Ribonucleases conformational structure

The secondary and tertiary structures of myoglobin and ribonuclease A illustrate the importance of packing in tertiary structures. Secondary structures pack closely to one another and also intercalate with (insert between) extended polypeptide chains. If the sum of the van der Waals volumes of a protein s constituent amino acids is divided by the volume occupied by the protein, packing densities of 0.72 to 0.77 are typically obtained. This means that, even with close packing, approximately 25% of the total volume of a protein is not occupied by protein atoms. Nearly all of this space is in the form of very small cavities. Cavities the size of water molecules or larger do occasionally occur, but they make up only a small fraction of the total protein volume. It is likely that such cavities provide flexibility for proteins and facilitate conformation changes and a wide range of protein dynamics (discussed later). 

No large conformational changes occur in the enzyme during catalysis, but many small movements take place. The structural basis for the catalytic power of ribonuclease thus resides in several different features tight, specihc binding of a strained conformation of the substrate, general acid-base catalysis by His-12 and His-119, and preferential stabilization of the transition state by ionic interactions with Lys-41. 

The fact that a denatured protein can spontaneously return to its native conformation was demonstrated for the first time with ribonuclease, a digestive enzyme (see p. 266) consisting of 124 amino acids. In the native form (top right), there are extensive pleated sheet structures and three a helices. The eight cysteine residues of the protein are forming four disulfide bonds. Residues His-12, Lys-41 and His-119 (pink) are particularly important for catalysis. Together with additional amino acids, they form the enzyme s active center. 

For ribonuclease A the occurrence of conformational changes and the occurrence of acid-base catalysis has been well documented. The overall mechanism can be envisaged as follows. The enzyme exists in dynamic equilibrium between two forms differing in the structure of the active site groove. The substrate is bound almost as rapidly as it can diffuse to the active site. Binding of the substrate induces a conformational change that... 

In a more recent study using circular dichroism, Pflumm and Beychok (313) have fitted the observed curve for RNase-A (see Figs. 11c and d) weighted mixtures of the characteristic bands for helix from poly-L-glutamic acid and / structure from poly-L-lysine. The data are compatible with 11.5% helix and 33% / conformation. Ribonuclease-S and RNase-A have almost identical CD spectra from 198 to 300 nm. The spectrum of S-protein is markedly different from the other two. 

Fig. 9. The conformation adopted by a leucine-rich repeat (LRR) is that of a /9-strand followed by an o-helix. In porcine ribonuclease inhibitor, a /9-strand (residues 2-8) is connected to an o-helix (residues 14—27) by a connecting loop (residues 9-13). A horseshoe-shaped structure is formed and is exemplified in the crystal structure of ribonuclease inhibitor (PDB 1A4Y Kobe and Deisenhofer, 1993). This has an inner concave surface formed by curved /9-sheets and an outer convex surface formed by oh el ices. The leucines and other large apolar residues form the hydrophobic core of the structure.

Kostrewa, D., H.W. Choe, U. Heinemann, and W. Saenger. 1989. Crystal structure of guanosine-free ribonuclease T1, complexed with vanadate(V), suggests conformation change upon substrate binding. Biochemistry 28 7592-7600. 

Fig. 2. Temperature dependence of the partial specific heat capacity for pancreatic ribonuclease A (RNase), hen egg-white lysozyme (Lys), sperm whale myoglobin (Mb), and catalase from Thermus thermophilus (CTT). The flattened curves are for RNase and Lys with disrupted disulfide cross-links and for apomyoglobin, when polypeptide chains have a random coil conformation without noticeable residual structure (Privalov et al., 1988).

The procedures and calculations described in this chapter provide considerable insight into the factors affecting the conformations of polypeptides and proteins. The computer programs for gramicidin-S, oxytocin, vasopressin, etc., can also be used for larger structures—of the size of ribonuclease and lysozyme—although the required computer time is considerably increased. 

Ribonuclease, the enzyme that hydrolyzes ribonucleic acids (Chap. 7), contains four disulfide bonds that help to stabilize its conformation. In the presence of 6 M guanidine hydrochloride, to weaken hydrogen bonds and hydrophobic interactions, and 1 mM mercaptoethanol, to reduce the disulfide bonds, all enzymatic activity is lost, and there is no sign of residual secondary structure. On removing the guanidine hydrochloride by dialysis or gel filtration, enzymatic activity is restored, the native conformation is regained, and correct disulfide bonds are reformed. 

Many other examples of outwardly complex molecular structures, whose salient architectural features appear to self-assemble from their constituent building blocks, have been documented [16]. The formation of the DNA double helix from its constituent chains is perhaps the quintessential example, whilst the perfect reconstitution of the intact tobacco mosaic virus from its constituent RNA and protein monomers also exhibits all the hallmarks of a cooperative self-assembly process [17]. The same is true of ribonuclease. Reconstitution of this enzyme in the presence of mercaptoethanol, to allow reversible exchange of the four disulfide bridges, proceeds smoothly to generate eventually only the active conformation from many possible isomeric states [18], In each of these cases, the thermodynamic stability of the product is vital in directing its synthesis. These syntheses could therefore be termed product-directed. 

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