Protein Structure
Carboxypeptidase A
Alpha Chymotrypsin
Ribonuclease A
Receptor Sites
Double-Helix B-DNA


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In addition to sites in proteins which bind specific substrate molecules to perform catalytic reactions, proteins also contain receptor sites which, when occupied by specific “regulator” molecules, alter protein shapes and permit them to form functional complexes with other proteins and substrate molecules. When regulator molecules leave those binding sites, water must move in and kinetically bond together as covalent units to bridge between polar atoms before the sites return to their inactive resting states. Once again, water is dynamic – covalently hydrogen-bonded linear elements form and exchange rapidly with surface water.

Glycogen Phosphorylase – An ATP/AMP Binding Site 

One of the first receptor proteins to be analyzed in detail was an enzyme which cleaves glucose molecules from the ends of polymeric glycogen (starch) molecules in the liver.58 Like the two enzymes analyzed above, this one is soluble in water but, unlike those, it requires either adenosine monophosphate (AMP) or adenosine triphosphate (ATP) to occupy a receptor binding site to hold the protein in the proper conformation to activate the reaction site.

Adenosine monophosphate and adenosine triphosphate in the binding site of a glycogen phosphorylase enzyme.

As shown above, binding within the site is provided by amine and amide peptides in coils above and below and amine and amide peptides on the left and right. Note that only slight changes in conformation of the binding groups are required to bind these two different nucleotides but that the ribose ring of ATP must rotate clockwise to permit binding.  Although an hexagonal lattice of water molecules is shown in the site, only short linear segments span between the binding atoms at any instant. Once regulator molecules leave, binding groups most likely move closer together in a less-hydrated, inactive resting state.

Membranal Receptor Sites

Before we consider additional receptor sites, it is important to realize that many of them are in proteins which pass through cell membranes. Most of them are composed of helical coils which are adjacent to the fatty acid chains of alpha-state phospholipids which dynamically kink back and forth in quantized fashion in the lipid zone of the membrane.59 The phosphate head groups provide a variety of hydrogen-bonding relationships with surface water.60 In fact, many membranes are composed of 1/1 phospholipid/cholesterol complexes with flat cholesterol molecules (as shown) rotating around their axes to keep the fatty-acid chains in their high-energy alpha  kinked-motion state.59

Polypeptide coils forming a pore through an alpha-state cholesterol/lecithin biomembrane.

In spite of the high internal energy, the bilayer lipid zone has a relatively constant width of about 40.5 Angstroms.  This is an important “harmonic” distance because it corresponds with the length of 19 linearly hydrogen-bonded water molecules (4.5A x 9) and 27 peptides in a tight helical coil (1.5A x 27).20,61,  Although very few water molecules are present in pores when they are closed, when they open, water molecules must span the space to coordinate passage of protons or specific ions in and out of the cell.  Of course, most membranal proteins are far more complex than the tetramer shown above.

Signal Transduction Protein and a Transport Protein passing through a cholesterol/lecithin biomembrane.

In fact, most of them are composed of at least seven helical coils which assemble in the same fashion as the enzymes described above outside the membrane and rotate their coils on entering the membrane or they are inserted directly into the membrane from the ribosome.  Often, they are composed of several identical or similar units which combine within the membrane to form functional assemblies. Usually, regulator binding sites, as shown above, are near the outer surface of the cell.62 

There are two basic types of membranal receptor proteins: those which bind regulator molecules on the outside of one or more coils to change the orientation of one or more coils inside and those which bind near the outside to open pores for ions and molecules to pass in or out of the cell. Movement of signal transduction coils inside the cell alters the binding with enzymatic proteins and activates functions inside.  On the other hand, the binding of acetyl choline to sites on both sides of a transport pore, turns two coils, opens the pore and permits sodium ions to enter nerve cells and initiate depolarization and pulse conduction.63 Now we look at the structures of a number of neurotransmitter and hormone molecules.20,64

Neurotransmitters and Steroidal Hormones

After viewing the intimate role transient linear hydration plays in the assembly and function of proteins, it should come as no surprise that the dimensions of natural molecules which bind to receptor sites and activate functions are similar to those of ordered elements of water molecules.

Six major regulator molecules mimic the dimensions of linear hydrogen-bonded elements of water molecules.

As you can see, all of these molecules which bind in activating sites on outer surfaces of membranal receptor proteins have polar oxygen or nitrogen atoms in positions of water molecules in linearly-ordered elements. Some of them, like acetyl choline and histamine, are neurotransmitters which are released from nerve endings to open sodium ion pores in nerve and muscle cells. Others, like serotonin and adrenaline, by altering coil positions in membranal transduction proteins, activate enzymes to carry out reactions inside the cells.

Linear elements of hydration bridge between binding groups in steroidal hormone receptor binding sites.

Although cholesterol is an important component of membrane, enzymatic removal of its tail produces a large number of steroidal hormones with polar atoms on both ends which mimic linear elements of six or seven water molecules. In contrast with most of the neurotransmitters shown above, these hormones are produced in specific endocrine organs and released into the blood stream. They are transported into cells to regulate protein production. A more detailed look at steroidal hormones will be included later.

The insulin molecule mimics cubic hydration water in order to displace ordered water in binding sites.

Insulin, which was discussed in detail earlier, is representative of a more complex class of polypeptide hormones which are released from ribosomes as linear elements and spontaneously fold to produce hormones with receptor-binding properties. Each one has spatial features of cubic water so they, like those shown above, can bind to receptor proteins in spaces which are occupied by ordered water when the regulator molecules are not present. Now we will look at a few receptor sites in membranal proteins.


Bacterial D-Aspartic Acid

One of the first transduction proteins to be isolated and the binding site deciphered was a receptor protein from a bacterium which binds D-aspartic acid.65 This D amino acid is not present in most organisms but is common in bacteria.

Water fills the receptor binding site of a bacterial protein before being displaced by D-Aspartic Acid.

The aspartate binding site is on the outer surface of the membrane between four helical polypeptide segments which pass through the membrane. The binding site is formed by five peptides: two anionic tyrosines, two cationic arginines and a threonine. The phenol ring of the upper tyrosine peptide is directed downward into the membrane with its carbonyl oxygen above.  The other tyrosine holds the lower arginine in a precise position to bind the aspartate molecule.

Since D-aspartic acid exists in aqueous solution as an anion with a net negative charge, it is attracted to the binding site by the two positively-charged arginines on the upper surface. Most likely, the site is hydrated in its resting state, as shown above, by five water molecules which simply bridge across as transient linear elements between the polar atoms. Remember, the site is not static - water molecules continually move in and out in kinetic quantized fashion and occupy a variety of positions. Those shown are simply high probability positions based on minimal hydration.

As the D-aspartate molecule enters, it pulls the right-hand arginine one water unit toward the center, rotating the coil anticlockwise to bind and activate an enzyme inside the cell.  Note that two water molecules remain in the activated site. As aspartate leaves, the site hydrates and then returns to its more hydrated resting state.

Human Dopamine

The third receptor site to be examined was reported by Chien and coworkers in 2010.66 Like many receptor proteins being examined today, this one required the use of a large antagonist molecule, Eticolpride, to hold the site in an inactive resting-state conformation and several point mutations in the protein to obtain an interpretably X-ray diffraction pattern.

Human Dopamine receptor binding site with the antagonist Eticlopride in the site.

Only the critical binding groups (aspartate D, histadine H, serine S and tryptophane W) are included in the illustrations.  As you can see, the Eticlopride molecule effectively fills the site leaving little or no room for water. In fact, the molecule fills the site so completely that the hydroxyl group of serine is forced away from the binding molecule next to the chlorine atom.  In the absence of the blocking molecule, transient triplets of water molecules bridge between the binding peptides. The aspartate carboxyl, D, faces the back coil. 

As the dopamine agonist molecule moves into the open site, helical coil V, which passes vertically through the membrane, rotates clockwise to permit histadine and serine to bind to the phenolic oxygens of dopamine while permitting its cationic nitrogen to bond with the anionic aspartate between the coils.  In this case, hydration involves the same number of water molecules in both the resting and activated states. Just as the activation of the aspartate receptor protein involved a slight turn of a coil, activation of this dopamine receptor appears to involve the same type of transduction mechanism.


One of the most important receptor proteins in nerve and muscle cells, employs the small acetylcholine molecule as its agonist.67 The cholinergic system involves a number of different receptor proteins with a number of different binding sites but the one which has received the most attention was isolated from the Torpedo electric eel and studied in detail by Professor Nigel Unwin and his coworkers.68

The acetyl choline molecule is responsible for regulating many physiological functions in animals.

Like the previous receptor proteins, this one also passes through the membrane but, unlike those, this one involves two identical binding sites on opposite sides of a pore which open on activation of both sites to permit sodium ions to enter nerve and muscle cells.  Since acetylcholine plays a vital role in muscle contraction, blocking agents, like curare, have been used for centuries by natives on the tips of darts and arrows to paralyze animals.

The receptor binding site of a cholinergic receptor protein with the acetyl choline molecule bound in the site.

Mechanical operation of the binding site is quite amazing and complex. In the occupied activated-state, the site is dehydrated with a positively-charged acetycholine molecule holding two cysteine sulfides in perfect position to neutralize the charge. On leaving the site, water molecules enter as crossed triplets to bridge between the polar atoms but the site quickly hydrates and opens wide with the cysteine-cysteine loop dropping down on the right.

This moves polypeptide chains on both sides of the protein, rotates trans-membrane coils attached to the ends of the chains and closes a pore which admits sodium ions into a nerve or muscle cell. As you can see, acetylcholine activation involves a dramatic decrease in hydration and an increase in local hydration entropy.  Activation is unique in that it involves no formal hydrogen bonds between the agonist molecule and the binding site – the molecule appears to be suspended in the site.


Although the position of the curare molecule in the binding site has not been reported, it has a structure which conforms so uniquely to positions of binding groups in the open state that an attempt has been made to derive a binding model.  As can be seen below, the curare molecule is extremely large compared to acetylcholine and has two cationic centers rather than one.

The large circular curare molecule bound in the open cholinergic receptor binding site.

As illustrated above, the relaxed binding site is highly hydrated with water molecules in dynamic motion in many conformations other than those shown in the idealized cubic lattice. In addition to the cysteines and tyrosine, an aspartate peptide in front provides a circle of anionic atoms in the open site.

As can be seen in the Front View above, the curare molecule completely covers the open site - displacing all of the water above it to prevent the entry of acetylcholine and other agonists. The two cysteines are positioned directly below the ammonium ion centers in the curare molecule with the terminal alcohol of the tyrosine phenol hydrogen-bonded to curare’s ether oxygens.  By covering the site and providing a planar upper surface for hydration stability, curare not only prevents activation by acetylcholine, it prevents the site from closing due to thermal agitation. This is important because these sites are often in dynamic, muscle-contracting tissues.

An Opiate Receptor - Met Enkephalin

One of the most intensely-studied physical maladies of man is pain.  Literally, hundreds of extracts from plants have been used to alleviate it and thousands of studies have been performed to develop more effective analgesics.

However, it was not until 1975 that Professor John Hughes isolated two pentapeptides from rat brain which, when injected back into brains, relieved pain.69 Thousands of subsequent studies have illustrated that these central nervous system compounds, methionine enkephalin and leucine enkephalin, are two of the primary receptor-binding agents which control the sensation of pain.


The met enkephalin molecule.

Based on NMR studies, met enkephalin (tyrosine-glycine-glycine-phenylalanine-methionine) adopts several conformations when suspended in a mixture of lipid and water but the globular form shown on the left above is the one which most likely occupies a number of opiate receptor sites.70  In order to illustrate bonding within the site, the molecule is oriented with the tyrosine, T, and glycine, G, peptides in front with the phenylalanine, F, and methionine, M, peptides behind. The cationic amine of tyrosine is on the left with its phenolic oxygen close enough to the carboxylate of methionine to be bridged by a single water molecule. In this form, about 60% of the outer surface, on the front and back associate with lipid - polar atoms are on the ends and the front.  If this is the correct configuration of met enkephalin in the binding site, then opiates which bind to the same site must mimick, to some degree, the same spatial distribution of polar, lipid and ionic groups.

Unfortunately, no published crystallographic or NMR information appears to be available for met enkephalin in the binding site, so we can only assume that the conformation selected is the correct one.  Since conformations of regulator proteins like insulin and calmodulin are the same in solution as in their receptor binding sites, it may be true for met enkephalin as well.  First, we will look at a proposed site for enkephalin and then at three different opiate analgesics and a blocking agent.

An Opiate Receptor Site TLH Model

Although no specific model has been reported for an opiate receptor site, evidence suggests that at least one of the sites has the same basic structure as human dopamine receptor described previously.66 Thus, model-building began with that basic structure and the assumption of similar conformations in the activated and blocked states.

The met enkephalin molecule bound in a proposed site in an opiate receptor protein.

In the view above, the entire molecule has been placed in the hypothetical site with tyrosine spanning between an anionic aspartate, D, behind the left coil, and the cationic amine of lysine, K, behind the right-hand coil. Since these two binding peptides are directed toward the center of the site, we are looking through the coils to see them.  The lysine amine is bridged between the phenolic oxygen and the upper methionine carboxylate oxygen.

Transiently-ordered water and the front three peptides of the met enkephalin molecule binding in a proposed site.

By viewing only the front section on the right above, you can get a better idea of critical bonding relationships. As illustrated, the tyrosine amine not only hydrogen bonds to aspartate D, it also bonds to an adjacent serine with the first glycine carbonyl bonded to the cysteine sulfhydryl on the right-hand coil. As the met enkephalin molecule leaves the site, water most likely enters to bridge between and stabilize polar groups on opposite sides of the site. As you can see, as many as four water molecules bridge as covalent quantized elements across the site. However, once again, even though a static cubic lattice of probability positions is shown, water within the site is dynamic.

Opiate Analgesics

Although a broad variety of molecular structures exhibit opiate analgesic activity, morphine, demerol and methadone represent three of the major classes.71 As illustrated below, the cationic amine and anionic phenolic hydroxyl group of morphine bridge across the site with the alcohol hydrogen-bonded to the cysteine sulfur. It is interesting that the cationic amines of all three analgesics, even though they bond with the same aspartate D on the left-hand coil, are in substantially different spatial positions.

Morphine, demerol and methadone in the derived opiate receptor binding site in its activating conformation.

In contrast to the morphine molecule, which tends to occupy the space of met enkephalin, the demerol molecule is positioned so far below the lysine nitrogen that it cannot hydrogen bond with it. Its ethyl ester carbonyl bridges between serine on the left and cysteine on the right. In fact, water molecules may transiently hydrogen bond from the lysine amine down to the ethyl ester. This would permit the cationic charge of the lysine amine to be distributed through the ester oxygen to the sulfur atom and place water molecules adjacent to the aromatic ring of demerol.

Methadone, with its two aromatic phenyl rings, is a complex molecule to view. It has a cationic amine which hydrogen bonds to the aspartate carboxylate and a ketone oxygen which hydrogen bonds to the cysteine sulfur - one of its aromatic rings is between the right-hand coils and the other is between the back coils. 


Like most receptor proteins, the opiate receptor is activated by a number of agonist regulators and is blocked by a number of antagonists. Naloxone, which was sythesized from morphine, is one of the most effective, long-acting antagonists.72 Its structure is similar to morphine but differs in a number of critical ways. First, it has a ketone at the position A rather than an alcohol. Second, the double bond in the ring at B is saturated.  Third: an alcohol is inserted at C.  Fourth: the methyl group on the nitrogen is replaced by an allyl group. Numerous changes in the structure of morphine produce a broad variety of binding properties and pharmacological effects but naloxone is one of the most effective blocking agents. Prolonged action suggests that chemical bonding may be involved.

The naloxone molecule bound in the derived opiate binding site in its activating and blocked (resting) states.

Since activation of the human dopamine recepter, which was presented previously, involves a clockwise rotation of the vertical right-hand coil, the figure on the left illustrates naloxone in its activating binding position in the site. Some structural modifications of the morphine molecule exhibit both activating as well as blocking properties. However, naloxone exhibits primarily blocking activity. Thus, instead of remaining in an activating conformation, the naloxone molecule tilts its lower section foreward to permit the hydroxyl on the central ring to hydrogen bond with serine S and the cysteine sulfur atom to bond with the ketone carbonyl carbon to form a ketal with the new hydroxyl group hydrogen-bonded to the central alcohol.  This turns the right-hand coil counter-clockwise, holds the site in its resting state, blocking processes within the cell.  Since this binding involves the formation of a chemical bond between the cysteine sulfur and the naloxone ketone, binding is more permanent and long-lasting.

Of course, the proposals presented above, with respect to the opiate receptor, are hypothetical and must await the results of experimental studies before being considered as valid.   

Steroidal Hormones

Another important class of regulators, which are synthesized enzymatically by oxidizing off the side chain of cholesterol, is the steroidal hormones. As mentioned before, cholesterol is a critical component of cell membrane but an equally-important source of a large variety of hormones and bile acids.73

Dimensional correlations between an element of transient Linear hydration and four hormonal molecules.

As illustrated above, the cholesterol molecule is the spatial analog of an ordered element of water molecules. Even though each of the hormones illustrated above mimics the length of six water molecules, each one has a different combination of polar groups on the ends to bind with different arrangements of binding groups in receptor sites.  Other steroids, like cortisone and aldosterone mimic dynamic linear elements of seven water molecules, rather than six.


The testosterone molecule in its receptor binding site.

The testosterone receptor above was reported by Professor R. Breton in 2006.74 It has pairs of peptides on the ends to provide for precise binding and specific hydrophobic peptides to fill the lipid space above and below the molecule.  Although details of the resting state have not been published, one or more of the coils above or below the site most likely rotates to partially close the space. However, a dynamic transient linear element of six water molecules most likely occupies the site as the testosterone molecule enters or leaves.

The fact that sonication, with no agonist molecules present, activates some receptors suggests that, under the influence of high thermal energy, water molecules may occupy receptor sites in ordered forms and provide activation. In fact, receptor sites may be in equilibrium between the resting and activated states but do not remain in active conformations long enough to activate functional processes. It is truly amazing that the steroidal nucleus in the cholesterol molecule serves as the source of so many vital hormone structures.

Ribosomal Binding Sites - Transfer RNA’s

Before we leave the topic of receptor proteins, we should consider the structural characteristics of a class of small nucleic acids called transfer-RNAs. They, like other nucleic acids, wrap spontaneously to produce functional forms and are believed to have been produced at random in an early phase of molecular formation on earth.  Once again, forms which were stable in the aqueous environment and provided for cooperative functions and reproductive capability survived - those which did not, were chewed up by hydrolytic enzymes and converted back to nucleotides. 

As you can see, t-RNAs are unique in that they have a geometry which fits perfectly into the framework of quantized cubic lattice patterning.75 This precise shape is extremely important because, in performing their functions in protein synthesis, they must fit into a number of binding sites in ribosomes which, like the binding sites described above, most likely, in their open forms, have transient elements of linear hydration within them.

The transfer RNA molecule and its amino acid-attaching enzyme.

Transfer RNAs are fundamentally important because each living cell contains 21 or more of them to match the 21 different amino acids which compose polypeptides. All t-RNAs have the same basic geometry but each has a different triplet sequence of nucleotides (adenosine, guanosine, uridine and cytosine) in the left, loop-end of the molecule.

In addition, each cell contains at least 21 different enzymes, with the structure shown above, which bind to the t-RNAs, to attach a specific amino acid to the open end of the t-RNA based on the triplet code at the loop end. With a specific peptide tied to one end of a t-RNA and a specific triplet code on the other end, they bind to sites on ribosomes to attach the peptides together in sequences defined by complimentary triplet codes in long linear messenger RNAs. As you can see, not only the t-RNAs, but the t-RNA/enzyme complexes which form the peptidyl-t-RNAs satisfy cubic hydration patterning. This provides for maximum stability and, at the same time, the capability of forming complexes with the ribosome or with other molecules involved in polypeptide formation.

Although ribosomes are extremely large and difficult to visualize, it is not hard to imagine that quantized transiently-ordered elements of water must be involved in guiding peptidyl-t-RNAs into and out of binding sites. In spite of the complexity of the processes, polypeptide synthesis is extremely rapid.  Once again, the reason is that the processes most likely are all integrated and directed by Transient Linear Hydration and Cubic Hydration Patterning.

Of course, you might ask: how it is possible for a single quantized probability pattern to produce the myriad of molecules which are present within living cells? Often it is stated that no snowflake is like another, even though each one is composed of the same hexagonal lattice. If that were true, then there might well be an almost limitless number of molecular forms which might conform to the cubic lattice.  Of course, the number is not limitless - in fact, constraints of transient linear hydration guided molecular evolution to only those forms which could function harmoniously within the environment of Cubic Hydration Patterning. Without those constraints, enzymes would not function efficiently and there would be no spatial or genetic control.

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