Journal of Clinical Nutrition & Dietetics

Description

A group of two or more polypeptide chains that are linked together is called a protein complex or multi-protein complex. Protein complexes are a type of quaternary structure, and they are distinct from multi-enzyme complexes, which contain multiple catalytic domains in a single polypeptide chain. Non-covalent protein interactions link the proteins in a protein complex. The majority of biological processes, if not all of them, are built on these complexes. It is evident that the cell is made up of modular supra-molecular complexes, each of which has its own distinct biological function. By being close together, the speed and selectivity of binding interactions between enzymatic complexes and substrates can be greatly increased, resulting in increased cellular efficiency. The task of determining the components of a complex is made more difficult by the fact that many of the methods used to enter cells and isolate proteins are by their very nature disruptive to such massive complexes.

Non-Obligate Protein Complexes

The proteasome for molecular degradation and the majority of RNA polymerases are two examples of protein complexes. Protein complex formation can be similar to phosphorylation in that it can either activate or inhibit one or more of the members of the complex. Numerous protein complexes can be formed by individual proteins. The same complex may perform multiple functions depending on a variety of factors, just as different complexes perform distinct functions. The model organism Saccharomyces cerevisiae (yeast) is particularly useful for understanding many protein complexes. In 2021, researchers used deep learning software Rose TTA Fold and Alpha Fold to solve the structures of 712 eukaryotic complexes for this relatively simple organism. The elucidation of the majority of its protein complexes is currently on going 6000 yeast proteins were compared to those of 2026 other fungi and 4325 other eukaryotic organisms. Non-obligate protein complexes are the complexes made by proteins that can form a stable, well-folded structure on their own in vivo without the help of another protein. However, some proteins can be found as part of a protein complex that stabilizes the individual proteins and cannot be found alone to create a stable, well-folded structure. Obligatory protein complexes refer to these kinds of protein complexes. Permanent protein complexes have a relatively long half-life, whereas transient protein complexes form and break down in vivo. Note that there is no clear distinction between obligate and non-obligate interactions; rather, there exists a continuum between them that depends on various conditions, such as pH, protein concentration, and so on. However, there are important distinctions between the properties of transient interactions and permanent/stable interactions: The interacting proteins on the two sides of a stable interaction have a greater tendency to be co-expressed than those on the two sides of a transient interaction in fact, the probability of co-expression between two transiently interacting proteins is not higher than that between two random proteins. On the other hand, transient interactions are much less co-localized than stable interactions. Even though they are transient by nature, transient interactions are very important for cell biology: These interactions make up the majority of gene regulation and signal transduction in the human interactome, and proteins with intrinsically disordered regions (IDR: Transient regulatory and signaling interactions are found to be more prevalent in regions of protein that exhibit dynamic inter-converting structures in the native state.

Binary or Transient Interactions in the Yeast

The centrality-lethality rule, as suggested by some early studies, suggested a strong correlation between essentiality and the degree of protein interaction. However, subsequent analyses have revealed that this correlation is weak for binary or transient interactions (such as the yeast two-hybrid). On the other hand, the correlation is robust for networks of stable co-complex interactions. The finding that essentiality is a property of molecular machines (i.e., complexes) rather than individual components led Wang et al. to the conclusion that essentiality is a property of molecular machines (i.e., complexes). Ryan noted that essential genes are more likely to have high co-complex interaction degrees because larger protein complexes are more likely to be essential. Modular essentiality was the term used by these researchers to describe the observation that complete complexes appear to be essential. They also demonstrated that complexes typically consist of either essential or non-essential proteins rather than exhibiting a random distribution. However, this is not a one-size-fits-all phenomenon: Only about 26% of yeast complexes (105/401) contain only essential or non-essential subunits. Proteins may not fold completely in either transient or permanent complexes because fuzzy protein complexes have more than one structural form or dynamic structural disorder in the bound state. As a result, certain complexes may engage in ambiguous interactions that shift in response to environmental signals. Post-translational modifications, protein interactions, or alternative splicing modify the conformational ensembles of fuzzy complexes to fine-tune the affinity or specificity of interactions. As a result, different ensembles of structures result in different (even opposite) biological functions. Within the eukaryotic transcription machinery, these mechanisms are frequently utilized for regulation. The "centrality-lethality" rule, as suggested by some early studies, suggested a strong correlation between essentiality and the degree of protein interaction. However, subsequent analyses have revealed that this correlation is weak for binary or transient interactions such as the yeast two-hybrid. On the other hand, the correlation is robust for networks of stable co-complex interactions. The finding that essentiality is a property of molecular machines (i.e., complexes) rather than individual components led Wang to the conclusion that essentiality is a property of molecular machines (i.e., complexes). Ryan noted that essential genes are more likely to have high co-complex interaction degrees because larger protein complexes are more likely to be essential. Modular essentiality was the term used by these researchers to describe the observation that complete complexes appear to be essential. They also demonstrated that complexes typically consist of either essential or non-essential proteins rather than exhibiting a random distribution. However, this is not a one-size-fits-all phenomenon: Only about 26% of yeast complexes contain only essential or non-essential subunits. Fats are used as both energy sources and storage for energy that isn't needed right away in humans or many other animals. When burned or metabolized, a gram of fat produces approximately 9 food calories. Fats are also important sources of essential fatty acids, which are required in the diet. Vitamins A, D, E, and K can only be digested, absorbed, and transported in conjunction with fats because they are fat-soluble.