Protein structure and function

85262_largeProtein Structure and Function

Gregory Petsko & Dagmar Ringe

Oxford University Press, 2009

Keyword:  biochemical functions of proteins, enzyme proteins, resonance

This book is summarised simply as a useful recent text book on protein with no reference to consciousness. The summary is provided, because  of the indications, highlighted on the rest of this site, that the physical presence of consciousness in the brain is in some bound up with the mechanism of protein, which even in conventional research reveals itself as a quantum engine. This suggests that if we are to understand the physical basis of consciousness, we need to deepen our knowledge of the processes of protein.

The biochemical functions of proteins include binding, catalysis by means of enzyme proteins, molecular switches, and proteins serving as structural components. Proteins present diverse surfaces that facilitate interaction with other molecules. Many proteins maintain a fine balance between structural stability and the flexibility needed to perform their functions. The diversity of proteins derives from the chemical differences in the side chains of the constituent amino acids.

Proteins are formed out of 20 amino acids. The sequence of amino acids in a protein is governed by the sequence of the gene that codes for a particular protein. An amino acid is represented by a codon consisting of three nucleotides. This is known as its primary structure. The primary structure governs the type of secondary structure adopted by the protein which are mostly alpha helices or beta strands The backbone is the same for all amino acids comprising the amino group (NH2), the alpha carbon and the carboxylic acid group (COOH). These are repeating elements in a backbone from which 20 different side chains protrude, characterising the 20 different types of amino acid. The amino acids are held together in a polypeptide chain by peptide or amide bonds formed by a covalent bond between an amino group in one amino acid and a carboxylic acid in another one. Beyond this, alpha helices, beta strands and other protein elements can be folded into what is known as a tertiary structure. This folded configuration is seen as necessary for a polypeptide to function as a protein. Finally, many proteins are formed by the conjunction of folded chains from more than one polypeptide. The protein must be stable but at the same time not so rigid that it cannot perform its function.

Resonance:  The peptide bond is described as being responsible for some of the properties of polypeptide chains in water. The stability of the chain is due to a property called resonance. Resonance is the delocalisation of bonding electrons over more than one bond. This work to increase the stability of the bonding, and also increases the polarity or dipole moment of the bond. The peptide bond accounts for most of the covalent bonding within protein. Apart from this, protein is held together by weak polar or opposite charge interactions. The binding power of these interactions is only a fraction of that of a covalent bond, but this is compensated by the large number of such weak interactions in protein. The most important of such interaction are van der Waals forces and hydrogen bonds.

Van der Waals forces:  Van der Waals forces occur when fluctuating electron clouds, for instance those around a group of bonded atoms induce a fluctuating dipole of opposite polarisation on a neighbouring atom, to which they are not otherwise bonded. This type of bonding often occurs in the hydrophobic chains of proteins. Van der Waal forces are particularly weak, but the large number of such interactions in protein total to a substantial amount of energy.

Hydrogen bonds arise when a hydrogen atom is covalently bound to a more negative atom such as oxygen, leaving the hydrogen atom with positive charge that can attract it to a neighbouring negatively charged atom. The atom to which the hydrogen atom is covalently bound is called the donor atom and the non-bonded atom is called the acceptor atom.

Water is important in respect of hydrogen bonding. Water molecules can form hydrogen bond with one another, a property which is responsible for the liquidity of water at ambient temperatures. Hydrogen bonding is also important for the folding and stability of protein. Water molecules bond to polar (charged) groups in proteins influence the hydrogen bonds formed between the groups. Polar groups on the surface of a protein can interact with water molecules nearly as strongly as with other proteins. In a protein nearly all potential hydrogen bonds are taken up with other protein or water molecules. In the interior of proteins, remote from most water, hydrogen bonds are usually between proteins and can increase the structural stability of protein.

Side chains:  The different amino acids are characterised by their side chains having different interactions with other proteins and with water. Some side chains are hydrophobic meaning that they are non-polar or not electrically charges, and tend to avoid water, associate with one another and engage only in van der Waals interactions. This is the basis of the hydrophobic effect. Other side chains are hydrophilic. This means that they are polar (electrically charged) and interact both with water and with other hydrophilic chains. The hydrophilic chains can interact with one another and with water by means of hydrogen bonds between the opposite charges of dipoles molecules. A third category known as amphipathic can have both polar and non-polar properties.

Proteins often have a globular form with a tightly packed core of hydrophobic proteins. The backbone is formed into regular segments that constitute the secondary structure of the protein. There are three main types of such elements, alpha helix, beta (or pleated ) sheets and beta turns. Alpha helices and beta sheets comprise a network of hydrogen bonds. The beta turn causes the polypeptide chain to reverse direction and makes the folding of the protein possible. Beta turns are often on the surface of proteins and form hydrogen bonds with water molecules.

Alpha helices are the most common secondary element in protein. All the amide bonds except the first in the helix are hydrogen bonded to one another, resulting in a cylindrical structure formed by a hydrogen bonded backbone, while the outside of the cylinder is studded by side chains. The side chains govern the interaction of the helix with other protein. Alpha helices are common in proteins that span the membranes of cells. Individual peptide dipoles in the alpha helix can align to form a macrodipole. In this, the dipole moments of all the amide bonds are forced to point in the same direction, which is approximately parallel to the axis of the helix. This helix dipole contributes to the binding of charged molecules by proteins.

The beta sheet involves hydrogen bonds between two or more strands. There are three types of configuration, parallel where the strands run in the same direction, anti-parallel, where they run in opposite directions  and mixed sheets. A common feature in protein is where a sheet curves round  so that the ends create hydrogen bonds, and take on a barrel form. The interior of this barrel is lined with hydrophobic side chains. Some side chains are more suited to linking to beta sheets than to alpha helices.

The tertiary structure of a protein is governed by the sequence of amino acids which is encoded by a gene. The primary structure contains the information needed to specify th folded state. The compact nature of proteins is down to the hydrophobic effect, which is  driven by the clustering of hydrophobic side chains. The hydrophobic groups are brought close together, which allows van der Waals interactions to take place. The polar hydrophilic chains tend to cluster on the outside of the compact shape.

In folded protein, the secondary structure becomes compact and is stabilised by numerous weak interactions. The tertiary structure creates a complex surface shape that allows protein to interact with small molecules that may bind in clefts of with macromolecules with complementary surface regions.

Bound water – an integral part of protein:  Bound water molecules on the surface of folded protein are important to the function of protein. This water is more ordered than normal liquid water. Some polar groups on the surface of folded protein must remain in contact with water molecules. There is a layer of bound water on the surface of folded proteins. These form hydrogen bonds  with polar groups in both the backbone and side groups of the protein and with one another. There are several water molecules per amino acid. A few additional water molecules are trapped inside the protein. The authors say that the interaction between the bound water molecules and the protein means the water molecules should be regarded as part of the tertiary structure of the protein.

The packing of the protein secondary structures serves to bury hydrophobic side chains inside the protein, leaving very little empty space inside the protein. This structure is held together by van der Waals forces between non-polar groups and hydrogen bonds between polar groups. The effectiveness of these forces is enhanced by the close packing of the atoms in the protein. Despite this dense packing in the protein core, there remain cavities which can contain polar groups interacting with a few water molecules, or alternatively cavities hydrophobic chains and no water molecules.

Some proteins do not exist in a water environment, but are instead embedded in the hydrophobic interiors of lip bilayer membranes around cells and organelles. The inside of membranes is a non-polar environment and the side chains of transmembrane proteins are hydrophobic. Alpha helices are the most common secondary structure in membrane proteins.

The protein tertiary structure is maintained by the summing of many weak forces. The resulting folding structure is only marginally stable at ambient temperature. The energy released by the formation of many weak interactions is balanced by the loss of entropy when the protein folds into a more compact form. The dependence of protein on weak interactions means there is enough thermal energy in organism for weak interactions to break and reform.

Many proteins are globular, with polypeptide chains coiled up into compact shapes. Larger proteins usually fold into two or more globules or domains. Most domains have 200 amino acids or less. Domains have hydrophobic cores maximising the number of van der Waals interactions within the protein. The various folding patterns for protein can be seen as solutions to the same problem,which is how to maximise the exposure of hydrophilic groups to water, while minimising the exposure of hydrophobic groups. The creation of a hydrophobic core is often part of this solution.

A relatively limited number of ways of folding are used to create a much greater diversity of proteins. The same tertiary structure folds appear in many different types of proteins. Some ways of folding protein are particularly common. The four (alpha) helix bundle is common in oxygen and electron transport, while a structure called globin fold containing eight alpha helices allows the formation of hydrophobic pockets in domain interiors. Many proteins are assemblies of between two and six or more polypeptide chains. Protein assemblies composed of more than one polypeptide chain are oligomers and are known as dimers, trimers etc according to how may chains they have.

Complementarity:  Protein surfaces are irregular  This enables proteins to bind to specific ligands or other proteins and this also allows the formation of quaternary structures, where more than one polypeptide chain can come together in a protein complex. The fit between different protein surfaces involves the weak bonds that hold complexes together and hydrogen bonds. This property of complementarity is observed in all protein binding. Complementarity is necessary because of the many weak interactions involved. With alpha helices, hydrophobic side chains fit into spaces on an interacting helix. The weak bonds holding subunits together are the same as those involved in proteinprotein interfaces. Water molecules are more often involved at protein interfaces than in the interior of proteins, although some water molecules may become trapped in the interior of proteins. Thus protein complexes are built up through the interaction of complementary binding surfaces. Responses to the binding of another molecule to protein are important in protein function. The binding of a particular ligand can shift a protein from an inactive to an active state. Ligand binding can also change the quaternary structure of protein, usually by changing the relationship between subunits.

Ligand binding involves non-covalent interactions between ligands and the protein surface. These are the same type of bonds as those used within protein. Specific binding is a function of the shape and charge distribution of the protein surface, providing complementarity for the ligand. These are called ligand binding sites. These are a function of the 3-dimensional structure of the protein. When a polypeptide chain folds into a three dimensional structure it creates internal cavities and clefts and pockets on the surface. These regions can have micro-environments that are different from the rest of the protein, for example a hydrophobic environment. This can enable the binding of a hydrophobic ligand, such as a lipid, or in the case of a strong electrostatic field it could bind a calcium ion.

Many important ligands are small molecules, and cavities with micro-environments can facilitate the binding of these. The structural flexibility of protein can allow the ligand to diffuse through the protein.  Binding sites are usually at the interface between protein domains, if the protein has multiple domains. Ligand binding sites are usually characterised by a large amount of hydrophobic surface area. Smaller hydrophobic patches can be  involved in signal transduction involving kinases, phosphates and G-proteins.

A protein has around it at least one layer of bound water which should be considered as an integral part of the protein. This water is more ordered than normal liquid water. Proteins are also important as structures within the cell. Structural proteins can provide a framework for dynamic processes, such as the tracks along which proteins and protein complexes can be transported.  Complementary surfaces on repeating secondary structures such as alpha helices and beta strands provide one way of generating the large number of weak interactions needed to stabilise protein. In signalling within cells kinases, and phosphates can assemble on scaffold proteins that guide them and give them spatial organisation.

Enzymes:  The authors remark on the extraordinary efficiency of enzymes, which are mainly proteins. In free solution the reactions required by living organism would require tens of millions of years at ambient temperatures. Only high temperature life would be possible. The rate of reaction with enzymes is 10^17 times faster than in free solution. Even into modern times, it was considered possible that such some special feature lay behind the efficiency of enzymes, but this is now found to be a function of known properties such as the precise orientation of the ligand, weak interactions and polarised bonds. Van der Waals interactions with non-polar groups on the enzyme and charge distribution in the protein are involved.

It is remarked that the genomes of mammals are not much larger than those of plants, and that higher organism contain too few genes. It is becoming apparent that the short fall from the expected number of genes is made up by the regulatory function of proteins including enzymes. Enzymes can double as as signalling proteins or in protein synthesis. The precise location within the cell where a protein exercises its function is a major aspect of the regulation of function.

Regulation of protein:  The precise regulation is essential for the smooth functioning of protein, because of the very crowded packing of most proteins. So-called effector molecules can bind non-covalently and modify the conformational structure of the protein. Ligands may bind to sites remote from the active site and thus activate or inhibit a protein. Extracellular stimulus by a hormone or regulatory at molecule at very low concentrations can produce a major change in the activity of enzymes. Several regulatory influences may work on any one protein. Signalling pathways, such as protein kinases are under the control of several different mechanisms. Proteins that regulate cell function are often constructed from a number of small domains. Nearly all proteins appear to be constrained in some way by their position within complexes, organelles, vesicles, membranes etc.  The guidance of protein kinases is a good example of this, while phosphorylation modifies a cell for binding by other proteins at a specific site. Evidence suggests that even cell membranes are not random soups, but have patches known as lipid rafts  that target binding locations on proteins. Scaffold proteins are also important for regulation by binding several proteins at the same time to promote interaction. Molecular switches are a special set of proteins that control the ‘on’ and ‘off’ aspect of cellular activity, and are governed by the difference between the triphosphate and diphosphate form of a nucleotide. Most switches involve the protein GTPase or ATPase switching GTP into GDP or ATP similarly. 

Cooperativity:  Cooperativity is an important feature of protein. The binding of a single ligand molecule to a protein makes it easier or alternatively more difficult for a second or later molecule to bind. This applies to either to the activation or inhibition of a protein, and means that a much lower concentration of ligands is required than if this was not the case. Further to this, the binding of a small molecule to a protein surface can cause structural changes at a distance from the binding site. Because of the close packing of atoms in a globular sprotein, it means that small changes in side or main chains can cause conformational changes at different locations.

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