Hydrophobins are small amphiphilic extracellular proteins produced by filamentous fungi; they are surface-active proteins, and their functions are mainly related to their ability to self-assemble into amphipathic monolayers at hydrophobic–hydrophilic interfaces. Depending on their hydropathy patterns and purification requirements, they are classified into class I and class II; both present eight conserved cysteines throughout their sequence, forming four disulfide bridges, which generate four loops that give stability to the protein in its monomeric and folded forms. Class I hydrophobin loops are more extended than class II hydrophobin loops, resulting in differences in assembly on divergent surfaces, additionally accompanied by conformational changes in the protein structure. In the monomer hydrophobin glycosylated form, hydrophobins are rich in β-sheet structure, while being assembled at the water–air interface increases the content of the β-sheet in their structure and is at the interface with water, and a hydrophobic solid such as Teflon also induces the formation of an α-helix structure. The monolayers generated by class I are stable structures called fibrils or rodlets, and class II only produces aggregates. Class I presents a glycosylated chain in its sequence; this causes the formation of the α-helix structure, promoting ordered assemblies, which entails their stability and high insolubility. Fibrils could be dissociated with trifluoroacetic acid and formic acid, which unfolds the protein, while 60% ethanol and 2% sodium dodecyl sulfate solutions dissociate class II aggregates.

The reasons underlying the oligomeric nature of some proteins such as triosephosphate isomerase (TIM) are unclear. It has been proposed that this enzyme is an oligomer, mainly because of its stability rather than for functional reasons. To address this issue, the reversible denaturation and renaturation of the homodimeric TIM from baker's yeast (Saccharomyces cerevisiae) induced by guanidinium chloride and urea have been characterized by spectroscopic, functional and hydrodynamic techniques. The unfolding and refolding of this enzyme are not coincident after ‘conventional’ equilibrium times. Unfolding experiments did not reach equilibrium, owing to a very slow dissociation and/or unfolding process. By contrast, equilibrium was reached in the refolding direction. The simplest equilibrium pathway compatible with the obtained data was found to be a three-state process involving an inactive and expanded monomer. The Gibbs energy changes for monomer folding (ΔGfold0 = −16.6±0.7kJ·mol-1) and monomer association (ΔGassoc0 = −70.3±1.1kJ·mol-1) were calculated from data obtained in the two denaturants. From an analysis of the present data and data from the literature on the stability of TIM from different species and for other β/α barrels, and model simulations on the effect of stability in the catalytic activity of the enzyme, it is concluded that the low stability of the monomers is neither the only, nor the main, cause for the dimeric nature of TIM. There is interplay between function and stability.

Plants are a valuable source of specialized metabolites that provide a plethora of therapeutic applications. They are natural defenses that plants use to adapt and respond to their changing environment. Decoding their biosynthetic pathways and understanding how specialized plant metabolites (SPMs) respond to biotic or abiotic stress will provide vital knowledge for plant biology research and its application for the future sustainable production of many SPMs of interest. Here, we focus on the proteomic approaches and strategies that help with the study of plant-specialized metabolism, including the: (i) discovery of key enzymes and the clarification of their biosynthetic pathways; (ii) study of the interconnection of both primary (providers of carbon and energy for SPM production) and specialized (secondary) metabolism; (iii) study of plant responses to biotic and abiotic stress; (iv) study of the regulatory mechanisms that direct their biosynthetic pathways. Proteomics, as exemplified in this review by the many studies performed to date, is a powerful tool that forms part of omics-driven research. The proteomes analysis provides an additional unique level of information, which is absent from any other omics studies. Thus, an integrative analysis, considered versus a single omics analysis, moves us more closely toward a closer interpretation of real cellular processes. Finally, this work highlights advanced proteomic technologies with immediate applications in the field.