Subunit in protein

FIGURE 15.22. Assembly of subunits in proteins. Shown are two subunits of the enzyme D-xylose isomerase, forming a dimer by a one-armed embrace. (a) Line drawing connecting Co, carbon atoms, and (b) computer-generated view of the molecule with atoms with van der Waals radii on each Co, carbon atom. No side chains are shown in either diagram. In (a) one monomer is illustrated with black spheres, and the other with white spheres, in order to differentiate between them. (Courtesy H. L. Carrell)... 

Describes the arrangement of subunits in proteins with more than one polypeptide chain... 

Quaternary structure refers to the arrangement of chains (or subunits) in proteins. It is maintained by interactions between amino acids on the individual chains. 

Protein molecules that have only one chain are called monomeric proteins. But a fairly large number of proteins have a quaternary structure, which consists of several identical polypeptide chains (subunits) that associate into a multimeric molecule in a specific way. These subunits can function either independently of each other or cooperatively so that the function of one subunit is dependent on the functional state of other subunits. Other protein molecules are assembled from several different subunits with different functions for example, RNA polymerase from E. coli contains five different polypeptide chains. 

Steinbacher, S., et al. Crystal structure of P22 tailspike protein interdigitated subunits in a thermostable trimer. Science 265 383-386, 1994. 

Deisenhofer, J., et al. Structure of the protein subunits in the photosynthetic reaction center of Rhodopseudomonas viridis at 3 A resolution. Nature 318 618-624, 1985. 

Class 1 and class II MHC molecules bind peptide antigens and present them at the cell surface for interaction with receptors on T cells. The extracellular portion of these molecules consists of a peptide-binding domain formed by two helical regions on top of an eight-stranded antiparallel p sheet, separated from the membrane by two lower domains with immunoglobulin folds. These domains are differently disposed between the two protein subunits in class I and class II molecules. 

Figure 16.S Schematic illustration of the way the 60 protein subunits are arranged around the shell of safellite tobacco necrosis virus. Each subunit is shown as an asymmetric A. The view is along one of the threefold axes, as in Figure 16.3a. (a) Three subunifs are positioned on one triangular tile of an Icosahedron, in a similar way to that shown in 16.4a. The red lines represent a different way to divide the surface of the icosahedron into 60 asymmetric units. This representation will be used in the following diagrams because it is easier to see the symmetry relations when there are more than 60 subunits in the shells, (b) All subunits are shown on the surface of the virus, seen in the same orientation as 16.4a. The shell has been subdivided into 60 asymmetric units by the red lines. When the corners are joined to the center of the virus, the particle is divided into 60 triangular wedges, each comprising an asymmetric unit of the virus. In satellite tobacco necrosis virus each such unit contains one polypeptide chain...

Figure 16.6 A T = 3 icosahedral virus structure contains 180 subunits in its protein shell. Each asymmetric unit (one such unit is shown in thick lines) contains three protein subunits A, B, and C. The icosahedral structure is viewed along a threefold axis, the same view as in Figure 16.5. One asymmetric unit is shown in dark colors.

The asymmetric unit contains one copy each of the subunits VPl, VP2, VP3, and VP4. VP4 is buried inside the shell and does not reach the surface. The arrangement of VPl, VP2, and VP3 on the surface of the capsid is shown in Figure 16.12a. These three different polypeptide chains build up the virus shell in a way that is analogous to that of the three different conformations A, C, and B of the same polypeptide chain in tomato bushy stunt virus. The viral coat assembles from 12 compact aggregates, or pen tamers, which contain five of each of the coat proteins. The contours of the outward-facing surfaces of the subunits give to each pentamer the shape of a molecular mountain the VPl subunits, which correspond to the A subunits in T = 3 plant viruses, cluster at the peak of the mountain VP2 and VP3 alternate around the foot and VP4 provides the foundation. The amino termini of the five VP3 subunits of the pentamer intertwine around the fivefold axis in the interior of the virion to form a p stmcture that stabilizes the pentamer and in addition interacts with VP4. 

Role of the Amino Acid Sequence in Protein Structure Secondary Structure in Protein.s Protein Folding and Tertiary Structure Subunit Interaction.s and Quaternary Structure... 

FIGURE 10.37 Gap Juoctioos consist of hexameric arrays of cylindrical protein subunits in the plasma membrane. The subunit cylinders are tilted with respect to the axis running through the center of the gap Junction. A gap Junction between cells is formed when two hexameric arrays of subunits in separate cells contact each other and form a pore through which cellular contents may pass. Gap Junctions close by means of a twisting, sliding motion in which the subunits decrease their tilt with respect to the central axis. Closure of the gap Junction is Ca -dependent. 

Perhaps the most significant case of catalysis by RNA occurs in protein synthesis. Harry F. NoIIer and his colleagues have found that the peptidyl transferase reaction, which is the reaction of peptide bond formation during protein synthesis (Figure 14.24), can be catalyzed by 50S ribosomal subunits (see Chapter 12) from which virtually ail of the protein has been removed. These... 

FIGURE 15.9 Monod-Wyman-Changeux (MWC) model for allosteric transitions. Consider a dimeric protein that can exist in either of two conformational states, R or T. Each subunit in the dimer has a binding site for substrate S and an allosteric effector site, F. The promoters are symmetrically related to one another in the protein, and symmetry is conserved regardless of the conformational state of the protein. The different states of the protein, with or without bound ligand, are linked to one another through the various equilibria. Thus, the relative population of protein molecules in the R or T state is a function of these equilibria and the concentration of the various ligands, substrate (S), and effectors (which bind at f- or Fj ). As [S] is increased, the T/R equilibrium shifts in favor of an increased proportion of R-conformers in the total population (that is, more protein molecules in the R conformational state). 

A complete set of intermolecular potential functions has been developed for use in computer simulations of proteins in their native environment. Parameters have been reported for 25 peptide residues as well as the common neutral and charged terminal groups. The potential functions have the simple Coulomb plus Lennard-Jones form and are compatible with the widely used models for water, TIP4P, TIP3P and SPC. The parameters were obtained and tested primarily in conjunction with Monte Carlo statistical mechanics simulations of 36 pure organic liquids and numerous aqueous solutions of organic ions representative of subunits in the side chains and backbones of proteins... 

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