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1.
Metabolomics ; 20(4): 68, 2024 Jun 28.
Article in English | MEDLINE | ID: mdl-38941046

ABSTRACT

INTRODUCTION: Exploring metabolic changes within host E. coli through an untargeted metabolomic study of T7L variants overexpression to optimize engineered endolysins for clinical/therapeutic use. AIM AND OBJECTIVE: This study aims to assess the impact of overexpressing T7L variants on the metabolic profiles of E. coli. The two variants considered include T7L-H37A, which has enhanced lytic activity compared to its wild-type protein, and T7L-H48K, a dead mutant with no significant activity. METHODS: 1H NMR-based metabolomics was employed to compare the metabolic profiles of E. coli cells overexpressing T7L wild-type protein and its variants. RESULTS: Overexpression of the T7L wild-type (T7L-WT) protein and its variants (T7L-H48K and T7L-H37A) was compared to RNAP overexpression in E. coli cells using 1H NMR-based metabolomics, analyzing a total of 75 annotated metabolites, including organic acids, amino acids, sugars, and nucleic acids. The results showed distinct clustering patterns for the two T7L variant groups compared with the WT, in which the dead mutant (H48K) group showed clustering close to that of RNAP. Pathway impact analysis revealed different effects of T7L variants on E. coli metabolic profiles, with T7L-H48K showing minimal alterations in energy and amino acid pathways linked to osmotic stress compared to noticeable alterations in these pathways for both T7L-H37A and T7L-WT. CONCLUSIONS: This study uncovered distinct metabolic fingerprints when comparing the overexpression of active and inactive mutants of T7L lytic enzymes in E. coli cells. These findings could contribute to the optimization and enhancement of suitable endolysins as potential alternatives to antibiotics.


Subject(s)
Escherichia coli , Metabolome , Metabolomics , Escherichia coli/metabolism , Escherichia coli/genetics , Metabolomics/methods , Viral Proteins/metabolism , Viral Proteins/genetics , Bacteriophage T7/genetics , Bacteriophage T7/metabolism , Mutation , DNA-Directed RNA Polymerases/metabolism , DNA-Directed RNA Polymerases/genetics
2.
Mech Ageing Dev ; 220: 111944, 2024 May 21.
Article in English | MEDLINE | ID: mdl-38782074

ABSTRACT

Age-related inflammation or inflammaging is a critical deciding factor of physiological homeostasis during aging. Cardiovascular diseases (CVDs) are exquisitely associated with aging and inflammation and are one of the leading causes of high mortality in the elderly population. Inflammaging comprises dysregulation of crosstalk between the vascular and cardiac tissues that deteriorates the vasculature network leading to development of atherosclerosis and atherosclerotic-associated CVDs in elderly populations. Leukocyte differentiation, migration and recruitment holds a crucial position in both inflammaging and atherosclerotic CVDs through relaying the activity of an intricate network of inflammation-associated protein-protein interactions. Among these interactions, small immunoproteins such as chemokines play a major role in the progression of inflammaging and atherosclerosis. Chemokines are actively involved in lymphocyte migration and severe inflammatory response at the site of injury. They relay their functions via chemokine-G protein-coupled receptors-glycosaminoglycan signaling axis and is a principal part for the detection of age-related atherosclerosis and related CVDs. This review focuses on highlighting the detailed intricacies of the effects of chemokine-receptor interaction and chemokine oligomerization on lymphocyte recruitment and its evident role in clinical manifestations of atherosclerosis and related CVDs. Further, the role of chemokine mediated signaling for formulating next-generation therapeutics against atherosclerosis has also been discussed.

3.
ACS Omega ; 8(50): 48233-48250, 2023 Dec 19.
Article in English | MEDLINE | ID: mdl-38144138

ABSTRACT

Retinoblastoma (Rb) is the most common pediatric eye cancer. To identify the biomarkers for early diagnosis and monitoring the progression of Rb in patients, mapping of the alterations in their metabolic profiles is essential. The present study aims at exploring the metabolic disparity in serum from Rb patients and controls using NMR-based metabolomics. A total of 72 metabolites, including carbohydrates, amino acids, and organic acids, were quantified in serum samples from 24 Rb patients and 26 controls. Distinct clusters of Rb patients and controls were obtained using the partial least-squares discriminant analysis (PLS-DA) model. Further, univariate and multivariate analyses of unilateral and bilateral Rb patients with respect to their age-matched controls depicted their distinct metabolic fingerprints. Metabolites including 2-phosphoglycerate, 4-aminobutyrate, proline, O-phosphocholine, O-phosphoethanolamine, and Sn-glycero-3-phosphocholine (Sn-GPC) showed significant perturbation in both unilateral and bilateral Rb patients. However, metabolic differences among the bilateral Rb cases were more pronounced than those in unilateral Rb cases with respect to controls. In addition to major discriminatory metabolites for Rb, unilateral and bilateral Rb cases showed specific metabolic changes, which might be the result of their differential genetic/somatic mutational backgrounds. This further suggests that the aberrant metabolic perturbation in bilateral patients signifies the severity of the disease in Rb patients. The present study demonstrated that identified serum metabolites have potential to serve as a noninvasive method for detection of Rb, discriminate bilateral from unilateral Rb patients, and aid in better understanding of the RB tumor biology.

4.
Invest Ophthalmol Vis Sci ; 64(11): 26, 2023 08 01.
Article in English | MEDLINE | ID: mdl-37603355

ABSTRACT

Purpose: To identify the genes and pathways responsible for treatment resistance (TR) in retinoblastoma (RB) by analyzing serum small extracellular vesicles (sEVs) of patients with TR active RB (TR-RB) and completely regressed RB (CR-RB). Methods: Serum-derived sEVs were characterized by transmission electron microscopy and nanoparticle tracking analysis. sEV transcriptome profiles of two TR-RB and one CR-RB with good response (>20 years tumor free) were compared to their age-matched controls (n = 3). Gene expression data were analyzed by the R Bioconductor package. The CD9 protein and mRNA expression of CD9, CD63, and CD81 were studied in five RB tumors and two control retinae by immunohistochemistry and quantitative reverse transcription-polymerase chain reaction. Results: The isolated serum sEVs were round shaped and within the expected size (30-150 nm), and they had zeta potentials ranging from -10.8 to 15.9 mV. The mean ± SD concentrations of sEVs for two adults and four children were 1.1 × 1012 ± 0.1 and 5.8 × 1011 ± 1.7 particles/mL. Based on log2 fold change of ±2 and P < 0.05 criteria, there were 492 dysregulated genes in TR-RB and 184 in CR-RB. KAT2B, VWA1, CX3CL1, MLYCD, NR2F2, USP46-AS1, miR6724-4, and LINC01257 genes were specifically dysregulated in TR-RB. Negative regulation of apoptotic signaling, cell growth, and proton transport genes were greater than fivefold expressed only in TR-RB. CD9, CD63, and CD81 mRNA levels were high in RB tumors versus control retina, with increased and variable CD9 immunoreactivity in the invasive areas of the tumor. Conclusions: Serum sEVs could serve as a potential liquid biopsy source for understanding TR mechanisms in RB.


Subject(s)
Extracellular Vesicles , Retinal Neoplasms , Retinoblastoma , Adult , Child , Humans , Retinoblastoma/genetics , Retina , Signal Transduction , Retinal Neoplasms/genetics
5.
Biochemistry ; 62(2): 330-344, 2023 01 17.
Article in English | MEDLINE | ID: mdl-35060722

ABSTRACT

The therapeutic use of bacteriophage-encoded endolysins as enzybiotics has increased significantly in recent years due to the emergence of antibiotic resistant bacteria. Phage endolysins lyse the bacteria by targeting their cell wall. Various engineering strategies are commonly used to modulate or enhance the utility of therapeutic enzymes. This study employed a structure-guided mutagenesis approach to engineer a T7 bacteriophage endolysin (T7L) with enhanced amidase activity and lysis potency via replacement of a noncatalytic gating residue (His 37). Two H37 variants (H37A and H37K) were designed and characterized comprehensively using integrated biophysical and biochemical techniques to provide mechanistic insights into their structure-stability-dynamics-activity paradigms. Among the studied proteins, cell lysis data suggested that the obtained H37A variant exhibits amidase activity (∼35%) enhanced compared to that of wild-type T7 endolysin (T7L-WT). In contrast to this, the H37K variant is highly unstable, prone to aggregation, and less active. Comparison of the structure and dynamics of the H37A variant to those of T7L-WT evidenced that the alteration at the site of H37 resulted in long-range structural perturbations, attenuated the conformational heterogeneity, and quenched the microsecond to millisecond time scale motions. Stability analysis confirmed the altered stability of H37A compared to that of its WT counterpart. All of the obtained results established that the H37A variant enhances the lysis activity by regulating the stability-activity trade-off. This study provided deeper atomic level insights into the structure-function relationships of endolysin proteins, thus aiding researchers in the rational design of engineered endolysins with enhanced therapeutic properties.


Subject(s)
Bacteriophages , Bacteriophages/metabolism , N-Acetylmuramoyl-L-alanine Amidase/genetics , N-Acetylmuramoyl-L-alanine Amidase/metabolism , Bacteriophage T7/genetics , Endopeptidases/chemistry
6.
Biochemistry ; 60(43): 3236-3252, 2021 11 02.
Article in English | MEDLINE | ID: mdl-34665609

ABSTRACT

The summarized amalgam of internal relaxation modulations and external forces like pH, temperature, and solvent conditions determine the protein structure, stability, and function. In a free-energy landscape, although conformers are arranged in vertical hierarchy, there exist several adjacent parallel sets with conformers occupying equivalent energy cleft. Such conformational states are pre-requisites for the functioning of proteins that have oscillating environmental conditions. As these conformational changes have utterly small re-arrangements, nuclear magnetic resonance (NMR) spectroscopy is unique in elucidating the structure-dynamics-stability-function relationships for such conformations. Helicobacter pylori survives and causes gastric cancer at extremely low pH also. However, least is known as to how the genome of the pathogen is protected from reactive oxygen species (ROS) scavenging in the gut at low pH under acidic stress. In the current study, biophysical characteristics of H. pylori DNA binding protein (Hup) have been elucidated at pH 2 using a combination of circular dichroism, fluorescence, NMR spectroscopy, and molecular dynamics simulations. Interestingly, the protein was found to have conserved structural features, differential backbone dynamics, enhanced stability, and DNA binding ability at low pH as well. In summary, the study suggests the partaking of Hup protein even at low pH in DNA protection for maintaining the genome integrity.


Subject(s)
Bacterial Proteins/metabolism , DNA-Binding Proteins/metabolism , Helicobacter pylori/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/physiology , Carrier Proteins/metabolism , Circular Dichroism/methods , DNA/chemistry , DNA/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/physiology , Entropy , Fluorescence , Helicobacter pylori/pathogenicity , Hydrogen-Ion Concentration , Magnetic Resonance Spectroscopy/methods , Molecular Conformation , Molecular Dynamics Simulation , Reactive Oxygen Species/metabolism , Solvents/chemistry , Temperature
7.
Int J Biol Macromol ; 172: 30-40, 2021 Mar 01.
Article in English | MEDLINE | ID: mdl-33440209

ABSTRACT

Global antimicrobial crisis and advent of drug resistant fungal strains has substantially distressed disease management for clinicians. Biodegradable silver nanoparticles (AgNps) emerge as an excellent alternative remedial option. In the current study, the anti-biofilm activity of microwave irradiated kappa-carrageenan (CRG) capped AgNps against Candida albicans, and Candida glabrata was investigated in terms of their effect on reactive oxygen species (ROS) generation, cellular morphology, biochemical composition, and the activity of enzymes of extracellular matrix. Minimum inhibitory concentration and fungicidal concentration value of CRG-AgNps against both Candida spp. ranged between 400 and 500 µg/mL. The 80% of Candida biofilm was inhibited and eradicated by CRG-AgNps at a concentration of ~300 µg/mL. Microscopic studies indicate that CRG-AgNps caused morphological damage through membrane disruption and pore formation. Further, CRG-AgNps generated ROS in a concentration-dependent manner and modulated the composition of Candida biofilm ECM by increasing the carbohydrate and eDNA content. CRG-AgNps also significantly inactivated the hydrolytic enzymes, thus hindering the biofilm forming ability. In conclusion, all these results suggest that the CRG-AgNps are potential antifungal agents against Candida biofilms, and they inhibit/eradicate the fungal biofilms through multiple signalling mechanisms.


Subject(s)
Antifungal Agents/pharmacology , Biofilms/drug effects , Candida/drug effects , Carrageenan/pharmacology , Metal Nanoparticles/chemistry , Silver/chemistry , Antifungal Agents/chemistry , Microbial Sensitivity Tests/methods
8.
Int J Biol Macromol ; 164: 3221-3234, 2020 Dec 01.
Article in English | MEDLINE | ID: mdl-32853623

ABSTRACT

Chemokines are a sub-group of chemotactic cytokines that regulate the leukocyte migration by binding to G-protein coupled receptors (GPCRs) and cell surface glycosaminoglycans (GAGs). Interleukin-8 (CXCL8/IL8) is one of the most essential CXC chemokine that has been reported to be involved in various pathophysiological conditions. Structure-function relationships of human IL8 have been studied extensively. However, no such detailed information is available on IL8 orthologs, although they exhibit significant functional divergence. In order to unravel the differential structure-dynamics-stability-function relationship of IL8 orthologs, comparative molecular analysis was performed on canine (laurasians) and human (primates) IL8 proteins using in-silico molecular evolutionary analysis and solution NMR spectroscopy methods. The residue level NMR studies suggested that, although the overall structural architecture of canine IL8 is similar to that of human IL8, systematic differences were observed in their backbone dynamics and low-energy excited states due to amino acid substitutions. Further, these substitutions also resulted in attenuation of stability and heparin binding affinity in the canine IL8 as compared to its human counterpart. Indeed, structural and sequence analysis evidenced for specificity of molecular interactions with cognate receptor (CXCR1) and glycosaminoglycan (heparin), thus providing evidence for a noticeable functional specificity and divergence between the two IL8 orthologs.


Subject(s)
Interleukin-8/genetics , Interleukin-8/metabolism , Amino Acid Sequence/genetics , Animals , Chemokines/metabolism , Chemokines, CXC/genetics , Dogs , Evolution, Molecular , Glycosaminoglycans/chemistry , Humans , Magnetic Resonance Spectroscopy/methods , Molecular Dynamics Simulation , Protein Binding/genetics , Protein Multimerization/genetics , Structure-Activity Relationship
9.
Int J Biol Macromol ; 156: 239-251, 2020 Aug 01.
Article in English | MEDLINE | ID: mdl-32289428

ABSTRACT

Chemokines are a sub-group of cytokines that regulate the leukocyte migration. Monocyte chemoattractant protein-1 (MCP/CCL2) is one of the essential CC chemokine that regulates the migration of monocytes into inflamed tissues. It has been observed that the primary sequences of CCL2 orthologs among rodents and primates vary significantly at the C-terminal region. However, no structural details are available for the rodentia family CCL2 proteins. The current study unravelled the structural, dynamics and in-silico functional characteristics of murine CCL2 chemokine using a comprehensive set of NMR spectroscopy techniques and evolutionary approaches. The study unravelled that the N-terminal portion of the murine CCL2 forms a canonical CC chemokine dimer similar to that of human CCL2. However, unlike human CCL2, the murine ortholog exhibits extensive dynamics in the µs-ms timescales. The presence of C-terminal region of the murine CCL2 protein/rodentia family is highly glycosylated, completely disordered, and inhibits the folding of the structured CCL2 regions. Further, it has been observed that the glycosaminoglycan binding surfaces of these orthologs proteins are greatly differed. In a nut shell, this comparative study provided the role of molecular evolution in generating orthologous proteins with differential structural and dynamics characteristics to engage them in specific molecular interactions.


Subject(s)
Chemokine CCL2/chemistry , Models, Molecular , Protein Conformation , Amino Acid Sequence , Animals , Binding Sites , Chemokine CCL2/genetics , Chemokine CCL2/metabolism , Chemokines/chemistry , Chemokines/metabolism , Cloning, Molecular , Evolution, Molecular , Gene Expression , Magnetic Resonance Spectroscopy , Mice , Phylogeny , Protein Binding , Protein Multimerization , Recombinant Proteins , Spectrum Analysis , Structure-Activity Relationship
10.
Int J Biol Macromol ; 151: 467-482, 2020 May 15.
Article in English | MEDLINE | ID: mdl-32084483

ABSTRACT

Protein nanocomposites have attracted considerable research interest in recent times owing to the combined advantageous properties of nanotechnology and proteins. Lysozyme holds enormous potential in various biomedical applications as it possesses antibacterial properties, anti-inflammatory, anti-cancer, and analgesic properties. Considering its multifunctional aspects, structural stability and ease of production and modification, special focus has been attributed to this protein. Nanocomposites have either been fabricated completely from lysozyme or have been conjugated to lysozyme considering its versatile biotechnological applications. The current review describes the recent advances of protein nanocomposites using lysozyme as a prime example. Along with the principles, techniques, and applications involved in protein based nanocomposites, this review also provides a comprehensive account of interactions between lysozyme and different nanoparticles. Numerous studies that have integrated the utilization of lysozyme and nanotechnology for a variety of applications have also been discussed at length.


Subject(s)
Nanocomposites/chemistry , Proteins/chemistry , Animals , Biocatalysis , Biosensing Techniques , Chemistry Techniques, Synthetic , Drug Delivery Systems , Humans , Lysosomes/chemistry , Nanotechnology , Structure-Activity Relationship , Theranostic Nanomedicine
11.
Biotechnol Biofuels ; 12: 2, 2019.
Article in English | MEDLINE | ID: mdl-30622644

ABSTRACT

BACKGROUND: Harnessing the halotolerant characteristics of microalgae provides a viable alternative for sustainable biomass and triacylglyceride (TAG) production. Scenedesmus sp. IITRIND2 is a fast growing fresh water microalga that has the capability to thrive in high saline environments. To understand the microalga's adaptability, we studied its physiological and metabolic flexibility by studying differential protein, metabolite and lipid expression profiles using metabolomics, proteomics, real-time polymerase chain reaction, and lipidomics under high salinity conditions. RESULTS: On exposure to salinity, the microalga rewired its cellular reserves and ultrastructure, restricted the ions channels, and modulated its surface potential along with secretion of extrapolysaccharide to maintain homeostasis and resolve the cellular damage. The algal-omics studies suggested a well-organized salinity-driven metabolic adjustment by the microalga starting from increasing the negatively charged lipids, up regulation of proline and sugars accumulation, followed by direction of carbon and energy flux towards TAG synthesis. Furthermore, the omics studies indicated both de-novo and lipid cycling pathways at work for increasing the overall TAG accumulation inside the microalgal cells. CONCLUSION: The salt response observed here is unique and is different from the well-known halotolerant microalga; Dunaliella salina, implying diversity in algal response with species. Based on the integrated algal-omics studies, four potential genetic targets belonging to two different metabolic pathways (salt tolerance and lipid production) were identified, which can be further tested in non-halotolerant algal strains.

12.
Arch Biochem Biophys ; 662: 121-128, 2019 02 15.
Article in English | MEDLINE | ID: mdl-30528777

ABSTRACT

Multigene families such as chemokines arose as a result of gene duplication events, followed by mutations and selection. GRO chemokines are three duplicated CXCL genes, comprising of CXCL1, CXCL2 and CXCL3 proteins. Comparative structural analysis of the two closely related paralog chemokines CXCL2 and CXCL3 in the current study indicated a variable electrostatic surface between them, and a specific hydrophobic pocket on the surface of CXCL3 that can bind naphthalene derivatives. Combined fluorescence and NMR analyses revealed that CXCL3 monomer can specifically bind to ANS (8-Anilinonaphthalene-1-sulfonic acid) with a stoichiometry of 1:1 by involving the residues belonging to the structural elements 310 helix and the α-helix. A close observation of the surfaces of these paralogs suggested that such a hydrophobic pocket is a resultant of inter-switch between a charged and a hydrophobic residue on the primary sequence of the two paralog proteins. Interestingly, the hydrophobic pocket is in the vicinity of GAG binding region of CXCL3, a molecular determinant in leukocyte trafficking. Such unique pockets/patches on specific chemokine surfaces can be exploited to design the naphthalene/small molecule based inhibitors against GAG binding to regulate their molecular interactions during the onset and progression of various types of cancers and inflammatory diseases.


Subject(s)
Amino Acids/metabolism , Chemokines, CXC/metabolism , Binding Sites , Humans , Hydrophobic and Hydrophilic Interactions
13.
Carbohydr Polym ; 206: 854-862, 2019 Feb 15.
Article in English | MEDLINE | ID: mdl-30553393

ABSTRACT

Maturation of bacterial biofilms and their resistance to recurrent antimicrobial agents results in convoluted infectious diseases. In the current study, kappa-Carrageenan (κ-Carrageenan/CRG), was used to formulate CRG-silver nanocomposites through a facile microwave green synthesis approach. CRG-Ag nanoparticles of size 50 ± 10 nm were obtained by using CRG as a reducing and stabilizing agent. CRG-Ag nanoparticles were highly effective against both S. aureus and P. aeruginosa mediated biofilms and acted as a broad spectrum antibacterial agent even after six months. CRG-Ag nanoparticles encapsulated in KCl cross-linked hydrogel also exhibited excellent thermal stability, and antimicrobial potency. All these results depict that CRG-Ag nanocomposites appear as a promising approach to eradicate bacterial biofilms in food packaging and biomedical applications.


Subject(s)
Anti-Bacterial Agents/pharmacology , Biofilms/drug effects , Carrageenan/chemistry , Metal Nanoparticles/chemistry , Nanocomposites/chemistry , Silver/pharmacology , Anti-Bacterial Agents/chemistry , Drug Stability , Green Chemistry Technology/methods , Hydrogels/chemical synthesis , Hydrogels/chemistry , Microbial Sensitivity Tests , Microwaves , Particle Size , Pseudomonas aeruginosa/drug effects , Silver/chemistry , Staphylococcus aureus/drug effects
14.
Curr Top Med Chem ; 18(20): 1719-1736, 2018.
Article in English | MEDLINE | ID: mdl-30360722

ABSTRACT

BACKGROUND: To carry out wide range of cellular functionalities, proteins often associate with one or more proteins in a phenomenon known as Protein-Protein Interaction (PPI). Experimental and computational approaches were applied on PPIs in order to determine the interacting partners, and also to understand how an abnormality in such interactions can become the principle cause of a disease. OBJECTIVE: This review aims to elucidate the case studies where PPIs involved in various human diseases have been proven or validated with computational techniques, and also to elucidate how small molecule inhibitors of PPIs have been designed computationally to act as effective therapeutic measures against certain diseases. RESULTS: Computational techniques to predict PPIs are emerging rapidly in the modern day. They not only help in predicting new PPIs, but also generate outputs that substantiate the experimentally determined results. Moreover, computation has aided in the designing of novel inhibitor molecules disrupting the PPIs. Some of them are already being tested in the clinical trials. CONCLUSION: This review delineated the classification of computational tools that are essential to investigate PPIs. Furthermore, the review shed light on how indispensable computational tools have become in the field of medicine to analyze the interaction networks and to design novel inhibitors efficiently against dreadful diseases in a shorter time span.


Subject(s)
Computational Biology/methods , Drug Design , Protein Interaction Mapping/methods , Small Molecule Libraries/chemistry , Small Molecule Libraries/therapeutic use , Disease/classification , Drug Therapy , Humans , Machine Learning , Proteins/metabolism , Structure-Activity Relationship
15.
Int J Biol Macromol ; 107(Pt A): 575-584, 2018 Feb.
Article in English | MEDLINE | ID: mdl-28928065

ABSTRACT

CXCL3 is a neutrophil activating chemokine that belongs to GRO subfamily of CXC chemokines. GRO chemokine family comprises of three chemokines GRO α (CXCL1), GROß (CXCL2), and GRO γ (CXCL3), which arose as a result of gene duplication events during the course of chemokine evolution. Although primary sequences of GRO chemokines are highly similar, they performs several protein specific functions in addition to their common property of neutrophil trafficking. However, the molecular basis for their differential functions has not well understood. Although structural details are available for CXCL1 and CXCL2, no such information regarding CXCL3 is available till date. In the present study, we have successfully cloned, expressed, and purified the recombinant CXCL3. Around 15mg/L of pure recombinant CXCL3 protein was obtained. Further, we investigated its functional divergence and biophysical characteristics such as oligomerization, thermal stability and heparin binding etc., and compared all these features with its closest paralog CXCL2. Our studies revealed that, although overall structural and oligomerization features of CXCL3 and CXCL2 are similar, prominent differences were observed in their surface characteristics, thus implicating for a functional divergence.


Subject(s)
Chemokine CXCL1/chemistry , Chemokine CXCL2/chemistry , Chemokines, CXC/chemistry , Cloning, Molecular/methods , Heparin/chemistry , Amino Acid Sequence , Animals , Chemokine CXCL1/genetics , Chemokine CXCL1/metabolism , Chemokine CXCL2/genetics , Chemokine CXCL2/metabolism , Chemokines, CXC/genetics , Chemokines, CXC/metabolism , Crystallography, X-Ray , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Heparin/metabolism , Humans , Mice , Models, Molecular , Primates , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Protein Multimerization , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Rodentia , Sequence Alignment , Sequence Homology, Amino Acid
16.
R Soc Open Sci ; 4(9): 171059, 2017 Sep.
Article in English | MEDLINE | ID: mdl-28989790

ABSTRACT

Chemokines are chemotactic cytokines involved in leucocyte trafficking to infected tissue. Growth-related oncogene (GRO) chemokines namely CXCL1, CXCL2 and CXCL3 are neutrophil activating chemokines sharing a conserved three-dimensional structure, but encompassing functional diversity due to gene duplication and evolutionary events. However, the evolutionary mechanisms including selection pressures involved in diversification of GRO genes have not yet been characterized. Here, we performed comprehensive evolutionary analysis of GRO genes among different mammalian species. Phylogenetic analysis illustrated a species-specific evolution pattern. Selection analysis evidenced that these genes have undergone concerted evolution. Seventeen positively selected sites were obtained, although the majority of the protein is under purifying selection. Interestingly, these positively selected sites are more concentrated on the C-terminal/glycosaminoglycan (GAG) binding and dimerization segment compared to receptor binding domain. Substitution rate analysis confirmed the C-terminal domain of GRO genes as the highest substituted segment. Further, structural analysis established that the nucleotide alterations in the GAG binding domain are the source of surface charge modulation, thus generating the differential GAG binding surfaces and multiple binding sites as per evolutionary pressure, although the helical surface is primordial for GAG binding. Indeed, such variable electrostatic surfaces are crucial to regulate chemokine gradient formation during a host's defence against pathogens and also explain the significance of chemokine promiscuity.

17.
Regen Med ; 12(4): 431-457, 2017 04.
Article in English | MEDLINE | ID: mdl-28621207

ABSTRACT

Regeneration of tissue structure with the aid of bioactive polymer matrices/composites and scaffolds for respective applications is one of the emerging areas of biomedical engineering. Recent advances in conjugated glycosaminoglycan (GAG) hybrids using natural and synthetic polymers have opened new avenues for producing a wide variety of resorbable polymer matrices. These hybrid scaffolds are low-immunogenic, highly biocompatible and biodegradable with incredible mechanical and tensile properties. GAG-based resorbable polymeric matrices are being exploited in migration of stem cells, cartilage and bone replacement/regeneration and production of scaffolds for various tissue engineering applications. In the current review, we will discuss the role of GAG-based resorbable polymer matrices in the field of regenerative medicine.


Subject(s)
Glycosaminoglycans/chemistry , Polymers/chemistry , Tissue Engineering/methods , Animals , Humans , Regeneration , Regenerative Medicine , Tissue Scaffolds/chemistry
18.
Front Mol Biosci ; 4: 100, 2017.
Article in English | MEDLINE | ID: mdl-29387686

ABSTRACT

Prerequisite for structural studies on G protein-coupled receptors is the preparation of highly concentrated, stable, and biologically active receptor samples in milligram amounts of protein. Here, we present an improved protocol for Escherichia coli expression, functional refolding, and reconstitution into bicelles of the human neuropeptide Y receptor type 2 (Y2R) for solution and solid-state NMR experiments. The isotopically labeled receptor is expressed in inclusion bodies and purified using SDS. We studied the details of an improved preparation protocol including the in vitro folding of the receptor, e.g., the native disulfide bridge formation, the exchange of the denaturating detergent SDS, and the functional reconstitution into bicelle environments of varying size. Full pharmacological functionality of the Y2R preparation was shown by a ligand affinity of 4 nM and G-protein activation. Further, simple NMR experiments are used to test sample quality in high micromolar concentration.

19.
Recent Pat Biotechnol ; 10(3): 235-263, 2016.
Article in English | MEDLINE | ID: mdl-27745543

ABSTRACT

BACKGROUND: Unraveling the comprehensive networks of molecular signaling in various cellular processes and redesign/rewire them as per human wish is the ultimate dream of the biomedical researchers. Recent advances in the experimental and computational biophysics have provided us with enormous amount of protein sequences and a wide variety of structural information. Protein engineering is a fledging field and a creative process to design the target proteins or signaling networks with desirable structure and functions. OBJECTIVE: Protein engineering has been a powerful tool in bioengineering for last couple of decades for generating vast numbers of useful enzymes/proteins that possess huge therapeutic and industrial potential. Now it is the high time to review the existing technologies and tune these methods for a desirable purpose as per the demand of biotechnological/biomedical applications. RESULTS: Numerous engineering approaches have been developed to generate synthetic protein universe with desired specificity and enhanced performance in comparison to their natural counterparts. The current review provides a glimpse of several of the important computational and experimental methods that are being widely used under the categories of rational design, de novo design, directed evolution and combinatorial approach. CONCLUSIONS: This review shed light on the technicalities, advantages and pitfalls of the existing methodologies along with their applications, recent patents obtained using the engineered proteins and the current and future perspectives of protein engineering techniques.


Subject(s)
Drug Design , Models, Chemical , Protein Engineering/methods , Proteins/chemistry , Proteins/ultrastructure , Sequence Analysis, Protein/methods , Combinatorial Chemistry Techniques/methods , Computer Simulation , Models, Molecular
20.
Glycoconj J ; 33(1): 1-17, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26635091

ABSTRACT

Immune regulation is a complex biological signaling pathway in which several classes of biomolecules and small molecules play a complacent role to mediate this process. Glycoimmunology is a rapidly evolving research area that deals with the structure, binding interactions and immunological functions of glycans. Great deal of information regarding proteins and nucleic acids in molecular recognition events have been established owing to their well-established structural features and straight forward replication, transcription and translation principles. However considering the complexities of template free synthesis and structural heterogeneity, role of carbohydrates in immune regulation are still unsung to a large extent. In the current review, we illuminate the canonical structural features, emerging and significant pathophysiological functions of glycosaminoglycans (GAGs), the negatively charged linear carbohydrate molecules that are primarily present on all types of cell surfaces and extra cellular matrix. A snap shot of their association with protein counterparts of diversified protein families has been updated exclusively to provide mechanistic insights into their cellular signaling functions. Eventually, this review throws light on the recent biomedical/biotechnological advances of GAG based biomarkers, nutraceuticals, therapeutics, and nanocomposites for inflammatory, immune disorders and their invaluable contribution in tissue engineering.


Subject(s)
Carbohydrate Metabolism, Inborn Errors/drug therapy , Glycosaminoglycans/metabolism , Immune System Diseases/drug therapy , Signal Transduction , Animals , Glycosaminoglycans/immunology , Glycosaminoglycans/therapeutic use , Humans
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