Nanoscale machines in nature

Part two of the Biology brief in The Economist is Cells and how to run them: All life is made of cells, and cells depend on membranes

A few of the main ideas are the following. Cells are either prokaryotic (bacterium) or eukaryotic (animals). Cell membranes are made of lipids that spontaneously form structures due to an interplay between hydrophobic and hydrophilic interactions. The boundary of prokaryotic cells is the membrane. Eukaryotic cells are more complex, containing many organelles (mitochondria), whose boundary are membranes.

Cells are little factories that can multiply themselves and perform distinct biological functions. It requires energy to maintain the cell shape and for it to manufacture new things. Inside and out is maintained by a difference in the concentration of protons (hydrogen ions) across the membrane. There are two aspects to this. First, the electron transport chain produces the protons. Second, a specific protein in the membrane, ATP synthase, pumps protons across the membrane.

The electron transfer chains are driven either by respiration or photosynthesis. 

Energy for processes in the cell is provided by breaking ATP down to ADP. The reverse process is driven by the kinetic energy of rotation (at about 6000 rpm) of the part of the ATP synthase protein.  ATP is Adenosine triphosphate.

To me the amazing/awesome/cool/miraculous thing is what the hardware can do. These are nanoscale chemical machines and factories. The video below shows a simulation of the ATP synthase protein that is located within cell membranes. It acts as a proton pump to maintain the concentration imbalance between the outside and inside of the cell and to convert ADP to ATP.

I learnt from this how the ATP synthase spins in only one direction and the rotation corresponds to sequential conformational changes in the protein subunits.

There is a beautiful discussion of the underlying physics in a chapter in Biological Physics by Phil Nelson. I have written a brief summary here.

The underlying quantum chemistry is explored in

Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase

Shayantani Mukherjee and Arieh Warshel

The beautiful mathematics and physics of virions

Next Monday I am giving a seminar, ``The mathematics and physics of virions", for the virtual Pandemic Seminar of the UQ School of Mathematics and Physics. Most of the talks so far have been about modeling the spread of the virus and the effect of social distancing measures. In contrast, I will look at phenomena at a much smaller scale.

The past month I have taken a crash course in what is known about the structure and properties of virions (single virus nanoparticles). There is some fascinating and beautiful mathematics and condensed matter physics involved. A nice place to start is this short animation video that shows how the Dengue fever virus replicates itself.



Three important questions for any virus are the following.

1. What is the structure of the virion?
In particular, what is the structure of the viral capsid, i.e. the protein shells that encapsulate the genome of the virus?

2. How does the capsid self assemble?

3. How is the genetic material packaged inside the capsid?

Handwashing with sanitiser works because hydrophobic interactions cause the breakup of the membrane that encases the virion. This is the same soft matter physics as when soap removes dirt.

The role of anti-viral drugs is to interrupt/sabotage any of the steps in the multi-step process of the action or duplication of the virion. Thus, finding answers to any of the three questions above may facilitate the development of anti-viral drugs or vaccines.

Here are a few of the articles I have found fascinating and helpful.

Geometry as a Weapon in the Fight Against Viruses
Reidun Twarock

On Virus Growth and Form 
Roya Zandi, Bogdan Dragnea, Alex Travesset, Rudolf Podgornik

TRIM5α self-assembly and compartmentalization of the HIV-1 viral capsid 
Alvin Yu, Katarzyna A. Skorupka, Alexander J. Pak, Barbie K. Ganser-Pornillos, Owen Pornillos, Gregory A. Voth

The figure below (taken from the second article above) shows the structure of the capsid of five different virions. The number of proteins in all of them is an integer multiple of 60.

Left to right: Satellite Tobacco Mosaic virus (composed of 60 proteins); L-A virus (120 proteins); Dengue virus (180 proteins); Chlorosome Vigna virus (180 proteins); Sindbis virus (240 proteins).

In the next post, I will explain the geometric origin of this quantisation.

Bouncing soap bubbles

My wife and I are often looking for new science demonstrations to do with children. The latest one she found was "bouncing soap bubbles".



For reasons of convenience [laziness?] we actually bought the kit from Steve Spangler.
It is pretty cool.

A couple of interesting scientific questions are:

Why do the gloves help?

The claim is that the grease on your hands makes bursting the bubbles easier.

Why does glycerin make the soap bubbles stronger?

Why does "ageing" the soap solution for 24 hours lead to stronger bubbles?

Journal of Chemical Education is often a source of good ideas and science discussions. Here are two relevant articles.

Clean Chemistry: Entertaining and Educational Activities with Soap Bubbles 
Kathryn R. Williams

Soap Films and the Joy of Bubbles
Mary E. Saecker

The challenge of writing books on water

Biman Bagchi has just published a new book,
Water in Biological and Chemical Processes: From Structure and Dynamics to Function 

Cambridge University Press sent me a complimentary copy to review. I am slowly working through it and will write a detailed review when I am done.

I think this is a very challenging subject to write a book on for at least three reasons. First, the scope of the topic is immense. Furthermore, it is multi-disciplinary spanning physics, chemistry, and biology, with a strong interaction between experiment, theory, and simulation. Second, although there have been some significant advances in the last few decades there is real state of flux, with a fair share of controversies, advances, and fashions. Finally, which audience do you write for? Experimental biochemists or theoretical physicists or somewhere in between.

Although this is an incredibly important and challenging topic few authors have taken up the challenge. One who has is Arieh Ben-Naim

Molecular Theory of Water and Aqueous Solutions, Part I: Understanding Water (2009)

Molecular Theory of Water and Aqueous Solutions Part II: The Role of Water in Protein Folding, Self-Assembly and Molecular Recognition (2011)

This was a topic of great interest to my late father. He wrote two comprehensive reviews with John Edsall, published in Advances in Biophysics

Water and proteins. I. The significance and structure of water; its interaction with electrolytes and non-electrolytes (1977) [does not seem to be available online]

Water and proteins. II. The location and dynamics of water in protein systems and its relation to their stability and properties (1983)

Classic earlier books include:

The Structure and Properties of Water
 by David Eisenberg and Walter Kauzmann
(1969, reissued in 2002 by Oxford UP in their Classic Texts in the Physical Sciences)

A seven volume series, Water: A comprehensive treatise, edited by Felix Franks

At the popular level there is
Life's Matrix: A Biography of Water 
(2001) by Philip Ball

Questions about protein folding

What is the physical code that relates the amino acid sequence to a proteins native structure?
How do proteins fold so fast?
Can protein structure be computationally predicted?

These are highlighted as key questions in a nice readable review in Science The Protein Folding problem, 50 years on by Ken Dill and Justin MacCallum.

The article gives a sober assessment of limited but significant achievements and the substantial challenges ahead.

Why you might worry about classical models of water

A nagging question for the whole field of (classical) molecular dynamics simulations of biomolecules is whether they can have an adequate description of water. This is particularly important because almost all biomolecular processes involve subtle interactions of the biomolecule of interest with its aqueous environment.

I learnt a lot from reading the article On the origin of the redshift of the OH stretch in Ice Ih: evidence from the momentum distribution of the protons and the infrared spectral density, by C. J. Burnham, G. F. Reiter, J. Mayers, T. Abdul-Redah, H. Reichert and H. Dosch.

They highlight several problems and state:

Clearly there is something missing from water models. All of the above difficulties have been consistently tackled by experimentalists, but they remain either unrecognized or unacknowledged by much of the simulation community.

Here are the 4 main difficulties they list concerning the differences between the properties of a water monomer and the water molecule in ice Ih [most common phase of ice]:

1. the magnitude of the measured anharmonicity parameter of the OH stretch X_OH (=difference between 1/2 of the second overtone frequency and the fundamental) of the OH stretch in the condensed phase is increased from 87 cm-1 in the gas-phase to 134 cm-1 in ice Ih. This behavior cannot be reproduced by a simple anharmonic oscillator (such as a Morse oscillator), for which elongation of the OH stretch by the ice H-bond results in a decrease in |XOH|.

2. the enormous observed increase (25 fold) of the integrated IR intensity in the OH stretch mode in ice compared to that of the gas-phase monomer. Most water models (even including polarizable ones) predict almost no increase at all.

3. The gas-phase molecular dipole moment derivative with respect to the OH stretch is observed to be in a direction some 25 degrees outside of the OH stretch vector. In contrast, it is observed that this derivative becomes nearly parallel to the OH vector in ice.

4. The HOH angle increases from the gas-phase value of 104.5 to 107 degrees in ice. This is in contrast to virtually all empirical water models, which predict a lowering of the HOH angle from the gas-phase value.

The authors propose their own (classical) solution to these problems.
I am not in a position to judge the validity or reasonableness of the solution.
However, I have a prejudice that ultimately the origins of these problems is that the H-bond has a significant covalent and quantum character.

Molecules of chocolate

The Journal of Chemical Education paper on chocolate based demonstrations discusses three key classes of molecules.
Triglyceride is a major component of cocoa butter. It is hydrophobic.

Serotonin is a major component of cocoa powder. It is is largely hydrophilic and so will dissolve in water.

Lecithin is an emulsifier [just like egg which leads to formation of a stable emulsion of oil and vinegar in a salad], an amphiphilic molecule, which promotes mixing of cocoa solids and cocoa butter.

  

Communicating the sweetness of science

Finding and doing cool science demos to impress children is not hard. However, the problem is that it is easy to fall into the trap that they become more like a magic show and communicate little about science. A grand challenge is actually performing demos that teach school children to think scientifically and critically. Framing questions and investigating possible answers for oneself is completely different from saying "gee whiz! this is so cool!" and just learning scientific names and mantras.

There is a really nice article in the Journal of Chemical Education, The Science of Chocolate: Interactive Activities on Phase Transitions, Emulsification, and Nucleation. It describes a series of demonstrations that can be done with children (and their parents). I am going to try this next week! (at a holiday kids club my church is running).

The demonstrations [described in the Supplementary material] focus on answering three questions:

• Why does chocolate usually melt in my mouth, not my hand?
• Why does chocolate feel smooth?
• Why does chocolate snap when you break it and have sheen?

The demonstrations provide a nice way to see in a memorable manner how changes in material composition change material properties.

Deconstructing protein phase diagrams

In the process of coming up with new exam questions for my undergraduate thermodynamics and condensed matter course I came across the following pressure-temperature phase diagram for the protein ribonuclease A at pH 2.0.

It is taken from a 1995 Biochemistry paper and I came across it in the wonderful text by Dill and Bromberg.
[Aside: I wondered if the water freezing was an issue but all along the curve the solvent water is liquid because dP/dT is negative for the liquid-solid line of pure water].

Natural scientific questions are:

• What are the mechanisms of "cold" and pressure-induced denaturation? 
• What are the associated changes in protein structure?
• Is this a generic type of phase diagram for proteins?
• What role does water and hydrophobic interactions play?

A nice review article from 2002 by Smeller discusses how these diagrams are indeed generic and their shape can be understood in terms of a simple thermodynamic theory due to Hawley in 1971.
One simply expands the Gibbs free energy change to second order in T and P relative to some reference pressure P0 and temperature T0,

The pressure induced denaturation can then lead to a volume contraction. This is explained in microscopic terms in a 1998 PNAS paper by Hummer et al.,

The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins

which shows
Pressure-denatured proteins, unlike heat-denatured proteins, retain a compact structure with water molecules penetrating their core. 

Do literature reviews matter?

In 1983, when I was a budding young student heading off to Princeton to do a physics Ph.D. I had the privilege of spending some time with an elderly John Edsall, an eminent Harvard biochemist, who was friend and collaborator of my father. I asked him if he had any advice for me. I expected him to say something profound and give me a long list of suggestions. He thought for a while and said, "Well I am not sure but I guess it is important to know the literature on what you are working on."
I am not sure to what extent I took on board this advice over the next decade.
But, now I think this was very good advice. The reason is knowing the literature can save you a lot of time.  If you are trying to do something someone else has already done then
-perhaps there is no point in trying it yourself
or
-you may be able to use what they have done to do something even better.

It is amazing what a discerning Google Scholar search can pick up. On the other hand, you need to be careful you don't spend all your time downloading and reading papers. Also, don't assume your supervisor knows the literature.

Male frog protein whips up a broth

For the biophysics class BIPH3001 students are required to select one recent scientific paper of interest to them and give a presentation to the class. This week one student, Heather Nutt, selected a 2009 Biophysical Journal paper, 

Ranaspumin-2: Structure and Function of a Surfactant Protein from the Foam Nests of a Tropical Frog

Her slides are here.

At first I thought this topic was a little obscure but it turns out to be fascinating. Below I highlight some of the things I found particularly interesting from the paper abstract. 

Ranaspumin-2 (Rsn-2) is a monomeric, 11 kDa surfactant protein identified as one of the major foam nest components of the túngara frog (Engystomops pustulosus), with an amino acid sequence unlike any other protein described so far. We report here on its structure in solution as determined by high-resolution NMR analysis, together with investigations of its conformation and packing at the air-water interface using a combination of infrared and neutron reflectivity techniques. Despite the lack of any significant sequence similarity, Rsn-2 in solution adopts a compact globular fold characteristic of the cystatin family, comprising a single helix over a four-stranded sheet, in a motif not previously associated with surfactant activity. The NMR structure of Rsn-2 shows no obvious amphiphilicity that might be anticipated for a surfactant protein. This suggests that it must undergo a significant conformational change when incorporated into the air-water interface that may involve a hinge-bending, clamshell opening of the separate helix and sheet segments to expose hydrophobic faces to air while maintaining the highly polar surfaces in contact with the underlying water layer. This model is supported by direct observation of the relative orientations of secondary structure elements at the interface by infrared reflection absorption spectroscopy, and by protein packing densities determined from neutron reflectivity profiles.

The origin of molecular medicine

The data in the Figure above changed the face of medical research.

It showed for the first time that disease can have a molecular basis.

It was another great scientific achievement and bold discovery of Linus Pauling.

The Figure is discussed in chapter 8 of Nelson's Biological Physics: Energy, Information, Life. He states:

In a historic discovery, Linus Pauling and coauthors showed in 1949 that the red blood cells of sickle-cell patients contained a defective form of hemoglobin. Today we know that the defect lies in parts of hemoglobin called the β-globin chains, which differ from normal β-globin by the substitution of a single amino acid, from glutamic acid to valine in position six. This tiny change (β-globin has 146 amino acids in all) is enough to create a sticky (hydrophobic) patch on the molecular surface. The mutant molecules clump together, forming a solid fiber of fourteen interwound helical strands inside the red cell and giving it the sickle shape for which the disease is named. The deformed red cells in turn get stuck in capillaries, then damaged, and destroyed by the body, with the net effect of creating pain and anemia.

In 1949, the sequence of β-globin was unknown. Nevertheless, Pauling and coauthors pinpointed the source of the disease in a single molecule. They reasoned that a slight chemical modification to hemoglobin could make a correspondingly small change in its titration curve, if the differing amino acids had different dissociation constants. 

A nice article  about the history is by William Eaton.

Walter Kauzmann (1916 -2009): the master of thermodynamics

Walter Kauzmann was a pioneer in understanding condensed phases of matter. Two of his most important contributions to science (the hydrophobic interaction and a paradox concerning glasses) were made using his profound understanding of thermodynamics. He first introduced the notion of a hydrophobic interaction. Before any structures of proteins were known he deduced solely from thermodynamic data on the solvation of small organic molecules that a protein must fold so that the non-polar amino acids are predominantly in the centre of the protein. I discuss this in a lecture I often give to undergraduates at the University of Queensland in the course PHYS2020: Thermodynamics and Condensed Matter Physics.

Kauzmann wrote a beautiful article, Reminiscences of a life in protein physical chemistry, that I warmly recommend. One point he makes repeatedly in the article is that in science (and life) people will often believe what they want to believe rather than what the evidence before them suggests they should believe. The article recounts some of the "silly" things (from the perspective of our knowledge today) people believed about proteins in the 1950's, and how reluctant the advocates of these theories were to give up on them. Those of us trying to understand complex materials today, and especially biomolecular function, should be sobered and chastened by this lesson from history.

Kauzmann co-authored with David Eisenberg the definitive monograph on water and a beautiful "ancient" text, Quantum Chemistry (1957) which I found extremely helpful as an undergraduate and today.

Bruce Alberts testifies to Kauzmann's personal legacy in this fascinating article where he describes how Kauzmann mentored him. Alberts is currently the Editor in chief of the journal Science, a former past president of the National Academy of Sciences in the USA, and a co-author of the definitive text, The Molecular Biology of the Cell.

More about Kauzmann's life is available here. I was privileged to have some personal interaction with him, while a graduate student (in physics not chemistry) at Princeton, because he was a long-time friend of my late father. However, I did not realize what a great scientist he was and how much I could have learnt from him. Back then I was a some-what narrow-minded physicist who had not developed a fascination with problems at the interface of chemistry and physics. Youth is wasted on the young!