Fractal nature of protein surface roughness: a note on quantification of change of surface roughness in active sites, before and after binding

Silk-gelatin hybrid hydrogel: a potential carrier for RNA therapeutics

RNA-based therapeutics have exhibited remarkable potential in targeting genetic factors for disease intervention, exemplified by recent mRNA vaccines for COVID-19. Nevertheless, the intrinsic instability of RNA and challenges related to its translational efficiency remain significant obstacles to the development of RNA as therapeutics. This study introduces an innovative RNA delivery approach using a silk fibroin (SF) and positively charged gelatin (Gel) hydrogel matrix to enhance RNA stability for controlled release. As a proof of concept, whole-cell RNA was incorporated into the hydrogel to enhance interactions with RNA molecules. Additionally, molecular modeling studies were conducted to explore the interactions between SF, collagen, chitosan (Chi), and the various RNA species including ribosomal RNAs (28S, 18S, 8.5S, and 5S rRNAs), transfer RNAs (tRNA-ALA, tRNA-GLN, and tRNA-Leu), as well as messenger RNAs (mRNA-GAPDH, mRNA-β actin, and mRNA-Nanog), shedding light on the RNA-polymer interaction and RNA stability; SF exhibits a more robust interaction with RNA compared to collagen/gel and chitosan. We confirmed the molecular interactions of SF and RNA by FTIR and Raman spectroscopy, which were further supported by AFM and contact angle measurement. This research introduces a novel RNA delivery platform and insights into biopolymer-RNA interactions, paving the way for tailored RNA delivery systems in therapeutics and biomedical applications.

Multiscale Water Dynamics on Protein Surfaces: Protein-Specific Response to Surface Ions

Proteins function in crowded aqueous environments, interacting with a diverse range of compounds, and among them, dissolved ions. These interactions are water-mediated. In the present study, we combine field-dependent NMR relaxation (NMRD) and theory to probe water dynamics on the surface of proteins in concentrated aqueous solutions of hen egg-white lysozyme (LZM) and bovine serum albumin (BSA). The experiments reveal that the presence of salts (NaCl or NaI) leads to an opposite ion-specific response for the two proteins: an addition of salt to LZM solutions increases water relaxation rates with respect to the salt-free case, while for BSA solutions, a decrease is observed. The magnitude of the change depends on the ion identity. The developed model accounts for the non-Lorentzian shape of the NMRD profiles and reproduces the experimental data over four decades in Larmor frequency (10 kHz to 110 MHz). It is applicable up to high protein concentrations. The model incorporates the observed ion-specific effects via changes in the protein surface roughness, represented by the surface fractal dimension, and the accompanying changes in the surface water residence times. The response is protein-specific, linked to geometrical aspects of the individual protein surfaces, and goes beyond protein-independent Hofmeister-style ordering of ions.

Apparent scaling of virus surface roughness-An example from the pandemic SARS-nCoV

This paper investigates the scaling of the surface roughness of coronavirus, including the SARS-nCoV based on fractal and spectral analyses of their published electron microscopy images. The box-counting fractal dimensions obtained are subjected to ANOVA tests for statistical significance. Results show that the SARS-nCoV particles could not statistically be resolved by their shape on the basis of the fractal dimension values, but they could be distinguished from the earlier SARS-CoV particles. MANOVA test results require interaction of factors used for classifying virions into different types. The topological entropies, a measure of randomness in a system, measured for the images of varying size show correlation with the fractal dimensions. Spectral analyses of our data show a departure from power-law self-similarity, suggesting an apparent scaling of surface roughness over a band of maximum an order of magnitude. The spectral crossover that corresponds to characteristic length scale may represent average viral size. Our results may be useful in inferring the nature of surface-contact between the viral and human cell, causing infection and also in providing clues for new drugs, although it is too early to say. In addition, limitations of this study, including possible ways to avoid the bias in scaling exponents due to the use of different techniques are discussed.

Ras isoforms: signaling specificities in CD40 pathway

Background

Ras are small cellular GTPases which regulate diverse cellular processes. It has three isoforms: H-Ras, K-Ras, and N-Ras. Owing to the N-terminus (1–165 residues) sequence homology these isoforms were thought to be functionally redundant. However, only K-Ras-deficient mice but not H-Ras- and N-Ras-deficient mice show embryonic lethality. Similarly, mutations in a given Ras isoform are associated with a particular type of cancer. Moreover, we have previously reported that Ras isoforms perform unique functions in Leishmania major infection. Thus, Ras isoforms are implicated to have signaling and functional specificity but the mechanism remains to be elucidated.

Result

Using CD40 as a model receptor, we showed that depending on the strength of signaling, specific Ras isoforms are activated. Weak CD40 signal activates N-Ras, whereas strong signal activates H-Ras and K-Ras. Additionally, we showed that suppression of N-Ras expression reduced CD40-induced extracellular signal–regulated kinase-1/2 (ERK-1/2) activation and Interleukin (IL)-10 production; whereas suppression of H-Ras or K-Ras reduced CD40-induced p38 mitogen-activated protein kinase (p38MAPK) activation and IL-12 production. Furthermore, we showed that Ras isoforms have activator (GEF) specificity as weak CD40 signal-activated N-Ras requires Sos-1/2 whereas strong CD40 signal-activated H-Ras/K-Ras requires Ras-GRP as the guanine-nucleotide exchange factor (GEF) inducing ERK-1/2- or p38MAPK-mediated IL-10 or IL-12 productions, respectively, in macrophages. Silencing of syk reduced CD40-induced N-Ras activation but silencing of lyn inhibited H-Ras and K-Ras activation. In CD40 signaling, Ras isoforms also showed effector specificity; while H-Ras and K-Ras showed specificity for phosphatidyl inositol-3 kinase activation at high dose of CD40 stimulation, N-Ras primarily associated with Raf-1 at low dose of CD40 stimulation. Moreover, fractal analysis showed that functional site surface roughness for H-Ras (SurfaceFD = 2.39) and K-Ras (SurfaceFD = 2.39) are similar but significantly different from N-Ras (SurfaceFD = 2.25).

Conclusion

The activator and effector specificities of Ras isoforms in CD40 signaling indicated their differential involvement in CD40 pathway and in maintaining the reciprocity. Our observations reveal Ras-regulated signaling outcome and its potential for developing Ras isoform-targeted immunotherapy and prophylaxis.

Graphical abstract

Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions

G protein-coupled receptors (GPCRs) control cellular signaling and responses. Many of these GPCRs are modulated by cholesterol and polyunsaturated fatty acids (PUFAs) which have been shown to co-exist with saturated lipids in ordered membrane domains. However, the lipid compositions of such domains extracted from the brain cortex tissue of individuals suffering from GPCR-associated neurological disorders show drastically lowered levels of PUFAs. Here, using free energy techniques and multiscale simulations of numerous membrane proteins, we show that the presence of the PUFA DHA helps helical multi-pass proteins such as GPCRs partition into ordered membrane domains. The mechanism is based on hybrid lipids, whose PUFA chains coat the rough protein surface, while the saturated chains face the raft environment, thus minimizing perturbations therein. Our findings suggest that the reduction of GPCR partitioning to their native ordered environments due to PUFA depletion might affect the function of these receptors in numerous neurodegenerative diseases, where the membrane PUFA levels in the brain are decreased. We hope that this work inspires experimental studies on the connection between membrane PUFA levels and GPCR signaling.

Our current picture of cellular membranes depicts them as laterally heterogeneous sheets of lipids crowded with membrane proteins. These proteins often require a specific lipid environment to efficiently perform their functions. Certain neuroreceptor proteins are regulated by membrane cholesterol that is considered to be enriched in ordered membrane domains. In the brain, these very same domains also contain a fair amount of polyunsaturated fatty acids (PUFAs) that have also been discovered to interact favorably with many receptor proteins. However, certain neurological diseases—associated with the inadequate functioning of the neuroreceptors—seem to result in the decrease of brain PUFA levels. We hypothesized that this decrease in PUFA levels somehow inhibits receptor partitioning to cholesterol-rich domains, which could further compromise their function. We verified our hypothesis by an extensive set of computer simulations. They demonstrated that the PUFA–receptor interaction indeed leads to favorable partitioning of the receptors in the cholesterol-rich ordered domains. Moreover, the underlying mechanism based on the shielding of the rough protein surface by the PUFAs seems to be exclusive for multi-helical protein structures, of which neuroreceptors are a prime example.

Self-organization, entropy and allostery

Allostery is a fundamental regulatory mechanism in biology. Although generally accepted that it is a dynamics-driven process, the exact molecular mechanism of allosteric signal transmission is hotly debated. We argue that allostery is as a part of a bigger picture that also includes fractal-like properties of protein interior, hierarchical protein folding and entropy-driven molecular recognition. Although so far all these phenomena were studied separately, they stem from the same common root: self-organization of polypeptide chains and, thus, has to be studied collectively. This merge will allow the cross-referencing of a broad spectrum of multi-disciplinary data facilitating progress in all these fields.

Surfaceome and Proteosurfaceome in Parietal Monoderm Bacteria: Focus on Protein Cell-Surface Display

The cell envelope of parietal monoderm bacteria (archetypal Gram-positive bacteria) is formed of a cytoplasmic membrane (CM) and a cell wall (CW). While the CM is composed of phospholipids, the CW is composed at least of peptidoglycan (PG) covalently linked to other biopolymers, such as teichoic acids, polysaccharides, and/or polyglutamate. Considering the CW is a porous structure with low selective permeability contrary to the CM, the bacterial cell surface hugs the molecular figure of the CW components as a well of the external side of the CM. While the surfaceome corresponds to the totality of the molecules found at the bacterial cell surface, the proteinaceous complement of the surfaceome is the proteosurfaceome. Once translocated across the CM, secreted proteins can either be released in the extracellular milieu or exposed at the cell surface by associating to the CM or the CW. Following the gene ontology (GO) for cellular components, cell-surface proteins at the CM can either be integral (GO: 0031226), i.e., the integral membrane proteins, or anchored to the membrane (GO: 0046658), i.e., the lipoproteins. At the CW (GO: 0009275), cell-surface proteins can be covalently bound, i.e., the LPXTG-proteins, or bound through weak interactions to the PG or wall polysaccharides, i.e., the cell wall binding proteins. Besides monopolypeptides, some proteins can associate to each other to form supramolecular protein structures of high molecular weight, namely the S-layer, pili, flagella, and cellulosomes. After reviewing the cell envelope components and the different molecular mechanisms involved in protein attachment to the cell envelope, perspectives in investigating the proteosurfaceome in parietal monoderm bacteria are further discussed.

Protein surface roughness accounts for binding free energy of Plasmepsin II-ligand complexes

The calculation of absolute binding affinities for protein-inhibitor complexes remains as one of the main challenges in computational structure-based ligand design. The present work explored the calculations of surface fractal dimension (as a measure of surface roughness) and the relationship with experimental binding free energies of Plasmepsin II complexes. Plasmepsin II is an attractive target for novel therapeutic compounds to treat malaria. However, the structural flexibility of this enzyme is a drawback when searching for specific inhibitors. Concerning that, we performed separate explicitly solvated molecular dynamics simulations using the available high-resolution crystal structures of different Plasmepsin II complexes. Molecular dynamics simulations allowed a better approximation to systems dynamics and, therefore, a more reliable estimation of surface roughness. This constitutes a novel approximation in order to obtain more realistic values of fractal dimension, because previous works considered only x-ray structures. Binding site fractal dimension was calculated considering the ensemble of structures generated at different simulation times. A linear relationship between binding site fractal dimension and experimental binding free energies of the complexes was observed within 20 ns. Previous studies of the subject did not uncover this relationship. Regression model, coined FD model, was built to estimate binding free energies from binding site fractal dimension values. Leave-one-out cross-validation showed that our model reproduced accurately the absolute binding free energies for our training set (R²  = 0.76; <|error|> =0.55 kcal/mol; SD_error  = 0.19 kcal/mol). The fact that such a simple model may be applied raises some questions that are addressed in the article.