SARomics Biostructures Blog

SARomics Biostructures determines structures of an industrially important ω-transaminase

2012-02-15T04:22:00.000-08:00

SARomics Biostructures recently published an article in FEBS Journal describing four crystal structures of an industrially important enzyme in different conformational states. The work was the result of a collaboration with researchers at the Royal Institute of Technology (KTH) in Stockholm and AstraZeneca in Södertälje. The collaboration was financed by the Swedish Innovation Agency VINNOVA through the BIO-AMINES grant.

The enzyme whose structure was revealed is an ω-transaminase that transfers amino groups between molecules. This group of enzymes has received quite some industrial attention due to their ability to accept inexpensive amines, such as isopropylamine, as amino donors, in combination with a capacity to produce highly enantiomerically pure chiral amino compounds, which are important both as pharmaceuticals and as key chiral intermediates for the agrochemical, chemical and pharmaceutical industries.

The structures give insight into the conformational changes associated with binding of the enzyme’s cofactor PLP. Unexpectedly large conformational changes in three loops were seen, apparently driven by binding of the PLP molecule’s phosphate group. The enzyme was captured in a state without PLP, in another with PLP, and finally in a form where some the molecules in the crystal were in a mixture of the two states. Most importantly, the structures pave the way for further complexes with appropriate ligands and an exploration of the enzyme’s enantiomeric preference, with a view to enhancing it even further.

SARomics Biostructures contributes to fundamental understanding of ligand and water binding to a protein

2012-01-03T04:21:00.000-08:00

SARomics Biostructures recently contributed to an exciting article in Biochemistry where ultra-high resolution X-ray crystallography was combined with a plethora of complementary biophysical and theoretical techniques such as NMR, ITC and molecular dynamics simulations to probe the nature of water binding and hydrogen bonding in the active site of the medically important carbohydrate binding protein galectin-3. The results showed that the ligand binding site of Gal3C is highly pre-organized to recognize a sugar-like framework of oxygen atoms, but that the water molecules in the binding site are highly dynamic, none of them staying in place for more than about 1 nanosecond. The results are important for drug design, where one of the major unsolved problems in the prediction of absolute free energies of binding is the treatment of ligand and solvent entropy.

One of the structures, a complex of galectin-3 with lactose, broke the current resolution record for data collected at the MAX-lab synchrotron in Lund, with data stretching all the way to 0.86 Å. At this resolution it begins to be possible to see the hydrogen atoms in the binding site and thus to analyze hydrogen bonding patterns in detail, an aspect that is ambiguous in X-ray structures at more typical resolutions. The academic groups with whom SARomics collaborated on this project are now taking the analysis one step further by using neutron diffraction to study unambiguously the positions of the protons.

This is the second publication on Gal3C to which SARomics has contributed. The collaboration reflects SARomics interest in the fundamental aspects of ligand recognition, which feeds into our commercial experimental and in silico offerings.

Saraboji K, Håkansson M, Genheden S, Diehl C, Qvist J, Weininger U, Nilsson UJ, Leffler H, Ryde U, Akke M & Logan DT (2011) The carbohydrate-binding site in galectin-3 is pre-organized to recognize a sugar-like framework of oxygens: ultra-high resolution structures and water dynamics. Biochemistry, Article ASAP.

Report from XIXth Protein Structure Determination in Industry Meeting or PSDI 2011

2011-11-26T11:57:00.000-08:00

Date: Nov. 13-15, 2011
Place: Stenungsbaden Yacht Club, Gothenburg area, Sweden
Narrator: Maria Håkansson, Senior scientist at SARomics Biostructures

It is quite simple to say that I utterly enjoyed the PSDI 2011 meeting and leave it like that.

Going into details then; what is it that separates a good meeting from a great one? Is it the mixture of people, old friends and new acquaintances, sharing a common interest and the latest news in the field? Is it the topics of the lectures covering drug ability, fragment screening and structures of GPCRs in complex with antagonists or agonists? The simplest reminder of these complexes you get every time you drink a coke or take a cup of coffee since caffeine is inhibiting one of them (Adenosine A2A). Is it the presentation of biophysical methods, which technique freaks like me embrace? The most used techniques seems to be the one’s below:

Thermal shift assays by QPCR
Surface plasmon resonance
Isothermal titration calorimetry
NMR

Also one entirely new technique was presented called ”Thermophoresis”. As the name implies it makes use of differences in diffusion at different temperatures for fluorescence labelled proteins and protein-ligand complexes very much like standard electrophoresis. I don’t see the immediate use of it but it is always a comfort to know that there are people thinking outside the box.

With these methods in combination with biological assays and X-ray crystallography it is possible to develop fragments into high affinity ligands and potential drug candidates. Don’t you believe me? Go to the next PSDI 2012 meeting.

New publication with a structure contributed by SARomics Biostructures

2011-08-26T07:01:00.000-07:00

Recent work by SARomics Biostructures' Co-founder Mikael Akke, and a structure contributed by the company has been selected for the latest issue of JACS Select ( http://pubs.acs.org/JACSbeta/jvi/issue12.html ).

"Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3",
Carl Diehl, Olof Engström, Tamara Delaine, Maria Håkansson, Samuel Genheden, Kristofer Modig, Hakon Leffler, Ulf Ryde, Ulf J. Nilsson, and Mikael Akke. J. Am. Chem. Soc. (2010) 132, 14577-89 ( http://pubs.acs.org/stoken/beta/select/abs/10.1021/ja105852y ).

About JACS Select: In order to both highlight and further explain topics of interest to a diverse audience, the Journal of the American Chemical Society has launched JACS Select, an online feature conceived and designed to showcase significant recent publications. Articles are selected based on their high scientific quality and broad appeal.