Microbially induced carbonate precipitation with Arthrobacter creatinolyticus: An eco-friendly strategy for mitigation of chromium contamination.

Chromium contamination from abandoned industrial sites and inadequately managed waste disposal areas poses substantial environmental threat. Microbially induced carbonate precipitation (MICP) has shown promising, eco-friendly solution to remediate Cr(VI) and divalent heavy metals. In this study, MICP was carried out for chromium immobilization by an ureolytic bacterium Arthrobacter creatinolyticus which is capable of reducing Cr(VI) to less toxic Cr(III) via extracellular polymeric substances (EPS) production. The efficacy of EPS driven reduction was confirmed by cellular fraction analysis. MICP carried out in aqueous solution with 100 ppm of Cr(VI) co-precipitated 82.21% of chromium with CaCO3 and the co-precipitation is positively correlated with reduction of Cr(VI). The organism was utilized to remediate chromium spiked sand and found that MICP treatment decreased the exchangeable fraction of chromium to 0.54 ±â€¯0.11% and increased the carbonate bound fraction to 26.1 ±â€¯1.15% compared to control. XRD and SEM analysis revealed that Cr(III) produced during reduction, influenced the polymorph selection of vaterite during precipitation. Evaluation of MICP to remediate Cr polluted soil sample collected from Ranipet, Tamil Nadu also showed effective immobilization of chromium. Thus, A. creatinolyticus proves to be viable option for encapsulating chromium contaminated soil via MICP process, and effectively mitigating the infiltration of Cr(VI) into groundwater and adjacent water bodies.

Genetically encoded biocompatible anti-coagulant protein-coated coronary artery stents drive endothelialization.

In response to the critical demand for advancements in coronary artery stents, this study addresses the challenges associated with arterial recoil and restenosis post-angioplasty and the imperative to encourage rapid re-endothelialization for minimizing thrombosis risks. We employed an innovative approach inspired by mussel adhesion, incorporating placental anticoagulant protein (AnnexinV) on stent design. The introduction of a post-translationally modified catecholic amino acid L-3,4-dihydroxyphenylalanine (L-Dopa), mimicking mussel characteristics, allowed for effective surface modification of Stainless steel stents through genetic code engineering in AnnexinV (AnxDopa). The efficacy of AnxDopa was analyzed through microscale thermophoresis and flow cytometry, confirming AnxDopa's exceptional binding with phosphatidylserine and activated platelets. AnxDopa coated stainless steel demonstrates remarkable bio-, hemo-, and immuno-compatibility, preventing smooth muscle cell proliferation, platelet adhesion, and fibrin formation. It acts as an interface between the stent and biological fluid, which facilitates the anticoagulation and rapid endothelialization. Surface modification of SS verified through XPS analysis and contact angle measurement attests to the efficacy of AnxDopa mediated surface modification. The hydrophilic nature of the AnxDopa-coated surface enhanced the endothelialization through increased protein absorption. This approach represents a significant stride in developing coronary stents with improved biocompatibility and reduced restenosis risks, offering valuable contributions to scientific and clinical realms alike.

Photocrosslinkable triple helical protein with enhanced higher-order formation for biomaterial applications.

Bacterial collagen, produced via recombinant DNA methods, offers advantages including consistent purity, customizable properties, and reduced allergy potential compared to animal-derived collagen. Its controlled production environment enables tailored features, making it more sustainable, non-pathogenic, and compatible with diverse applications in medicine, cosmetics, and other industries. Research has focused on the engineering of collagen-like proteins to improve their structure and function. The study explores the impact of introducing tyrosine, an amino acid known for its role in fibril formation across diverse proteins, into a newly designed bacterial collagen-like protein (Scl2), specifically examining its effect on self-assembly and fibril formation. Biophysical analyses reveal that the introduction of tyrosine residues didn't compromise the protein's structural stability but rather promoted self-assembly, resulting in the creation of nanofibrils-a phenomenon absent in the native Scl2 protein. Additionally, stable hydrogels are formed when the engineered protein undergoes di-tyrosine crosslinking under light exposure. The hydrogels, shown to support cell viability, also facilitate accelerated wound healing in mouse fibroblast (NIH/3T3) cells. These outcomes demonstrate that the targeted inclusion of functional residues in collagen-like proteins enhances fibril formation and facilitates the generation of robust hydrogels using riboflavin chemistry, presenting promising paths for research in tissue engineering and regenerative medicine.

Biomimetic design of fibril-forming non-immunogenic collagen like proteins for tissue engineering.

Collagen, a key component of extracellular matrix serves as a linchpin for maintaining structural integrity and functional resilience. Concerns over purity and immunogenicity of animal-derived collagens have spurred efforts to develop synthetic collagen-based biomaterials. Despite several collagen mimics, there remains limited exploration of non-immunogenic biomaterials with the capacity for effective self-assembly. To combat the lacuna, collagen like protein (CLP) variants were rationally designed and recombinantly expressed, incorporating human telopeptide sequences (CLP-N and CLP-NC) and bioactive binding sites (CLP-NB). Circular dichroism analyses of the variants confirmed the triple helical conformation, with variations in thermal stability and conformation attributed to the presence of telopeptides at one or both ends of CLP. The variants had propensity to form oligomers, setting the stage for fibrillogenesis. The CLP variants were biocompatible, hemocompatible and supported cell proliferation and migration, particularly CLP-NB with integrin-binding sites. Gene expression indicated a lack of significant upregulation of inflammatory markers, highlighting the non-immunogenic nature of these variants. Lyophilized CLP scaffolds maintained their triple-helical structure and offered favorable biomaterial characteristics. These results accentuate the potential of designed CLP variants in tissue engineering, regenerative medicine and industrial sectors, supporting the development of biocompatible scaffolds and implants for therapeutic and cosmetic purposes.

Collagen Mimicry with a Short Collagen Model Peptide.

Mimicking triple helix and fibrillar network of collagen through collagen model peptide(CMP) with short GPO tripeptide repeats is a great challenge. Herein, a minimalistic CMP comprising only five GPO repeats [(GPO)5 ] is presented. This novel approach involves the fusion of ultrashort peptide with the synergetic power of π-system and ß-sheet formation to short CMP (GPO)5 . Accordingly, a hydrogel-forming, fluorenylmethoxycarbonyl (Fmoc)-functionalized ultrashort peptide (NFGAIL) is fused at the N-terminus and phenylalanine at the C-terminus of (GPO)5 (Fmoc-NFGAIL-(GPO)5 -F-COOH, FmP-5GPO). At room temperature, it forms a robust triple helix in aqueous buffer solution and has a relatively high melting point of 35 °C. The fluorenyl motif stabilizes the triple helix by aromatic π-π interactions as in its absence, triple helix is not formed. NFGAIL, which forms a ß-sheet, also aids in triple helix stabilization via intermolecular hydrogen bonding and hydrophobic interactions. FmP-5GPO forms highly entangled nanofibrils with a micrometer length, which have excellent cell viability. The achievement of stable triple helix and fibrils in such a short CMP(FmP-5GPO) sequence is a challenging feat, and its significance in CMP-based biomaterials is undeniable. The present strategy highlights the potential for developing new CMP sequences through intelligent tuning of fusion peptides and GPO repeats.

Redirecting the JAK-STAT signal blocks the SARS-CoV-2 replication.

The distinct disease progression patterns of severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) indicate diverse host immune responses. SARS-CoV-2 severely impairs type I interferon (IFN) cell signaling, resulting in uncontrolled late-phase lung damage in patients. For better pharmacological properties, cytokine modifications may sometimes result in a loss of biological activity against the virus. Here, we employed the genetic code expansion and engineered IFN-ß, a phase II clinical cytokine with 3-amino tyrosine (IFN-ß-A) that reactivates STAT2 expression in virus-infected human cells through JAK/STAT cell signaling without affecting signal activation and serum half-life. This study identified that genetically encoded IFN-ß-A might stabilize the protein-receptor complex and trigger JAK-STAT cell signaling, which is a promising modality for controlling SARS-CoV-2 infection.

π-System Functionalization Transforms Amyloidogenic Peptide Fragment of Human Islet Amyloid Polypeptide into a Super Hydrogelator.

While a considerable number of ultra-short/short amyloid peptides have been reported to form 3D supramolecular hydrogels, they all possess high minimum gelation concentration (MGC) (≥1 wt%), which preclude their applications. In this context, we demonstrate that functionalisation of a well-known amyloidogenic ultra-short peptide fragment NFGAIL (IAPf) of human Islet amyloid polypeptide with a π-system (Fluorenyl, Fm) at the N-terminus of the peptide (Fm-IAPf) yield not only highly thermostable hydrogel at physiological pH but also exhibited super gelator nature as the MGC (0.08 wt%) falls below 0.1 wt%. Various experimental results confirmed that aromatic π-π interactions from fluorenyl moieties and hydrogen bonding interactions between the IAPf drive the self-assembly/fibril formation. Fm-IAPf is the first super hydrogelator derived from amyloid-based ultra-short peptides, to the best of our knowledge. We strongly believe that this report, i. e., functionalization of an amyloid peptide with π-system, provides a lead to develop super hydrogelators from other amyloid-forming peptide fragments for their potential applications.

Electrochemical Response of Redox Amino Acid Encoded Fluorescence Protein for Hydroxychloroquine Sensing.

The sudden rise in the demand has led to large-scale production of hydroxychloroquine (HCQ) in the global market for various diseases such as malaria, rheumatic arthritis, and systemic lupus erythematous and prophylactic treatment of early SARS-CoV-2 outbreak. Thorough monitoring of HCQ intake patients is in high demand; hence, we have developed a redox amino acid encoded fluorescent protein-based electrochemical biosensor for sensitive and selective detection of HCQ. This electrochemical biosensor is generated based on the two-electron transfer process between redox amino acid (3,4-dihydroxy-L-phenylalanine, DOPA) encoded bio-redox protein and the HCQ forms the conjugate. The DOPA residue in the bio-redox protein specifically binds with HCQ, thereby producing a remarkable electrochemical response on the glassy carbon electrode. Experimental results show that the developed biosensor selectively and sensitively detects the HCQ in spiked urine samples. The reagent-free bio-redox capacitor detects HCQ in the range of 90 nM to 4.4 µM in a solution with a detection limit of 58 nM, signal to noise ratio of 3:1, and strong anti-interference ability. Real-time screening, quantification, and relative mean recoveries of HCQ on spiked urine samples were monitored through electron shuttling using bio-redox protein and were found to be 97 to 101%. Overall, the developed bio-redox protein-based sensor has specificity, selectivity, reproducibility, and sensitivity making it potentially attractive for the sensing of HCQ and also applicable to clinical research.

Engineering microbial cells with metal chelating hydroxylated unnatural amino acids for removable of synthetic pollutants from water.

Lead (Pb2+) is a well-known heavy metal and toxic synthetic industrial pollutant in the ecosystem and causes severe threats to living organisms. It is paramount to develop a sustainable microbial engineering approach to remove synthetic pollutants from the environment. Genetic code engineering is emerging as an important microbial engineering tool in biosciences to biosynthesis congener protein production beyond the canonical set of natural molecules and expand the chemistries of living cells. Here, we prepare cells expressing unnatural amino acid encoded congener proteins for effectively removable toxic synthetic industrial pollutants (Pb2+) with high binding efficiency. Native and the developed congener proteins expressing cells adapted the Langmuir and Sips adsorption model that recommends uniform adsorption with Pb2+ ions. This could be due to a more significant number of functional groups on the protein surface. Fluorescence spectroscopic, field emission scanning electron microscope, X-ray photoelectron spectroscopic analysis, and protein-metal molecular stimulation coordination allowed us to explore the role of hydroxylation on Pb2+ adsorption. The bioreactor filled with immobilized protein-containing active granules showed >90% of lead removal in the contaminated water samples. The desorption of bound Pb2+ from GFP and its variants were studied by varying the pH to reuse the proteins for subsequent usage. We observed that about 70% of the GFP and its variants could be recycled and >75% of fluorescence efficiency could be recovered. Among all the variants, GFPHPDP exhibits high affinity and maintains the reusability efficiency in 7 consecutive cycles. These results suggest that genetic code engineering of cells encoding unnatural amino acids could be a next-generation microbial engineering tool for manipulating and developing the microbial strain's selective and effective removal of synthetic pollutants from the environment.

Building biomaterials through genetic code expansion.

Genetic code expansion (GCE) enables directed incorporation of noncoded amino acids (NCAAs) and unnatural amino acids (UNAAs) into the active core that confers dedicated structure and function to engineered proteins. Many protein biomaterials are tandem repeats that intrinsically include NCAAs generated through post-translational modifications (PTMs) to execute assigned functions. Conventional genetic engineering approaches using prokaryotic systems have limited ability to biosynthesize functionally active biomaterials with NCAAs/UNAAs. Codon suppression and reassignment introduce NCAAs/UNAAs globally, allowing engineered proteins to be redesigned to mimic natural matrix-cell interactions for tissue engineering. Expanding the genetic code enables the engineering of biomaterials with catechols - growth factor mimetics that modulate cell-matrix interactions - thereby facilitating tissue-specific expression of genes and proteins. This method of protein engineering shows promise in achieving tissue-informed, tissue-compliant tunable biomaterials.

Recombinant and genetic code expanded collagen-like protein as a tailorable biomaterial.

Collagen occurs in nature with a dedicated triple helix structure and is the most preferred biomaterial in commercialized medical products. However, concerns on purity, disease transmission, and the reproducibility of animal derived collagen restrict its applications and warrants alternate recombinant sources. The expression of recombinant collagen in different prokaryotic and eukaryotic hosts has been reported with varying degrees of success, however, it is vital to elucidate the structural and biological characteristics of natural collagen. The recombinant production of biologically functional collagen is restricted by its high molecular weight and post-translational modification (PTM), especially the hydroxylation of proline to hydroxyproline. Hydroxyproline plays a key role in the structural stability and higher order self-assembly to form fibrillar matrices. Advancements in synthetic biology and recombinant technology are being explored for improving the yield and biomimicry of recombinant collagen. It emerges as reliable, sustainable source of collagen, promises tailorable properties and thereby custom-made protein biomaterials. Remarkably, the evolutionary existence of collagen-like proteins (CLPs) has been identified in single-cell organisms. Interestingly, CLPs exhibit remarkable ability to form stable triple helical structures similar to animal collagen and have gained increasing attention. Strategies to expand the genetic code of CLPs through the incorporation of unnatural amino acids promise the synthesis of highly tunable next-generation triple helical proteins required for the fabrication of smart biomaterials. The review outlines the importance of collagen, sources and diversification, and animal and recombinant collagen-based biomaterials and highlights the limitations of the existing collagen sources. The emphasis on genetic code expanded tailorable CLPs as the most sought alternate for the production of functional collagen and its advantages as translatable biomaterials has been highlighted.

Valorization of tannery solid wastes for sustainable enzyme induced carbonate precipitation process.

Biocementation via enzyme induced carbonate precipitation (EICP) is an emerging ground improvement technique that utilizes urease for calcium carbonate precipitation. Usage of expensive laboratory grade chemicals in EICP hinders its implementation at field level applications. In this study, the feasibility of utilizing solid wastes generated from leather industry was investigated for EICP process. Initially, the proteinaceous fleshing waste was used as nitrogen source for production of an extracellular urease from Arthrobacter creatinolyticus MTCC 5604 followed by its subsequent use in EICP with suspended solids of tannery lime liquor, as alternative calcium source. The calcium ion solution was prepared by treating suspended solids of lime liquor with 1 N HCl. The EICP was optimum with 1000 U of urease, 1.0 M urea and 1.0 M CaCl2.2H2O for test tube experiments. Sand solidification experiments under optimal conditions with five times addition of cementation solution yielded a maximum unconfined compressive strength (UCS) of 810 kPa with laboratory grade CaCl2.2H2O and 780 kPa with calcium from lime liquor. The crystalline phases and morphology of the CaCO3 precipitate were analyzed by XRD, FTIR and SEM-EDX. The results showed the formation of more stable calcite in EICP with calcium obtained from lime liquor, while calcite and vaterite polymorphs were obtained with CaCl2.2H2O. Utilization of fleshing waste and lime liquor in EICP could reduce the pollution load and sludge formation that are generated during the pre-tanning operations of leather manufacturing. The results indicated the viability of process to achieve cost effective and sustainable biocementation for large scale applications.

Three-dimensional tailor-made collagen-like proteins hydrogel for tissue engineering applications.

Despite the potential tunable properties of blank slate collagen-like proteins (CLP), an alternative to animal-originated collagen, assembling them into a stable 3D hydrogel to mimic extracellular matrix is a challenge. To address this constraint, the CLP (without hydroxyproline, CLPpro) and its variants encoding functional unnatural amino acids such as hydroxyproline (CLPhyp) and 3,4-dihydroxyphenylalanine (CLPdopa) were generated through genetic code engineering for 3D hydrogel development. The CLPhyp and CLPdopa were chosen to enhance the intermolecular hydrogen bond interaction through additional hydroxyl moiety and thereby facilitate the self-assembly into a fibrillar network of the hydrogel. Hydrogelation was induced through genipin as a cross-linker, enabling intermolecular cross-linking to form a hydrogel. Spectroscopic and rheological analyses confirmed that CLPpro and its variants maintained native triple-helical structure, which is necessary for its function, and viscoelastic nature of the hydrogels, respectively. Unlike CLPpro, the varients (CLPhyp and CLPdopa) increased pore size formation in the hydrogel scaffold, facilitating 3T3 fibroblast cell interactions. DSC analysis indicated that the stability of the hydrogels got increased upon the genetic incorporation of hydroxyproline (CLPhyp) and dopa (CLPdopa) in CLPpro. In addition, CLPdopa hydrogel was found to be relatively stable against collagenase enzyme compared to CLPpro and CLPhyp. It is the first report on 3D biocompatible hydrogel preparation by tailoring CLP sequence with non-natural amino acids. These next-generation tunable CLP hydrogels open a new venue to design synthetic protein-based biocompatible 3D biomaterials for tissue engineering applications.

Role of heavy metals (copper (Cu), arsenic (As), cadmium (Cd), iron (Fe) and lithium (Li)) induced neurotoxicity.

Parkinson's disease (PD) is a neurodegenerative condition characterized by the dopamine (DA) neuronal loss in the substantia nigra. PD impairs motor controls symptoms such as tremor, rigidity, bradykinesia and postural imbalance gradually along with non-motor problems such as olfactory dysfunction, constipation, sleeping disorder. Though surplus of factors and mechanisms have been recognized, the precise PD etiopathogenesis is not yet implied. Reports suggest that various environmental factors play a crucial role in the causality of the PD cases. Epidemiological studies have reported that heavy metals has a role in causing defects in substantia nigra region of brain in PD. Though the reason is unknown, exposure to heavy metals is reported to be an underlying factor in PD development. Metals are classified as either essential or non-essential, and they have a role in physiological processes such protein modification, electron transport, oxygen transport, redox reactions, and cell adhesion. Excessive metal levels cause oxidative stress, protein misfolding, mitochondrial malfunction, autophagy dysregulation, and apoptosis, among other things. In this review, we check out the link between heavy metals like copper (Cu), arsenic (As), cadmium (Cd), iron (Fe), and lithium (Li) in neurodegeneration, and how it impacts the pathological conditions of PD. In conclusion, increase or decrease in heavy metals involve in regulation of neuronal functions that have an impact on neurodegeneration process. Through this review, we suggest that more research is needed in this stream to bring more novel approaches for either disease modelling or therapeutics.

Insights in the structural understanding of amyloidogenicity and mutation-led conformational dynamics of amyloid beta (Aß) through molecular dynamics simulations and principal component analysis.

Abnormal protein aggregation in the nervous tissue leads to several neurodegenerative disorders like Alzheimer's disease (AD). In AD, accumulation of the amyloid beta (Aß) peptide is proposed to be an early important event in pathogenesis. Significant research efforts are devoted so as to understand the Aß misfolding and aggregation. Molecular dynamics (MD) simulations complement experiments and provide structural information at the atomic level with dynamics without facing the same experimental limitations. Artificial missense mutations are employed experimentally and computationally for providing insights into the structure-function relationships of amyloid-ß in relation to the pathologies of AD. Present work describes the MD simulations for 100 ns so as to probe the structural and conformational dynamics of Aß1-42 assemblies and its mutants. Essential dynamics analysis with respect to conformational deviation of Cα was evaluated to identify the largest residual fluctuation of Cα. Conformational stability of all Aß mutants was analyzed by computing RMSD, deciphering the convergence is reached in the last 20 ns in all replicas. To highlight the low frequency mode of motion corresponding to the highest amplitude, atomic displacements seen in trajectory, distance pair principal component analysis (dpPCA) was performed, which adumbrated mutations strongly affect the conformational dynamics of investigated model when compared with wild type. Dynamic cross correlation matrix (DCCM) also suggests the conserved interactions of wild Aß and imply mutations in ß3-ß4 loop region induce deformity and residual fluctuations as observed from simulation. Present study indicate the mutational energy landscape which induces deformation leading to fibrillation.Communicated by Ramaswamy H. Sarma.

A deep dive into the darning effects of biomaterials in infarct myocardium: current advances and future perspectives.

Myocardial infarction (MI) occurs due to the obstruction of coronary arteries, a major crux that restricts blood flow and thereby oxygen to the distal part of the myocardium, leading to loss of cardiomyocytes and eventually, if left untreated, leads to heart failure. MI, a potent cardiovascular disorder, requires intense therapeutic interventions and thereby presents towering challenges. Despite the concerted efforts, the treatment strategies for MI are still demanding, which has paved the way for the genesis of biomaterial applications. Biomaterials exhibit immense potentials for cardiac repair and regeneration, wherein they act as extracellular matrix replacing scaffolds or as delivery vehicles for stem cells, protein, plasmids, etc. This review concentrates on natural, synthetic, and hybrid biomaterials; their function; and interaction with the body, mechanisms of repair by which they are able to improve cardiac function in a MI milieu. We also provide focus on future perspectives that need attention. The cognizance provided by the research results certainly indicates that biomaterials could revolutionize the treatment paradigms for MI with a positive impact on clinical translation.

Genetically encoded dihydroxyphenylalanine coupled with tyrosinase for strain promoted labeling.

Protein modifications through genetic code engineering have a remarkable impact on macromolecule engineering, protein translocation, protein-protein interaction, and cell biology. We used the newly developed molecular biology approach, genetic code engineering, for fine-tuning of proteins for biological availability. Here, we have introduced 3, 4-dihydroxy-l-phenylalanine in recombinant proteins by selective pressure incorporation method for protein-based cell labeling applications. The congener proteins treated with tyrosinase convert 3, 4-dihydroxy-l-phenylalanine to dopaquinone for strain-promoted click chemistry. Initially, the single-step Strain-Promoted Oxidation-Controlled Cyclooctyne-1,2-quinone Cycloaddition was studied using tyrosinase catalyzed congener protein and optimized the temporally controlled conjugation with (1R,8S,9s)-Bicyclo[6.1.0]non-4-yn-9-ylmethanol. Then, the feasibility of tyrosinase-treated congener annexin A5 with easily reactive quinone functional moiety was conjugated with fluorescent tag dibenzocyclooctyne-PEG4-TAMRA for labeling of apoptotic cells. Thus, the congener proteins-based products demonstrate selective cell labeling and apoptosis detection in EA.hy926 cells even after the protein modifications. Hence, genetic code engineering can be coupled with click chemistry to develop various protein-based fluorescent labels.

Beyond protein tagging: Rewiring the genetic code of fluorescent proteins - A review.

Fluorescent proteins (FP) are an integral part of modern biology due to its diverse biochemical and photophysical properties. The boundaries of FP have been extended through conventional mutagenesis and directed evolution approaches. Engineering of FP based on the standard genetic code consisting of 20 amino acids with limited functional groups restrict its diversification. Degeneracy of genetic code has helped in covering this substantial gap through genetic code engineering, wherein introduction of unnatural amino acid (UAA) analogues resulted in a collection of FP with varying properties. This review features the work carried till date in the area of FP incorporated with UAAs and explores strategies employed for incorporation, impact of UAAs in chromophore and surrounding residues and changes in inherent properties of FP. The long-standing association of FP as a tool for high throughput screening of orthogonal aaRS/tRNA pairs used in site specific incorporation of UAAs is expounded. Insertion of UAAs in FP has enabled their use in contemporary fields such as biophotovoltaics, bioremediation, biosensors, biomaterials and imaging of acidic vesicles. Thus, expansion of genetic code of FP is envisaged to rejig the existing spectra of colors and future research initiative in this direction is expected to glow brighter and brighter.