAD dependent amine oxidase lysine specific demethylase 1 (LSD1). The peptides differ only at a single stereocenter, but display a major difference in binding affinity. Their Raman optical activity (ROA) spectra are most likely dominated by the C-terminus, obscuring the analysis of the epimeric macrocycle. By employing NMR spectroscopy, we show a difference in conformational behavior between the two compounds and that the LSD1 bound conformation of the most potent compound is present to a measurable extent in aqueous solution. In addition, we illustrate that Molecular Dynamics (MD) simulations produce ensembles that include the most important solution conformations, but that it remains problematic to identify relevant conformations with no a priori knowledge from the large conformational pool. Furthermore, this work highlights the importance of understanding the scope and limitations of the available techniques for conducting conformational analyses. It also emphasizes the importance of conformational selection of a flexible ligand in molecular recognition.

Solvation and the secondary structure of a proline-containing dipeptide: insights from VCD spectroscopy

In this study we investigate the IR and VCD spectra of the diastereomeric dipeptide Boc-Pro-Phe-(n-propyl) 1 in chloroform-d₁ (CDCl₃) and the strongly hydrogen bonding solvent dimethylsulfoxide-d₆ (DMSO-d₆). From comparison of the experimental spectra, the amide II spectral region is identified as marker signature for the stereochemistry of the dipeptide: the homochiral LL-1 features a (+/-)-pattern in the amide II region of the VCD spectrum, while the amide II signature of the diastereomer LD-1 is inverted. Computational analysis of the IR and VCD spectra of LL-1 reveals that the experimentally observed amide II signature is characteristic for a β_I-turn structure of the peptide. Likewise, the inverted pattern found for LD-1 arises from a β_II-turn structure of the dipeptide. Following a micro-solvation approach, the experimental spectra recorded in DMSO-d₆ are computationally well reproduced by considering only a single solvent molecule in a hydrogen bond with N-H groups. Considering a second solvent molecule, which would lead to a cleavage of intramolecular hydrogen bonds in 1, is found to give a significantly worse match with the experiment. Hence, the detailed computational analysis of the spectra of LL- and LD-1 recorded in DMSO-d₆ confirms that the intramolecular hydrogen bonding pattern, that stabilizes the β-turns and other conformations of LL- and LD-1 in apolar solvents, remains intact. Our findings also show that it is essential to consider solvation explicitly in the analysis of the IR and VCD spectra of dipeptides in strongly hydrogen bonding solvents. As the solute-solvent interactions affect both conformational preferences and spectral signatures, it is also demonstrated that this inclusion of solvent molecules cannot be circumvented by applying fitting procedures to non-solvated structures.

The effect of protein backbone hydration on the amide vibrations in Raman and Raman optical activity spectra

Raman and specifically Raman optical activity (ROA) spectroscopy are very sensitive to the solution structure and conformation of biomolecules. Because of this strong conformational sensitivity, density functional theory (DFT) calculations are often used to get a better understanding of the experimentally observed spectral patterns. While e.g. for carbohydrate structure the water molecules that surround the solute have been demonstrated to be of vital importance to get accurate modelled ROA spectra, the effect of explicit water molecules on the calculated ROA patterns of peptides and proteins is less well studied. Here, the effect of protein backbone hydration was studied using DFT calculations of HCO-(l-Ala)5-NH2 in specific secondary structure conformations with different treatments of the solvation. The effect of the explicit water molecules on the calculated spectra mainly arises from the formation of hydrogen bonds with the amide C[double bond, length as m-dash]O and N-H groups. Hydrogen bonding of water with the C[double bond, length as m-dash]O group determines the shape and position of the amide I band. The C[double bond, length as m-dash]O bond length increases upon formation of C[double bond, length as m-dash]OH2O hydrogen bonds. The effect of the explicit water molecules on the amide III vibrations arises from hydrogen bonding of the solvent with both the C[double bond, length as m-dash]O and N-H group, but their contributions to this spectral region differ: geometrically, the formation of a C[double bond, length as m-dash]OH2O bond decreases the C-N bond length, while upon forming a N-HH2O hydrogen bond, the N-H bond length increases.

Tracking Conformational Changes in Phosvitin throughout a Crowding-Agent-Based Titration

The sensitivity of Raman optical activity (ROA) towards small conformational changes is explored by tracking the structural changes in an intrinsically disordered protein-phosvitin-induced by different concentrations of crowding agent. It is shown that ROA is capable of tracking small conformational changes involving β-sheet and α-helical secondary structural properties of the protein. Furthermore, it is indicated that the influences of the crowding agents employed, Ficoll 70 and dextran 70, on the structural properties of phosvitin differ significantly, with the structural changes induced by the presence of Ficoll 70 being more pronounced and already being visible at a lower concentration. The data also suggest that some spectral changes do not arise from a change in the secondary structure of the protein, but are related to differences in interaction between the phosphorylated residues of the protein and the sugar-based crowding agent.