Domain-structured

J. C. Randall, ed., NMR and Macromolecules, Sequence, Dynamic, and Domain Structure, MCS Symposium Series, No. 247, American Chemical Society,... 

CA Orengo, AD Michie, S Jones, DT Jones, MB Swindells, JM Thornton. CATH—A hierarchic classification of protein domain structures. Stnrcture 5 1093-1108, 1997. 

Several motifs usually combine to form compact globular structures, which are called domains. In this book we will use the term tertiary structure as a common term both for the way motifs are arranged into domain structures and for the way a single polypeptide chain folds into one or several domains. In all cases examined so far it has been found that if there is significant amino acid sequence homology in two domains in different proteins, these domains have similar tertiary structures. 

Domains are formed by different combinations of secondary structure elements and motifs. The a helices and p strands of the motifs are adjacent to each other in the three-dimensional structure and connected by loop regions. Sequentially adjacent motifs, or motifs that are formed from consecutive regions of the primary structure of a polypeptide chain, are usually close together in the three-dimensional structure (Figure 2.20). Thus to a first approximation a polypeptide chain can be considered as a sequential arrangement of these simple motifs. The number of such combinations found in proteins is limited, and some combinations seem to be structurally favored. Thus similar domain structures frequently occur in different proteins with different functions and with completely different amino acid sequences. 

On the basis of simple considerations of connected motifs, Michael Leviff and Cyrus Chothia of the MRC Laboratory of Molecular Biology derived a taxonomy of protein structures and have classified domain structures into three main groups a domains, p domains, and a/p domains. In ct structures the core is built up exclusively from a helices (see Figure 2.9) in p structures the core comprises antiparallel p sheets and are usually two P sheets packed... 

The four-helix bundle is a common domain structure in a proteins... 

The most frequent of the domain structures are the alpha/beta (a/P) domains, which consist of a central parallel or mixed P sheet surrounded by a helices. All the glycolytic enzymes are a/p structures as are many other enzymes as well as proteins that bind and transport metabolites. In a/p domains, binding crevices are formed by loop regions. These regions do not contribute to the structural stability of the fold but participate in binding and catalytic action. 

The a/p-barrel structure is one of the largest and most regular of all domain structures, comprising about 250 amino acids. It has so far been found in more than 20 different proteins, with completely different amino acid sequences and different functions. They are all enzymes that are modeled on this common scaffold of eight parallel p strands surrounded by eight a helices. They all have their active sites in very similar positions, at the bottom of a funnel-shaped pocket created by the loops that connect the carboxy end of the p strands with the amino end of the a helices. The specific enzymatic activity is, in each case, determined by the lengths and amino acid sequences of these loop regions which do not contribute to the stability of the fold. 

Antiparallel beta (P) structures comprise the second large group of protein domain structures. Functionally, this group is the most diverse it includes enzymes, transport proteins, antibodies, cell surface proteins, and virus coat proteins. The cores of these domains are built up by p strands that can vary in number from four or five to over ten. The P strands are arranged in a predominantly antiparallel fashion and usually in such a way that they form two P sheets that are joined together and packed against each other. 

Figure S.12 Schematic diagram of the path of the polypeptide chain In one domain (the blue region in Figure 5.11) of the y-crystallln molecule. The domain structure is built up from two P sheets of four antiparallel p strands sheet 1 from p strands 1, 2, 4, and 7 and sheet 2 from strands 3, 5, 6, and 8.

A relevant question to ask at this stage is, do the topological identities displayed in the diagram reflect structural similarity We can now see that topologically the polypeptide chain is divided into four consecutive Greek key motifs arranged in two domains. How similar are the domain structures to each other, and how similar are the two motifs within each domain ... 

Figure 11.8 Topology diagrams of the domain structure of chymotrypsin. The chain is folded into a six-stranded antiparallel p barrel arranged as a Greek key motif followed by a hairpin motif.

The overall structure of the variable domain is very similar to that of the constant domain, hut there are nine p strands instead of seven. The two additional p strands are inserted into the loop region that connects p strands C and D (red in Figure 15.8). Functionally, this part of the polypeptide chain is important since it contains the hypervariahle region CDR2. The two extra p strands, called C and C", provide the framework that positions CDR2 close to the other two hypervariahle regions in the domain structure (Figure 15.8). 

For each of the 500 or so different domain structures that have so far been observed, we might at best know about a dozen of these different possible sequences. It is not trivial to recognize the general sequence patterns that are common to specific domain structures from such a limited knowledge base. 

Figure 3.8. Schematic representation of the polystyrene domain structure in styrene-butadiene-styrene triblock copolymers. (After Holden, Bishop and Legge )...

FIGURE 6.34 Sheet structures formed from andparallel arrangements of /3-strands, (a) Streptomyces suh i x Xu inhibitor, (b) glutathione reductase domain 3, and (c) the second domain of glyceraldehyde-3-phosphate dehydrogenase represent minimal andparallel /S-sheet domain structures. In each of these cases, an andparallel /S-sheet is largely exposed to solvent on one face and covered by helices and random coils on the other face. (Jane Richardson)... 

These interactions involve adhesion proteins called selectins, which are found both on the rolling leukocytes and on the endothelial cells of the vascular walls. Selectins have a characteristic domain structure, consisting of an N-terminal extracellular lectin domain, a single epidermal growth factor (EGR) domain, a series of two to nine short consensus repeat (SCR) domains, a single transmembrane segment, and a short cytoplasmic domain. Lectin domains, first characterized in plants, bind carbohydrates... 

A very special type of ABA block copolymer where A is a thermoplastic (e.g., styrene) and B an elastomer (e.g., butadiene) can have properties at ambient temperatures, such as a crosslinked rubber. Domain formations (which serves as a physical crosslinking and reinforcement sites) impart valuable features to block copolymers. They are thermoplastic, can be eaisly molded, and are soluble in common solvents. A domain structure can be shown as in Fig. 2. 

Figure 2 Schematic representation of the domain structure of styrene-butadiene-styrene block copolymer.

It turns out that, in the CML, the local temporal period-doubling yields spatial domain structures consisting of phase coherent sites. By domains, we mean physical regions of the lattice in which the sites are correlated both spatially and temporally. This correlation may consist either of an exact translation symmetry in which the values of all sites are equal or possibly some combined period-2 space and time symmetry. These coherent domains are separated by domain walls, or kinks, that are produced at sites whose initial amplitudes are close to unstable fixed points of = a, for some period-rr. Generally speaking, as the period of the local map... 

Whereas XRD patterns of the thin crystalline films provide information on the orientation and lattice distances perpendicular to the substrate, AFM has proven to be a powerful technique for obtaining structural information of thin-lilm surfaces of conjugated materials 195 j. AFM imaging of the surface of a thin (10 nm) annealed film of Ooct-OFV5 confirmed the domain structure of the annealed Ooct-... 

Adaptor Proteins. Figure 1 Adaptor protein domains. A scheme of the domain structures of some well-characterized adaptor proteins is shown. Descriptions of domain characteristics are in main text except C2, binds to phospholipids GTPase activating protein (GAP) domain, inactivates small GTPases such as Ras Hect domain, enzymatic domain of ubiquitin ligases and GUK domain, guanylate kinase domain. For clarity, not all domains contained within these proteins are shown. 

Calpains. Figure 1 Domain structures of calpain superfamily. Figure kindly provided by Dr. Hiroyuki Sorimachi, Laboratory of Biological Function, University of Tokyo, Japan. 

---