Renewable Methanol from Industrial Carbon Emissions: A Dead End or Sustainable Way Forward?

As the urgency to achieve net-zero emissions by 2050 intensifies, industries face an imperative to reimagine their role in the fight against climate change. One promising avenue arises from the realization that industrial emissions, often deemed pollutants, can be the building blocks of a circular economy strategy. By directly utilizing these carbon emissions as raw materials, we can produce net-zero or low-carbon fuels, carbonates, polymers, and chemicals.

Potential phytochemical inhibitors of SARS-CoV-2 helicase Nsp13: a molecular docking and dynamic simulation study.

The SARS-CoV-2 helicase Nsp13 is a promising target for developing anti-COVID drugs. In the present study, we have identified potential natural product inhibitors of SARS-CoV-2 Nsp13 targeting the ATP-binding site using molecular docking and molecular dynamics (MD) simulations. MD simulation of the prepared crystal structure of SARS-CoV-2 Nsp13 was performed to generate an ensemble of structures of helicase Nsp13 capturing the conformational diversity of the ATP-binding site.

Interdigitation of Lipids Induced by Membrane-Active Proteins.

The membrane-active protein Nogo-66 is found to induce interdigitation in dimyristoylphosphocholine membranes. Extensive molecular dynamics simulations have been employed to probe the interactions of Nogo-66 with these model membranes. This phase change happens when the temperature is close to the main transition temperature of the membrane (T) and only in the presence of the protein.

Sequence fingerprints distinguish erroneous from correct predictions of intrinsically disordered protein regions.

More than 60 prediction methods for intrinsically disordered proteins (IDPs) have been developed over the years, many of which are accessible on the World Wide Web. Nearly, all of these predictors give balanced accuracies in the ~65%-~80% range. Since predictors are not perfect, further studies are required to uncover the role of amino acid residues in native IDP as compared to predicted IDP regions.

The structure of DLP12 endolysin exhibiting alternate loop conformation and comparative analysis with other endolysins.

The lytic enzyme, endolysin, is encoded by bacteriophages (phages) to destroy the peptidoglycan layer of host bacterial cells. The release of phage progenies to start the new infection cycle is dependent on the cell lysis event. Endolysin encoded by DLP12 cryptic prophage is a SAR endolysin which is retained by the bacterium presumably due to the benefit it confers.

MPDB: Molecular Pathways Brain Database.

Molecular Pathways Brain Database (MPDB), is a novel database for molecular information of the brain pathways and is an initiative to provide an organized platform for researchers in the field of neuro-informatics. The database currently has information from 1850 molecules for three different sensory pathways namely olfactory transduction, photo transduction and long-term potentiation. The usefulness of the database is demonstrated by an analysis of the olfactory transduction pathway which helps understand their olfactory specifity and further indicates that some of the molecules have evolved independently among these organisms as per the need of time and function.

Characterization of Salmonella typhi OmpC and OmpF porins engineered with HIV-gp41 epitope on the surface loops.

Porins form trimers in the outer membrane and help transport nutrients and waste products across the bacterial cell membrane. Porin loops are suitable candidates as display systems due to their high immunogenicity and presentation at the bacterial cell surface. In this study, Salmonella typhi porins (OmpC and OmpF) engineered with the Kennedy peptide from gp41 of HIV were characterised.

Sequence and structural perspectives of bacterial β-stranded porins.

Porins are integral membrane proteins found in the outer membrane of bacteria, mitochondria and chloroplasts. Herein, we have reviewed sequence and structural understanding about bacterial porins. The first porin structure from Rhodobacter capsulatus at 1.

Functional fragments of disorder in outer membrane β barrel proteins.

The traditional view of "sequence-structure-function" has been amended by the discovery of intrinsically disordered proteins. Almost 50% of PDB structures are now known to have one or more regions of disorder, which are involved in diverse functions. These regions typically possess low aromatic content and sequence complexity as well as high net charge and flexibility.

Mutational probing of the forkhead domain of the transcription factor FOXL2 provides insights into the pathogenicity of naturally occurring mutations.

Mutations of the transcription factor FOXL2, involved in cranio-facial and ovarian development, lead to the Blepharophimosis Syndrome. Here, we have systematically replaced the amino acids of the helices of the forkhead domain (FHD) of FOXL2 by glycine residues to assess the impact of such substitutions. A number of mutations lead to protein mislocalization, aggregation and to partial or complete loss of transactivation ability on a series of luciferase reporter systems.

Functional exploration of the adult ovarian granulosa cell tumor-associated somatic FOXL2 mutation p.Cys134Trp (c.402C>G).

Background: The somatic mutation in the FOXL2 gene c.402C>G (p.Cys134Trp) has recently been identified in the vast majority of adult ovarian granulosa cell tumors (OGCTs) studied.

HNHDb: a database on pattern based classification of HNH domains reveals functional relevance of sequence patterns and domain associations.

The HNH Database is a collection and sequence-based classification of HNH domain proteins. The database contains about 1913 HNH domain containing proteins, and is classified into 10 subsets based on the sequence pattern. Each of these subsets has unique signature sequences.

Differential functional effects of novel mutations of the transcription factor FOXL2 in BPES patients.

Mutations of the transcription factor FOXL2, involved in cranio-facial and ovarian development lead to the Blepharophimosis-Ptosis-Epicanthus Inversus Syndrome (BPES) in human. Here, we describe nine mutations in the open reading frame of FOXL2. Six of them are novel: c.

In vitro and in vivo study on the secretion of the Gly367Arg mutant myocilin protein.

Purpose: Mutations in the myocilin gene (MYOC) leading to a perturbed outflow of aqueous in the trabecular meshwork (TM) has been associated with the pathophysiology of glaucoma. This study examines the expression of normal and mutant myocilin (Gly367Arg) in cultured TM cells.

Methods: Normal and mutant MYOC cDNA constructs were used to transfect the TM cells.

Consensus based validation of membrane porins.

Porins are outermembrane beta-barrel proteins. They have varied biological functionality ranging from phage receptors, immunogenicity, pathogenicity to apoptosis. However, only a small number has been structurally and functionally characterised.

A review of genetic and structural understanding of the role of myocilin in primary open angle glaucoma.

Primary open angle glaucoma (POAG) is the most common form of glaucoma and the second leading cause of blindness in the world. Discovery of the candidate gene MYOC (TIGR/MYOC) encoding the protein myocilin, believed to have a role in cytoskeletal function, might play a key role in understanding the pathogenesis of POAG. MYOC is expressed in many ocular tissues, including trabecular meshwork (TM), a specialised eye tissue essential in regulating intraocular pressure (IOP).

A simulation model of Escherichia coli osmoregulatory switch using E-CELL system.

Background: Bacterial signal transduction mechanism referred to as a "two component regulatory systems" contributes to the overall adaptability of the bacteria by regulating the gene expression. Osmoregulation is one of the well-studied two component regulatory systems comprising of the sensor, EnvZ and the cognate response regulator, OmpR, which together control the expression of OmpC and OmpF porins in response to the osmolyte concentration.

Results: A quantitative model of the osmoregulatory switch operative in Escherichia coli was constructed by integrating the enzyme rate equations using E-CELL system.

Analysis of the lambdoid prophage element e14 in the E. coli K-12 genome.

Background: Many sequenced bacterial genomes harbor phage-like elements or cryptic prophages. These elements have been implicated in pathogenesis, serotype conversion and phage immunity. The e14 element is a defective lambdoid prophage element present at 25 min in the E.

HNH family subclassification leads to identification of commonality in the His-Me endonuclease superfamily.

The HNHc (SMART ID: SM00507) domain (SCOP nomenclature: HNH family) can be subclassified into at least eight subsets by iterative refinement of HMM profiles. An initial clustering of 323 proteins containing the HNHc domain helped identify the subsets. The subsets could be differentiated on the basis of the pattern of occurrence of seven defining features.

Evaluation and understanding of myocilin mutations in Indian primary open angle glaucoma patients.

Purpose: To screen for mutations in the MYOC gene of patients with Primary Open Angle Glaucoma (POAG) in India and to better understand the mutations using a possible model of myocilin.

Methods: We analyzed DNA for mutations in 107 subjects with POAG and 90 normal control subjects. The exonic sequences of the MYOC gene from all subjects were amplified by Polymerase Chain Reaction (PCR).