Influence of friction on protein folding

Dr. Neil Canter, Contributing Editor | TLT Tech Beat August 2012

Researchers examine the effects of internal friction during the protein-folding process.

KEY CONCEPTS
• Proteins tend to function in living organisms by going through a folding process, enabling them to move to the lowest possible free energy state.
• Two types of internal friction must be examined in the folding process. The first is due to solvent interaction with the protein, while the second originates from the internal interactions of the amino acids in the protein chain.
• According to a new study, internal friction plays a bigger role in affecting protein folding than originally anticipated.

AS RESEARCHERS FURTHER EXPLORE THE ROLE OF FRICTION ON THE ATOMIC SCALE, there becomes more of a realization of its importance in influencing how atoms interact with each other. Through the use of nanotribology, frictional effects are being studied with the use of the atomic force microscope.

In a previous TLT article, a newly developed empirical approach was used to observe how friction takes place on the atomic scale (1). A layer of charged polystyrene spheres with a small radius of 1.95 microns suspended in water were passed through a light-created surface. Atomic interactions led to the formation of kink and antikink regions on the surface. Kinks involve areas where atoms slide together, while in antikinks they move apart. The presence of both environments has now been confirmed from theoretical predictions.

Proteins play important roles in the functioning of living organisms. Enzymes that facilitate physiological processes such as respiration are composed of proteins. Dr. Everett Lipman, associate professor in the physics department at the University of California, Santa Barbara in Santa Barbara, Calif., says, “Proteins are composed of strings of amino acids that do not like to be stretched but prefer to be folded. Folding enables proteins to move towards the lowest possible free energy state.”

Figure 3 shows an amino acid chain folding into a three-dimensional protein.


Figure 3. Internal friction has been found to influence the folding of the protein Csp more than originally anticipated. (Courtesy of the University of California, Santa Barbara)

Lipman characterizes unfolded proteins as messy balls that take some time to find the right path to fold up. A competition exists between entropy increase, which favors the disorganized unfolded ball and energetic interactions with the solvent and among parts of the protein, and causes it to adopt its compact folded shape.

Protein folding is studied in an artificial manner using a denaturant to disrupt the environment. Researchers search for the path taken by a protein to fold down in an arrangement where the free energy state is minimized.

Lipman indicates that there are two important factors that need to be taken into consideration as the protein folds. He says, “The protein has to fold into a particular shape and fulfill a specific function. It cannot take an infinite time to fold because proteins can be degraded by the cell if there is a delay.”

Speed is very important in protein folding. Lipman indicates that neurodegenerative diseases are linked to protein aggregation. He adds, “This aggregation is not seen in healthy patients.”

The same friction that tribologists deal with every day affects the rate of protein folding and can delay the process. In this case, the researchers refer to this phenomenon as internal friction.

Lipman says, “There are two types of friction that must be considered. Friction occurs due to the type of solvent interacting with the protein. A second type originates from the internal interactions of the amino acids in the protein chain as they bang up against each other slowly during folding.”

He adds, “Internal friction is caused by the interactions between parts of the protein, while solvent interactions are considered external friction. We measure the contribution of internal friction by gradually reducing the solvent viscosity. The reconfiguration time then drops and in the absence of internal friction, we would expect the extrapolated reconfiguration time at zero solvent viscosity to be zero. Instead, it approaches a finite value, which we interpret as indicating the effect of internal friction.”

Quantification of the friction found during protein folding has been difficult. A new technique has now been used to overcome this problem.

MICROFLUIDIC MIXING
Lipman and his fellow researchers were able to study the frictional effect on protein folding by using microfluidic mixing to control the environmental conditions. He says, “We used a denaturant so that the protein folded under non-natural conditions. The mixing was done on a scale that is faster than the folding time of the protein. An unfolded protein was studied under conditions where it wanted to fold.”

Lipman continues, “Under native conditions, we think the protein reconfigures in tens to hundreds of nanoseconds, but folding takes 12 milliseconds, as the protein explores new configurations, many of which must be tried to find the transition state from which the protein can fold.”

The researchers studied a small cold-shock protein from the bacterium Thermotoga maritime, which is known as Csp. Lipman says, “This is a simple, basic protein that is always found in one of only two states and represents a good model system.”

Internal friction was evaluated through the use of glycerol as the solvent. The concentration of the denaturant used was varied to assess how it impacted the rate of protein folding. Guanidinium chloride was used as the denaturant in this study.

The researchers found that internal friction plays a bigger role in affecting the folding of proteins than was anticipated. Ultimately, the question that needs to be answered is how the sequence of amino acids in the protein chain affects the rate and type of folding. Lipman says, “It is too early to tell whether the approach we used to study Csp can be applied to other proteins.”

A good analogy is that the study of protein folding is similar to the function of VI Improvers in lubricants under changing temperature conditions. Further information can be found at Lipman’s web page here.

Lipman indicates future work will involve studying internal friction in other proteins. Detailed information can be found in a recent article on this work (2).

REFERENCES
1. Canter, N. (2012), “Observation of Friction on Microscopic Length Scales,” TLT, 68 (4), pp. 8-9.
2. Soranno, A., Buchli, B., Nettles, D., Cheng, R., Spath, S., Pfeil, S., Hoffmann, A., Lipman, E., Makarov, D. and Schuler, B. (2012), “Quantifying Internal Friction in Unfolded and Intrinsically Disordered Proteins with Single-Molecule Spectroscopy,” Proceedings of the National Academy of Sciences, doi/10.1073/pnas.1117368109.


Neil Canter heads his own consulting company, Chemical Solutions, in Willow Grove, Pa. Ideas for Tech Beat items can be sent to him at neilcanter@comcast.net.