Conformational properties of enzymes

Transcription

1 Conformational properties of enzymes; Physics of enzyme substrate interactions; Electronic conformational interactions, cooperative properties of enzymes Mitesh Shrestha

2 Conformational properties of enzymes All proteins, and hence enzymes, are inherently flexible molecules due to the non-covalent nature of their folded 3D structure. While crystal structures make it convenient to think of a protein as existing in a single state, in reality a protein exists in a range of conformations often with relatively small energy differences between them. In enzymes the differences between these conformations can have important functional consequences. For instance, the conformation that can bind the substrate may be different from that required for catalysis to occur.

3 Conformational properties of enzymes The importance of conformational change in enzyme catalysis has long been appreciated. The classic example is the theory of induced fit, which proposes a general mechanism of substrate binding whereby an `open' form of the enzyme binds the substrate, and in doing so closes around the substrate into a `closed' form. Catalysis takes place in the closed form and the enzyme opens again to release the product.

4 Conformational properties of enzymes The observed conformational changes between states are categorized into four different types of motion: Loop motions: Movements of small (2 10 residues) segments of structure. Domain motions: Movements of protein domains, connected by a hinge region. Side chain rotation: Rotation of side chains which alters the position of the functional atoms of the side chain. Secondary structure change.

5 Allosteric Enzymes Allosteric enzymes are enzymes that change their conformational ensemble upon binding of an effector, which results in an apparent change in binding affinity at a different ligand binding site. This "action at a distance" through binding of one ligand affecting the binding of another at a distinctly different site, is the essence of the allosteric concept. Allostery plays a crucial role in many fundamental biological processes, including but not limited to cell signaling and the regulation of metabolism. Allosteric enzymes need not be oligomers as previously thought, and in fact many systems have demonstrated allostery within single enzymes. In biochemistry, allosteric regulation (or allosteric control) is the regulation of a protein by binding an effector molecule at a site other than the enzyme's active site. The site to which the effector binds is termed the allosteric site. Allosteric sites allow effectors to bind to the protein, often resulting in a conformational change involving protein dynamics. Effectors that enhance the protein's activity are referred to as allosteric activators, whereas those that decrease the protein's activity are called allosteric inhibitors.

6 Conformational properties of enzymes

7 Physics of enzyme substrate interactions When an enzyme binds its substrate, it forms an enzyme-substrate complex. This complex lowers the activation energy of the reaction and promotes its rapid progression by providing certain ions or chemical groups that actually form covalent bonds with molecules as a necessary step of the reaction process. Enzymes also promote chemical reactions by bringing substrates together in an optimal orientation, lining up the atoms and bonds of one molecule with the atoms and bonds of the other molecule. This can contort the substrate molecules and facilitate bond-breaking. The active site of an enzyme also creates an ideal environment, such as a slightly acidic or non-polar environment, for the reaction to occur. The enzyme will always return to its original state at the completion of the reaction. One of the important properties of enzymes is that they remain ultimately unchanged by the reactions they catalyze. After an enzyme is done catalyzing a reaction, it releases its products.

8 Electronic conformational interactions The electronic conformational interactions must be considered as the basic mechanisms of enzymatic activity. We have to distinguish between the oxidative-reductive enzymes which serve directly for the electron transfer (cytochromes, etc), and enzymes, acting as catalysts of chemical transformation of some substrates, i.e. the transfer of atoms. In the first case direct electron transfer occurs, changing for example, the charge of the iron atom of the heme group. In the second case the electron transfer does not occur but as the substrate molecule bound at the active site of enzyme produces a perturbing action at the atoms of this site, changes of their electronic states occur. It is actually a perturbation because the substrate is bound by weak interactions. As the same weak interactions are responsible for the potential surfaces of internal rotations, the change of interactions during the formation of the enzyme substrate complex (ESC) produces a change of conformation of the enzyme or of the substrate or of both of them.

9 Cooperative properties of enzymes Molecular binding is an interaction between molecules that results in a stable physical association between those molecules. Cooperative binding occurs in binding systems containing more than one type, or species, of molecule and in which one of the partners is not monovalent and can bind more than one molecule of the other species. For example, consider a system where one molecule of species A can bind two molecules of species B. Species A is called the receptor and species B is called the ligand. Binding can be considered "cooperative" if the binding of the first molecule of B to A changes the binding affinity of the second B molecule, making it more or less likely to bind. In other words, the binding of B molecules to the different sites on A do not constitute mutually independent events. Co operativity can be positive or negative. Cooperative binding is observed in many biopolymers, including proteins and nucleic acids. Cooperative binding has been shown to be the mechanism underlying a large range of biochemical and physiological processes.

10 Cooperative properties of enzymes Threonine deaminase was one of the first enzymes suggested to behave like hemoglobin and shown to bind ligands cooperatively. It was later shown to be a tetrameric protein. Another enzyme that has been suggested early to bind ligands cooperatively is aspartate trans-carbamoylase. Although initial models were consistent with four binding sites, its structure was later shown to be hexameric by William Lipscomb and colleagues.