Themed collection Exploring proteins and their interactions

33 items
Open Access Review Article

Chemogenetics of cell surface receptors: beyond genetic and pharmacological approaches

In this review, we describe chemogenetics of cell surface receptors. This approach using designer ligands allows for rapid and selective control of the designer receptor function without affecting the endogenous systems.

Graphical abstract: Chemogenetics of cell surface receptors: beyond genetic and pharmacological approaches
From the themed collection: Exploring proteins and their interactions
Open Access Review Article

An overview of methods for the structural and functional mapping of epitopes recognized by anti-SARS-CoV-2 antibodies

This mini-review presents a critical survey of techniques used for epitope mapping on the SARS-CoV-2 Spike protein. An additional focus is an analytical appraisal of different deep mutational scanning workflows.

Graphical abstract: An overview of methods for the structural and functional mapping of epitopes recognized by anti-SARS-CoV-2 antibodies
From the themed collection: Exploring proteins and their interactions
Open Access Review Article

Segmental and site-specific isotope labelling strategies for structural analysis of posttranslationally modified proteins

Selective isotope labeling facilitates the analysis of effects of posttranslational modifications on protein structure and function.

Graphical abstract: Segmental and site-specific isotope labelling strategies for structural analysis of posttranslationally modified proteins
From the themed collection: Exploring proteins and their interactions
Open Access Review Article

Targeting protein–protein interactions in the DNA damage response pathways for cancer chemotherapy

Targeting protein–protein interactions within the DNA damage response (DDR) pathways with small molecule inhibitors is reviewed here as a strategy to design novel cancer chemotherapeutics.

Graphical abstract: Targeting protein–protein interactions in the DNA damage response pathways for cancer chemotherapy
From the themed collection: Exploring proteins and their interactions
Open Access Review Article

Aggregation of protein therapeutics enhances their immunogenicity: causes and mitigation strategies

Protein aggregation of biotherapeutics increases their immunogenicity, leading to immune-mediated adverse effects. In this review we discuss immune activation pathways, causes of aggregation and mitigation strategies.

Graphical abstract: Aggregation of protein therapeutics enhances their immunogenicity: causes and mitigation strategies
From the themed collection: Exploring proteins and their interactions
Open Access Review Article

Modulators of protein–protein interactions as antimicrobial agents

This review describes recent efforts towards the modulation of protein–protein interactions in infectious bacteria.

Graphical abstract: Modulators of protein–protein interactions as antimicrobial agents
From the themed collection: Exploring proteins and their interactions
Open Access Review Article

Metal transport mechanism of the cation diffusion facilitator (CDF) protein family – a structural perspective on human CDF (ZnT)-related diseases

A mechanistic analysis and structural perspective of cation diffusion facilitator (human ZnT) related diseases.

Graphical abstract: Metal transport mechanism of the cation diffusion facilitator (CDF) protein family – a structural perspective on human CDF (ZnT)-related diseases
From the themed collection: Exploring proteins and their interactions
Open Access Review Article

The chemical biology of coronavirus host–cell interactions

Chemical biology strategies can play important roles in studying the complexity of SARS-CoV-2–host interactions at molecular level detail.

Graphical abstract: The chemical biology of coronavirus host–cell interactions
Open Access Review Article

Neighborhood watch: tools for defining locale-dependent subproteomes and their contextual signaling activities

We discuss chemical-genetic means to mine locale-specific proteins of functional relevance and whose behaviors are pharmacologically malleable.

Graphical abstract: Neighborhood watch: tools for defining locale-dependent subproteomes and their contextual signaling activities
From the themed collection: Exploring proteins and their interactions
Open Access Communication

Protein–protein interaction based substrate control in the E. coli octanoic acid transferase, LipB

Lipoic acid, an essential cofactor produced in all organisms, diverts octanoic acid from type II fatty acid biosynthesis through a highly specific protein–protein interaction. This study characterizes how different substrates influence this interface to control chain length specificity.

Graphical abstract: Protein–protein interaction based substrate control in the E. coli octanoic acid transferase, LipB
From the themed collection: Exploring proteins and their interactions
Open Access Communication

Aquaporin-driven hydrogen peroxide transport: a case of molecular mimicry?

The combination of advanced atomistic simulations provides complete analysis of the atomistic basis of molecular transduction of H2O2 across aquaporins.

Graphical abstract: Aquaporin-driven hydrogen peroxide transport: a case of molecular mimicry?
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Biochemical and structural characterization of Haemophilus influenzae nitroreductase in metabolizing nitroimidazoles

The nitroreductase of Haemophilus influenzae metabolizes clinically used nitroimidazoles, generates dimeric metabolites and anaerobically sensitizes an E. coli mutant to antibiotics. We further uncover its biochemical and structural details.

Graphical abstract: Biochemical and structural characterization of Haemophilus influenzae nitroreductase in metabolizing nitroimidazoles
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Computational design and experimental characterisation of a stable human heparanase variant

A mutant heparanase that exhibits wild type structure and activity but can be heterologously produced in bacterial protein expression systems.

Graphical abstract: Computational design and experimental characterisation of a stable human heparanase variant
From the themed collection: Exploring proteins and their interactions
Open Access Paper

The identification and characterization of an oxalyl-CoA synthetase from grass pea (Lathyrus sativus L.)

Kinetic and structural analysis of a novel oxalyl-CoA synthetase isolated from grass pea (Lathyrus sativus L.).

Graphical abstract: The identification and characterization of an oxalyl-CoA synthetase from grass pea (Lathyrus sativus L.)
From the themed collection: Exploring proteins and their interactions
Open Access Paper

A COVID-19 vaccine candidate composed of the SARS-CoV-2 RBD dimer and Neisseria meningitidis outer membrane vesicles

Soberana01 is composed of the SARS-CoV-2 dimeric RBD and Neisseria meningitidis outer membrane vesicles (OMVs) adsorbed on alum. This vaccine induces a potent neutralizing immune response and shows potential against SARS-CoV-2 variants of concern.

Graphical abstract: A COVID-19 vaccine candidate composed of the SARS-CoV-2 RBD dimer and Neisseria meningitidis outer membrane vesicles
From the themed collection: Celebrating Latin American Chemistry
Open Access Paper

Identification of fragments binding to SARS-CoV-2 nsp10 reveals ligand-binding sites in conserved interfaces between nsp10 and nsp14/nsp16

By fragment screening using X-ray crystallography we identified four ligands revealing ligand-binding sites in interfaces between SARS-CoV-2 nsp10 and nsp14/nsp16. The nsp14/10 interaction is weak and therefore could be disrupted by small molecules.

Graphical abstract: Identification of fragments binding to SARS-CoV-2 nsp10 reveals ligand-binding sites in conserved interfaces between nsp10 and nsp14/nsp16
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Origin, toxicity and characteristics of two amyloid oligomer polymorphs

Self-assembly of lysozyme can generate two amyloids oligomer polymorphs with distinct characteristics and toxicity. Both polymorphs are off-pathway from amyloid fibril assembly.

Graphical abstract: Origin, toxicity and characteristics of two amyloid oligomer polymorphs
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Members of the Legionella pneumophila Sde family target tyrosine residues for phosphoribosyl-linked ubiquitination

During infection, Legionella pneumophila translocates hundreds of effectors into host cells. Among these, the Sde family effector SdeC catalyzes atypical ubiquitination of host targets at tyrosine, not only serine, residues.

Graphical abstract: Members of the Legionella pneumophila Sde family target tyrosine residues for phosphoribosyl-linked ubiquitination
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Computational design and experimental characterization of a photo-controlled mRNA-cap guanine-N7 methyltransferase

Guided by computational design, we engineered a light-dependent 5' cap guanine-N7 methyltransferase by bridging the substrate-binding cleft with an azobenzene derivative.

Graphical abstract: Computational design and experimental characterization of a photo-controlled mRNA-cap guanine-N7 methyltransferase
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Lysine succinylation on non-histone chromosomal protein HMG-17 (HMGN2) regulates nucleosomal DNA accessibility by disrupting the HMGN2–nucleosome association

Succinylated HMGN2, prepared by a ‘thiol–ene reaction’, disrupted the association of HMGN2 with the nucleosome and increased nucleosomal DNA accessibility.

Graphical abstract: Lysine succinylation on non-histone chromosomal protein HMG-17 (HMGN2) regulates nucleosomal DNA accessibility by disrupting the HMGN2–nucleosome association
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Elongation rate and average length of amyloid fibrils in solution using isotope-labelled small-angle neutron scattering

We demonstrate a solution method that allows both elongation rate and average length of amyloid fibrils to be independently determined.

Graphical abstract: Elongation rate and average length of amyloid fibrils in solution using isotope-labelled small-angle neutron scattering
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Mechanisms of allosteric and mixed mode aromatase inhibitors

Identification of multiple ligand binding sites in aromatase.

Graphical abstract: Mechanisms of allosteric and mixed mode aromatase inhibitors
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Intermediary conformations linked to the directionality of the aminoacylation pathway of nonribosomal peptide synthetases

In-solution analysis of conformational changes of NRPS adenylation and peptidyl-carrier protein domains under catalytic conditions reveals a new intermediary conformation.

Graphical abstract: Intermediary conformations linked to the directionality of the aminoacylation pathway of nonribosomal peptide synthetases
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Membrane composition and lipid to protein ratio modulate amyloid kinetics of yeast prion protein

This study provides a mechanistic description of how the membrane composition and lipid to protein ratio modulate amyloid kinetics of yeast prion protein.

Graphical abstract: Membrane composition and lipid to protein ratio modulate amyloid kinetics of yeast prion protein
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Combined computational and intracellular peptide library screening: towards a potent and selective Fra1 inhibitor

Here we describe library design coupled with computational and intracellular screening as an effective methodology to derive an antagonist that is selective for Fra1 relative to Jun counterparts.

Graphical abstract: Combined computational and intracellular peptide library screening: towards a potent and selective Fra1 inhibitor
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Substrate inhibition by the blockage of product release and its control by tunnel engineering

Substrate inhibition can be caused by substrate binding to the enzyme–product complex and can be controlled rationally by targeting enzyme access tunnels.

Graphical abstract: Substrate inhibition by the blockage of product release and its control by tunnel engineering
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Protein degradation profile reveals dynamic nature of 20S proteasome small molecule stimulation

Small molecule stimulators of the 20S core particle of the proteasome can lead to the degradation of a variety of protein substrates.

Graphical abstract: Protein degradation profile reveals dynamic nature of 20S proteasome small molecule stimulation
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Site-specific modification and segmental isotope labelling of HMGN1 reveals long-range conformational perturbations caused by posttranslational modifications

Using protein semi-synthesis, segmentally isotope-labelled variants of nucleosome-binding protein HMGN1 were generated with site-specific posttranslational modifications to explore their structural and functional effects.

Graphical abstract: Site-specific modification and segmental isotope labelling of HMGN1 reveals long-range conformational perturbations caused by posttranslational modifications
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Bypassing the requirement for aminoacyl-tRNA by a cyclodipeptide synthase enzyme

Cyclodipeptide synthases recognize a minimalistic substrate to produce cyclic dipeptides in a tRNA-independent manner.

Graphical abstract: Bypassing the requirement for aminoacyl-tRNA by a cyclodipeptide synthase enzyme
From the themed collection: Exploring proteins and their interactions
Open Access Paper

In silico peptide-directed ligand design complements experimental peptide-directed binding for protein–protein interaction modulator discovery

Using the protein–protein interaction of Mcl-1/Noxa, two methods for efficient modulator discovery are directly compared.

Graphical abstract: In silico peptide-directed ligand design complements experimental peptide-directed binding for protein–protein interaction modulator discovery
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Met80 and Tyr67 affect the chemical unfolding of yeast cytochrome c: comparing the solution vs. immobilized state

The motional regime affects the unfolding propensity and axial heme coordination of the Met80Ala and Met80Ala/Tyr67Ala variants of yeast iso-1 cytochrome c.

Graphical abstract: Met80 and Tyr67 affect the chemical unfolding of yeast cytochrome c: comparing the solution vs. immobilized state
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Sub-stoichiometric inhibition of IAPP aggregation: a peptidomimetic approach to anti-amyloid agents

Naphthalimide-appended oligopyridylamide peptidomimetic modulate islet amyloid polypeptide amyloidogenesis and disaggregate preformed oligomers and fibrils into non-toxic conformations at substoichiometric concentration.

Graphical abstract: Sub-stoichiometric inhibition of IAPP aggregation: a peptidomimetic approach to anti-amyloid agents
From the themed collection: Exploring proteins and their interactions
Open Access Paper

Haemoglobin(βK120C)–albumin trimer as an artificial O2 carrier with sufficient haemoglobin allostery

Recombinant haemoglobin [rHb(βK120C)] was coupled with two human serum albumins (HSAs), yielding a rHb(βK120C)–HSA2 heterotrimer, which shows a sigmoidal O2 equilibrium curve and sufficient Hb allostery identical to those of native Hb.

Graphical abstract: Haemoglobin(βK120C)–albumin trimer as an artificial O2 carrier with sufficient haemoglobin allostery
From the themed collection: Exploring proteins and their interactions
33 items

About this collection

The study of proteins, their structure and function, interactions and roles in disease is a vast topic encompassing a range of different approaches, techniques and tools. Work in this collection reflects the variety and scope of this area of chemical biology research, including studies on the mechanisms of aromatases, coronavirus host-cell interactions, the mapping of epitopes, and much more. Protein structure, function and protein-protein interactions are all included.

This collection intends to highlight the importance of multidisciplinary research at the chemistry-biology interface.  Much of this exciting and ground-breaking research on proteins and their interactions is collated here for you to explore.

New articles on the topic will be added periodically.

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