Why do electrons flow in proteins in a single direction?


Heliobacter reaction center
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Photosynthesis is the most important biological process driving the biosphere. It harnesses the energy of sunlight, and provides us with our main sources of food and fuel. The study of photosynthesis has allowed scientists not only to understand the intricacies of how organisms use light to drive their metabolism, but has also paved the way for technological advances into sustainable energy sources.

The photosynthetic process first came into being roughly 3.5-3.8 billion years ago, before Earth's atmosphere contained oxygen. Photosynthesis works by using specialized membrane proteins, called photosynthetic reaction centers, which collect the energy from light and use it to pump electrons across a biological membrane from one cellular electron carrier to another, resulting in conversion of electromagnetic (i.e. light) energy into chemical energy, which the organism can use.

A great deal of research has determined that these reaction centers appeared just once on the planet, and have since diversified to perform different sorts of chemistry. Despite the diversification, the reaction centers retain the same overall architecture, reflecting their common origin.

During the last 3 billion years these proteins have been elaborated and changed and it has been difficult to reconstruct what happened over this enormous period of time. However, we do know that one of them developed the ability to oxidize water, releasing oxygen. This changed the world irrevocably, and allowed for life as we know it today.

The earliest ancestor of current photosynthetic bacteria is not known, but heliobacteria share a common ancestor with cyano and green sulfur bacteria and are viewed as closest to the primary ancestor. A recent Science paper by Kevin Redding, a professor in the School of Molecular Sciences (SMS) in the College of Liberal Arts and Sciences and Raimund Fromme, associate research professor (SMS) and a researcher in the Biodesign Institute's Center for Applied Structural Discovery (CASD), (Science  2017357,  1021– 1025,  DOI: 10.1126/science.aan5611) released the X-ray  structure of the heliobacterium reaction center where the energy of light is converted to the movement of electrons between two sides of the bacterial membrane.

Redding, who is also director of ASU’s Center for Bioenergy and Photosynthesis , is the PI on a current department of energy (DOE) Energy Biosciences grant, with Matyushov and Singharoy as co-PIs.

“This discovery opened the door to theoretical and computational modeling of charge transport in these bacterial reaction centers,” explains professor Dmitry Matyushov (SMS and department of physics). “Electrons hop, by quantum mechanical tunneling, between organic molecules, known as cofactors, immersed into these large protein complexes.”

Experimental studies have established that the electron arrives, within a few picoseconds, to a cofactor called A0, but where it goes afterwards is still a mystery. The final destination for the electron is to hop to the ferredoxin protein docking at the reaction center on the opposite side of the membrane, but the ``bus stops’’ between A0 and ferredoxin are not quite clear.

The X-ray crystal structure suggested that the electron can potentially go to either the iron-sulfur cluster ~18 Å away from A0 or potentially land on a menaquinone cofactor. To establish the electron transport pathway, graduate student Adam Pirnia from Matyushov’s lab built the first computational model of the heliobacterial reaction center and ran high-performance molecular dynamics simulations to see how motions of the protein, hydration water, and the bacterial membrane facilitate tunneling electron hops.

Building this, largest to date computational model, to study protein electron transfer required help from associate professor Abhishek Singharoy (SMS and CASD) who is an expert in high-performance simulations of large biomolecular complexes. The problem turned out to be highly complex demanding significant quantum mechanical calculations performed by Setare Sarhangi, a postdoctoral fellow from Matyushov’s group.

Theoretical modeling combined quantum calculations with molecular dynamics simulations to deliver a clear answer to the mechanism question: the iron-sulfur cofactor is too far for electron tunneling and menaquinone is the preferred electron acceptor. In addition, and more importantly, simulations have shed light on some long-standing questions that have haunted the field for decades.

“No one had extended these kinds of calculations of electron transfer to distances as long as we're trying to do here,” states Redding. “This is a rate that we have, or at least we think we have, experimentally measured. We're trying to monitor electron transfer from a donor to an acceptor within this protein but what we're really measuring is the electron leaving the donor. 

We've never actually experimentally seen the electron arriving at the acceptor because spectroscopically it doesn't make a very large difference in the spectrum so it's difficult to see. Until now we've merely assumed that the electron’s leaving here and we know it ends up there. We don't see in the structure any likely intermediates for electron transfer so we assume that it's a direct hop. However Dmitry’s results show that according to the best calculations their best rate is at least three orders of magnitude slower than what we see experimentally. Clearly, we have a mystery on our hands.”

Why do electrons flow in one direction in bacterial reaction centers and respiratory chains of mitochondria? Photosynthetic reaction centers operate as molecular diodes, allowing rectification of the electric current and unidirectional charge flow. Rules of thermodynamics suggest that there is insufficient thermodynamic driving force to channel electrons into a vectorial flux. The group’s simulations have shown that reaction center complexes move with different speeds (are dynamically anisotropic) depending on where the electron resides. The protein is much faster for the forward hop than for the backward transition. A sluggish protein holds onto the electron in its final destination, thus slowing down the reverse reaction.

“These new findings bring protein dynamics into the forefront of the discussion of how protein media facilitate cross-membrane electron flow in respiratory chains of bacteria and animals,” says Matyushov.

This work has just been published in the Journal of Physical Chemistry B

All biological energy comes from this process of separating charge across the biological membrane. The biological machinery either takes the energy from light or from chemical bonds of the organic food that we eat to create microscopic batteries with plus and minus charges across the lipid membrane. We are now learning that protein complexes inserted in these membranes, and serving as conduits of electron conduction, do it by slowing themselves down close to the electron’s final destination. The final ``bus stop’’ for the electron is the longest wait.