Rubisco

Rubisco is the world's most abundant protein. It is present in large quantities in every plant, and other light harvesting organisms. It is the sole responsible protein for CO2 fixation and has thus caught great attention for a long time. What if we could enhance this protein and make crops grow faster? Also in light of global warming it is of great importance to understand nature's natural way of recycling CO2 from the atmosphere.


Despite being crucial to every light harvesting organism, rubisco is notoriously sluggish in CO2 fixation. Rubisco from different plants and algea works at different speeds and we would like to know what exactly makes Rubisco efficient. To understand how Rubisco works we need to know its structure, biochemstry and dynamics. Several varieties of Rubisco have now been purified and crystallized, giving in insight in de variety among different species. The quest is now to comprehend what specific structural differences contribute to its efficiency or lack thereof. The methods we use for studying this problem are Molecular Dynamics and X-ray Crystallography.

...molecular dynamics carbon dioxyde
protein structures
X-ray crystallography...
We study mutational effect on protein dynamics, the geometrical restrictions for active side residues and interface interaction. The enzyme RuBisCO comprises 16 subunits: 8 small and 8 large units. They pack together in an intricate way whereby 2 large units complements each others active site. 2x4 large units pack together in a ring shape manner. 4 small units are placed on top and on the bottom of the large units, thus creating numerous interactions. Generally, the small units influence the stability and specificity of the large units, whereas the large units are the actual production sites. The interconnectivity affects catalysis, either in specificity or catalytic rate.

Protein G and the Protein Folding Problem

Cirrus Levinthal pointed out in the 1960's that there seems to be a paradox in getting into the folded native state for a given protein. In a very simplified way, one can assume that each amino acid can choose to be in one of three different energetically favourite backbone conformations. For a medium sized protein of 100 amino acids, this means that there are 3 to the power of 100 possible backbone conformations. Sampling all these would take ages, yet proteins fold within microseconds. Clearly, proteins use a better way of finding their native state. From this, the protein folding problem is formulated easily:

"Given the amino acid sequence of a polypeptide chain, how does it fold to its native conformation?"

My Masters Thesis dealt with this problem by doing protein folding simulations and analysing the results. The subject of study is Staphylococ Protein G, segment B1: a 56 residue, globular protein with a four-stranded beta-sheet and an alpha helix. Molecular Dynamics simulations of the folding of Protein G was were performed, using Gromacs software.

Movie

Movie 5.4 MBThis movie shows a short molecular dynamics simulation of protein G. It covers a 10 nano second time period. What you can see is the collapse of an extended structure to a smaller, less exposed form. Hydrophobic side chains are coloured white, otherwise only the backbone atoms are shown. Now and then, some flickering slashed lines appear; they are hydrogen bonds, using a broad 'bond' definition in sense of distance and angle. Click and enjoy the molecular motion.