Impact of protein conformational diversity on AlphaFold predictions.

MOTIVATION: After the outstanding breakthrough of AlphaFold in predicting protein 3D models, new questions appeared and remain unanswered. The ensemble nature of proteins, for example, challenges the structural prediction methods because the models should represent a set of conformers instead of single structures. The evolutionary and structural features captured by effective deep learning techniques may unveil the information to generate several diverse conformations from a single sequence. Here, we address the performance of AlphaFold2 predictions obtained through ColabFold under this ensemble paradigm. RESULTS: Using a curated collection of apo-holo pairs of conformers, we found that AlphaFold2 predicts the holo form of a protein in ∼70% of the cases, being unable to reproduce the observed conformational diversity with the same error for both conformers. More importantly, we found that AlphaFold2's performance worsens with the increasing conformational diversity of the studied protein. This impairment is related to the heterogeneity in the degree of conformational diversity found between different members of the homologous family of the protein under study. Finally, we found that main-chain flexibility associated with apo-holo pairs of conformers negatively correlates with the predicted local model quality score plDDT, indicating that plDDT values in a single 3D model could be used to infer local conformational changes linked to ligand binding transitions. AVAILABILITY AND IMPLEMENTATION: Data and code used in this manuscript are publicly available at https://gitlab.com/sbgunq/publications/af2confdiv-oct2021. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Environmentally Induced Changes of Commercial Carbon Nanotubes in Aqueous Suspensions. Adaptive Behavior of Bacteria in Biofilms.

The effects of environmental factors such as sunlight irradiation and the presence of humic acid (HA) on the physicochemical properties of commercial multiwall carbon nanotubes (MWCNT) suspended in a simulated inorganic matrix (SIM) and their impacts on bacteria growing in biofilms were evaluated. Both solar irradiation and the presence of HA lead to the dissolution of adsorbed metals on the MWCNT, which are residues of synthesis catalysts. Also, preferential adsorption of certain HA components on the MWCNT induces important modifications in the aliphatic/aromatic relationship of HA components in solution and the generation and release of new moieties. Results demonstrated that the variation of such physicochemical parameters strongly affects the interactions of MWCNT with Pseudomonas aeruginosa sessile bacteria. Thus, the number of attached bacteria increased, and stress responses such as decrease in bacterial size were found in the presence of sunlight-irradiated MWCNT with a particular distribution of extracellular polymeric substances (EPS) strands. A shielding effect was observed when HA was added. It was concluded that physicochemical alterations caused by environmental conditions (with/without irradiation, presence/absence of HA) on MWCNT-containing SIM trigger distinctive adaptive behavior of bacteria in biofilms. This information must be taken into account in the development of biologically assisted treatments for organic metal co-contamination of MWCNT-containing media since MWCNT discharge alters the physicochemical properties and composition of the aqueous environment and the response of the biofilms that interact with it.

Staphylococcus aureus biofilm eradication by the synergistic effect exerted by PEG-coated silicon dots immobilized in silica films and light irradiation.

Immobilization of PEG-covered silicon dots, PEGSiDs, on glass substrates was performed following a simple strategy involving particle embedding by a sol-gel process forming a silica film on glass slides. The obtained films, denoted as fSiO x -PEGSiD, constitute a water-wettable, strongly supported, photoluminescent glass coating. The films showed high capacity for photosensitizing singlet oxygen (1O2) in the UVA when immersed in water. Staphylococcus aureus colonies formed on fSiO x -PEGSiDs modified glasses revealed the inhibition of bacterial adhesion and bacterial growth leading to the formation of loosely-packed and smaller S. aureus colonies. Upon 350 nm light irradiation of the biofilmed fSiO x -PEGSiDs -modified glasses, S. aureus growth was inhibited and bacteria killed reducing the number of living bacteria by three orders of magnitude. Eradication of attached bacteria was achieved by the synergistic effect exerted by a less adherent fSiO x -PEGSiDs surface that inhibits biofilm formation and the ability of the surface to photosensitize 1O2 to kill bacteria.