To Fold Or Not To Fold?

An exploration ofthe exciting worldof protein folding for high school chemistry or biology teachers and students.

Claudia Winkler and Gary Benz

Animation of the folding of villin, a well known protein

Activity 1 - Vocabulary Sharpen your skills!• What do the following words mean:

amino-acids, bonds, carbon, folding, hydrogen, nitrogen, oxygen, protein, polymer, residue, sulfur, synthesize, villin?

• We will briefly explore their meaning in the next few pages, so that the concepts we are introducing in the slides ahead might be clearer.

Vocabulary: Amino-Acid• Amino-acids are the building

blocks of proteins. • They are characterized by

the presence of a carboxyl group (COOH) and an amino group (NH3) attached to the same carbon (called alpha carbon).

• The letter R represents succinctly the “rest” to which the amino-acid group is attached.

Vocabulary: Chemical Bonds• Except for noble gases which have achieved the state of

“nirvana” for their atoms, i.e. they have a complete outer shell of electrons, all other elements in nature pair up with other elements to complete their outer shell. This process is called “chemical bonding”.

• Bonds most relevant to organic chemistry are: covalent bonds and hydrogen bonds.

– Covalent bonds are characterized by sharing of electrons between the atoms “bonding with each other” to form a molecule.

– Hydrogen bonds keep together polar molecules, i.e. molecules which have uneven distribution of electric charge.

– Hydrogen bonds can also occur between part of the same

polymer when there is charge polarity between different parts of the polymer.

Vocabulary: Carbon• (Latin: carbo, charcoal)

Carbon, an element of prehistoric discovery, is very widely distributed in nature. It is found in abundance in the sun, stars, comets, and atmospheres of most planets.

• Carbon is the source of energy for life through carbohydrates, just like a burning log is a source of energy to a cold room.

Atomic number

6

Atomic Symbol C

Atomic mass 12.011 u

Electron Configuration

[He]2s22p2

Vocabulary: Hydrogen• (Greek: hydro, water,

and genes, forming) Hydrogen is the most abundant of all elements in the universe.

• The heavier elements were originally made from Hydrogen or from other elements that were originally made from Hydrogen.

• Used in rocket fuel.

Atomic number

1

Atomic symbol

H

Atomic mass 1.0070 u

Electron Configuration

1s1

Vocabulary: Oxygen• Greek: oxys, sharp, acid,

and genes, forming; acid former) Oxygen is the third most abundant element found in the sun. Oxygen is vital to the respiration of living organisms.

• Oxygen is responsible for the bright red and yellow-green colors of the Aurora.

• Essential element for combustion (i.e. burning).

Atomic number

8

Atomic symbol

O

Atomic mass 15.9994 u

Electron Configuration

[He]2s22p4

Vocabulary: Nitrogen• (Latin Nitrum, Greek.

Nitron, native soda; genes, forming)

• Nitrogen gas (N2) makes up 78.1% of the Earth’s air, by volume.

• Nitrogen is found in all living systems as part of the makeup of biological compounds.

• Ammonia (NH3) is the most important commercial compound of nitrogen, with a very pungent smell, used in cleaning supplies.

Atomic number

7

Atomic symbol

N

Atomic mass 14.00674

Electron Configuration

[He]2s22p3

Vocabulary: Sulfur• (Sanskrit, sulvere; Latin

sulpur) Known to the ancients; referred to in Genesis as brimstone.

• Sulfur occurs native in the vicinity of volcanoes and hot springs.

• It is widely distributed in nature in various minerals (iron pyrites, galena, sphalerite, cinnabar, stibnite, gypsum, epsom salts, celestite, barite, etc.)

• Sulfur is found in meteorites.

Atomic number

16

Atomic symbol

S

Atomic mass 32.6

Electron Configuration

[Ne]3s23p4

Yellowstone hot springs

Vocabulary: Proteins• Proteins are necklaces of amino acids, i.e. long chain

molecules. Proteins are the basis of how biology gets things done.

• As enzymes, they are the driving force behind all of the biochemical reactions which makes biology work.

• As structural elements, they are the main constituent of our bones, muscles, hair, skin and blood vessels.

• As antibodies, they recognize invading elements and allow the immune system to get rid of the unwanted invaders.

Vocabulary: (Protein) Folding• Proteins are formed by unique sequences of

amino-acids. However, only knowing the sequence tells us little about what the protein does and how it does it.

• In order to carry out their function (for instance as enzymes or antibodies), proteins must take on a particular shape, also known as a "fold." Thus, proteins are truly amazing machines: before they do their work, they assemble themselves! This self-assembly is called "folding."

Vocabulary: Polymer• Polymers are chemical compound

with high molecular weight consisting of a number of structural units (called monomers) linked together by covalent bonds.

• A structural unit is a group having two or more bonding sites.

• Many polymers occur in nature, such as silk, cellulose, caoutchouc (latex), which is natural rubber coming from the rubber tree, and proteins. Many others are man made (such as plastic), foam.

Rubber tree

Vocabulary: Residue• When amino acids connect with each

other to form a a specific protein, they do so through a special kind of covalent bond that is called “peptide bonds”.

• In the formation of the bond, water is released. What remains is called a “residue”. Residues are the beads of the necklace we introduced before.

Vocabulary: Synthesize

• To synthesize means to bring together. In chemistry it means to make a product from other products.

• For instance A+B -> C means that element A is added to element B to synthesize element C.

• Since the incredible development of Organic Chemistry in the 1900s, thousands of new compounds have been synthesized, in the fields of textiles, building materials, plastic, paints, cosmetics, etc.

Vocabulary: Villin• Villin is a protein that

gives structure to intestinal villi (shown in the model to the right).

• Intestinal villi augment

the surface of the intestine to increase food absorption.

• However intestinal villi need to be “stabilized”, to add rigidity.

Why Villin?

• We chose villin as a model for protein folding.

• Villin is a well known protein whose folding processes have been studied and are understood among the scientific community.

Villin is a protein• It is made up of 36 amino acid “residues”.

• It has been heavily studied experimentally and by simulation since it is perhaps one of the smallest, fastest folding proteins.

What makes proteins different from each other?• Proteins are synthesized as linear

polymers (i.e. chains) of amino acids.

• Once formed, the protein chain, does not remain straight for long.

Form determines function

• Suppose you have some molten iron. You may turn it into nails, hammers, wrenches, etc. What makes these tools different from each other is their form (i.e. their shape and structure)

• Similarly proteins, though basically being built as similar chains of amino acids, very rapidly fold onto their own “correct” form, so as to be able to carry out the function that is assigned to them

Folding is critical• When proteins do not fold correctly (i.e. they "mis-

fold") there can be serious effects, including many well known diseases, such as Alzheimer's, mad cow disease (also known as Creutzfeldt-Jakob disease, prions, bovine spongiform encephalopathy, scrapie) and Parkinson's disease.

• Understanding protein folding is critical in the medical and clinical professions and as such it is the subject of extensive research.

Villin folds• Immediately after the villin

polymer is synthesized, it starts to fold over itself to form a perfectly defined geometrical structure.

• There is only one “correct” shape that villin can fold into to perform its biological actions.

Villin model

• To represent folding in villin, we have built a model.

• The purpose of this model, to be displayed on the floor of the Exploratorium, is to simulate the correct folding of villin.

Activity 2: Building a model

• You will build a villin model which simulates the proper folding of villin.

• “Snack” description

Protein folding time scale• Proteins self-assemble, i.e. fold,

amazingly quickly: some as fast as a millionth of a second.

• While this time is very fast on a person's timescale, it's remarkably long for computers to simulate.

Why is protein folding difficult to simulate on a computer?

• It takes about a day to simulate a nanosecond (1/1,000,000,000 of a second) on a computer.

• Unfortunately, proteins fold on the tens of microsecond timescale (10,000 nanoseconds).

• Thus, it would take 10,000 CPU days to simulate folding -- i.e. it would take 30 CPU years! That's a long time to wait for one result!

A Solution: Distributed Dynamics

• Dr. Pande’s group at Stanford University has developed a new way to simulate protein folding by dividing the work between multiple parallel processors in a new way -- with a near linear speed up in the number of processors. Thus, with 1000 processors, it is possible to break the microsecond barrier and help unlock the mystery of how proteins fold.

• The parallel processors are personal computers connected to the web. The computational power of these computers is used when they are in an idle state.

Folding@Home

• Folding@Home 1.0 has been a success. During the one year period from October 2000 to October 2001, Dr. Pande’s groups was able to computationally fold several small, fast folding proteins, with experimental validation of our method.

• They are now working to further develop their method, and to apply it to more complex and interesting proteins and protein folding and misfolding questions.

Folding@Home • Everybody can help the project by

downloading and running our client software on their computer

• For every computer that joins the project, there is a commensurate increase in simulation speed.

• Download the software now and be part of an exciting research that can benefit advancements in medicine and biology!

Using the down time of your computer connected to the web

• The Folding@Home client (console or screen saver) shows real time visualizations of the protein simulations being performed.

• The molecule drawn is the current atomic configuration ("fold") of the protein being simulated on your computer.

Suggested reading for teachers and students

• Michael Crichton, Prey, Harper Collins, 2002

• How the cows turned mad, Maxime Schwartz, University of California Press, 2003

• Jeremy Cherfas, The human genome, Dorling Kindersely, 2002

• Mark Ratner & Daniel Ratner, Nanotechnology, Prentice Hall

Credits

• CPIMA provided leadership and vision.

• Dreyfus Foundation provided financial support.

• The Exploratorium in San Francisco supported us a hands-on approach to science philosophy.

Thank you !