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Learn more Check out. Citing Literature. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. In general, domains vary in length from between about 50 amino acids up to amino acids in length.
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Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin. Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimeric proteins. The concept of the domain was first proposed in by Wetlaufer after X-ray crystallographic studies of hen lysozyme  and papain  and by limited proteolysis studies of immunoglobulins.
In the past domains have been described as units of:. Each definition is valid and will often overlap, i. Nature often brings several domains together to form multidomain and multifunctional proteins with a vast number of possibilities. Domains can either serve as modules for building up large assemblies such as virus particles or muscle fibres, or can provide specific catalytic or binding sites as found in enzymes or regulatory proteins.
An appropriate example is pyruvate kinase see first figure , a glycolytic enzyme that plays an important role in regulating the flux from fructose-1,6-biphosphate to pyruvate. It is seen in many different enzyme families catalysing completely unrelated reactions. There is debate about the evolutionary origin of this domain. One study has suggested that a single ancestral enzyme could have diverged into several families,  while another suggests that a stable TIM-barrel structure has evolved through convergent evolution.
The TIM-barrel in pyruvate kinase is 'discontinuous', meaning that more than one segment of the polypeptide is required to form the domain. This is likely to be the result of the insertion of one domain into another during the protein's evolution. It has been shown from known structures that about a quarter of structural domains are discontinuous.
The primary structure string of amino acids of a protein ultimately encodes its uniquely folded three-dimensional 3D conformation. Generally proteins have a core of hydrophobic residues surrounded by a shell of hydrophilic residues. Since the peptide bonds themselves are polar they are neutralised by hydrogen bonding with each other when in the hydrophobic environment.
This gives rise to regions of the polypeptide that form regular 3D structural patterns called secondary structure. Some simple combinations of secondary structure elements have been found to frequently occur in protein structure and are referred to as supersecondary structure or motifs. Covalent association of two domains represents a functional and structural advantage since there is an increase in stability when compared with the same structures non-covalently associated. Structural alignment is an important tool for determining domains.
Several motifs pack together to form compact, local, semi-independent units called domains. Domains are the fundamental units of tertiary structure, each domain containing an individual hydrophobic core built from secondary structural units connected by loop regions. The packing of the polypeptide is usually much tighter in the interior than the exterior of the domain producing a solid-like core and a fluid-like surface.
Protein tertiary structure can be divided into four main classes based on the secondary structural content of the domain.
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Domains have limits on size. Larger domains, greater than residues, are likely to consist of multiple hydrophobic cores. Many proteins have a quaternary structure , which consists of several polypeptide chains that associate into an oligomeric molecule. Each polypeptide chain in such a protein is called a subunit. Domain swapping is a mechanism for forming oligomeric assemblies. Domain swapping can range from secondary structure elements to whole structural domains.
It also represents a model of evolution for functional adaptation by oligomerisation, e. Nature is a tinkerer and not an inventor ,  new sequences are adapted from pre-existing sequences rather than invented. Domains are the common material used by nature to generate new sequences; they can be thought of as genetically mobile units, referred to as 'modules'.
Often, the C and N termini of domains are close together in space, allowing them to easily be "slotted into" parent structures during the process of evolution. Many domain families are found in all three forms of life, Archaea , Bacteria and Eukarya. Examples can be found among extracellular proteins associated with clotting, fibrinolysis, complement, the extracellular matrix, cell surface adhesion molecules and cytokine receptors. Molecular evolution gives rise to families of related proteins with similar sequence and structure. However, sequence similarities can be extremely low between proteins that share the same structure.
Protein structures may be similar because proteins have diverged from a common ancestor. Alternatively, some folds may be more favored than others as they represent stable arrangements of secondary structures and some proteins may converge towards these folds over the course of evolution. All proteins should be classified to structural families to understand their evolutionary relationships.
Structural comparisons are best achieved at the domain level. For this reason many algorithms have been developed to automatically assign domains in proteins with known 3D structure; see ' Domain definition from structural co-ordinates '. The CATH domain database classifies domains into approximately fold families; ten of these folds are highly populated and are referred to as 'super-folds'. Super-folds are defined as folds for which there are at least three structures without significant sequence similarity. Many domains in eukaryotic multidomain proteins can be found as independent proteins in prokaryotes,  suggesting that domains in multidomain proteins have once existed as independent proteins.
Multidomain proteins are likely to have emerged from selective pressure during evolution to create new functions. Various proteins have diverged from common ancestors by different combinations and associations of domains. Modular units frequently move about, within and between biological systems through mechanisms of genetic shuffling:. The simplest multidomain organization seen in proteins is that of a single domain repeated in tandem. The giant 30, residue muscle protein titin comprises about fibronectin-III-type and Ig-type domains. Genetically engineered mutants of the chymotrypsin serine protease were shown to have some proteinase activity even though their active site residues were abolished and it has therefore been postulated that the duplication event enhanced the enzyme's activity.
Modules frequently display different connectivity relationships, as illustrated by the kinesins and ABC transporters. The kinesin motor domain can be at either end of a polypeptide chain that includes a coiled-coil region and a cargo domain. Not only do domains recombine, but there are many examples of a domain having been inserted into another.
Sequence or structural similarities to other domains demonstrate that homologues of inserted and parent domains can exist independently. An example is that of the 'fingers' inserted into the 'palm' domain within the polymerases of the Pol I family. An evolutionary domain will be limited to one or two connections between domains, whereas structural domains can have unlimited connections, within a given criterion of the existence of a common core.
Several structural domains could be assigned to an evolutionary domain.
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This superdomain is found in proteins in animals, plants and fungi. A key feature of the PTP-C2 superdomain is amino acid residue conservation in the domain interface. Many experimental folding studies have contributed much to our understanding, but the principles that govern protein folding are still based on those discovered in the very first studies of folding. Anfinsen showed that the native state of a protein is thermodynamically stable, the conformation being at a global minimum of its free energy.
Folding is a directed search of conformational space allowing the protein to fold on a biologically feasible time scale. The Levinthal paradox states that if an averaged sized protein would sample all possible conformations before finding the one with the lowest energy, the whole process would take billions of years. Therefore, the protein folding process must be directed some way through a specific folding pathway. The forces that direct this search are likely to be a combination of local and global influences whose effects are felt at various stages of the reaction.
Advances in experimental and theoretical studies have shown that folding can be viewed in terms of energy landscapes,   where folding kinetics is considered as a progressive organisation of an ensemble of partially folded structures through which a protein passes on its way to the folded structure. This has been described in terms of a folding funnel , in which an unfolded protein has a large number of conformational states available and there are fewer states available to the folded protein. As TF displays both chaperone and PPIase activity in vivo and in vitro [ 16 , 17 ], it has been the subject of considerable interest in co-production experiments — despite the fact that the majority of newly synthesised polypeptides do not require it for de novo folding [ 18 ].
Nevertheless, TF co-production led to a 4-fold increase in expression of an anti-digoxin Fab antibody fragment in the E. Similarly, a 3. TF co-production can also be synergistic with that of Hsp70 family members DnaK-DnaJ-GrpE, as observed in a temperature-dependent effect on guinea pig liver transglutaminase production [ 22 ] and vasostatin [ 23 ], which may be linked to TF's reported in vivo role in enhancing cell viability at low temperatures [ 24 ].
In an attempt to determine the mode of action of TF, mutants with very low PPIase activities were found to enhance soluble production of an adenylate kinase to the same extent as wildtype TF [ 25 ], indicating that the effect of TF on at least some recombinant proteins may be due to its chaperoning rather than isomerisation activity. The observation that human FKBP12, which has PPIase but no chaperone-like activity, did not improve expression of a thiosulfate sulfurtransferase enzyme that benefitted from co-production of an archaeal FKBP [ 26 ] provides additional evidence that many of the positive effects of PPIases in foreign protein production may relate to their chaperone-like rather than their isomerisation activity.
The h eat s hock p rotein 70 Hsp70 family of proteins are ubiquitous, highly conserved molecules whose predominant unifying feature is the ability to bind short, linear hydrophobic regions of polypeptides [ 27 , 28 ]. In addition to their role under heat stress, they assist in folding of newly translated polypeptides and subcellular trafficking of polypeptides under normal physiological conditions. Members of the family contain an ATPase domain and a more variable, peptide-binding domain and polypeptide binding and release is carried out in a cycle between an ATP-bound DnaK molecule with low substrate affinity and a high substrate affinity, ADP-bound state [ 29 ].
DnaK-DnaJ-GrpE chaperones are most commonly overproduced with cytoplasmic recombinant proteins, due to their own location in the cytoplasm. This approach has enabled the successful production of a number of proteins otherwise produced mainly or exclusively as inclusion bodies, such as a single-chain antibody fragment scFv; [ 33 ] , human tyrosine kinases Csk, Fyn and Lck [ 34 ], an Acinetobacter cyclohexanone monooxygenase [ 35 ], and a cedar pollen allergen [ 36 ].
This improved production is generally due to increased solubility of recombinant targets rather than an increase in cellular production levels, though Nishihara and co-workers [ 17 ] reported a decrease in total murine endostatin concomitant with increased levels of soluble protein upon DnaK-DnaJ-GrpE overproduction. It should, however, be noted that increased solubility is not always accompanied by an increase in protein quality and so determination of solubility may not always provide an accurate picture of correct folding, as reported in a study of the effects of DnaK levels on a misfolding-prone GFP fusion protein [ 41 , 42 ].
Conversely, DnaK-DnaJ have little effect on the solubility and negative effects on the production and activity of numerous proline-rich targets [ 17 , 39 , 43 ], which emphasises the benefits of attempting to "match" chaperones to hypothetical bottlenecks in target protein production. Other workers have reported that protein aggregation could be prevented when DnaK-DnaJ-GrpE were co-expressed at 2—3 times wild type levels but that higher chaperone concentrations resulted in a reduced yield of recombinant protein [ 36 ].
These results highlight a recurring theme in this field, that chaperone overproduction must be regulated to meet the additional needs of the host cells, rather than serving to add to cellular stress through the high-level production of an irrelevant protein product [ 44 ]. The relatively recent availability, both commercial and non-commercial, of sets of E.
The successes reported with a variety of molecules from combining chaperones in this manner [ 17 , 44 — 47 ] and the ease of carrying out such broad screens means this type of approach will continue to provide an obvious starting point for researchers looking to improve expression of otherwise intransigent proteins. Hsp70 co-production has also been employed to beneficial effect with heterologous proteins produced in the E.
A fold increase in the yield of a scFv antibody fragment was observed upon co-producing DnaK-DnaJ-GrpE [ 48 ], while export of human granulocyte-colony stimulating factor [ 49 ], granulocyte-macrophage colony-stimulating factor and interleukin [ 50 ] were greatly improved upon production of DnaK and DnaJ. In all cases, the amount of total cellular protein remained unchanged. A variation on this approach saw export of DnaJ itself to the E. GroEL is characterised by a fascinating double ring-shaped structure composed of 14 identical subunits, stacked in 2 back to back heptameric rings, which together form a hollow cylinder containing a nucleotide binding site facing into the central channel [ 52 ].
GroEL acts by binding unfolded polypeptide at either of the outer ends of its inner cavity through hydrophobic interactions [ 53 , 54 ]. This is followed by capping of the cavity by its Hsp10 family co-chaperonin GroES, which exists as a single heptameric ring with a hollow dome-shape structure [ 55 ] to create a closed environment, with a capacity of approximately 86 kDa [ 56 ], in which substrate folding is favoured. Cycles of peptide binding and release are driven by ATP binding and hydrolysis, promoting a structural stretching of the guest protein until a sufficiently native state is reached such that exposed hydrophobic regions are no longer available to be bound in the GroEL cavity [ 57 ].
The demonstration that GroESL mediated folding of an kDa aconitase protein that could not be encapsulated in the central GroEL cavity led more recently to the identification of a less efficient trans mechanism of polypeptide folding by GroEL, in which polypeptides are not encapsulated and the chaperone appears to act more as a holdase, suppressing off-pathway aggregation reactions, than as a foldase [ 58 ]; reviewed in [ 59 ]. Overproduction of GroESL has proven a highly productive approach to overcoming polypeptide folding problems in E.
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A sample of proteins whose total or functional yield in the E. In spite of this impressive track record and the fact that GroEL has been demonstrated to support the folding of a majority of newly translated polypeptides in E. There are numerous reports of GroESL failing to improve protein solubility [ ] or rescue recombinant proteins from inclusion bodies [ ], even where co-production of Hsp70 family members was successful [ 22 , 37 , 48 ].
Overproduction of GroESL has also been found to lead to reduced enzyme activity [ 21 ] and lower viability of host cells during protein production [ 48 ]. These failings may reflect a degree of polypeptide specificity on the part of GroESL, as potentially evident in its differing effects on the expression of two human aromatase variants that differ only by a single amino acid residue [ 94 ].
Similarly, as discussed above with Hsp70 family members, GroESL overproduction has notably failed to improve the production of proteins with complex disulfide patterns [ 38 , , ] or in which peptidyl-prolyl cis - trans isomerisation is limiting [ ] as the production bottleneck in such cases presumably lies outwith the remit of its chaperoning role.
Combining GroESL with DnaK-DnaJ-GrpE has proven significantly less fruitful, with numerous examples of losses up to total of positive effects on solubility or activity upon addition of the second chaperone family to the experimental setup [ 21 , 33 , 48 , ]. As these multi-chaperone experiments usually have the singular objective of increasing target protein yields, however, they typically lack the detailed mechanistic studies necessary to delineate the effects of individual chaperones.
While some success has resulted from co-producing chaperones such as DnaK with periplasm-destined recombinant proteins, comparably little success has accrued with GroES and GroEL. Thus it appears that, while GroESL overproduction represents a prime choice for investigation of folding defects of recombinant proteins expressed in the cytoplasm, it is typically unable to overcome bottlenecks associated with periplasmic production. Recombinant production of membrane proteins in E. There are few reports of co-production of molecular chaperones with membrane proteins in E.
Amongst these, the expression and solubility of the HrcA repressor from Helicobacter pylori were dramatically increased upon induction of heat shock proteins by elevated temperature [ ] while overexpression of GroESL led to significantly improved expression of the human liver cytochrome P 2B6 [ ] and a DnaK-DnaJ combination reduced inclusion body formation by the CorA bacterial magnesium transporter [ 66 ].
While the present body of literature does not make a particularly compelling case for adding chaperones to membrane protein production experiments in E. Small heat shock proteins sHsps are a ubiquitous group of proteins that tend to exist in vivo as macromolecular complexes, the stoichiometry of which varies between different sHsps reviewed in [ ].
They bind non-native proteins with a high degree of promiscuity in an ATP-independent manner and their slowness of substrate release has led to speculation that they may function primarily as reservoirs of unfolded protein in times of stress. It is also likely that, upon removal of the physiological stress, they interact with other chaperones such as the Hsp70 group, leading to peptide release and ATP-dependent folding [ , ].
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Their native activity has led to some interest recently in their potential usefulness in increasing the solubility of heterologous proteins in E. Overproduction of IbpAB led to increased production of E. Co-production of hexadecameric murine Hsp25, meanwhile, fused to an ompA signal peptide, increased the amount of functional tPA variant in the E.
In their approach, protein production and chaperone co-production was followed by a period of inhibition of protein synthesis to allow chaperone-mediated refolding of misfolded or aggregated polypeptides. The overall effect of co-overproduction of IbpAB was an increase in the solubility of 20 of 23 proteins tested, including 12 that could not be produced in soluble form in the absence of IbpAB [ 47 ].
One of the most common of these is thioredoxin Trx , as discussed later in the context of disulfide bond metabolism. ClpB, meanwhile, is a large, star-shaped hexameric molecule that interacts with the DnaK chaperone system in a currently unresolved manner to disaggregate insoluble polypeptide aggregates reviewed in [ ].
This potential is borne out by the observation that, while various combinations of Hsp60 and Hsp70 proteins could dissolve macromolecular aggregates of human basic fibroblast growth factor, this typically was not concomitant with increased solubility of the target unless ClpB was also overproduced [ 44 ]. Overproduction of tRNA molecules specific for E. A further approach to chaperoning heterologous proteins in E.
Proteins destined for the non-reducing environment of the periplasm are most commonly secreted using the Sec sec retion family [ ]. Cytosolic SecB associates with unfolded proteins in an ATP-independent manner and delivers them to SecA, the site of preprotein entry into the membrane-bound translocase [ , ]. Translocation is achieved through the SecEY complex, which forms a pore through which the preprotein passes [ , ], and involves the action of SecG, which "lubricates" the pore for insertion of a SecA domain [ , ] and SecD and SecF, which prevent reverse translocation of the preprotein [ ].
In addition to the sec pathway, a less well characterised twin-arginine translocation tat pathway of membrane translocation also exists [ ]. The essential components of this pathway are the TatA, TatB and TatC integral membrane proteins, which recognise a critical twin arginine motif in the N-terminal signal sequence of polypeptide substrates.
Unlike the sec system, the Tat pathway can transport proteins across the cytoplasmic membrane in a fully folded state Figure 2 ; [ , ]. Furthermore, two distinct systems, the first employing a homologue of the eukaryotic signal recognition particle called the f ifty- f our h omologue Ffh; [ ] and its FtsY receptor and the second the kDa cytoplasmic protein YidC [ ], are involved primarily in targeting integral membrane pre proteins to the inner membrane in E.
The possible membrane translocation routes of recombinant polypeptides, and their subsequent folding in the periplasm, are represented in Figure 2. Membrane translocation and periplasmic folding in E. Most polypeptides cross the cytoplasmic membrane in an unfolded conformation using the Sec translocase 1 , following delivery to SecA at the inner surface of the membrane by DnaK or SecB chaperones. Polypeptides with highly hydrophobic signal sequences or transmembrane domains may, however, be recognised by Ffh which, together with its FtsY receptor, can target the polypeptide to either the Sec machinery or to the YidC translocase 2.
Alternatively, the twin-arginine translocation Tat machinery is responsible for the translocation of already folded proteins 3 , typically with bound metal cofactors. While manipulation of the Sec pathway initially concentrated largely on the SecEY tranlocase, the disappointing results led to most studies focussing instead on the SecA and SecB proteins that deliver polypeptides to the translocase. Even then, results remained unspectacular: SecB overproduction resulted in increased solubility and a higher yield of a penicillin acylase, though enzyme activity was not increased [ ], while SecB and SecF overproduction led to 3- and 2-fold increases, respectively, in the periplasmic activity of a penicillin amidase [ ].
Comparatively little analysis of tat gene overexpression has been carried out, though overexpression of tatABC , in combination with manipulation of physiological conditions, led to a fold increase in the level of a green fluorescent protein that otherwise rapidly saturates the tat translocation machinery [ ]. Co-expression of phage shock protein A PspA can also relieve saturation of protein export via this pathway [ ] while Han and co-workers [ ] demonstrated that knocking out the sHsps IbpA and IbpB led to enhanced secretion of enhanced green fluorescent protein EGFP from Aequorea victoria via both the sec and tat secretion pathways.
The recent demonstration that DnaK and SlyD chaperones serve as general Tat signal-binding proteins [ , ], in tandem with the promising outcomes of the limited investigation of the pathway to date, is likely to focus increased attention on using the tat machinery to improve periplasmic expression over the coming years. Overall, while E. Instead, the bottleneck for production is usually more likely to involve maintenance of polypeptides in a non-aggregated, translocation-competent form in the cytoplasm or in avoidance of aggregation in the periplasm subsequent to membrane translocation.
Following membrane translocation, folding of the heterologous polypeptide takes place in the periplasmic space Figure 2. While disulfide bond formation and peptidyl-prolyl cis - trans isomerisation can occur here, no general molecular chaperones that prevent non-productive folding reactions had been identified until relatively recently, when a variety of molecules such as Skp, FkpA, SurA and DegP were independently isolated and characterised. Skp is an E.
Skp co-production led to delayed cell lysis and improved production of single-chain antibody fragments scAbs; [ ] , higher yields and increased antigen binding activity of scFvs [ ], improved functional production of phage-displayed scFvs [ ] and improved production and secretion of a Fab fragment [ ].
Meanwhile, a signal sequence-less Skp has also been used to increase the yield of active Fab fragment in the cytoplasm of an E. Skp co-production has also been utilised, in combination with protein engineering, to achieve high-level secretion of three single-chain T cell receptors [ ], which, though structurally similar to antibody fragments, have traditionally proven difficult to produce in active form in E. Skp has been also found to enhance the E.
It is active in the same pathway as Skp, with SurA active in a parallel chaperone pathway. DegP overproduction has been found to reduce inclusion body formation in the periplasm and to increase the activity of penicillin acylase in E. Formation of stable disulfide bonds is confined to the oxidising periplasmic environment in E. DsbA catalyses disulfide bond formation by transferring its own active site disulfide to the target protein, leaving DsbA in a reduced form, whereupon it is reoxidised by the cytoplasmic membrane-bound DsbB.
DsbB in turn passes its electrons to the respiratory chain to regenerate its own oxidised state. Other Dsb proteins in E.