HYDRATION QUANTIZATION OF RECEPTOR BINDING SITES

J. C. Collins, PhD

MOLECULAR PRESENTATIONS
178 West Shore Drive, Valatie, NY 12184

Molepres2000@aol.com

Dedicated to the late Professor William S. Johnson The University of Wisconsin Stanford University, to Professor Carl Djerassi Wayne State University Stanford University and to My Wife, Betty

The Author:
Dr. Collins received his degrees in Chemistry from Wayne University in Michigan and the University of Wisconsin. After employment at General Motors Research, E. I. Dupont and Sterling Drug, he accepted a position at Illinois Wesleyan University as Chairman of the Chemistry Department and Associate Professor. I n 1967, he returned to Sterling Drug to direct drug research at Sterling Winthrop Research Institute until l987 when he retired to devote full time to his driving interest in the role of water in the living cell. He has a number of publications and patents to his credit and has had a synthetic organic reagent The Collins Reagent named after him. However, natural molecular shape and cellular hydration have been his primary interests for many years. In this short treatise, he provides a pictorial view of how water mole cules most likely occupy quantized probability positions within receptor binding sites. Hydration Quantization of Receptor Binding Sites Strange as it may seem, this work has been placed on the Internet for your enjoyment. Download it if you like and share it with whomever you like. My only desire, is that you enjoy it. Questions and comments can be addressed to the a u t h o r at m o l e p re s 2 0 0 0 @ a o l. co m Illustrations were developed on R R R Apple Macintosh and Dell comWe b S i t e s : p u t e r s u s i n g A d o b e R I l l u s t r a t o r R. Quantized Spatial Control Within Living Cells Data for strucural analyses and the preparation of drawings were w w w . l i n e a r w a t e r. c o m obtained from the published literHydration Quantization of Receptor Binding Sites ature. Custom physical modelw w w. m o l e p re s. c o m building was per formed primarily w i t h Framework R molecular model A Creation Story from Atoms to the Living Cell par ts (Prentice Hall, Englewood w w w. m o l e c u l a rc re a t i o n . c o m Cli s, NJ 07632).

Hydration Quatization of Receptor Binding Sites

CONTENTS
Glycine Receptor Site 1 2 Strychnine Curare Enkephalin An Opiate Receptor Binding Site Opiate Analgesic Binding Naloxone Steroidal Hormone Receptors Testosterone Receptor Ion Binding Sites References 11 12 13 14 15 16 17 18 19 20 21-23

Cover, Dedication, Author, Preface Introduction Water

Quantized Proton Coupling

Neurotransmitters and Regulators An Adenosine Triphosphate Receptor Site Hydration Quantization Membranal Receptors Bacterial D-Aspartate Receptor Site Dopamine Receptor Site Acetylcholine Receptor Site

3
4 5 6 7 8 9 10

Hydration Quantization of Receptor Binding Sites

Preface

Receptor sites are spaces within cellular protein molecules which, when occupied by regulator molecules, like those of hormones and neurotransmitters, hold them in particular conformations. When held in those spatial forms, enzymatic and transport functions in other regions of the proteins are turned on or turned off. In fact, drug molecules often bind in those sites to activate or block essential functions. Thus, detailed structural studies are performed on receptor proteins, not only to determine how they regulate particular functions, but to aid in the design of new drugs to produce specific pharmacological responses. As might be expected, the isolation and structural determination of these extremely complex molecules are difficult and time consuming and precautions must be taken to insure that isolated entities preserve the structural features of the natural, functional systems. To permit detailed X-ray and spectral analysis of binding sites, receptor proteins often are crystallized with large regulator molecules in the sites. However, when not occupied by regulator molecules, the sites are occupied by water molecules. Although the prevailing view seems to be that water molecules are so dynamic that they do not occupy specific locations in the sites, it is likely that they do occupy probability positions to hold the sites in open conformations, to delocalize charge and to participate in the entrance and release of the regulator molecules. Thus, it is critical for probability hydration models to be developed in order to interpret the properties of these extremely important sites. The purpose of this article is to begin that process by presenting quantized hydration models for five receptor binding sites which have been defined experimentally and for a number which have not been determined.

Hydration Quantization of Receptor Binding Sites

Introduction

Forty years ago, in an extensive molecular model-building program, the dimensions of regulator molecules, like hormones and neurotransmitters, were found to mimic linear hydrogen-bonded segments of water molecules. At first, it seemed that the correlations were simply a coincidence, but, as more correlations were noted, even in lipids and proteins, it appeared that natural molecules might simply be spatial analogs of ordered units of the aqueous environment in which they had evolved; that ordered units of water molecules might occupy receptor sites in proteins when the natural regulators are not present. Since water molecules form linear, hydrogen-bonded elements adjacent to surfaces, a proposal was presented at the American Chemical Society Meeting in Quebec Canada in 1993 that spatial order within living cells and spaces within receptor sites might be defined by transient linear elements of water molecules. However, little or no evidence was available for the existance of linear elements in liquid water and limited information was available on the structures of binding sites, so the proposals were rejected as pure speculation. In spite of that rejection and the rejection of multiple submissions to scientific journals, two books and three web sites were presented to promote the concept of Transient Linear Hydration. Based on recently-published evidence that the molecules of water in the liquid state exhibit quantum mechanical properties, the three web sites have been modified to include this important new information and quantized hydration models for a number of receptor sites are presented here. However, the concept that protons and water molecules may be providing spatial order within living cells is not new - it was proposed by Erwin Schrodinger in 1944 and, again in 1972, by Szent Gyorgi.
1,2

Hydration Quantization of Receptor Binding Sites

Water
H

2
H
O
H H

Before we venture into the analysis of receptor sites, it is essential that we understand the structural and structuring properties of water molecules. As polarized entities, with two positively-charged protons on two corners of the oxygen atom and two negativelycharged electron orbitals at the other two corners, water molecules are like magnets which attract each other to form hydrogen

H
O

H
O

H
O

H
H
O

bonds. Since very little energy is involved in forming and breaking these bonds, the processes are extremely rapid: about a million millionth of a second, 10 -12 seconds.3 Although hydrogen bonds are only about 1/10th as strong as chemical bonds between atoms, they are strong enough to have dramatic structural effects on molecules dissolved or suspended in liquid water.4 In ice, water molecules are hydrogen-bonded together in relatively rigid lattices but, in the liquid state, they are randomly distributed, rapidly forming and breaking hydrogen bonds with each other. Classically, each liquid water molecule, at any instant, was considered hydrogen-bonded with four others.5 However, high speed neutron bombardment has demonstrated that, at any instant, each water molecule is hydrogen bonded only to two other water molecules.6 Thus, in liquid water, a dominant form is the linear triplet shown above 7 but as many as six water molecules may assemble into linear elements adjacent to hydrocarbon surfaces.8 In surface elements, hydrogen-bond strength is lower than in bulk water but linear order is significantly greater. 9 In fact, recent studies suggest that water molecules do not move smoothly from one alignment to another: instead, they jump in quantized fashion from one bonding relationship to another.10 As illustrated on the next page, they move by large-amplitude angular jumps, rather than the commonly accepted sequence of of small diffusive steps. Motions conform with principles of Quantum Mechanics rather than Newtonian Physics.
11

Hydration Quantization of Receptor Binding Sites

Quantized Proton Coupling

Thus, extension and contraction in hydrogen-bonded elements of water molecules appear to occur in quantized steps, possibly through an intermediate cyclic trimer.12 However, a critical portion of the water molecule is not the oxygen atom but the nuclei of hydrogen atoms, the protons. Often we forget _ + Dimer _ + Cyclic Trimer _
Trimer

that the proton is a subatomic entity with a radius similar to that of the electron; it also exhibits particle and wavelike properties. In fact, ultra high-speed neutron irradiation of liquid water at 10 -18 seconds, detects only 1.5 protons per water molecule, not 2, because of their wave-like properties. Water molecules are unique in that they contain two spin-coupled protons which, like electrons, couple with neighbors to produce entanglement.
14 13

_
Quantized Proton Entanglement Model

Although dynamic wave entanglement is most likely critical in the delocalization of charge and regulation

of motion within living cells, specific hydrogen-bonded states of water molecules most likely are important in the confines of regulator binding sites. Since groups like anionic carboxyls and cationic amines, often occupy critical positions in binding sites, proton transfer from one water molecule to the next through hydrogen-bonded networks also may play a role in minimizing the charge potential in open hydrated states. Quantized shifts from one hydrogen-bonded state to another also must be involved in the movement of molecules in and out of binding sites.
15 15

+
Proton Transfer Stabilization

Hydration Quantization of Receptor Binding Sites

Neurotransmitters and Regulators

+ +

Forty years ago, in a program of constructing permanent accurate models of neurotransmitters, hormones and drugs, it was surprising to find that linear dimensions corresponded closely to linear segments of hydrogen-bonded water molecules with unit linear dimension of about 2.3 Angstroms.
16

Serotonin

Glycine Acetylcholine

At first, it seemed simply to be a coincidence, but, as even more models were constructed, it appeared that hydrogen-bonded water molecules might be holding receptor sites in particular conformations when regulator molecules were not present.

Histamine

Adrenaline

Gama-amino Butyric Acid

Dopamine

Prostaglandin-PGE 2

In fact, based on the information presented above, it appears that not only hydrogen-bonding but proton quantization may be involved in directing and binding regulator molecules into those sites. Although detailed studies have not been performed on probable locations of water molecules in such sites, information is available on the cores of specialized proteins which form hydrated channels through biological membranes. Even though water molecules within those channels are present as short linear segments, they exhibit the property of tunneling which permits protons to pass through the membrane.17 Thus, proton transfer and entanglement may be occurring in the confines of the channels and in hydrated receptor sites as well. However, based on the principles of quantum mechanics, water molecules within receptor sites must be considered to occupy probability positions rather than specific positions as illustrated in the figures.
14

Hydration Quantization of Receptor Binding Sites

An Adenosine Triphosphate Receptor Site

AMP ATP

Since the adenosine triphosphate molecule, ATP, is in every living cell and regulates essential processes in thousands of different functional proteins, it is important to start with one of its binding sites.
18

ribose

adenine

ribose

adenine

In contrast to most of the proteins included in this presentation, glycogen phosphorylase is an enzyme which removes glucose molecules from the ends of liver glycogen molecules to produce glucose-1-phosphate. The protein was chosen because it has two regulator sites, both of which bind ATP and adenosine monophosphate, AMP. In the upper figures, the molecules are displayed in their binding conformations. The middle figures illustrate how they bind in the site and, in the lower left, the proposed hydration model. Hydration overlays are on the right. It is important to note that water, in binding within the site, is in its fully-extended, cubic, space-filling form. Water molecules lose entropy in binding sites, so it is important for a minimal number to be involved at any instant.
ATP + + AMP +
arginines

+ _ + _

Hydration Quantization of Receptor Binding Sites

Hydration Quantization
ATP
R N

In viewing the hydration gure for the ATP-binding site at the right, it must be realized that the water molecules displayed are not all in the site all of the time and that they occupy only quantized, probability positions. It is as if a time-lapse picture were taken of the site with only the locations of idealized probability identi ed. Proton entanglement and linear hydrogen bonds in the site distribute positive charges on the arginine (R) and lysine (K) groups throughout the space. Note that even though the central ribose ring

+
K

+
N

of the ATP molecule, which usually is in the extended form as it is in AMP in the receptor site on page 5, is forced behind the adenine ring to t within the hydration-ordered space. Cyclic adenosine monophosphate, c-AMP, a molecule which is produced from ATP, also regulates functions in almost every living cell. Like ATP, it binds in multiple receptor proteins and adopts a number of conformations to satisfy binding groups within those sites. In its extended form, it binds in spaces de ned by six
Cyclic AMP Activated Site
+
_

Arginine

Glutmate Serine
+

linear water molecules. In this case, charges on the arginine and glutamate groups are viewed as neutralized by the formation of counter ions on adjacent water molecules by proton transfer. Below is an entanglement model.

Quantized Charge Delocalization

Hydration Quantization of Receptor Binding Sites

Membranal Receptors
HYDRATION PORE

Before we consider additional receptor sites, it is important to realize that many of them are in proteins composed of helical coils which pass through cell membranes. Most of these membranes are composed of dynamic, puckered fatty-acid chains of alpha-state phospholipids complexed with cholesterol molecules. The cholesterol molecules, which are shown as the at gures, spin around their axes to keep the membrane in motion and yet provide structural stability.
19
o

The lipid region, as illustrated schematically on right, is about 40 A thick, the same dimension as 17 water molecules bridging between the carbonyl oxygens of the fatty acids on both sides.
16,19

As mentioned before, protons tunnel through freely.17

water passing through channel proteins such as these is composed of several short linear segments but
SIGNAL TRANSDUCTION TRANSPORT

Two types of receptor proteins span this type of membrane: 1) those which, by binding a regulator molecule, move helical segments and alter processes within the cell and 2) those which, by binding regulators, permit ions or molecules to enter or leave the cell. Single or multiple regulators may be involved in activation.

Hydration Quantization of Receptor Sites

Bacterial D-Aspartate Receptor Site

Aspartate Activated State
+ _ _
T _ W

One of the first signal transduction proteins to be isolated and the binding

site deciphered was a receptor protein

from a bacteria which binds D-aspartic acid.
20

Hydrated Active State

Y

Y W R

This aminoacid is not present in

_
R T

most organisms but is common in bacteria. The aspartate-binding site in the protein is on the outer surface of the membrane with four helical polypeptide segments passing through the membrane.

+ _
R Y

+ _ _ R

Inactive Resting State

Since D-aspartic acid exists in aqueous solution with a net negative charge, two of the binding groups are positively-charged arginines (R). The aromatic ring of the upper binding tyrosine peptide (Y ) is directed downward with its oxygen binding two water molecules ( W ) which bridge across to the two carboxyl groups of aspartate. As the aspatate leaves, three water molecules most likely take its place. However, the arginines are highly-charged and additional water molecules most likely move into the site to delocalize the charge as aspartate leaves. This either rotates the right-hand helix clockwise or moves it to the right to turn off a process within the cell. It must be remembered that only a limited number of water molecules will be in the site at any instant. Also, the increase in quantized hydration and the movement of one column may alter the position of one or more of the other columns.
_ + _ +
R

Hydration Quantization of Receptor Binding Sites

Dopamine Receptor Site

Quantized Hydration of a Dopamine Receptor
Antagonist Blocked State
H

The third receptor site to be examined was reported in 2010. Like many receptor proteins being examined today, this one required extensive modi cation with the introduction of point mutations to enhance thermal stability and the use of a large binding molecule to hold the site in a particular con guration for crystallization. The antagonist Eticlopride was used to obtain an interpretable X-ray di raction pattern.
+ +
Chlorine Atom 21

Hydrated Blocked State

H

_
D

+ _
S

V
D

+ _
S

Eticlopride Antagonist

Dopamine Activated State

H

Hydrated Activated State + _

S

_ Dopamine Agonist

+ _

+ _
S

Only the critical binding groups, (aspartate D, Histadine H, serine S and tryptophan W ) are included in the illustrations. As you can see, the Eticopride molecule e ectively lls the site leaving little or no room for water molecules. In fact, the molecule lls the site so completely that the oxygen atom of the serine group, S, is forced down away from the binding molecule. Model studies suggest that, with dopamine agonist in the site, the helical polypeptide column V turns clockwise, turning the histadine away from the site, permitting serine to bind to the dopamine oxygen. Like the aspartate receptor, column movement most likely activates a process within the cell.

Hydration Quantization of Receptor Binding Sites

Acetylcholine Receptor Site

22

10

One of the most important receptors in the body, which is in both muscle and nerve cells, is the cholinergic system involving the small acetylcholine molecule as the agonist. Several different types of receptors are activated by acetylcholine with a number of different binding sites but the one which has received the most attention by Dr. Nigel Unwin and his coworkers was isolated from the Torpedo electric eel.
23

ACETYLCHOLINE

Activation of the

receptor protein, rotates a helical segment which passes through cell membrane which opens a pore and permits sodium ions to enter the cell. Antagonists, such as curare, by binding to the site, prevent sodium entry and block nerve pulse transmission and muscle contraction.
24

The receptor site involves two chain loops: one with a tryptophane, W, the other with two cysteines, C, and a tyrosine, Y. As the positively-charged acetylcholine molecule moves into the site, it displaces the water, draws the Cys/Cys loop up toward the trytophane, draws tyrosine upward, moves the polypeptide chain and opens a sodium pore in the membrane. Since the acetylcholine molecule is small, it moves rapidly in and out of the site. As it leaves, water molecules move in rapidly to occupy the space followed more molecules to return the site to its open, fully hydrated form. Y
_

OPEN BINDING SITE

ACETYLCHOLINE BINDING

CLOSED SITE HYDRATION

+ _
Y

C Y

Hydration Quantization of Receptor Binding Sites

Glycine Receptor Site

_ +
Glycine

11

Although detailed information regarding the glycine receptor site has not been published, DNA cloning and structural studies indicate that the binding site has the same basic cysteine/cysteine-loop structure as the acetylcholine site.25 However, based on the quantized linear hydration analysis, the tyrosine peptide in the cys/cys loop of the acetylcholine binding site is replaced by a cationic arginine peptide, R, to provide for unique binding of the glycine molecule. A peptide other than tryptophane, W, may be in the upper loop but studies suggest that it may be in most cys/cys-loop receptor sites.26 Once again, in viewing the hydration model, it is extremely important to realize that, even though water molecules are illustrated in specific locations, they are extremely dynamic and continually jumping from one electron-coupled or proton coupled position to another. Also, it is important to realize that the orientation of hydration planes in the site is defined by the external spatial structure of the protein. As illustrated in the Protein Assembly section of this site, orientations of hydration are defined early in protein assembly, thus, the same basic hydration patterns should be involved in all cys/cys-loop receptor sites. W
OPEN RECEPTOR SITE FOR GLYCINE GLYCINE BINDING ACTIVATED STATE HYDRATION

_ +
R
_

+ C _ +
R

_ +
R

Hydration Quantization of Receptor Binding Sites

Strychnine
_ +

12

Just as acetylcholine binds to its receptor protein to close the site and open a pore in nerve cell membrane to admit positive sodium ions, glycine binds to a receptor protein to open a pore to admit negative chloride ions. By binding to the glycine site in its open form, strychnine blocks the site and the opening of the pore.
23

Glycine Strychnine

Although the binding of strychnine has not been defined experimentally, it appears, based on the concept of quantized linear hydration,

that the relatively-flat strychnine molecule displaces a planar segment of hydrating water molecules above the ionic binding groups. With its cationic amine hydrogen bonded to the sulfur atom in front, its aromatic ring involved in charge transfer with the other sulfur atom below it and its amide group hydrogen-bonded to the cationic nitrogens of the arginine behind and below it, the strychnine molecule blocks glycine activation. As can be seen from the models, the large size of strychnine relative to glycine is important to cover the site and displace the water.
HYDRATION OVERLAY VIEWED FROM ABOVE
amide

OPEN BINDING SITE HYDRATION

STRYCHNINE BINDING

+ R

+ R

+
C

Hydration Quantization of Receptor Binding Sites

Curare
+
CURARE

13

Although the curare molecule is complex and difficult to view in the acetylcholine receptor, it has received so much attention as a receptor-binding agent, that it should be included in any presentation on receptors. South American Indians dipped the points of their arrows and darts in the juice of an herb which contained d-tubocurarine because it binds to the same receptor as acetylcholine and nicotine.

It keeps the binding site in its open state and prevents the contraction of muscles. Its action is extremely rapid when injected into the blood stream. As illustrated above, the molecule is a large ring composed of four aromatic rings with cationic amines at both ends. It is much larger than acetylcholine because it must displace a large number of water molecules in the open site. When viewed on the edge, as shown below, it has a planar upper surface, like the linear element of water it displaces in the site and its cations are close to the two anionic sulfur atoms of the cysteines in the loop. Notice its spatial analogy with planeordered water. Y
_
VIEW THROUGH IDEALIZED HYDRATION ABOVE

CURARE BINDING

OPEN ACETYLCHOLINE BINDING SITE

HYDRATION ANALOG

+ _

_ +

Hydration Quantization of Receptor Binding Sites

Enkephalin
MET ENKEPHALIN
+
F T M G G

14

One of the most intensely-studied physical maladies of man is pain. Herbs and extracts of all kinds have been used to alleviate it and intense studies have been performed to nd more e ective analgesic agents. However, it was not until 1975 that Professor John Hughes isolated two pentapeptides from rat brain which, when injected back into brains, relieved pain.
27

Thousands

of subsequent studies illustrated that these two central nervous system compounds, methionine enkephalin and leucine enkephalin, are the primary receptor-binding agents which control the sensation of pain.
28

Although the basic structures of the receptor proteins which bind these systemic agonist molecules and analgesics like morphine and demerol are similar to those which bind dopamine, binding groups within the sites appear to be di erent. In fact, a number of opioid receptor proteins, with di erent binding properties, have been isolated but limited data is available with regard to the details of binding within the sites.
29

Based on NMR studies, met enkephlin (tyrosine-glycine-glycine-phenyl alanine-methionine) adopts several conformations when suspended in a mixture of lipid and water but the spherical form shown above is the one which most likely occupies a number of the receptor sites.
30

In this form, about 60% of the

outer surface associates with lipid but most of its polar atoms are directed outward to hydrogen bond with groups around it in the receptor sites. In order to illustrate bonding within the site, the molecule has been oriented so the tyrosine peptide, T, and a glycine, G, are in front with the phenyl alanine, F, and methionine, M, behind. The cationic amine of tyrosine is on the left with its phenolic oxygen close enough to the anionic carboxylate of methionine to be bridged by a single water molecule where the negative charge is shown in the illustration.

Hydration Quantization of Receptor Binding Sites

An Opiate Receptor Binding Site

D K

15

In the upper view, the entire molecule is placed within the hypothetical site with the tyrosin peptide bound between an anionic aspartate, D, on the left and a cationic lysine, K, on the right. Since opiates regulate many cellular functions, it is likely that there are several di erent sets of binding groups. As you can see in the upper gure, the molecule is so complex that it is di cult to identify critical binding. However, based on the structural studies performed on many synthetic opiates, three groups on the front of the molecule, as pictured at the right, are critical. Tyrosine,Y, bridges across the space occupied by four hydrogen-bonded water molecules in the hydrated site shown below, while the tyrosine carbonyl and the rst glycine bridge over to the cysteine sulfur, C. Remember, even though the water molecules are pictured in a ridged lattice, they are only probability positions; they continually move in and out of the site. Also, you should note that the enkephalin molecule and hydration analog are somewhat spherical like a bucky-ball.
_ + _ +
A

D _ +

Y _

+
C

Hydration Quantization of Receptor Binding Sites

Opiate Analgesic Binding

_ +

16

Although a broad variety of molecular structures exhibit analgesic opiate activity, morphine, demerol and methadone represent three of the major structural classes. As illustrated at the right, the cationic amine and phenolic oxygen of the morphine molecule bind to the same aspartic acid and lysine peptides as the enkephlins, with the alcoholic oxygen bonded to sulfur. On the other hand, the aromatic ring of demerol is held out away from the helical column so far that water can bridge from the lysine nitrogen to the cysteine sulfur. The sulfur atom, in turn, hydrogen bonds to the oxygen of the ester with the terminal methyl of the ester adjacent to the alanine methyl (A). Methadone is a complex molecule to view. It has an amine which hydrogen-bonds to the aspartate, D, and a ketone oxygen which bonds with the cysteine sulfur, C. One of the its phenyl rings is pointed directly at the helix in a location which brings it close enough to sulfur atom to be stabilized by charge-transfer. The other phenyl ring, behind the ketone, points directly away from the site toward the more open side of the site. Based on this proposed receptor model, each of these molecules appears to bind and activate the same site but each in a significantly di erent manner.
Methadone
_ + _ +
27

_
+

Morphine

+ _

Demerol

Hydration Quantization of Receptor Binding Sites

Naloxone
Active State Binding
_ + _
+

17 Active State Hydration

Like most receptor proteins, those which bind morphine to produce analgesia also bind antgonists to block the e ects.31 Naloxone, which is pictured above bound to the opiate site, is an extremely e ective antagonist which not only reverses the e ects of agonists, like mor-

Blocked State Binding

Blocked State Hydration

phine, but produces a prolonged blockade. In the upper gure, naloxone is pictured bound to the site in a manner similar to morphine, with the allyl group on the nitrogen pointing toward the column in the back. However, sulfur atoms readily add to carbonyl carbons to form sulfhydryls so, by rotating the right helix counter clockwise and the left helix clockwise, the cysteine sulfur can bond chemically to the carbonyl carbon. This places the newly-formed hydroxyl in a position to hydrogen-bond to the neigboring hydroxyl. With the methyl group of the alanine A rotated forward, the allyl group can move foreward next to the helix and coordinate with the proton on the neigboring alchhol. Since sulfhydrylformation is reversible, naloxone binding is reversible but is more long-lasting than normal agonist binding.

Hydration Quantization of Receptor Binding Sites

Steroidal Hormone Receptors

Cholesterol

18

Last, but not least, let us look at a few steroidal hormones, all of which are produced by the oxidation of cholesterol in various organs of the body, all control a wide variety of functions and all are approximately the length of six linearly hydrogen-bonded water molecules. In a previous section, cholesterol was displayed as a component of phospholipid membrane. As can be seen in the gure at the right, the cholesterol molecule simulates a linear hydration unit of nine

water molecules. It is interesting that the two vertical water molecules are in the spatial locations of the two vertical methyl groups in cholesterol. However, most of the cholesterol molecule is lipophillic, so it is doubtful that open sites which bind it would by hydrated by more than a single linear element of 9 water molecules. Likewise, the hormones shown on the right all have lipophillic central regions; receptor sites which binding them most likely are hydrated by linear segments of six water molecules. Even though their structures are quite similar, they bind to di erent receptor proteins and produce di erent physiological e ects. On next page, we will look at a testosterone binding site which was reported by K. Pereira in 2006.
33 32

Steroidal Hormones

Estradiol

Progesterone

Testosterone

Androstendione

Hydration Quantization of Receptor Binding Sites

Testosterone Receptor
TESTOSTERONE RECEPTOR BINDING SITE

19

It is amazing that a receptor site, such as the one illustrated on the right, could have evolved with glutamine-Q, arginine-R, threonine-T and asparagine-B groups in precise positions to bind the testosterone molecule. 33 And yet, proteins did not develop in a void. Water occupies all voids in and around natural molecules. In fact, most of the time, water molecules occupy receptor and enzyme-binding sites. Thus, it should not be surprising that many proteins might have formed at random which could bind six hydrogen-bonded molecules. As molecules move in and out of binding sites, speci c water molecules participate in the process. Only when we accept the fact that water actively particticipants in the processes, can we begin to understand how cells can function in such an e cient manner.
Q R T B

Hydration Quantization of Receptor Binding Sites

Ion Binding Sites

20

As pointed out on the previous page, one might conclude that space within the site was de ned by the testosterone molecule. However, we must remember, we are not dealing with the chicken and the eggmost likely, water came rst. Thus far, we have emphsized the importance of linearity in water but small ions delocalize their charge by binding water molecules in concentric spheres around them.
34

When con-

centrations of ions such as sodium and calcium increase rapidly during depolarization in nerve and muscle cells, free-water within the cells shifts from its linear, resting-state orientation to a circularly-polarized state and molecules within rapidly shift to alternative conformations - it is the change in environmental water and the locations of ions which produce changes within the cells. Thus, binding sites for hydrated ions,
+ like Na(H 2 O) 6 , Ca(H 2 O) +2 and Cl(H 2 O) 6 , and their presence in water play a vital role in regulating cell function. 6 _
35

Tetrototoxin, the extremely toxic pu er sh poison, mimics the spatial structure of Na(H 2 O) 6 . It binds tightly to sodium-transport sites preventing nerve-cells from going from resting to excited states.
-2
36

Likewise,

the diuretic drug molecule, dihydrochlorothiazide, binds to sites in kidney-cell membranes which normally bind the complex hydrated dichloride ion, (H 2 O) 3 Cl(H 2 O)5 Cl(H 2 O) 3 . By blocking chloride ion uptake into kidney cells, sodium ion uptake is blocked and water around it is excreted into the ducts.37 Until now, the coupling of electrons to form spatial structures and provide for the transfer of energy has dominated science and technology. Hopefully, this presentation will draw attention to the fact that the coupling of protons to form transient structural elements in liquid water played a critical role in the development of natural molecules; it plays a critical role in regulating the motions and interactions of molecules and ions in living cells and will play a critical role in a new age of advancements in medicine and technology.

Hydration Quantization of Receptor Binding Sites

References

21

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