The cell's ironing: protein folding and folding surveillance

Proteins are highly organised structures: they're folded into particular conformations;associated with other protein subunits and have different levels of organisation (see previous post).

But how do they achieve their folded state?

(1) How do proteins fold?

We all like help-so do proteins

Sometimes it is easier when someone helps you fold away your clothes. Same for proteins-yes they are largely self-folding. But what happens when this goes wrong?

Chaperones are part of the cell’s emergency services attending various accidents (misfolded proteins) but in a disaster they all flood to the scene (when a cell is under stress).Many chaperones are heat shock proteins (Hsp) and are highly abundant when a cell is under stress (during nutrient starvation, extreme temperatures, exposure to toxins etc).

Aggregates can easily form when hydrophobic regions of the protein can end up on the outer surface of the misfolded or partially folded protein and will attract other misfolded proteins with exposed hydrophobic residues (as the cell has an aqueous environment the water fearing residues want to bury themselves in the core of a protein).  In a living cell it not just empty space (imagine trying to fold your washing in a crowd without elbowing anyone!). Chaperones help the protein fold in the most energetically favorable way as well as preventing the unwanted binding of other proteins during the folding process.

Some molecular chaperones (Chaperonins-Hsp60) act like a huge tent in the middle of the crowd where you can fold your washing without people getting in the way. They completely isolate the protein from the environment of the cytosol.

(2)Bacterial  Hsp60 (GroEL) and associates Hsp10 (GroES)

Whilst other chaperones (Hsp70) bind to a region of the protein to aid folding like having a group of people who are designated to aid in folding of washing-it is their job.

(3) Hsp70 binds to hydrophobic regions to aid folding

Chaperones are not just involved in folding they’re also important for unfolding, refolding and trafficking.  Chaperones work by an ATP* dependent mechanism: they bind to hydrophobic regions of a misfolded (non-native) protein.

One size of chaperone doesn't fit all:
There are different classes of molecular chaperones (they are usually classified by their molecular weight).  Hsp60 (chaperonins) ,Hsp70,Hsp90 and Hsp100 systems. The numbers indicate the molecular mass of each Hsp protein subunit.

Focusing on the chaperones involved in protein folding:  namely- Hsp60,70 and 90.
They generally act under two systems Hsp70 and Hsp60 (chaperonins).

Hsp70 interacts with newly synthesised proteins and releases them . Whilst chaperonins  (Hsp60) are large cylindrical protein complexes ( figure 3) (composed of several polypeptide chains-quarternary structure: an outfit (see previous post)).They enclose the proteins for folding. The two systems act sequentially Hsp70 act on newly synthesised proteins and then chaperonins assist folding of proteins that do not reach their correct folded state by Hsp70 alone.

So imagine you (Hsp70)are folding your washing and your Mum (Hsp60) is stood by your side and when something is difficult to fold or you have not folded it correctly your Mum takes over to ensure correct folding.

The Hsp90 system functions downstream of Hsp60. It acts in the late folding stages of proteins involved in cellular signalling and development. Both Hsp70 and Hsp90 can direct proteins for degradation.

It is now like your Grandma (Hsp90) has joined the folding party; smoothing out the creases of odd item that your Mum (Hsp60) has missed.

Folding avoids creases but what does it mean for proteins?

When proteins fold they gain a particular shape which is important for the function of that protein. It may allow it to associate with other proteins to form a complex.

It has been suggested that the decline in the cell’s ability to correctly fold proteins and maintain correct protein folding (proteostasis) declines with age. This can allow the formation of protein aggregates which are involved in many neurodegenerative diseases such as Alzheimer’s and Parkinsons disease. Finding out more about chaperone mediated surveillance of proteins is vital as these diseases become more prevalent in our aging society.

(4) Comparison of a healthy neuron with a Alzheimer's neuron with protein aggregates ( Beta amyloid plaques and neurofibrillary tangles)

*ATP= Adenosine triphosphate is the energy currency of the cell. It is a phosphorylated nucleotide that is made and consumed by all cells and drives chemical reactions

References

Hartl F, Bracher A, Hayer-Hartl M., 2011. Molecular chaperones in protein folding and proteostasis., Nature reviews., 475., pp324-332

Lodish H et. Al., 2008., 6^th Ed., Molecular cell biology., W.H.Freeman., New York

Saibil H., 2013. Chaperone machines for protein folding, unfolding and disaggregation., Nature reviews., 14., pp631-632

Images

(1) Left: https://thelaundrycenter.com/blog/tag/wash-and-fold-laundry-service/

      Right: http://ocw.mit.edu/courses/biology/7-343-protein-folding-misfolding-and-human-disease-fall-2004/

(2) Left: http://www.terra-nova.co.uk/tents-and-spares/tent-inner/

     Right: http://www.tulane.edu/~biochem/med/groel.gif

(3) Top: http://www.singaporelaundry.com/articles/how-to-fold-clothes.html

      Bottom: http://www.pnas.org/content/103/16/6166/F1.expansion.html

(4) https://sites.google.com/site/bme365ralzheimers/pathophysiology

If proteins were in my wardrobe: folding and organisation

So my blog has been very quiet (apologies). A new start to the academic year so a new blog post!


When you open your wardrobe, how does it look?

Like this?

(1) Clean and tidy

...Or admittedly more like this?

(2) Disorganized and messy

Many things in molecular cell biology can appear rather chaotic on the surface. Proteins look like highly higgledy piggledy molecules. When  actually they’re pretty organised things: structurally complex and sophisticated molecules of life.

How the cell folds its wardrobe

Amino acid sequence: The shape of a protein is determined by its amino acid sequence (primary structure)- the threads of the garments (20 types in total). They can be grouped into different categories according to their side chains-acidic, basic, uncharged polar and nonpolar.

(3) 20 Amino acids 

Non covalent bonds also influence the folding of proteins: hydrogen bonds, ionic bonds and Van der Waals attractions.

Environment: The cell has a very aqueous environment which affects a proteins shape, making it very compact. The non polar side chains are hydrophobic (water-fearing) bury themselves in the core of the proteins whilst the polar (hydrophilic- water-loving) side chains interact with water and so tend to gather on the outside of the protein.

When completing a task we often look for the easiest way to accomplish the task with minimal cost (whatever that may be) Proteins do the same: they fold into a shape of the lowest energy (i.e energetically favourable to maintain- the easiest way to fold).

Organisation of protein structure

Unlike my wardrobe proteins have a very organised structure that can be broken down into four categories:

(4) Categories of protein structure 

Many proteins have large structures (of one very long string on amino acids folded up) which gives a further unit of organisation: the protein domain.

 This is a length of the protein which is between 40 and 350 amino acids (stitches) in length. This length folds independently to the other regions of the protein like different parts of a shirt (collar, sleeve,  the pocket) are all still part of one shirt but and useless on their own yet still independent.

Different protein domains often are associated with different functions.

Items in a cells wardrobe (some examples)

Src protein kinase:  One of the many secretaries of the cell. It acts in signalling cascades by adding phosphate groups from high energy donor molecules like ATP to substrate molecules.
A protein formed of four different domains (each has a different function).

The SH2 and SH3 domains are involved in regulation whilst the catalytic domain and the activation loop play a role in the catalytic activity of the kinase.

(5) Src Kinase Hck

Haemoglobin: Found in red blood cells and vital for the transport of oxygen around the body and also has roles in the transport of carbon dioxide and hydrogen ions. It is a multi-subunit protein: two α subunits (two protein chains of 141 amino acids-stitches) and two β subunit (two protein chains of 146 amino acids-stitches).

(6) Haemoglobin

So next time you open your wardrobe to put your clean clothes away (freshly synthesized (nascent) proteins) think about how organised our cells are: folding proteins and packaging them to be sent to various locations within the cell. How organised is your wardrobe?

Upcoming posts
More about protein organisation and folding-why and the cellular machinery involved
What happens when folding goes wrong?

References

Alberts B et al., 2008., 5^th Ed., Molecular biology of the cell., New York., Garland Science

Berg  J et al., 2011., 7^th Ed., Biochemistry., New York, W. H. Freeman

Images

(1)  (https://www.flickr.com/photos/8011986@N02/4211768335/)

(2) (http://imgarcade.com/1/messy-bedroom/)

(3) (http://www.personal.psu.edu/staff/m/b/mbt102/bisci4online/chemistry/chemistry8.htm)

(4) (Adapted from: http://en.wikipedia.org/wiki/Protein_structure_prediction)

(5) (Adapted from: http://mysbfiles.stonybrook.edu/~tomiller/dualrole.htm)

(6) (Adapted from: http://www.rcsb.org/pdb/general_information/news_publications/newsletters/2004q4/education_corner.html)

I'm sorry, bio-what??!!-A brief plug for biochemistry

University is a time where you meet lots of new people. Being in a new city and getting involved in a new community. You get asked the three questions a zillion times:

1)What's your name?

2)Where are you from?

3)What are you studying?



A tip for you all!

 

Okay so I study biochemistry. But I thought I'd give an insight into how diverse a subject it is.

Biochemistry is not quite a fusion of your biology and chemistry lessons you might've had at school
It is much more than that!

Biochemistry is at the heart of many areas of the life sciences such as genetics, cell biology, energy and metabolism, plant biology and development of disease.

Lubert Stryer, the famous biochemist and author of Biochemistry (W.H. Freeman & Co.), states that biochemistry is “rapidly progressing from a science performed almost entirely at the laboratory bench to one that may be explored through computers. Its practical approach applies the molecular aspects of chemistry to the vast variety of biological systems."

 The thing I love about studying biochemistry is taking a 'simple' cell and finding out the intricate mechanisms that enable that cell to function. For example protein synthesis: DNA is transcribed into messenger RNA (ribonucleic acid, a molecule similar to a single strand of DNA). The code of bases that the mRNA contains is transcribed by ribosomes into a chain of amino acids joined by peptide bonds a.k.a a protein.

That may sound simple summarised in just a few short sentences.But it's far from it!  And that is only one example!

Molecular biology shows that there is to life that meets the eye which makes me feel privileged to be studying biochemistry.

Upcoming posts
Sugar and sweetners-What's the difference?