Hydrodynamic Radii of Intrinsically Disordered Proteins: Fast Prediction by Minimum Dissipation Approximation and Experimental Validation.

The diffusion coefficients of globular and fully unfolded proteins can be predicted with high accuracy solely from their mass or chain length. However, this approach fails for intrinsically disordered proteins (IDPs) containing structural domains. We propose a rapid predictive methodology for estimating the diffusion coefficients of IDPs.

Diversity of hydrodynamic radii of intrinsically disordered proteins.

Intrinsically disordered proteins (IDPs) form an important class of biomolecules regulating biological processes in higher organisms. The lack of a fixed spatial structure facilitates them to perform their regulatory functions and allows the efficiency of biochemical reactions to be controlled by temperature and the cellular environment. From the biophysical point of view, IDPs are biopolymers with a broad configuration state space and their actual conformation depends on non-covalent interactions of its amino acid side chain groups at given temperature and chemical conditions.

Masquerade of Polish Society-Psychological Determinants of COVID-19 Precautionary Behaviors.

The risk of contracting COVID-19 was a very specific situation of uncertainty and ambi-guity, and of course, cognitively interesting for psychologists studying the determinants of behaviors of different personality types. In this study, we set our sights on trying to find a correlation between adherence to wearing masks and receiving vaccinations and having certain character traits that we thought might influence preventive behavior or not. We focused on the Dark Triad-psychopathy, Machiavellianism and narcissism-as well as social approval and the need for cognition closure, as these traits have previously been linked to heightened conspiracy mentalities.

Regiospecific O → N Acyl Migration as a Methodology to Access l-Altropyranosides with an 2,4-Differentiation.

Pseudaminic acid and its biosynthetic altropyranoside precursors are bacterial components currently being investigated toward novel antibacterial strategies. One structural feature associated with these naturally occurring flagellar carbohydrates is the different -acylation patterns on the two amido functionalities, posing a synthetic challenge. A new one-pot methodology is reported and a scope of diverse 2/4-differentiated analogs are presented via a Staudinger reduction-mediated regiospecific O3 → N4 acyl migration, followed by an autonomous 2-acylation.

An efficient and scalable synthesis of 2,4-di--acetyl-l-altrose (l-2,4-Alt-diNAc).

Bacterial nonulosonic acids such as pseudaminic acids and others constitute a family of 9-carbon monosaccharides that contain a common 3-deoxy-2-ketoacid fragment but differ in their stereochemistries at 5 stereogenic centers between C-4 to C-8. Their unique structures make them attractive targets for use as antigens in vaccinations to combat drug-resistant bacterial infections and their challenging stereochemistries have attracted considerable attention from chemists. In this work we report the development of an improved synthesis for 2,4-di--acetyl-l-altrose (l-2,4-Alt-diNAc), which is a key hexose required for the chemical and chemoenzymatic synthesis of pseudaminic acids.

Distinct type II opsins in the eye decode light properties for background adaptation and behavioural background preference.

Crypsis increases survival by reducing predator detection. Xenopus laevis tadpoles decode light properties from the substrate to induce two responses: a cryptic coloration response where dorsal skin pigmentation is adjusted to the colour of the substrate (background adaptation) and a behavioural crypsis where organisms move to align with a specific colour surface (background preference). Both processes require organisms to detect reflected light from the substrate.

Nanoecotoxicology study of the response of magnetic O-Carboxymethylchitosan loaded silver nanoparticles on Artemia salina.

Magnetic silver nanoparticles (MNPAg) are interesting nanotechnology materials with borderless environmental science, that can be used to disinfect water contaminated with pathogenic bacteria. The use of MNPAg leads to increased risk of nanomaterial contamination in the environment, especially natural water sources, with harmful effects on the ecosystem. This study investigating survival and enzyme activity of magnetic O-carboxymethylchitosan loaded silver nanoparticle on Artemia salina.

Structural Dynamics of the GW182 Silencing Domain Including its RNA Recognition motif (RRM) Revealed by Hydrogen-Deuterium Exchange Mass Spectrometry.

The human GW182 protein plays an essential role in micro(mi)RNA-dependent gene silencing. miRNA silencing is mediated, in part, by a GW182 C-terminal region called the silencing domain, which interacts with the poly(A) binding protein and the CCR4-NOT deadenylase complex to repress protein synthesis. Structural studies of this GW182 fragment are challenging due to its predicted intrinsically disordered character, except for its RRM domain.

Molecular recognition of mRNA 5' cap by 3' poly(A)-specific ribonuclease (PARN) differs from interactions known for other cap-binding proteins.

The mRNA 5' cap structure plays a pivotal role in coordination of eukaryotic translation and mRNA degradation. Poly(A)-specific ribonuclease (PARN) is a dimeric exoribonuclease that efficiently degrades mRNA 3' poly(A) tails while also simultaneously interacting with the mRNA 5' cap. The cap binding amplifies the processivity of PARN action.

Towards novel efficient and stable nuclear import signals: synthesis and properties of trimethylguanosine cap analogs modified within the 5',5'-triphosphate bridge.

A trimethylguanosine (TMG) cap is present at the 5' end of several small nuclear and nucleolar RNAs. Recently, it has been reported that the TMG cap is a potential nuclear import signal for nucleus-targeting therapeutic nucleic acids and proteins. The import is mediated by recognition of the TMG cap by the snRNA transporting protein, snurportin1.

Structural basis for nematode eIF4E binding an m(2,2,7)G-Cap and its implications for translation initiation.

Metazoan spliced leader (SL) trans-splicing generates mRNAs with an m(2,2,7)G-cap and a common downstream SL RNA sequence. The mechanism for eIF4E binding an m²²⁷G-cap is unknown. Here, we describe the first structure of an eIF4E with an m(2,2,7)G-cap and compare it to the cognate m⁷G-eIF4E complex.

Global architecture of human poly(A)-specific ribonuclease by atomic force microscopy in liquid and dynamic light scattering.

Deadenylation is the initial and often rate-limiting step in the main pathways of eukaryotic mRNA decay. Poly(A)-specific ribonuclease (PARN) is a eukaryotic enzyme that efficiently degrades mRNA poly(A) tails. Structural and functional studies have shown that human PARN is composed of at least three functional domains, i.

Thermodynamics of molecular recognition of mRNA 5' cap by yeast eukaryotic initiation factor 4E.

Molecular mechanisms underlying the recognition of the mRNA 5' terminal structure called "cap" by the eukaryotic initiation factor 4E (eIF4E) are crucial for cap-dependent translation. To gain a deeper insight into how the yeast eIF4E interacts with the cap structure, isothermal titration calorimetry and the van't Hoff analysis based on intrinsic protein fluorescence quenching upon titration with a series of chemical cap analogs were performed, providing a consistent thermodynamic description of the binding process in solution. Equilibrium association constants together with thermodynamic parameters revealed similarities and differences between yeast and mammalian eIF4Es.

Structural insights into parasite eIF4E binding specificity for m7G and m2,2,7G mRNA caps.

The eukaryotic translation initiation factor eIF4E recognizes the mRNA cap, a key step in translation initiation. Here we have characterized eIF4E from the human parasite Schistosoma mansoni. Schistosome mRNAs have either the typical monomethylguanosine (m(7)G) or a trimethylguanosine (m(2,2,7)G) cap derived from spliced leader trans-splicing.

Structural basis of m(7)GpppG binding to poly(A)-specific ribonuclease.

Poly(A)-specific ribonuclease (PARN) is a homodimeric, processive, and cap-interacting 3' exoribonuclease that efficiently degrades eukaryotic mRNA poly(A) tails. The crystal structure of a C-terminally truncated PARN in complex with m(7)GpppG reveals that, in one subunit, m(7)GpppG binds to a cavity formed by the RRM domain and the nuclease domain, whereas in the other subunit, it binds almost exclusively to the RRM domain. Importantly, our structural and competition data show that the cap-binding site overlaps with the active site in the nuclease domain.

Diverse role of three tyrosines in binding of the RNA 5' cap to the human nuclear cap binding complex.

The heterodimeric nuclear cap-binding complex (CBC) specifically recognizes the monomethylguanosine 5' cap structure of the eukaryotic RNA polymerase II transcripts such as mRNA and U snRNA. The binding is essential for nuclear maturation of mRNA, for nuclear export of U snRNA in metazoans, and for nonsense-mediated decay of mRNA and the pioneer round of translation. We analysed the recognition of the cap by native human CBC and mutants in which each tyrosine that stacks with the 7-methylguanosine moiety was replaced by phenylalanine or alanine and both tyrosines were replaced by phenylalanines.

Structural changes of eIF4E upon binding to the mRNA 5' monomethylguanosine and trimethylguanosine Cap.

Recognition of the 5' cap by the eukaryotic initiation factor 4E (eIF4E) is the rate-limiting step in the ribosome recruitment to mRNAs. The regular cap consists of 7-monomethylguanosine (MMG) linked by a 5'-5' triphosphate bridge to the first transcribed nucleoside, while some primitive eukaryotes possess a N (2), N (2),7-trimethylguanosine (TMG) cap structure as a result of trans splicing. Mammalian eIF4E is highly specific to the MMG form of the cap in terms of association constants and thermodynamic driving force.

A multifunctional RNA recognition motif in poly(A)-specific ribonuclease with cap and poly(A) binding properties.

Poly(A)-specific ribonuclease (PARN) is an oligomeric, processive and cap-interacting 3' exoribonuclease that efficiently degrades mRNA poly(A) tails. Here we show that the RNA recognition motif (RRM) of PARN harbors both poly(A) and cap binding properties, suggesting that the RRM plays an important role for the two critical and unique properties that are tightly associated with PARN activity, i.e.

Novel way of capping mRNA trimer and studies of its interaction with human nuclear cap-binding complex.

Binding of mRNA 5' cap by the nuclear cap-binding complex (CBC) is crucial for a wide variety of mRNA metabolic events. The interaction involving the CBP20 subunit of CBC is mediated by numerous hydrogen bonds and by stacking of the tyrosine sidechains with two first bases of the capped mRNA. To examine a possible role of a longer mRNA chain in the CBC-cap recognition, we have synthesized an mRNA tetramer using a novel way of capping an RNA trimer and determined its affinity for CBC by fluorescence titration.

Specificity of recognition of mRNA 5' cap by human nuclear cap-binding complex.

The heterodimeric nuclear cap-binding complex (CBC) binds to the mono-methylated 5' cap of eukaryotic RNA polymerase II transcripts such as mRNA and U snRNA. The binding is important for nuclear maturation of mRNAs and possibly in the first round of translation and nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans.