High-throughput prediction of protein conformational distributions with subsampled AlphaFold2.

This paper presents an innovative approach for predicting the relative populations of protein conformations using AlphaFold 2, an AI-powered method that has revolutionized biology by enabling the accurate prediction of protein structures. While AlphaFold 2 has shown exceptional accuracy and speed, it is designed to predict proteins' ground state conformations and is limited in its ability to predict conformational landscapes. Here, we demonstrate how AlphaFold 2 can directly predict the relative populations of different protein conformations by subsampling multiple sequence alignments.

Predicting Relative Populations of Protein Conformations without a Physics Engine Using AlphaFold2.

This paper presents a novel approach for predicting the relative populations of protein conformations using AlphaFold 2, an AI-powered method that has revolutionized biology by enabling the accurate prediction of protein structures. While AlphaFold 2 has shown exceptional accuracy and speed, it is designed to predict proteins' single ground state conformations and is limited in its ability to predict fold switching and the effects of mutations on conformational landscapes. Here, we demonstrate how AlphaFold 2 can directly predict the relative populations of different conformations of proteins and even accurately predict changes in those populations induced by mutations by subsampling multiple sequence alignments.

Predicting Relative Populations of Protein Conformations without a Physics Engine Using AlphaFold 2.

This paper presents a novel approach for predicting the relative populations of protein conformations using AlphaFold 2, an AI-powered method that has revolutionized biology by enabling the accurate prediction of protein structures. While AlphaFold 2 has shown exceptional accuracy and speed, it is designed to predict proteins' ground state conformations and is limited in its ability to predict conformational landscapes. Here, we demonstrate how AlphaFold 2 can directly predict the relative populations of different protein conformations by subsampling multiple sequence alignments.

Impact of pretreatments with ethanol and freezing on drying slice papaya: drying performance and kinetic of ultrasound-assisted extraction of phenolics compounds.

Background: Pretreatments of drying can represent an alternative to minimize the negative aspect process on the dry samples. Thus, the influence of ethanol (ET) and freezing (FG) as drying pretreatments was analyzed for slices of papaya. The slices (5 mm) were submitted for drying kinetics (60 °C and 1.

Covalent docking and molecular dynamics simulations reveal the specificity-shifting mutations Ala237Arg and Ala237Lys in TEM beta-lactamase.

The rate of modern drug discovery using experimental screening methods still lags behind the rate at which pathogens mutate, underscoring the need for fast and accurate predictive simulations of protein evolution. Multidrug-resistant bacteria evade our defenses by expressing a series of proteins, the most famous of which is the 29-kilodalton enzyme, TEM β-lactamase. Considering these challenges, we applied a covalent docking heuristic to measure the effects of all possible alanine 237 substitutions in TEM due to this codon's importance for catalysis and effects on the binding affinities of commercially-available β-lactam compounds.

A topological data analytic approach for discovering biophysical signatures in protein dynamics.

Identifying structural differences among proteins can be a non-trivial task. When contrasting ensembles of protein structures obtained from molecular dynamics simulations, biologically-relevant features can be easily overshadowed by spurious fluctuations. Here, we present SINATRA Pro, a computational pipeline designed to robustly identify topological differences between two sets of protein structures.

Correction: Influence of co-cultures of and probiotic lactobacilli on quality and antioxidant capacity parameters of lactose-free fermented dairy beverages containing (L.) Skeels pulp.

[This corrects the article DOI: 10.1039/C9RA08311A.].

Influence of co-cultures of s and probiotic lactobacilli on quality and antioxidant capacity parameters of lactose-free fermented dairy beverages containing (L.) Skeels pulp.

This study investigated the influence of probiotic lactobacilli in co-culture with on composition, physicochemical parameters, microbial viability, sensory acceptability, antioxidant capacity and protein profile of lactose-free fermented dairy beverages with added whey, β-galactosidase and jambolan ( (L.) Skeels) pulp. Three beverages (T1, T2 and T3) were prepared with TA-40 as starter culture.

Assessment of the hypoglycemic effect of Bixin in alloxan-induced diabetic rats: and studies.

The objectives of this study were to extract and purify Bixin from the seeds of and to evaluate its hypoglycemic activity , as well as, to conduct an study of selectivity on peroxisome proliferator-activated receptors via molecular docking and molecular dynamics simulations. Oral administration of Bixin (10 mg/kg) significantly reduced their glucose level that was alloxan-induced diabetic rats. Bixin showed selectivity on peroxisome proliferator-activated receptors (PPARs), particularly by the peroxisome proliferator-activated receptor gamma (PPARγ), which supports the hypoglycemic activity of Bixin.

Cell-Penetrating Peptide Mediates Intracellular Membrane Passage of Human Papillomavirus L2 Protein to Trigger Retrograde Trafficking.

Cell-penetrating peptides (CPPs) are short protein segments that can transport cargos into cells. Although CPPs are widely studied as potential drug delivery tools, their role in normal cell physiology is poorly understood. Early during infection, the L2 capsid protein of human papillomaviruses binds retromer, a cytoplasmic trafficking factor required for delivery of the incoming non-enveloped virus into the retrograde transport pathway.

Oil from the fruits of Pterodon emarginatus Vog.: A traditional anti-inflammatory. Study combining in vivo and in silico.

Ethnobotanical Relevance: The oil obtained from the fruits of Pterodon emarginatus Vog. (OPe) is used orally and topically, in traditional medicine for some purposes, such as acute and chronic inflammatory states as rheumatoid arthritis.

Materials And Methods: In this work, the anti-inflammatory activity of the OPe was demonstrated based on several animal models and presented an in silico study based on the 6α,7β-dihydroxy-vouacapan-17β-oic acid (DHVA) majority compound of the OPe to evaluate the interaction this compound, with cyclooxygenase-2 (COX-2) in 4COX (Mus musculus) and 5KIR (Homo sapiens) and molecular dynamics simulation.