hydration quantization of receptor binding sites by j.c. collins, phd

8/6/2019 Hydration Quantization of Receptor Binding Sites by J.C. Collins, PhD

1/28

MOLECULAR PRESENTATIONS

178 West Shore Drive, Valatie, NY 12184

[email protected]

HYDRATION QUANTIZATION OF

RECEPTOR BINDING SITES

J. C. Collins, PhD


2/28

Dedicated to the late

Professor William S. Johnson

The University of WisconsinStanford University,to

Professor Carl Djerassi

My Wife, Betty

Wayne State UniversityStanford University

and to


3/28

Dr. Coll ins received his degrees in Chemistry from Wayne Universit y

The Author:

in Michigan and t he Universit y of Wisconsin. After employmentat General Mot ors Research, E. I. Dupont and Sterl ing Drug, heaccepted a posit ion at Il l ino is Wesleyan Universit y as Chairman

of the Chemistry Department and Associate Professor. In 1967,he returned t o Sterli ng Drug to di rect d rug research at SterlingWinthrop Research Inst itute unti l l987 when he retired to devot efull time to his driving interest in t he role of water in the livingcell. He has a number of publ icat ions and patents to his creditand has had a synthet ic organic reagent The Coll ins Reagent named after him. However, natural molecular shape and cellularhydration have been his primary interests for many years. In thisshort t reatise, he provides a pictor ial view of how w ater mole-cules most l ikely occupy qu antized p robabilit y posit ionswithin receptor binding sites.

St range as it may seem, th is work has beenplaced on th e Internet for your enjoyment.Download it if you like and share it wi th whom-ever you l ike. My only desire, is that you enjoy it.Questions and comments can be addressed to t he

Web Si t es:

www. l inearwater .com

I l l u s t r a t i o n s w er e d e v el o p e d o n

A p p l e Macin t osh and Del l com-pu t e rs using Adobe I l l u s t r a t o r .D at a f o r s t r u c u r a l a n a l y se s a n dt h e p r e p ar at i o n o f d r aw i n g s w er eo b t a i n e d f r o m t h e p u b l i sh e d l i t e r -a t u r e . Cu s t o m p h y s i c a l mode l -b u i l d i n g w as p e r f o r m e d p r i m a r i l yw i t h Framework mol ecu la r mod e lp a r t s (Pre n t i c e H al l , En g l e w o o d

Cl i s, NJ 07632).

H y d r a t i o n Q u a n t i z a t i o n o f Re ce p t o r Bi n d i n g Si t e s

Qu a n t i z e d Sp a t i a l Co n t r o l W i t h i n L i v i n g Ce l l s

www.molepres .comH y d r a t i o n Q u a n t i z a t i o n o f Re ce p t o r Bi n d i n g Si t e s

www.molecu la rc rea t ion .comA Cr e a t i o n St o r y f r o m A t o m s t o t h e Li v i n g Ce l l

author at mol [email protected]

R RR R

R

R


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Water 2

Neurotransmitters and Regulators

Quantized Proton Coupling 3

4

6

7

Bacterial D-Aspart ate Receptor Site

Hydration Quantization

Membranal Receptors

Dopamine Receptor Site

8

9

Acetylcholine Receptor Site 10

Glycine Receptor Sit e 11

Strychnine 12

Curare 13

Enkephalin 14

An Opiate Receptor Binding Site 15

Opiate Analgesic Binding 16

Naloxone 17

Steroidal Hormone Receptors 18

Testosterone Receptor 19

Ion Binding Sites 20

References 21-23

An Adenosine Triphosphate Receptor Site 5

Introduction

Cover, Dedication, Author, Preface

1

CONTENTSof Recept or Binding Sit esHydration Quatization


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Receptor sites are spaces within cellular protein molecules which, when occupied by

Thus, detailed structural studies are performed on receptor proteins, not only to determine

how they regulate particular func tions, 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 cr ystal-

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 thosesites to activate or blockessential functions.

lized with large regulator molecules in the sites .

However, when not occupied by regulator molecules, the sites are occupied by water molecules.

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 numberwhich have notbeen determined.

Although the prevailing view seems to be that water molecules are so dynamic that they do not

1Prefaceof Receptor Binding SitesHydration Quantization


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Q


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Before we venture int o the analysis of receptor sites, it is essential

that we understand t he st ructural and st ructur ing propert ies of

watermolecules. As polarized ent it ies, wi th two posit ively-charged

protons on two corners of t he oxygen atom and two negatively-charged electron orbitals at the other two corners, water molecules

but as many as six water molecules may assemble into li near elements adjacent t o hydrocarbon surfaces.

In fact, recent studies suggest that water molecules do not move smoot hly from one alignment to another:

only to two ot her water molecules. Thus, in liquid water, a dominant form is the linear tr iplet shown above

are like magnets which att ract each other to form hydrogen

bonds. Since very lit t le energy is involved in forming and breaking these bonds, the processes are

extremely rapid : about a mil lion mill ionth of a second, 10 seconds.

Although hydrogen bonds are only about 1/10th as st rong as chemical bonds between atoms, they are

strong enough t o have dramatic st ructural effects on molecules dissolved or suspended in liquid

state, they are randomly distributed, rapidly forming and breaking hydrogen bonds with each other. Classically,

each l iquid water molecule, at any instant, was considered hydrogen-bonded wit h four others. However, high

speed neutron bombardment has demonstrated that, at any instant, each water molecule is hydrogen bonded

water. In ice, water molecules are hydrogen-bonded together in relat ively rigid latt ices but , in the liquid

H

O

H

H

OH

H

O

HH

O

H H

O

H H

O

HH

2Water

-12

4

3

6

11

7

8

instead, they jump in quantized fashion from one bonding relati onship to another. As ill ustrated on the

In surface elements, hydrogen-bond strength is lower than in bulk water but linear order is signif icantly greater.

next page, they move by large-amplit ude angular jumps, rather t han the commonly accepted sequence of

of small d if fusive steps. Mot ions conform wit h principles of Quantum Mechanics rather than Newtonian Physics.

9

10

5

of Recept or Binding Sit esHydration Quantization

H d ti Q ti ti


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Thus, extension and contraction in hydrogen-bonded elements

of water molecules appear to occur in quantized steps, possibly

Although dynamic wave entanglement is most likely

crit ical in the delocalizat ion of charge and regulation

of mot ion wit hin l iving cells, specific hydrogen-bonded states of water molecules most likely are

amines, oft en occupy crit ical posit ions in bind ing sites,

important in the confines of regulator bind ing sites. Since groups like anionic carboxyls and cat ionic

prot on t ransfer from one water molecule to the next

through hydrogen-bonded networks also may play a role

in minimizing the charge pot ential in open hydrated states.

another also must be involved in the movement ofmolecules in and out of b inding sit es.

Quantized shif ts from one hydrogen-bonded state to

th rough an int ermedi ate cyclic t rimer. However, a crit ical

like properti es. In fact, ult ra high -speed neut ron irradiation of liquid water at 10 seconds, detects only 1.5

prot ons per watermolecule, not 2, because of t heir w ave-like properties. Water mo lecules are unique in

that they contain two spin-coupled protons which, like

electrons, couple wit h neighbors to produce entanglement .

port ion of t he water molecule is not the oxygen atom butt he nuclei of hydrogen atoms, the pro tons. Often we forget

that the proton is a subatomic ent it y with a radius similar to that of t he electron; it also exhibit s part icle and wave-

12

13

14

15

-18

15

3Quantized Proton Coupling

Cyclic Trimer TrimerDimer ++

+_ _ _

Quant ized Proton Entanglement Model

+_

_

_

+

+

Proton Transfer Stabil ization

of Recept or Binding SitesHydration Quantization



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Neurotransmitters and Regulators 4

Acetylcholine

Prostaglandin-PGE

Glycine

Histamine

++

-

+

Gama-aminoButyric Acid

Serotonin

+

+

+

Dopamine

--

-

-

2

Adrenaline

+--

channels through biological membranes. Even though water mol ecules wit hin those channels are

present as short linear segment s, they exhib it the property of t unneling which permits protons to

pass through the membrane. Thus, prot on t ransfer and entanglement may be occurring in

the confinesof t he channels and in hydrated receptor sites as well . However, based on t he

principles of quantum mechanics, water molecules wi thin recept or sit es must be consideredto occupy probabilit y positions rather than specific positions as illustrated in the figures.

Forty years ago, in a program of construct ing

hormones and drugs, it was surpri sing to f ind that

permanent accurate models of neurot ransmit ters,

linear dimensions corresponded closely to linear

as even more models were constructed, it appeared

At f irst , it seemed simp ly t o be a coincidence, but ,

unit linear dimension of about 2.3 Angstroms.

segments of hydrogen-bonded water molecules with

that hydrogen-bonded water molecules might be

when regulator molecules were not present.

holding receptor sit es in parti cular conformations

sites. Although detailed studies have not been performed on probable locations of water molecules in

such sit es, information is available on the cores of specialized proteins which form hydrated

proton quantizat ion may be involved in di rect ing and binding regulator molecules into those

In fact, based on the information presented above, it appears that not only hydrogen-bonding but

16

14

17

of Recepto r Bind ing SitesHydration Quantization

A Ad i T i h h R SiHydration Quantization


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An Aden osin e Tr iph osph ate Recept or Site 5

Since the adenosine t riphosphate molecule, ATP,

AMP

AMP

ribose adenine adenineribose

arginines+ +

++

_ __

ATP

ATP

In cont rast to most of t he 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.

is in every l iving cell and regulates essent ial

processes in thousands of different functional

prot eins, it is import ant to start wit h one of i ts

binding sites.

The protein was chosen because it has two regu-

bind in the sit e and, in the lower left , the proposed

hydrat ion model. Hydration overlays are on the right .

It is import ant to note t hat water, in b inding

wi thin the sit e, is in i t s ful ly-extend ed, cubic,

space-fil ling form. Water molecules lose entropy

in b inding sites, so it is import ant for a min imalnumber to b e involved at any instant.

lator sit es, bot h of which bind ATP and adenosine

monophosphate, AMP. In the upper figures, the

molecules are displayed in t heir binding confor-

mations. The midd le figures il lustrate how they

18

+

+

of Receptor Binding Sit esHydration Quantization

H d i Q i i 6Hydration Quantization


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Hydr ation Quant ization 6

In viewing the hydration gure for the ATP-bind ing site at t he right ,

it must be realized that t he water molecules displayed are not all in

the site all of the time and that t hey occupy only quant ized, probabili ty

positions. It is as if a time-lapse picture were taken of the site with only

the locations of idealized probabil it y identi ed. Proton entangle-

ment and linear hydrogen bonds in the sit e distribute posit ive

charges on the arginine (R) and lysine (K) groups through-

Cyclic adenosine monophosphate, c-AMP, a molecule which is produced from ATP, also regulates

funct ions in almost every liv ing cell. Like ATP, it binds in mult iple receptor proteins and adopt s a

out the space. Note that even though t he central ribose ring

of t he ATP molecule, which usually is in t he extended form as it is in AMP in the receptor site on

page 5, is forced behind the adenine ring t o t wit hin t he hydrat ion-ordered space.

sati sfy binding groups with in

number of conformat ions to

those sit es. In it s extended form,

it binds in spaces de ned by six

and glu tamate groups are viewed as neutralized by t he form-

linear water molecules. In th is case, charges on t he arginine

Cyclic AMP Activated Site

Arginine

Glutmate

Serine

++_ _ +

+

+

__

_+_

Quantized Charge Delocalization

ATP

R

K

N

NN

ation of counter ions on adjacent water molecules by proton

transfer. Below is an entanglement model.

+

+


7M b l R tHydration Quantization


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7

17

19

16,19

Membr an al Receptor s

Before we consider addit ional receptor sit es, 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 fat t y-acid chains of alpha-state

phospholi pids complexed wit h cholesterol molecules. The cholesterol

molecules, which are shown as the at gures, spin around t heir axes to

keep t he membrane in mot ion and yet provide structural stabil it y.

carbonyl oxygens of the fat t y acids on both sides. As ment ioned before,

The lip id region, as il lustrated schematically on righ t, is about 40 A

thick, the same dimension as 17 water mo lecules bridging between the

Two t ypes of receptor p roteins span

this type of membrane: 1) those wh ich,

by binding a regulator molecule, move

helical segments and alter processes

wit hin t he cell and 2) those which,

by binding regulators, permi t i ons or

molecules to enter or leave the cell .

Single or mult iple regulators may be

involved in activat ion.

prot ons tunnel th rough freely.

water passing through channel p roteins such as these is composed of several shor t linear segments but

o

SIGNAL TRANSDUCTION TRANSPORT

HYDRATION PORE


Hydration Quantization B t i l D A t t R t Sit 8


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of Receptor SitesHydration Quantization Bacter ial D-Aspar ta te Recept or Site 8

One of the first signal transduct ion

most organisms but is common in

acid. This aminoacid is not present in

bacteria. The aspartate-binding sit e in

the protein is on the outer surface of t he

membrane wit h four helical polypeptide

segments passing through the membrane.

Since D-aspart ic acid exists in aqueous solut ion with a net negat ive

charge, two of the binding groups are positi vely-charged arginines (R).

The aromatic ring of the upper binding t yrosine peptide (Y) is directed

downward with it s oxygen binding t wo water molecules (W) which

bridge across to t he two carboxyl groups of aspartate.As the aspatate leaves, three water molecules most likely take its place.

However, the arginines are highly-charged and addit ional water molecules

most likely move int o the sit e to delocalize the charge as aspartate leaves. This eit her 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 wi ll be in the site at any instant. Also, the increase in quantized

hydration and the movement of one column may alter the posit ion of one or more of the other columns.

proteins to be isolated and the binding

sitedeciphered was a receptor protein

from a bacteria which binds D-aspart ic

+

+_

_

_

_

_

++

_

+

_

_Aspartate Activated State Hydrated Active State

Y Y

W

W

Y

R R

R

R R

T T

_

Inactive Resting State

20

_

++

_

Dopamine Receptor Site 9



14/28

Dopamine Receptor Site 9

Quan tized Hydr ation of a Dopam ine Receptor

Dopamine

Agonist

Eticlopride

Antagonist Blocked State Hydrated Blocked State

+

+ +

_

_

ChlorineAtom

Antagonist

The th ird recept or site to

mutations to enhance thermal

stabilit y and the use of a large

binding molecule to hold t he

site in a particular con gur-

at ion for crystallization. The

antagonist Et iclopride was

used to obtain an interpret-

able X-ray di raction pattern.Only the crit ical binding groups, (aspartate D, Histadine H, serine S and t rypt ophan W) are included in the

ill ustrations. As you can see, the Et icopride molecule e ectively lls the sit e leaving li tt le 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 poly-

peptide column V turns clockwise, turning t he histadine away from the site, permitt ing serine to bind to the

dopamine oxygen. Like the aspartate receptor, column movement most li kely act ivates a process within the cell .

be examined was reported21

in 2010. Like many recept or

prot eins being examined

today, this one requi red

extensive modi cation w ith

the introduction of point

Hydrated Activated StateDopamine Activated State

+

_

H

D

W

S

V +

_

H

HH

D

W

S

SS

V

+

__

+

_

VV

of Receptor Binding Sit esy

Acetylcholine Receptor Site 10Hydration Quantization


15/28

Acetylcholine Receptor Site 10

22

One of the most important receptors in the body, which is in both muscle and nerve cells,

Several diff erent t ypes of receptors are acti vated b y acetylchol ine wi th a number of

is the cholin ergic system i nvolving t he small acet ylcholine molecule as the agonist.

different bind ing sites but the one which has received t he most attent ion by Dr. NigelUnwin and his coworkers was isolated from the Torpedoelectr ic eel. Acti vati on of the

receptor protein, rotates a helical segment which passes through cell membrane

which opens a pore and permit s sodium ions to enter t he cell. Antagon ists, such as curare, by

binding to th e sit e, prevent sodium ent ry and bl ock nerve pulse transmission and m uscle cont racti on.

The receptor site invo lves two chain loops: one wit h a tr ypt ophane, W, the ot her wit h two cysteines, C, and

draws the Cys/Cys loop up t oward the trytophane, draws tyrosine upward, moves the polypept ide chain

and opens a sodium p ore in t he membrane. Since the acetylcholi ne molecule is small, it moves rapidl y in and

out of t he site.

As it leaves, wat er

molecules move in

to return t he site

to it s open, full y

hydrated form.

more molecules

the space fol lowed

rapidly to occupy

a tyrosine, Y. As the posit ively-charged acetylcholi ne molecule moves in to the sit e, it di splaces the water,

23

24

ACETYLCHOLINE BINDING

ACETYLCHOLINE

CLOSED SITE HYDRATIONOPEN BINDING SITE

+

_

__

CY

W

C

W

Y

C

W

Y

+

of Recepto r Bind ing Sitesy

Glycine Receptor Sitef R Bi di SiHydration Quantization 11


16/28

Glycine Receptor Siteof Receptor Binding Sit es 11

Although detailed information regarding t he glycine receptor site has not been

same basic cysteine/ cysteine-loop struct ure as the acetylcholine sit e. However, based

published, DNA cloning and structural studies ind icate that t he binding site has the

on the quantized linear hydration analysis, the tyrosine peptide in t hecys/cys loop ofthe acetylcholine binding sit e is replaced by a cationi c argin ine pept ide, R, to

provide for unique binding of t he glycine molecule.

A peptide other than t ryptophane, W, may be in the upper loop but studies suggest that it may be

in most cys/cys-loop receptor sit es. Once again, in viewing t he hydration model, it is extremely important

and continually jumping from one electron-coupled or proton coupled posit ion t o another. Also, it is

important to realize that the orientation of hydration p lanes in t he site is defined by t he external

spatial st ructure of the protein. As illustrated in the Protein Assembly section of t his site, orientations

of hydration are

defined early in

protein assembly,

thus, the same

basic hydrat ion

be involved in

patt erns should

all cys/cys-loop

receptor sites.

to realize that, even though water molecules are il lustrated in specific locat ions, they are extremely dynamic

Glycine

25

26

GLYCINE BINDING ACTIVATED STATE HYDRATIONOPEN RECEPTOR SITEFOR GLYCINE

+

_

+R

_

C

W

+

+__

R

C

W

+

_

R

C

W

Strychnine 12f R t Bi d i SitHydration Quantization


17/28

Strychnine 12

23

Just as acetylcholine binds to i ts receptor p rotein t o close the site

and open a pore in nerve cell membrane to admit posit ive sodium

ions, glycine binds to a receptor prot ein to open a pore to admit

negative chloride ions. By binding to the glycine sit e in it s open

mentally, it appears, based on t he concept of quant ized l inear hydration,

that the relat ively-flat st rychnine molecule displaces a planar segment of hydrating water

molecules above t he ionic binding groups. With itscationicamine hydrogen bonded to the

sulfu r atom in front , it s aromat ic ring involved in charge transfer wit h t he other sulfu r atom

of t he argin ine behin d and below it , th e st rychnine molecule blo cks glycine

below it and it s amide group hydrogen-bonded to the cationic nit rogens

activation. As can

be seen from t he

models, the large

size of st rychnine

relati ve to gl ycine

is import ant t o

cover the sit e and

displace the water.

form, st rychnine blocks the sit e and t he opening of t he pore.

Although t he binding of st rychnine has not been defined experi-

OPEN BINDING SITEHYDRATION

STRYCHNINE BINDING

VIEWED FROM ABOVE

amide

HYDRATION OVERLAY

Strychnine

++

_

__

Glycine

+

R

_

C

W

+

+

R C

W

of Recepto r Bind ing Sites

Curare 13of Recepto r Bind ing SitesHydration Quantization


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Curare 3

Although the curare molecule is complex and d iffi cult t o view in the acetylcholine

should be included in any presentation on receptors. South American Indians dipped

receptor, it has received so much att entio n as a recepto r-bind ing agent, t hat i t

the points of t heir arrows and dart s in t he juice of an herb which contained d-tubo-curarine because it binds to the same receptor as acetylchol ine and nicot ine.

It keeps the bin din g site in its open state and p revent s the cont ract ion of m uscles. Its action isextremely

rapid when injected into t he blood stream.

As ill ustrated above, the molecule is a large ring comp osed of fou r

aromati c rings with cati onic amines at bot h ends. It is much larger than

cules in t he open site. When viewed on t he edge, as show n below, it

has a planar upper surface, like t he linear element of water it displaces

in t he site and its

cations are close

to t he two anionic

sulfur atoms of

ogy wit h plane-

ordered water.

it s spat ial anal-

the loop. Notice

the cysteines in

acetyl choli ne because it must d isplace a large number of water mole-

CURARE

+

+

BINDING SITE

CURARE BINDING

HYDRATION

VIEW

IDEALIZED

THROUGH

HYDRATION

ABOVE

ANALOG

OPEN ACETYLCHOLINE

_

CY

WC

W

of Recepto r Bind ing Sites


Enkephalin 14


19/28

28

One of the most intensely-stud ied physical maladies of man is pain. Herbs

and extracts of all kinds have been used to alleviate it and int ense studies

have been performed to nd more e ecti ve analgesic agents. However, it was

not unt il 1975 that Professor John Hughes isolated two pentapeptides from rat

brain which, when injected back int o brains, relieved pain. Thousands

of subsequent stud ies ill ustrated that t hese two central nervous system com-

pound s, methion ine enkephalin and leucine enkephalin, are the pri mary

receptor-binding agents which control the sensat ion of pain.

Although t he basic structures of the receptor proteins which bind t hese systemic agonist molecules and

analgesics like morphine and demerol are simi lar to t hose which bind dopamine, binding groups wit hin t he

sites appear to be di erent. In fact, a number of opioid receptor p roteins, with di erent binding propert ies,

have been isolated but limit ed data is available with regard to t he details of binding wit hin t he sit es.

Based on NMR studies, met enkephl in (tyrosine-g lycine-glycine-phenyl alanine-methionine) adopts several

conformat ions when suspended in a mixture of lip id and water but the spherical form shown above

is the one which most l ikely occupies a number of the receptor sites. In thi s form, about 60% of the

bond w ith groups around it i n the receptor sites. In order to illustrate bonding wit hin the site,

outer surface associates wi th lipid but most of i ts polar atoms are directed outward to hydrogen

the molecule has been oriented so t he t yrosine pept ide, T, and a glycine, G, are in f ront wi th t he

phenyl alanine, F, and methionine, M, behind . The cat ionic amine of tyrosine is on the left wi th

it s phenol ic oxygen close enough to the anionic carboxylate of methionine to be bridged by a single

water molecule where the negat ive charge is shown in the illustration.

of Receptor Binding Sit es Enkephalin

MET ENKEPHALIN

T

M

F

GG

+ _

27

30

29

An Opiat e Receptor Bin din g Site 15



20/28

In the upper view, the enti re 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 opiatesregulate many cellular funct ions, it is likely that

there are several di erent sets of binding groups.

Remember, even though t he water molecules are

pictured in a ridged latt ice, they are only probabil it y

posit ions; they continually move in and out of t he

sit e. Also, you should note that the enkephalin

molecule and hydration analog are somewhat

spherical like a bucky-ball.

As you can see in t he 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 t he hydrated site

shown below, while the tyrosine carbonyl and the

rst glycine bridge over to t he cysteine sulfur, C.

An Opiat e Receptor Bin din g Site

++

__D

D

K

K

CG

GA

D

Y

++__

of Receptor Binding Sit es


21/28

Naloxone 17of Receptor Binding Sit esHydration Quantization


22/28

the cysteine sulfur can bond chemically to the carbonyl carbon. This places the newly-formed hydroxyl in a posit ion t o

hydrogen-bond to t he neigboring hydroxyl. With the methyl group of t he alanine A rotated forward, the allyl group can

move foreward next to the helix and coordinate with t he proton on the neigboring alchhol. Since sulfhydr yl-formation is reversib le, naloxone binding is reversible but is more long-lasti ng than normal agonist b inding.

Like most recept or Active State Binding

Blocked State Binding

Active State Hydration

proteins, those which

bind morphine to pro-

duce analgesia alsobind antgonists to

block the e ects.

Naloxone, which is

to the opiate sit e, is

an extremely e ective

antagonist which not

pictu red above bound

only reverses the e ects

phine, but produces a prolonged blockade.

of agonists, like mor-

In the upper gure, naloxone is pictured bound to the site in a manner similar to morphine, wit h t he allyl

group on the nit rogen point ing toward the column in the back. However, sulfur atoms readily add to

carbonyl carbons to form sulfhydr yls so, by rotati ng t he right helix counter clockwise and the left helix clockwise,

31

Blocked State Hydration

+

+

__

A

A

A

A

of Receptor Binding Sit es

Steroidal Horm on e Receptor s 18of Receptor Binding Sit esHydration Quantization


23/28

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 funct ions and all are approx-

imately 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 t he gure at t he right ,

the cholesterol molecule simulates a linear hydration unit of nine

water molecules. It is int erest ing that the two vert ical water molecules are in t he spatial locations of

the two vert ical methyl groups in cholesterol . However, most of the cholesterol molecule is lipophi lli c,

so it is doubt ful t hat 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

by l inear segment s of six water molecules. Even

have lipophil lic central regions; receptor sit es

which binding them most likely are hydrated

though t heir structures are qui te simi lar, they

we will look at a testosterone binding site

which was reported by K. Pereira in 2006.

bind to di erent receptor proteins and produce

di erent physiological e ects. On next page,32

33

Testosterone

Estradiol Progesterone

Cholesterol

Steroidal Hormones

Androstendione

p g

Testost eron e Receptor 19of Receptor Binding Sit esHydration Quantization


24/28

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 surpri sing that many proteins migh t have formed at

random which could bind six hydrogen-bonded molecules.

As molecules move in and out of binding sit es, spec-

i c water molecules part icipate in the process. Only when

It is amazing that a receptor site, such as the one ill ustrated

on the right , could have evolved with glutamine-Q, arginine-R,

threonine-T and asparagine-B groups in precise posit ions to

bind the testosterone molecule. And yet , proteins did not

we accept the

fact that water

act ively parti c-

ti cipants in t he

processes, can

we begin to un-

derstand how

cells can function

in such an e c-

ient manner.

33

R

Q B

T

TESTOSTERONE

RECEPTOR BINDING

SITE

Ion Bin din g Sites 20of Receptor Binding Sit esHydration Quantization


25/28

most l ikely, water came rst. Thus far, we have emphsized the impor tance of linearit y in water but small ions

delocalize their charge by binding water molecules in concent ric spheres around them. When con-

As point ed out on t he previous page, one might conclude that space wit hin t he site was de ned by t he

testosterone molecule. However, we must remember, we are not dealing w ith the chicken and t he egg-

centrat ions of i ons such as sodium and calcium increase rapidly during depolarization in nerve and muscle

cells, free-water wit hin t he cells shif ts from i ts linear, rest ing-state orientat ion to a circularly-polarized

state and molecules wi thin rapidly shift to alternative conformat ions - it is the change in environmental water

Tetrototoxin, the extremely toxic pu er sh poison, mimics the spatial structure of Na(H O) . It binds

t ight ly to sodium-transpor t sit es prevent ing nerve-cells from going from rest ing to excit ed states. Likewise,

li ke Na(H O) , Ca(H O) and Cl(H O) , and their presence in water play a vital role in regulati ng cell function.

and the locati ons of ions which produce changes wit hin t he cells. Thus, binding sit es for hydrated ions,

the diureti c drug molecule, dihydrochlorothiazide, binds to sites in kidney-cell membranes which normally

bind the complex hydrated dichlor ide ion, (H O) Cl(H O) Cl(H O) . By blocking chlor ide ion upt ake

int o kidney cells, sodium ion up take is blocked and water around it is excreted int o t he ducts.

Until now, the coupling of electrons to form spat ial st ructures and provide for t he transfer of energy has

dominated science and technology. Hopefull y, th is presentation will draw att ention to t he fact that the coupl ing

of protons to form t ransient st ructural elements in l iquid water played a crit ical role in t he development o f

natural molecules; it plays a crit ical role in regulating t he mot ions and interactions of molecules and

ions in li ving cells and w ill play a crit ical role in a new age of advancements in medicine and technology.

+

+

_

-2

+22

2

2 2 2

2 26

6

3 35

6 6

34

36

35

37

References 21of Recept or Binding Sit esHydration Quantization


26/28

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