Structured proteins and proteins with internal disorder

The point of view that a uniquely folded protein tertiary structure is required for the protein functioning has been prevailing in the literature quite recently. However of lately it has been found that many proteins in a cell have no such structure in an isolated state, though they have a well-defined function in physiological conditions. These proteins were named as proteins with natural or internal disorder. The portion of disordered regions in such proteins may vary from a sequence of several amino acids to a completely disordered sequence containing from tens to hundreds of amino acids. The main difference of these proteins from the structured (globular) ones is that they have no unique tertiary structure in an isolated state and acquire it after interaction with their partners. Their conformation in such a complex depends on the interacting partner and not only on their own amino acid sequence, which is specific for structured (globular) proteins. The problem of structural and functional relations in the structured proteins and proteins with internal disorder is discussed in this review. The complexity of the problem and its potential solutions are illustrated by the example of elongation factors EFlA.     

Structured proteins and proteins with intrinsic disorder

Until recently, the point of view that the unique tertiary structure is necessary for protein function has prevailed. However, recent data have demonstrated that many cell proteins do not possess such structure in isolation, although displaying a distinct function under physiological conditions. These proteins were named the naturally, or intrinsically, disordered proteins. The fraction of intrinsically disordered regions in such proteins may vary from several amino acid residues to a completely unordered sequence of several tens or even several hundreds of residues. The main distinction of these proteins from structured (globular) proteins is that they have no unique tertiary structure in isolation and acquire it only upon interaction with their partners. The conformation of these proteins in a complex is determined not only by their own amino acid sequence (as is typical of structured, or globular, proteins) but also by the interacting partner. This review discusses the structure-function relationships in structured and intrinsically disordered proteins. The intricateness of this problem and the possible ways to solve it are illustrated by the example of the EF1A elongation factor family.     

Tethering of proteins to RNAs by bacteriophage proteins

Many steps in the control of gene expression are dependent on RNA-binding proteins, most of which are bi-functional, in as much as they both bind to RNA and interact with other protein partners in a functional complex. A powerful approach to study the functional properties of these proteins in vivo, independently of their RNA-binding ability, is to attach or tether them to specifically engineered reporter mRNAs whose fate can be easily followed. Two tethering systems have been mainly used in eukaryotic cells, namely the MS2 coat protein system and the lambda N-B box system. In this review, we firstly describe several studies in which these tethering systems have been used and provide an overview of these applications. We next describe the major features of these two systems, and, finally, we highlight a number of points that should be considered when designing experiments using this approach.     

Docking proteins

Docking proteins comprise a distinct category of intracellular, noncatalytic signalling protein, that function downstream of a variety of receptor and receptor-associated tyrosine kinases and regulate diverse physiological and pathological processes. The growth factor receptor bound 2-associated binder/Daughter of Sevenless, insulin receptor substrate, fibroblast growth factor receptor substrate 2 and downstream of tyrosine kinases protein families fall into this category. This minireview focuses on the structure, function and regulation of these proteins.     

Membrane-bending proteins

Cellular membranes can assume a number of highly dynamic shapes. Many cellular processes also require transient membrane deformations. Membrane shape is determined by the complex interactions of proteins and lipids. A number of families of proteins that directly bend membranes have been identified. Most associate transiently with membranes and deform them. These proteins work by one or more of three types of mechanisms. First, some bend membranes by inserting amphipathic domains into one of the leaflets of the bilayer; increasing the area of only one leaflet causes the membrane to bend. Second, some proteins form a rigid scaffold that deforms the underlying membrane or stabilizes an already bent membrane. Third, some proteins may deform membranes by clustering lipids or by affecting lipid ordering in membranes. Still other proteins may use novel but poorly understood mechanisms. In this review, we summarize what is known about how different families of proteins bend membranes.     

Glycolipid-binding proteins

Proteins which bind glycolipids with high specificity are tentatively divided into two groups. One group consists of activator proteins involved in the catabolism of glycolipids by acid lysosomal hydrolases. Two activator proteins, GM2-activator and sphingolipid activator protein-1, are critically appraised on their glycolipid-binding properties and on their activity to facilitate the transfer of glycolipids. These proteins are glycoproteins localized in the lysosomes. Their molecular weights are in a range of 21 000-27 000, and isoelectric points are 4-5. Glycolipid transfer protein (GLTP) is included in the other group. GLTP purified from pig brain has a molecular weight of about 20 000 and an isoelectric point of 8.3. GLTP facilitates the transfer of various glycosphingolipids and glyceroglycolipids between membranes. The protein does not facilitate the transfer of phospholipids or cholesterol. GLTP binds galactosylceramide. The galactosylceramide-GLTP complex participates in the transfer reaction as the intermediate. Each protein in both groups binds glycolipids with a characteristic specificity to the sugar moiety. A stoichiometry of 1 mol of lipid per mol of protein has been found in all three proteins. Proteins in both groups seem to have a hydrophobic region on their surface, since all three proteins have been efficiently purified by hydrophobic chromatography.     

Antifreeze proteins

Antifreeze proteins comprise a structurally diverse class of proteins that inhibit the growth of ice. Recently, new AFP types have been discovered; more active AFPs have been isolated; antecedents have been recognized supporting the notion of recent, multiple origins; and detailed structures have emerged leading to models for their adsorption to ice     

Stomatin-domain proteins

The stomatin-domain defines a family of proteins that are found in all classes of life. The ubiquity of stomatin-family proteins and their high degree of homology suggest that they have a unifying cellular function, which has yet to be defined. The five stomatin family proteins in mammals show varying expression patterns and different sub-cellular distributions. In surveying the relevant literature, three common themes emerge; stomatin family members are oligomeric; they mostly localise to membrane domains; and in many cases, they have been shown to modulate ion channel activity. How oligomerisation and membrane localisation contribute to the modulation of channel function is unclear to date. Future studies into the precise structure and mechanism of stomatin-like proteins need to address these important questions to clarify the detailed cellular function of stomatin-domain containing proteins.     

Biofilm-associated proteins

Although exopolysaccharides are important and often essential compounds of the biofilm matrix, recent evidences suggest that a group of surface proteins plays a leading role during the development of the microbial communities. The first member of this group of proteins was described in a Staphylococcus aureus bovine mastitis isolate and was named Bap, for biofilm-associated protein. Later on, other surface proteins homologous to Bap and involved in biofilm development have been described in many gram-positive and gram-negative bacteria. In this review, we have summarized our knowledge about three members of this group of proteins: Bap of S. aureus, Esp of Enterococcus faecalis and BapA of Salmonella enterica ser. Enteritidis.