Ramachandran maps for side chains in globular proteins

Biocatalytic Preparation of High-Purity DHA-Enriched Partial Glycerides through Semirational Design and Modification of Lipase Lip1897

High-purity docosahexaenoic acid (DHA) partial glycerides (PG) supplements have promising market prospects. In this study, a novel lipolytic enzyme family I lipase Lip1897, derived from Streptomyces thermodiastaticus, was identified and modified to be applied to the enzymatic synthesis of high-purity docosahexaenoic acid partial glycerides (DHA-PG). Lip1897 displayed optimal activity and good stability at 55 °C and pH 5.0. Further study found that Lip1897 could catalyze the hydrolysis of DHA triglycerides (TG) and DHA ethyl esters (EE), the esterification of DHA, and the glycerolysis of docosahexaenoic acid ethyl esters (DHA-EE), which had good prospects for industrial application. To enhance the catalytic selectivity of Lip1897, semirational design and modification based on structural analysis were carried out, and the mutant Lip1897-H106W showed a 1.86-fold increase in glycerolysis activity. The molecular docking results indicated that the mutant bound to the substrate DHA-EE at lower energy and with a more stable conformation. Under the solvent-free system, Lip1897-H106W was employed to catalyze the glycerolysis of DHA-EE for the synthesis of DHA-PG, achieving a promising DHA-EE conversion rate of 95.02% and a high DHA-PG yield of 70.85%. The efficient glycerolysis for preparing high-purity DHA-PG was realized. This research provides a reference for enhancing the efficiency of specific configurational functional lipid biosynthesis through enzyme discovery and modification.

Amino-Acid Characteristics in Protein Native State Structures

The molecular machines of life, proteins, are made up of twenty kinds of amino acids, each with distinctive side chains. We present a geometrical analysis of the protrusion statistics of side chains in more than 4000 high-resolution protein structures. We employ a coarse-grained representation of the protein backbone viewed as a linear chain of Cα atoms and consider just the heavy atoms of the side chains. We study the large variety of behaviors of the amino acids based on both rudimentary structural chemistry as well as geometry. Our geometrical analysis uses a backbone Frenet coordinate system for the common study of all amino acids. Our analysis underscores the richness of the repertoire of amino acids that is available to nature to design protein sequences that fit within the putative native state folds.

Reviewing the Structure-Function Paradigm in Polyglutamine Disorders: A Synergistic Perspective on Theoretical and Experimental Approaches

Polyglutamine (polyQ) disorders are a group of neurodegenerative diseases characterized by the excessive expansion of CAG (cytosine, adenine, guanine) repeats within host proteins. The quest to unravel the complex diseases mechanism has led researchers to adopt both theoretical and experimental methods, each offering unique insights into the underlying pathogenesis. This review emphasizes the significance of combining multiple approaches in the study of polyQ disorders, focusing on the structure-function correlations and the relevance of polyQ-related protein dynamics in neurodegeneration. By integrating computational/theoretical predictions with experimental observations, one can establish robust structure-function correlations, aiding in the identification of key molecular targets for therapeutic interventions. PolyQ proteins' dynamics, influenced by their length and interactions with other molecular partners, play a pivotal role in the polyQ-related pathogenic cascade. Moreover, conformational dynamics of polyQ proteins can trigger aggregation, leading to toxic assembles that hinder proper cellular homeostasis. Understanding these intricacies offers new avenues for therapeutic strategies by fine-tuning polyQ kinetics, in order to prevent and control disease progression. Last but not least, this review highlights the importance of integrating multidisciplinary efforts to advancing research in this field, bringing us closer to the ultimate goal of finding effective treatments against polyQ disorders.

Analysis of SIKVAV's receptor affinity, pharmacokinetics, and pharmacological characteristics: a matrikine with potent biological function

Matrikines are biologically active peptides generated from fragments fragmentation of extracellular matrix components (ECM) that are functionally distinct from the original full-length molecule. The active matricryptic sites can be unmasked by ECM components enzymatic degradation or multimerization, heterotypic binding, adsorption to other molecules, cell-mediated mechanical forces, exposure to reactive oxygen species, ECM denaturation, and others. Laminin α1-derived peptide (SIKVAV) is a bioactive peptide derived from laminin-111 that participates in tumor development, cell proliferation, angiogenesis in various cell types. SIKVAV has also a potential pharmaceutical activity that may be used for tissue regeneration and bioengineering in Alzheimer's disease and muscular dystrophies. In this work, we made computational analyzes of SIKVAV regarding the ADMET panel, that stands for Administration, Distribution, Metabolism, Excretion, and Toxicity. Docking analyzes using the α3β1 and α6β1 integrin receptors were performed to fill in the gaps in the SIKVAV's signaling pathway and coupling tests showed that SIKVAV can interact with both receptors. Moreover, there is no indication of cytotoxicity, mutagenic or carcinogenic activity, skin or oral sensitivity. Our analysis suggests that SIKVAV has a high probability of interacting with peroxisome proliferator-activated receptor-gamma (NR-PPAR-γ), which has anti-inflammatory activity. The results of bioinformatics can help understand the participation of SIKVAV in homeostasis and influence the understanding of how this peptide can act as a biological asset in the control of dystrophies, neurodegenerative diseases, and tissue engineering.

Investigating the Mechanism of Action of Anti-Dengue Compounds as Potential Binders of Zika Virus RNA-Dependent RNA Polymerase

The World Health Organization (WHO) has designated the Zika virus (ZIKV) as a significant risk to the general public's health. Currently, there are no vaccinations or medications available to treat or prevent infection with the Zika virus. Thus, it is urgently required to develop a highly efficient therapeutic molecule. In the presented study, a computationally intensive search was carried out to identify potent compounds that have the potential to bind and block the activity of ZIKV NS5 RNA-dependent RNA polymerase (RdRp). The anti-dengue chemical library was subjected to high-throughput virtual screening and MM/GBSA analysis in order to rate the potential candidates. The top three compounds were then chosen. According to the MM/GBSA analysis, compound 127042987 from the database had the highest binding affinity to the protein with a minimum binding free energy of -77.16 kcal/mole. Compound 127042987 had the most stable RMSD trend and the greatest number of hydrogen bond interactions when these chemical complexes were evaluated further under a 100 ns molecular dynamics simulation. Compound 127042987 displayed the best binding free energy (GBind) of -96.50 kcal/mol, surpassing the native ligand binding energy (-66.17 kcal/mole). Thereafter, an MM/GBSA binding free energy study was conducted to validate the stability of selected chemical complexes. Overall, this study illustrated that compound 127042987 showed preferred binding free energies, suggesting a possible inhibitory mechanism against ZIKV-RdRp. As per this study, it was proposed that compound 127042987 could be used as a therapeutic option to prevent Zika virus infection. These compounds need to be tested in experiments for further validation.

Effects of the deletion and substitution of thioesterase on bacillomycin D synthesis

OBJECTIVES

The importance of thioesterase domains on bacillomycin D synthesis and the ability of different thioesterase domains to selectively recognize and catalyze peptide chain hydrolysis and cyclization were studied by deleting and substituting thioesterase domains.

RESULTS

No bacillomycin D analogs were found in the thioesterase-deleted strain fmbJ-ΔTE, indicating that the TE domain was essential for bacillomycin D synthesis. Then the thioesterase in bacillomycin D synthetases was replaced by the thioesterase in bacillomycin F, iturin A, mycosubtilin, plipastatin and surfactin synthetases. Except for fmbJ-S-TE, all others were able to synthesize bacillomycin D homologs because a suitable recombination site was selected, which maintained the integrity of NRPSs. In particular, the yield of bacillomycin D in fmbJ-IA-TE, fmbJ-M-TE and fmbJ-P-TE was significantly increased.

CONCLUSION

This study expands our understanding of the TE domain in bacillomycin D synthetases and shows that thioesterase has excellent potential in the chemical-enzymatic synthesis of natural products or their analogs.

A pH-responsive phosphoprotein washing fluid for the removal of phenanthrene from contaminated peat moss in the cold region

Oil pollution is one of the major environmental concerns in the petroleum industry. In this study, a cheap food-grade sodium caseinate (NaCas) was used as a pH-responsive washing fluid in the remediation of phenanthrene (PHE) affected peat moss. The effects of environmental factors on the removal of PHE were systematically investigated. The results showed that increasing NaCas concentration and washing temperature improved the PHE mobilization, while high salinity and humic acid dosage displayed a negative effect. The factorial analysis revealed that three individual factors and two interactions exhibited significant effects on the washing performance. Due to the pH-responsive property of NaCas, the turbidity, total organic carbon (TOC), and chemical oxygen demand (COD) of the washing effluent were remarkably reduced by simply adjusting the solution acidity, improving the practical application of such a washing method. Significantly, the toxicity modeling proved that NaCas can reduce the binding energy between PHE and superoxide dismutase (SOD) of the selected marine organism, and thus relieve the toxicity of PHE to the organisms. Given these advantages, NaCas-assisted washing can be a viable option for the remediation of contaminated peat moss.

In silico structural and functional characterization of Antheraea mylitta cocoonase

BACKGROUND

Cocoonase is a serine protease present in sericigenous insects and majorly involved in dissolving of sericin protein allowing moth to escape. Cocoon structure is made up of sericin protein which holds fibroin filaments together. Cocoonase enzyme hydrolyzes sericin protein without harming the fibroin. However, until date, no detailed characterization of cocoonase enzyme and its presence in wild silk moth Antheraea mylitta has been carried out. Therefore, current study aimed for detailed characterization of amplified cocoonase enzyme, secondary and tertiary structure prediction, sequence and structural alignment, phylogenetic analysis, and computational validation. Several computational tools such as ProtParam, Iterative Threading Assembly Refinement (I-TASSER), PROCHECK, SAVES v6.0, TM-align, Molecular Evolutionary Genetics Analysis (MEGA) X, and Figtree were employed for characterization of cocoonase protein.

RESULTS

The present study elucidates about the isolation of RNA, cDNA preparation, PCR amplification, and in silico characterization of cocoonase from Antheraea mylitta. Here, total RNA was isolated from head region of A. mylitta, and gene-specific primers were designed using Primer3 followed by PCR-based amplification and sequencing. The newly constructed 377-bp length sequence of cocoonase was subjected to in silico characterization. In silico study of A. mylitta cocoonase showed 26% similarity to A. pernyi strain Qing-6 cocoonase using Blastp and belongs to member of chymotrypsin-like serine protease superfamily. From phylogenetic study, it was found that A. mylitta cocoonase sequence is closely related to A. pernyi cocoonase sequence.

CONCLUSIONS

The present study revealed about the detailed in silico characterization of cocoonase gene and encoded protein obtained from A. mylitta head region. The results obtained infer the presence of cocoonase enzyme in the wild silkworm A. mylitta and can be used for cocoon degumming which will be a valuable and cost-effective strategy in silk industry.

Understanding structural variability in proteins using protein structural networks

Proteins perform their function by accessing a suitable conformer from the ensemble of available conformations. The conformational diversity of a chosen protein structure can be obtained by experimental methods under different conditions. A key issue is the accurate comparison of different conformations. A gold standard used for such a comparison is the root mean square deviation (RMSD) between the two structures. While extensive refinements of RMSD evaluation at the backbone level are available, a comprehensive framework including the side chain interaction is not well understood. Here we employ protein structure network (PSN) formalism, with the non-covalent interactions of side chain, explicitly treated. The PSNs thus constructed are compared through graph spectral method, which provides a comparison at the local and at the global structural level. In this work, PSNs of multiple crystal conformers of single-chain, single-domain proteins, are subject to pair-wise analysis to examine the dissimilarity in their network topologies and in order to determine the conformational diversity of their native structures. This information is utilized to classify the structural domains of proteins into different categories. It is observed that proteins typically tend to retain structure and interactions at the backbone level. However, some of them also depict variability in either their overall structure or only in their inter-residue connectivity at the sidechain level, or both. Variability of sub-networks based on solvent accessibility and secondary structure is studied. The types of specific interactions are found to contribute differently to structure variability. An ensemble analysis by computing the mathematical variance of edge-weights across multiple conformers provided information on the contribution to overall variability from each edge of the PSN. Interactions that are highly variable are identified and their impact on structure variability has been discussed with the help of a case study. The classification based on the present side-chain network-based studies provides a framework to correlate the structure-function relationships in protein structures.

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Monomeric, single domain protein structures can exhibit non-rigid behaviour and be highly variable.

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The comparison of protein structural networks can better discriminate conformations with similar backbones.

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Specific interactions between solvent accessible and inaccessible residues are poorly preserved.

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Network edge-variation offers insights on which interacting residues are likely to influence their dynamics and function.

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These side-chain network-based studies provide a framework to correlate protein structure-function relationships.

Reframing the Protein Folding Problem: Entropy as Organizer

It has been a long-standing conviction that a protein's native fold is selected from a vast number of conformers by the optimal constellation of enthalpically favorable interactions. In marked contrast, this Perspective introduces a different mechanism, one that emphasizes conformational entropy as the principal organizer in protein folding while proposing that the conventional view is incomplete. This mechanism stems from the realization that hydrogen bond satisfaction is a thermodynamic necessity. In particular, a backbone hydrogen bond may add little to the stability of the native state, but a completely unsatisfied backbone hydrogen bond would be dramatically destabilizing, shifting the U(nfolded) ⇌ N(ative) equilibrium far to the left. If even a single backbone polar group is satisfied by solvent when unfolded but buried and unsatisfied when folded, that energy penalty alone, approximately +5 kcal/mol, would rival almost the entire free energy of protein stabilization, typically between -5 and -15 kcal/mol under physiological conditions. Consequently, upon folding, buried backbone polar groups must form hydrogen bonds, and they do so by assembling scaffolds of α-helices and/or strands of β-sheet, the only conformers in which, with rare exception, hydrogen bond donors and acceptors are exactly balanced. In addition, only a few thousand viable scaffold topologies are possible for a typical protein domain. This thermodynamic imperative winnows the folding population by culling conformers with unsatisfied hydrogen bonds, thereby reducing the entropy cost of folding. Importantly, conformational restrictions imposed by backbone···backbone hydrogen bonding in the scaffold are sequence-independent, enabling mutation─and thus evolution─without sacrificing the structure.

Protein folding - seeing is deceiving

This Perspective is intended to raise questions about the conventional interpretation of protein folding. According to the conventional interpretation, developed over many decades, a protein population can visit a vast number of conformations under unfolding conditions, but a single dominant native population emerges under folding conditions. Accordingly, folding comes with a substantial loss of conformational entropy. How is this price paid? The conventional answer is that favorable interactions between and among the side chains can compensate for entropy loss, and moreover, these interactions are responsible for the structural particulars of the native conformation. Challenging this interpretation, the Perspective introduces a proposal that high energy (i.e., unfavorable) excluding interactions winnow the accessible population substantially under physical-chemical conditions that favor folding. Both steric clash and unsatisfied hydrogen bond donors and acceptors are classified as excluding interactions, so called because conformers with such disfavored interactions will be largely excluded from the thermodynamic population. Both excluding interactions and solvent factors that induce compactness are somewhat nonspecific, yet together they promote substantial chain organization. Moreover, proteins are built on a backbone scaffold consisting of α-helices and strands of β-sheet, where the number of hydrogen bond donors and acceptors is exactly balanced. These repetitive secondary structural elements are the only two conformers that can be both completely hydrogen-bond satisfied and extended indefinitely without encountering a steric clash. Consequently, the number of fundamental folds is limited to no more than ~10,000 for a protein domain. Once excluding interactions are taken into account, the issue of "frustration" is largely eliminated and the Levinthal paradox is resolved. Putting the "bottom line" at the top: it is likely that hydrogen-bond satisfaction represents a largely under-appreciated parameter in protein folding models.

Study on cocoonase, sericin, and degumming of silk cocoon: computational and experimental

Background

Cocoonase is a proteolytic enzyme that helps in dissolving the silk cocoon shell and exit of silk moth. Chemicals like anhydrous Na₂CO₃, Marseille soap, soda, ethylene diamine and tartaric acid-based degumming of silk cocoon shell have been in practice. During this process, solubility of sericin protein increased resulting in the release of sericin from the fibroin protein of the silk. However, this process diminishes natural color and softness of the silk. Cocoonase enzyme digests the sericin protein of silk at the anterior portion of the cocoon without disturbing the silk fibroin. However, no thorough characterization of cocoonase and sericin protein as well as imaging analysis of chemical- and enzyme-treated silk sheets has been carried out so far. Therefore, present study aimed for detailed characterization of cocoonase and sericin proteins, phylogenetic analysis, secondary and tertiary structure prediction, and computational validation as well as their interaction with other proteins. Further, identification of tasar silkworm (Antheraea mylitta) pupa stage for cocoonase collection, its purification and effect on silk sheet degumming, scanning electron microscope (SEM)-based comparison of chemical- and enzyme-treated cocoon sheets, and its optical coherence tomography (OCT)-based imaging analysis have been investigated. Various computational tools like Molecular Evolutionary Genetics Analysis (MEGA) X and Figtree, Iterative Threading Assembly Refinement (I-TASSER), self-optimized predicted method with alignment (SOPMA), PROCHECK, University of California, San Francisco (UCSF) Chimera, and Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) were used for characterization of cocoonase and sericin proteins. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), protein purification using Sephadex G 25-column, degumming of cocoon sheet using cocoonase enzyme and chemical Na₂CO₃, and SEM and OCT analysis of degummed cocoon sheet were performed.

Results

Predicted normalized B-factors of cocoonase and sericin with respect to α and β regions showed that these regions are structurally more stable in cocoonase while less stable in sericin. Conserved domain analysis revealed that B. mori cocoonase contains a trypsin-like serine protease with active site range 45 to 180 query sequences while substrate binding site from 175 to 200 query sequences. SDS-PAGE analysis of cocoonase indicated its molecular weight of 25–26 kDa. Na₂CO₃ treatment showed more degumming effect (i.e., cocoon sheet weight loss) as compared to degumming with cocoonase. However, cocoonase-treated silk cocoon sheet holds the natural color of tasar silk, smoothness, and luster compared with the cocoon sheet treated with Na₂CO₃. SEM-based analysis showed the noticeable variation on the surface of silk fiber treated with cocoonase and Na₂CO₃. OCT analysis also exemplified the variations in the cross-sectional view of the cocoonase and Na₂CO₃-treated silk sheets.

Conclusions

Present study enlightens on the detailed characteristics of cocoonase and sericin proteins, comparative degumming activity, and image analysis of cocoonase enzyme and Na₂CO₃ chemical-treated silk sheets. Obtained findings illustrated about use of cocoonase enzyme in the degumming of silk cocoon at larger scale that will be a boon to the silk industry.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-021-00125-2.

Chain stiffness bridges conventional polymer and bio-molecular phases

Chain molecules play important roles in industry and in living cells. Our focus here is on distinct ways of modeling the stiffness inherent in a chain molecule. We consider three types of stiffnesses-one yielding an energy penalty for local bends (energetic stiffness) and the other two forbidding certain classes of chain conformations (entropic stiffness). Using detailed Wang-Landau microcanonical Monte Carlo simulations, we study the interplay between the nature of the stiffness and the ground state conformation of a self-attracting chain. We find a wide range of ground state conformations, including a coil, a globule, a toroid, rods, helices, and zig-zag strands resembling β-sheets, as well as knotted conformations allowing us to bridge conventional polymer phases and biomolecular phases. An analytical mapping is derived between the persistence lengths stemming from energetic and entropic stiffness. Our study shows unambiguously that different stiffnesses play different physical roles and have very distinct effects on the nature of the ground state of the conformation of a chain, even if they lead to identical persistence lengths.

Stereochemical Assessment of (φ,ψ) Outliers in Protein Structures Using Bond Geometry-Specific Ramachandran Steric-Maps

Ramachandran validation of protein structures is commonly performed using developments, such as MolProbity. We suggest tailoring such analyses by position-wise, geometry-specific steric-maps, which show (φ,ψ) regions with steric-clash at every residue position. These maps are different from the classical steric-map because they are highly sensitive to bond length and angle values that are used, in our steric-maps, as observed in the residue positions in super-high-resolution peptide and protein structures. (φ,ψ) outliers observed in such structures seldom have steric-clash. Therefore, we propose that a (φ,ψ) outlier is unacceptable if it is located within the steric-clash region of a bond geometry-specific steric-map for a residue position. These steric-maps also suggest position-specific accessible (φ,ψ) space. The PARAMA web resource performs in-depth position-wise analysis of protein structures using bond geometry-specific steric-maps.

Local symmetry determines the phases of linear chains: a simple model for the self-assembly of peptides

We discuss the relation between the emergence of new phases with broken symmetry within the framework of simple models of biopolymers. We start with a classic model for a chain molecule of spherical beads tethered together, with the steric constraint that non-consecutive beads cannot overlap, and with a pairwise attractive square well potential accounting for the hydrophobic effect and promoting compaction. We then discuss the consequences of the successive breaking of spurious symmetries. First, we allow the partial interpenetration of consecutive beads. In addition to the standard high temperature coil phase and the low temperature collapsed phase, this results in a new class of marginally compact ground states comprising conformations reminiscent of α-helices and β-sheets, the building blocks of the native states of globular proteins. We then discuss the effect of a further symmetry breaking of the cylindrical symmetry on attaching a side-sphere to the backbone beads along the negative normal of the chain, to mimic the presence of side chains in real proteins. This leads to the emergence of a novel phase within the previously obtained marginally compact phase, with the appearance of more complex secondary structure assemblies. The potential importance of this new phase in the de novo design of self-assembled peptides is highlighted.