Do polyproline II helix associations modulate biomolecular condensates?

Architectonic principles of polyproline II helix bundle protein domains

Glycine rich polyproline II helix assemblies are an emerging class of natural domains found in several proteins with different functions and diverse origins. The distinct properties of these domains relative to those composed of α-helices and β-sheets could make glycine-rich polyproline II helix assemblies a useful building block for protein design. Whereas the high population of polyproline II conformers in disordered state ensembles could facilitate glycine-rich polyproline II helix folding, the architectonic bases of these structures are not well known. Here, we compare and analyze their structures to uncover common features. These protein domains are found to be highly tolerant of distinct flanking sequences. This speaks to the robustness of this fold and strongly suggests that glycine rich polyproline II assemblies could be grafted with other protein domains to engineer new structures and functions. These domains are also well packed with few or no cavities. Moreover, a significant trend towards antiparallel helix configuration is observed in all these domains and could provide stabilizing interactions among macrodipoles. Finally, extensive networks of Cα-H···OC hydrogen bonds are detected in these domains. Despite their diverse evolutionary origins and activities, glycine-rich polyproline II helix assemblies share architectonic features which could help design novel proteins.

Yeast profilin mutants inhibit classical nuclear import and alter the balance between actin and tubulin levels

Profilin is a small protein that controls actin polymerization in yeast and higher eukaryotes. In addition, profilin has emerged as a multifunctional protein that contributes to other processes in multicellular organisms. This study focuses on profilin (Pfy1) in the budding yeast Saccharomyces cerevisiae. The primary sequences of yeast Pfy1 and its metazoan orthologs diverge vastly. However, structural elements of profilin are conserved among different species. To date, the full spectrum of Pfy1 functions has yet to be defined. The current work explores the possible involvement of yeast profilin in nuclear protein import. To this end, a panel of well-characterized yeast profilin mutants was evaluated. The experiments demonstrate that yeast profilin (i) regulates nuclear protein import, (ii) determines the subcellular localization of essential nuclear transport factors, and (iii) controls the relative abundance of actin and tubulin. Together, these results define yeast profilin as a moonlighting protein that engages in multiple essential cellular activities.

Structure-function relationships in protein homorepeats

Homorepeats (or polyX), protein segments containing repetitions of the same amino acid, are abundant in proteomes from all kingdoms of life and are involved in crucial biological functions as well as several neurodegenerative and developmental diseases. Mainly inserted in disordered segments of proteins, the structure/function relationships of homorepeats remain largely unexplored. In this review, we summarize present knowledge for the most abundant homorepeats, highlighting the role of the inherent structure and the conformational influence exerted by their flanking regions. Recent experimental and computational methods enable residue-specific investigations of these regions and promise novel structural and dynamic information for this elusive group of proteins. This information should increase our knowledge about the structural bases of phenomena such as liquid-liquid phase separation and trinucleotide repeat disorders.

Combining Experiments and Simulations to Examine the Temperature-Dependent Behavior of a Disordered Protein

Intrinsically disordered proteins are a class of proteins that lack stable folded conformations and instead adopt a range of conformations that determine their biochemical functions. The temperature-dependent behavior of such disordered proteins is complex and can vary depending on the specific protein and environment. Here, we have used molecular dynamics simulations and previously published experimental data to investigate the temperature-dependent behavior of histatin 5, a 24-residue-long polypeptide. We examined the hypothesis that histatin 5 undergoes a loss of polyproline II (PPII) structure with increasing temperature, leading to more compact conformations. We found that the conformational ensembles generated by the simulations generally agree with small-angle X-ray scattering data for histatin 5, but show some discrepancies with the hydrodynamic radius as probed by pulsed-field gradient NMR spectroscopy, and with the secondary structure information derived from circular dichroism. We attempted to reconcile these differences by reweighting the conformational ensembles against the scattering and NMR data. By doing so, we were in part able to capture the temperature-dependent behavior of histatin 5 and to link the observed decrease in hydrodynamic radius with increasing temperature to a loss of PPII structure. We were, however, unable to achieve agreement with both the scattering and NMR data within experimental errors. We discuss different possible reasons for this including inaccuracies in the force field, differences in conditions of the NMR and scattering experiments, and issues related to the calculation of the hydrodynamic radius from conformational ensembles. Our study highlights the importance of integrating multiple types of experimental data when modeling conformational ensembles of disordered proteins and how environmental factors such as the temperature influence them.

Insight into polyproline II helical bundle stability in an antifreeze protein denatured state

The use of polyproline II (PPII) helices in protein design is currently hindered by limitations in our understanding of their conformational stability and folding. Recent studies of the snow flea antifreeze protein (sfAFP), a useful model system composed of six PPII helices, suggested that a low denatured state entropy contributes to folding thermodynamics. Here, circular dichroism spectroscopy revealed minor populations of PPII like conformers at low temperature. To get atomic level information on the conformational ensemble and entropy of the reduced, denatured state of sfAFP, we have analyzed its chemical shifts and {1H}-15N relaxation parameters by NMR spectroscopy at four experimental conditions. No significant populations of stable secondary structure were detected. The stiffening of certain N-terminal residues at neutral versus acidic pH and shifted pKa values leads us to suggest that favorable charge-charge interactions could bias the conformational ensemble to favor the formation the C1-C28 disulfide bond during nascent folding, although no evidence for preferred contacts between these positions was detected by paramagnetic relaxation enhancement under denaturing conditions. Despite a high content of flexible glycine residues, the mobility of the sfAFP denatured ensemble is similar for denatured α/β proteins both on fast ps/ns as well as slower μs/ms timescales. These results are in line with a conformational entropy in the denatured ensemble resembling that of typical proteins and suggest that new structures based on PPII helical bundles should be amenable to protein design.

BERT-PPII: The Polyproline Type II Helix Structure Prediction Model Based on BERT and Multichannel CNN

Predicting the polyproline type II (PPII) helix structure is crucial important in many research areas, such as the protein folding mechanisms, the drug targets, and the protein functions. However, many existing PPII helix prediction algorithms encode the protein sequence information in a single way, which causes the insufficient learning of protein sequence feature information. To improve the protein sequence encoding performance, this paper proposes a BERT-based PPII helix structure prediction algorithm (BERT-PPII), which learns the protein sequence information based on the BERT model. The BERT model's CLS vector can fairly fuse sample's each amino acid residue information. Thus, we utilize the CLS vector as the global feature to represent the sample's global contextual information. As the interactions among the protein chains' local amino acid residues have an important influence on the formation of PPII helix, we utilize the CNN to extract local amino acid residues' features which can further enhance the information expression of protein sequence samples. In this paper, we fuse the CLS vectors with CNN local features to improve the performance of predicting PPII structure. Compared to the state-of-the-art PPIIPRED method, the experimental results on the unbalanced dataset show that the proposed method improves the accuracy value by 1% on the strict dataset and 2% on the less strict dataset. Correspondingly, the results on the balanced dataset show that the AUCs of the proposed method are 0.826 on the strict dataset and 0.785 on less strict datasets, respectively. For the independent test set, the proposed method has the AUC value of 0.827 on the strict dataset and 0.783 on the less strict dataset. The above experimental results have proved that the proposed BERT-PPII method can achieve a superior performance of predicting the PPII helix.

AlphaFold 2 and NMR Spectroscopy: Partners to Understand Protein Structure, Dynamics and Function

The artificial intelligence program AlphaFold 2 is revolutionizing the field of protein structure determination as it accurately predicts the 3D structure of two thirds of the human proteome. Its predictions can be used directly as structural models or indirectly as aids for experimental structure determination using X-ray crystallography, CryoEM or NMR spectroscopy. Nevertheless, AlphaFold 2 can neither afford insight into how proteins fold, nor can it determine protein stability or dynamics. Rare folds or minor alternative conformations are also not predicted by AlphaFold 2 and the program does not forecast the impact of post translational modifications, mutations or ligand binding. The remaining third of human proteome which is poorly predicted largely corresponds to intrinsically disordered regions of proteins. Key to regulation and signaling networks, these disordered regions often form biomolecular condensates or amyloids. Fortunately, the limitations of AlphaFold 2 are largely complemented by NMR spectroscopy. This experimental approach provides information on protein folding and dynamics as well as biomolecular condensates and amyloids and their modulation by experimental conditions, small molecules, post translational modifications, mutations, flanking sequence, interactions with other proteins, RNA and virus. Together, NMR spectroscopy and AlphaFold 2 can collaborate to advance our comprehension of proteins.

Entering the second decade: FEBS Open Bio in 2022

FEBS Open Bio continues to go from strength to strength, with 2021 perhaps marking its most exciting year. In this Editorial, the Editor-in-Chief Miguel A. De la Rosa looks back at all the new developments of 2021 and forecasts the outlook for 2022.

Remarkably high solvatochromism in the circular dichroism spectra of the polyproline-II conformation: limitations or new opportunities?

Circular dichroism is a conventional method for studying the secondary structures of peptides and proteins and their transitions. While certain circular dichroism features are characteristic of α-helices and β-strands, the third most abundant secondary structure, the polyproline-II helix, does not exhibit a strictly conserved spectroscopic appearance. Due to its extended nature, the polyproline-II helix is highly accessible to the surrounding solvent; thus, the environment has a critical influence on the lineshape of the circular dichroism spectra of this structure. To showcase possible effects due to the medium, in this work, we report an experimental spectroscopic study of polyproline-II-forming oligomeric peptides in various environments: solvents, detergent micelles, and liposomes. Strikingly, the examination of an oligomeric peptide in a solvent series showed a remarkable 7 nm solvatochromic shift in the main negative band starting with hexafluoropropan-2-ol and moving to hexane. Furthermore, a previously predicted positive band below 200 nm was discovered in the spectra in nonpolar environments. In isotropic liposomes, the expected transition to the transmembrane state correlated with the appearance of a positive band at 228 nm. Our results demonstrate that changes in solvation should be taken into consideration when assessing the circular dichroism spectra of peptides expected to adopt the polyproline-II conformation. Although this precaution may complicate spectral analysis, characterization of solvent-induced spectral changes can generate new opportunities for testing the location of peptides in complex systems such as micelles or lipid bilayers.

Glycine-Rich Peptides from FUS Have an Intrinsic Ability to Self-Assemble into Fibers and Networked Fibrils

Glycine-rich regions feature prominently in intrinsically disordered regions (IDRs) of proteins that drive phase separation and the regulated formation of membraneless biomolecular condensates. Interestingly, the Gly-rich IDRs seldom feature poly-Gly tracts. The protein fused in sarcoma (FUS) is an exception. This protein includes two 10-residue poly-Gly tracts within the prion-like domain (PLD) and at the interface between the PLD and the RNA binding domain. Poly-Gly tracts are known to be highly insoluble, being potent drivers of self-assembly into solid-like fibrils. Given that the internal concentrations of FUS and FUS-like molecules cross the high micromolar and even millimolar range within condensates, we reasoned that the intrinsic insolubility of poly-Gly tracts might be germane to emergent fluid-to-solid transitions within condensates. To assess this possibility, we characterized the concentration-dependent self-assembly for three non-overlapping 25-residue Gly-rich peptides derived from FUS. Two of the three peptides feature 10-residue poly-Gly tracts. These peptides form either long fibrils based on twisted ribbon-like structures or self-supporting gels based on physical cross-links of fibrils. Conversely, the peptide with similar Gly contents but lacking a poly-Gly tract does not form fibrils or gels. Instead, it remains soluble across a wide range of concentrations. Our findings highlight the ability of poly-Gly tracts within IDRs that drive phase separation to undergo self-assembly. We propose that these tracts are likely to contribute to nucleation of fibrillar solids within dense condensates formed by FUS.

Membraneless organelles: a smart design for metabolic control

While most organelles are surrounded by membranes, cells also contain membraneless organelles, which remain separated in the cell by avoiding the mixture of their components with the surroundings. Actually, liquid–liquid phase separation provides a simple but smart mechanism for the cell to control the spatial localization and processing of molecules, without relying on membrane boundaries. This Special ‘In the Limelight’ section, entitled ‘Membraneless organelles’, consists of three review articles, each focused on a particular aspect. The first article deals with assembly of coacervates as mediated by polyproline II helices, as well as with condensate stability. The second article addresses the formation of protein–nucleic acid coacervates by prion‐like proteins and their link to human diseases. Finally, the last article focuses on mitochondrial cytochrome c translocation into the nucleus after DNA damage, with the subsequent inhibition of nucleosome assembly/disassembly activity of histone chaperones and its impact on chromatin dynamics and nuclear condensates.