Sandwalk.blogspot.com Strands and Sheets

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M O N D A Y , M A R C H 1 0 , 2 0 0 8

β Strands and β Sheets

The &alphahelix is oneform of

secondarystructure inproteins.When apolypeptidechaincontains therightsequence of amino acidsit can adopt

a helicalconformation.

There areother conformations commonly found in proteins. One of them is the β structure, which is characterized by longextended polpeptide chains in contrast to the compacthelix of the α helix. Single β strands are rarely found inproteins because the structure is not that much morestable than a random coil. However, when two adjacent β

strands line up they can from bridges of hydrogen bonds.This creates a very stable structure known as a β sheet.In the example shown (left) three parallel β strands lineup edge to edge to form a highly stable sheet withmultiple hydrogen bond (shown in yellow).

β sheets can also be formedwhen antiparallel β strandsalign edge to edge. As amatter of fact, the antiparallelconformation is more stable,

and more common, than theparallel conformation.

β strands are usually drawn

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SANDWALKS T R O L L I N G W I T H A S K E P T I C A L B I O C H E M I S T

L A U R E N C E A . M O R A N

Larry Moran is a Professor inthe Department of

Biochemistry at the University

of Toronto. You can contact

him by looking up his email

address on the University of

Toronto website.

S A N D W A L K

The Sandwalk is the path

behind the home of Charles

Darwin where he used to walk

every day, thinking about

science. You can see the path

in the woods in the upper left-

hand corner of this image.

R E C E N T C O M M E N T S

Page 1 of 19Sandwalk: β Strands and β Sheets

27/9/2011http://sandwalk.blogspot.com/2008/03/strands-and-sheets.html



as wide arrows with the tip of the arrow head representingthe C-terminal end of thepolypeptide chain. As shownin the cartoon on the right,the strands are often twisted

and the amino acid sidechains project above andbelow the plane of the βstrand.

The amino acid compositionof β strands tends to favorhydrophobic (water fearing) amino acid residues. The sidechains of these residues tend to be less soluble in waterthan those of more hydrophilic (water loving) residues. Asyou might imagine, β structures tend to be found inside

the core structure of proteins where the hydrogen bondsbetween strands are protected from competition withwater molecules.

One of the common motifs in proteins is the β sandwich,formed when two β sheets are stacked on top of oneanother. The example shown below is the coat protein of grass pollen grains [PDB 1BMW]. For those people whoare allergic to grass pollen, this protein is the main culprit.This example is the simplest form of a β sandwich sinceeach sheet consists of only two β strands.

In order to appreciatewhy this is such a stable(and common) motif weneed to add in the aminoacid side chains. (Theyare usually ignored in thekinds of structures shownabove so we can tracethe polypeptide

steve oberski wrote...@DennyIt's all in your tummy.Belief in God Boils Downto a Gut FeelingBy STEPHANIEPAPPAS - LIVESCIENCE.COMhttp://www.livescience.com/16151-god-belief-intuition.html

steve oberski wrote...@Denny Besides, I can’t figureout how atheists/naturalists/evolutionists

would be better at traversing thesedisciplines, if they insist that oneof the most common traits of humans doesn’t exist...Continue >>

steve oberski wrote...Ian H Spedding By presuming itsright to life you are keeping openthe unborn's options until ithas reached the stage when it canchoose for itself.By completely

denying the rights of the mother...Continue >>

Denny wrote... Allan, re. your comments about“Common Descent - we arelooking at the tips of a vastbranching tree.” A lot of us nolonger see a conventionalmetaphorical ‘tree of life’ thatshows simple life at...Continue >>

Allan Miller wrote...@Denny,I agree that “traversingthese disciplines with equal clarityand ease” is a challenge. That’s afocus of RTB – to bring together all the aspects of human life(natural, supernatural, personal...Continue >>

Denny wrote...Larry Moran said... “It's crap.Her last article—the only one Iread—contains factually incorrectstatements andmisrepresentations of the scientificliterature. That's typicalbehavior for...Continue >>

Denny wrote... Allan. Your word picture is helpful,but I never saw an illustration with“evolutionary theorists” at thecentral core.” When I think of theultimate meaning of life (not thenarrow focus of...

P R I N C I P L E S O F

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E D I T I O N





backbone.) In the figureon the right I've drawnthe hydrophobic sidechains in blue so you cansee how they clustertogether to form the

interior "filling" of thesandwhich. You can thinkof these hydrophobicregions as being like the oil in a mixture of oil and water.The oil droplets tend to come together to exclude thewater molecules. Similarly, the hydrophobic residues tendto come together in the middle of the protein and excludewater molecules. This is called hydrophobic interactionand it's one of the dominent weak forces n biochemistry.

Most proteins are made up of combinations of α helices

and β strands. The third kind of secondary structure isturns.

[Figures are from Horton et al. (2006) © Laurence A. Moran,

Pearson/Prentice Hall]

Horton, H.R., Moran, L.A., Scrimgeour, K.G., perry, M.D.and Rawn, J.D. (2006) Principles of Biochemisty .Pearson/Prentice Hall, Upper Saddle River N.J. (USA)

POSTED BY LARRY MORANAT 3:56 PM

LABELS:BIOCHEMISTRY

2 C O M M E N T S :

Some readers of this blogmay be under theimpression that my

personal opinionsrepresent the official

position of Canada, the

Province of Ontario, theCity of Toronto, theUniversity of Toronto, theFaculty of Medicine, or the Department of Biochemistry. All of theseinstitutions, plus every single one of my colleagues, students,friends, and relatives,want you to know that I do not speak for them.You should also know that they don't speak for me.

R E C E N T P O S T S

The Protein Engineer Sep 26, 2011 Two former undergraduatestudents of mine have started ablog called The ProteinEngineer.A blog started by twograduate students, 11000kilometres apart, on a quest todiscover, or otherwise...

Continue >>

Countries That ExecuteTheir Own CitizensSep 22, 2011 Most civilized, democraticcountries have abolished capitalpunishment. This is especially trueof those countries with a Christiantradition.The last execution inCanada took place in 1962 and...Continue >>

When Will They Ever Learn?Sep 17, 2011 In my class on ScientificMisconceptions and Controversies

we discuss the ways in whichscientific reasoning is used and

mwcsaid...

That's a good introduction to this structural element.I especially liked the discussion of amphipathicity instrands. Showing an integral membrane protein likeporin might reinforce the point, while also displaying

part of the great diversity of structures possible withβ strands.

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Tegumai Bopsulai, FCD said...

Web site aims to help mail-order brides"TORONTO (Reuters) - Canada can be a bewildering,even frightening place for immigrant women whoarrive as mail-order or Internet brides, but now they

have a new Web site to help smooth thetransition..."

THURSDAY, MARCH 13, 2008 9:32:00 AM





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The old argument of design in nature, as givenby Paley, which formerly seemed to me to be soconclusive, fails, now that the law of natural

selection has beendiscovered. We can nolonger argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, likethe hinge of a door by man. There seems to beno more design in thevariability of organic beings and in the actionof natural selection, thanin the course which thewind blows.

Charles Darwin(c1880)





Although I am fully convinced of the truth of the views given in thisvolume, I by no meansexpect to convinceexperienced naturalistswhose minds are stocked with a multitude of facts

all viewed, during a longcourse of years, from a

point of view directly opposite to mine. It is soeasy to hide our ignorance under suchexpressions as "plan of creation," "unity of design," etc., and to think that we give anexplanation when weonly restate a fact. Any one whose dispositionleads him to attach moreweight to unexplained

difficulties than to theexplanation of a certainnumber of facts will certainly reject thetheory.

Charles Darwin (1859)

Science reveals wherereligion conceals. Wherereligion purports toexplain, it actually resorts to tautology. Toassert that "God did it" is

no more than anadmission of ignorancedressed deceitfully as anexplanation...

Peter Atkins

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continue to do so,because its large realmand legitimate claimshave been so poorly attended by evolutionary scientists who cannot

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discern the beat of thisdifferent drummer whiletheir brains and earsremain tuned to only thesounds of general theory.

Stephen Jay Gould (2002) p.1339

The essence of Darwinism lies in itsclaim that natural selection creates the fit.Variation is ubiquitousand random in direction.

It supplies raw material only. Natural selectiondirects the course of evolutionary change.


Rudyard Kipling asked how the leopard got its

spots, the rhino itswrinkled skin. He called his answers "just-sostories." Whenevolutionists try toexplain form and behavior, they also tell ust-so stories—and the

agent is natural selection.Virtuosity in inventionreplaces testability as thecriterion for acceptance.


Since 'change of genefrequencies in

populations' is the'official' definition of evolution, randomnesshas transgressed Darwin's border and asserted itself as anagent of evolutionary change.


The first commandment for all versions of NOMA

might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important eventsin the history of natureby special interferenceknowable only throughrevelation and not accessible to science." Incommon parlance, werefer to such special interference as"miracle"—operationally defined as a unique and temporary suspension of natural law to reorder thefacts of nature by divinefiat.






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My own view is that conclusions about theevolution of humanbehavior should be based on research at least asrigorous as that used instudying nonhumananimals. And if you read the animal behavior ournals, you'll see that

this requirement sets thebar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry CoyneWhy Evolution Is True

I once made the remark that two thingsdisappeared in 1990: onewas communism, theother was biochemistry and that only one of themshould be allowed tocome back.

Sydney BrennerTIBS Dec. 2000

It is naïve to think that if a species' environment changes the species must adapt or else becomeextinct.... Just as achanged environment need not set in motionselection for new adaptations, new adaptations may evolvein an unchangingenvironment if new mutations arise that aresuperior to any pre-existing variations

Douglas Futuyma

One of the most frightening things in theWestern world, and inthis country in particular,is the number of peoplewho believe in things that are scientifically false. If someone tells me that theearth is less than 10,000years old, in my opinionhe should see a

psychiatrist.

Francis Crick





There will be no difficulty in computers beingadapted to biology. Therewill be luddites. But they will be buried.

Sydney Brenner

An atheist before Darwin

could have said, followingHume: 'I have noexplanation for complex biological design. All I know is that God isn't agood explanation, so wemust wait and hope that somebody comes up witha better one.' I can't helpfeeling that such a

position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might

have been logically tenable before Darwin,Darwin made it possibleto be an intellectually fulfilled atheist

Richard Dawkins

Another curious aspect of the theory of evolution isthat everybody thinks heunderstand it. I mean

philosophers, social scientists, and so on.While in fact very few

people understand it,actually as it stands, evenas it stood when Darwinexpressed it, and evenless as we now may beable to understand it inbiology.

Jacques Monod

The false view of evolution as a process of global optimizing hasbeen applied literally by engineers who, taken in

by a mistaken metaphor,have attempted to find globally optimal solutionsto design problems by writing programs that model evolution by natural selection.

Richard Lewontin


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Sandwalk.blogspot.com Strands and Sheets