Bimolecular quenching of tryptophan fluorescence in a membrane protein: Evolution of local solvation and environment during folding into a bilayer

Stress response proteins within biofilm matrixome protect the cell membrane against heavy metals-induced oxidative damage in a marine bacterium Bacillus stercoris GST-03

Biofilm formation is a key adaptive response of marine bacteria towards stress conditions. The protective mechanisms of biofilm matrixome proteins against heavy metals (Pb and Cd) induced oxidative damage in the marine bacterium Bacillus stercoris GST-03 was investigated. Exposure to heavy metals resulted in significant changes in cell morphology, biofilm formation, and matrixome composition. Biofilm-encased cells showed lower oxidative damage. Biofilm matrixome protein exhibited major conformational changes, with 100 % α-helix turned to 62.33 % and 69.64 % of random coil under Pb and Cd stress, respectively. Fluorescence quenching kinetics revealed slow interactions between biofilm matrixome proteins and heavy metals (Kq values < 2.0 × 1010). Thermodynamic analysis showed negative ∆G (-16.02 kJ/mol for Pb and -17.45 kJ/mol for Cd) and binding dissociation constant (KD) (1530 ± 157 μM for Pb and 875 ± 97.4 μM for Cd), indicating a stronger binding affinity of biofilm matrixome to heavy metals. Pb stress led to overproduction of detoxification proteins (YnaI, KhtS, Bacillopeptidase F), competence and sporulation proteins (RapF, CSSF, XkdP), while Cd exposure leads to overproduction of proteins involved in protein misfolding repair (YlxX, cysteine-tRNA ligase, YacP), DNA repair (YfkN), and redox balance (cysteine synthase, YdiK). The findings highlight the resilience of B. stercoris GST-03 to heavy metal stress in biofilm mode.

Triplet state spectroscopy reveals involvement of the buried tryptophan residue 310 in Glyceraldehyde-3-phosphate dehydrogenase (GAPD) in the interaction with acrylamide

Using conventional steady state and time resolved fluorescence study of the interaction between a multi-tryptophan protein and a quencher, it is difficult, if not impossible to identify the particular tryptophan residue/residues involved in the interaction. In this work we have exemplified the above contention using a multi-tryptophan protein, Glyceraldehyde-3-phosphate dehydrogenase (GAPD) from rabbit muscle having three tryptophan (Trp) residues at positions 84, 193 and 310 and a neutral quencher acrylamide in Tris buffer of pH 7.5. From the steady state and time resolved fluorescence quenching (at 298 K) with acrylamide Ksv, K and kq for the system have been calculated. Low temperature phosphorescence (LTP) spectra at 77 K of GAPD in suitable cryosolvent is known to exhibit two (0,0) bands corresponding to two tryptophan residues 193 and 310. Using the LTP study of free GAPD and GAPD - acrylamide it is possible to identify that the buried Trp 310 residue is specifically involved in the interaction with acrylamide. This is possible without doing any site-directed mutagenesis of GAPD which contains Trp residues at 84, 193 and 310. Tyrosine 320 is also specifically quenched. The results have been corroborated using the molecular docking studies. Molecular Dynamics simulation supports our contention of the involvement of Trp 310 and also shows that the other nearest residues of acrylamide are Val175 and Val232.

The Formation of β-Strand Nine (β9) in the Folding and Insertion of BamA from an Unfolded Form into Lipid Bilayers

Transmembrane proteins span lipid bilayer membranes and serve essential functions in all living cells. Membrane-inserted domains are of either α-helical or β-barrel structure. Despite their biological importance, the biophysical mechanisms of the folding and insertion of proteins into membranes are not well understood. While the relative composition of the secondary structure has been examined by circular dichroism spectroscopy in folding studies for several outer membrane proteins, it is currently not known how individual β-strands fold. Here, the folding and insertion of the β-barrel assembly machinery protein A (BamA) from the outer membrane of Escherichia coli into lipid bilayers were investigated, and the formation of strand nine (β₉) of BamA was examined. Eight single-cysteine mutants of BamA were overexpressed and isolated in unfolded form in 8 M urea. In each of these mutants, one of the residues of strand β₉, from R572 to V579, was replaced by a cysteine and labeled with the fluorophore IAEDANS for site-directed fluorescence spectroscopy. Upon urea-dilution, the mutants folded into the native structure and were inserted into lipid bilayers of dilauroylphosphatidylcholine, similar to wild-type BamA. An aqueous and a membrane-adsorbed folding intermediate of BamA could be identified by strong shifts in the intensity maxima of the IAEDANS fluorescence of the labeled mutants of BamA towards shorter wavelengths, even in the absence of lipid bilayers. The shifts were greatest for membrane-adsorbed mutants and smaller for the inserted, folded mutants or the aqueous intermediates. The spectra of the mutants V573C-, L575C-, G577C-, and V579C-BamA, facing the lipid bilayer, displayed stronger shifts than the spectra recorded for the mutants R572C-, N574C-, T576C-, and K578C-BamA, facing the β-barrel lumen, in both the membrane-adsorbed form and the folded, inserted form. This alternating pattern was neither observed for the IAEDANS spectra of the unfolded forms nor for the water-collapsed forms, indicating that strand β₉ forms in a membrane-adsorbed folding intermediate of BamA. The combination of cysteine scanning mutagenesis and site-directed fluorescence labeling is shown to be a valuable tool in examining the local secondary structure formation of transmembrane proteins.

Molecular interactions involved in the complexation process between buffalo whey proteins concentrate and folic acid

Using buffalo whey proteins as carrier agents of sensitive molecules raises an interesting approach allowing adding value and minimizing the pollution impact of this by-product. In this context, this work aims to explore the molecular interactions between buffalo whey proteins concentrate (BWPC) and folic acid (FA). For this purpose, fluorescence, UV and FTIR analysis were performed on aqueous or solid dispersions of a buffalo whey protein concentrate (5 μM) (BWPC), with variable concentrations (0-20 μM) of FA. Fluorescence and absorption data were fitted by Stern-Volmer, Beckett, Förster resonance energy transfer, and sphere-of-action models (R2 > 0.9). Derived results suggest that BWPC strongly bind to FA through non-covalent interactions and form ground-state complexes. Additionally, BWPC improves the photostability of FA against UV radiation, and chemical denaturation negatively affects the binding properties. Obtained results encourage further studies of BWPC as carrier agents, which could promote innovative applications for this under-utilized proteins source.