Understanding thermodynamic competitivity between biopolymer folding and misfolding under large-scale intermolecular interactions

Site specifically probing the unfolding process of human telomere i-motif DNA using vibrationally enhanced alkynyl stretch

The microscopic unfolding process of a cytosine-rich DNA forming i-motif by hemi-protonated base pairs is related to gene regulation. However, the detailed thermal unfolding mechanism and the protonation/deprotonation status of site-specific cytosine in DNA in a physiological environment are still obscure. To address this issue, a vibration-enhanced CC probe tagged on 5'E terminal cytosine of human telomere i-motif DNA was examined using linear and nonlinear infrared (IR) spectroscopies and quantum-chemistry calculations. The CC probe extended into the major groove of the i-motif was found using nonlinear IR results only to introduce a minor steric effect on both steady-state structure and local structure dynamics; however, its IR absorption profile effectively reports the cleavage of the hemi-protonated base pair of C1-C13 upon the unfolding with C1 remaining protonated. The temperature mid-point (Tm) of the local transition reported using the CC tag was slightly lower than the Tm of global transition, and the enthalpy of the former exceeds 60% of the global transition. It is shown that the base-pair unraveling is noncooperative, with outer base pairs breaking first and being likely the rate limiting step. Our results offered an in-depth understanding of the macroscopic unfolding characteristics of the i-motif DNA and provided a nonlinear IR approach to monitoring the local structural transition and dynamics of DNA and its complexes.

Physical and culinary analysis of long gluten-free extruded pasta based on high protein quinoa flour

The consumption of foods with high protein content from pseudocereals is of great industrial interest. Pasta has a high gluten content; consequently, obtaining these gluten-free products is a technological challenge. The products obtained from quinoa show excellent results in protein and fiber with low glycemic index. This work focused on studying the effect of quinoa fat on the production of long pasta by extrusion in different mixtures of hyperprotein quinoa (HHP). It was observed that formulations with high percentages of starch showed a higher expansion rate, due to a higher fat content. Likewise, extruded pastes showed higher values of brightness than those containing lower percentages of starch and crude fat. The fracturability results were associated with the resistance of the paste to the pressure exerted for its deformation, which does not exceed 3.73 mm. The formulations with lower fat content presented high values in fracture stress due to the low diffusion of water and lipids. It was shown that fat has an indirect influence with a strong correlation with the expansion index and fracture stress and a moderate correlation (p > 0.05) with Young's modulus, indicating that increasing the added fat content increases the percentage of mass loss by baking. The melting and cohesiveness of all components improved during extrusion due to the pregelatinization of cassava starch, the addition of defatted HHP and the availability of quinoa starch granules.

Transient misfolding dominates multidomain protein folding

Neighbouring domains of multidomain proteins with homologous tandem repeats have divergent sequences, probably as a result of evolutionary pressure to avoid misfolding and aggregation, particularly at the high cellular protein concentrations. Here we combine microfluidic-mixing single-molecule kinetics, ensemble experiments and molecular simulations to investigate how misfolding between the immunoglobulin-like domains of titin is prevented. Surprisingly, we find that during refolding of tandem repeats, independent of sequence identity, more than half of all molecules transiently form a wide range of misfolded conformations. Simulations suggest that a large fraction of these misfolds resemble an intramolecular amyloid-like state reported in computational studies. However, for naturally occurring neighbours with low sequence identity, these transient misfolds disappear much more rapidly than for identical neighbours. We thus propose that evolutionary sequence divergence between domains is required to suppress the population of long-lived, potentially harmful misfolded states, whereas large populations of transient misfolded states appear to be tolerated.

Single molecule kinetics investigations and molecular simulations are useful tools in elucidating protein assembly mechanisms. Here, the authors use these to show that even naturally occurring tandem repeats undergo transient misfolding and that assembly is much more complex than we previously understood.

Study of pH-induced folding and unfolding kinetics of the DNA i-motif by stopped-flow circular dichroism

Using the stopped-flow circular dichroism (SFCD) technique, we investigate the kinetics of the pH-induced folding and unfolding process of the DNA i-motif. The results show that the molecule can fold or unfold on a time scale of 100 ms when the solution pH is changed. It is also found that the folding and unfolding rates strongly depend on the solution pH. On the basis of quantitative data, we propose theoretical models to decipher the folding and unfolding kinetics. Our models suggest that the cooperativity of protons is crucial for both the folding and unfolding process. In the unfolding process, the cooperative neutralization of two protons (out of the total six protons in the i-motif molecule) is the only rate-limiting step. In the folding process, there exists a critical step in which three protons bind cooperatively to the DNA strand. These results offer an in-depth understanding of the folding and unfolding kinetics of the DNA i-motif and may give precise guidance for constructing novel nanodevices based on the DNA i-motif.