SteinBlog

Beilstein Symposium on Systems Chemistry, Day 3

Back after an afternoon of heavy hiking to Castle Boymont uphill from Schloss Korb. Great stuff.

Day 3, Morning Session on Macromolecular Interactions: P-P, P-NA, NA-Light

• Sara Linse of Lund report on her group’s work on Protein Interactions, Association and Fibrillation. Systems Chemistry is the study of molecules acting collectively, she proposes. Her focus of course is on proteins interacting and she show some micro array assays for protein association studies (and I learned another buzz word: Interactome :-)). The second part of her talk is dedicated to studies of the effect of nano particles on protein fibrillation. The nano particles she studies where about 200 nm in diameter, compared to about 70 nm for a typical protein in study. Her conclusions are quite alarming in that there are clear effect of nanoparticles on protein association, because of their small size nano particles can enter the organism by various mechanism – yet, because of the fact that many nano particles are made from known and risk-assessed materials, there no *new* risk assessments done accounting for the new properties that arise from the small size. It should be noted of course, that there is awareness for the new risks arising from nano particles and discussions are going on.
• Michele Vendruscolo of Cambridge talked about “Life on the Edge: Proteins are close to their Solubility Limits”. He shows an incredibly crowded picture of a yeast cell. Yet, a protein can visit most locations in a cell in a fraction of a second. Interestingly, the life time of a protein in a cell is only in the order of about 1 hour, after which it is recycled. He talks about the folding process of a protein and that dispite a well-defined folding funnel there can be many more states being adopted by a protein, potentially leading fibrilles. Michele shows a model to predict aggregation rates of proteins from the sequence. He concludes by giving another definitions of Systems chemistry being a strategy based on chemical principles to make predictions about cellular processes.
• Alexander Heckel of Frankfurt speaks about “Shedding Light on Nucleic Acids and DNA under Construction”. He shows examples from his research on light-induced transcription and light-induced RNA interference. In his second part he talks about DNA constructions. Alexander shows a very impressive animation of ATP synthase that I need to get my hands on.
• The morning session closes with a talk by Justin Roberts from Riverside, CA, USA, on High-Throughput Analysis of Nucleoside- and Nucleotide-binding by Proteins.

Day 3, Afternoon session on Chemical Spaces and Molecular Design

• Joseph Lehár of Cambridge, MA, USA, starts the afternoon talks with the topic “Systems Biology from Synergistic Chemical Combinations”. He is the first to talk about multi-drug (he calls it combination drugs). He highlights various multi-target mechanisms such as “cooperative targets”, “block compensation”, “circumvention of resistance”. His companies looks at combinations of all approved drugs and uses cell-based assays to screen them.
• Holger Wallmeier, independent consultant, speaks about “A Dynamical Supramolecular System for Chemical Biology – a Step towards Contiguous Structural Spaces”.
• The last research talk of the meeting is delivered by Gisbert Schneider of Frankfurt talking about “Molecular Design: Voyages to the (un)known”. He starts with musing about what Systems Chemistry is based on Darwin’s work on the Transmutation of Species. He continues with explaining different levels of abstraction for molecular representations leading to the definition of a pharmacophore space. In the following, Gisbert shows work with Self-Organising Maps (SOMs) on the discovery of pharmacophore spaces.
• My summary and closing remarks: We saw an enormously diverse set of talks, most of them dedicated to the study of biological phenomena. If this workshop was really on Systems Chemistry, this indicates that System Chemistry has to do something with Biology. My theory is that we add the view on molecular details to Systems Chemstry. A lot of reports focus on understanding the parts, but there were indeed interesting insights into the properties of biological systems, such as the talk by Danchin. I enjoyed the meeting a lot and would love to see a follow-up – the problem is far from solved – with a greater emphasis on the fundamental problems of systems simulations on varying scales – dynamic scale switching, so to say. Only the application of first-principles at places where detail is required will allow us to make meaningful prediction, for example in the prediction of drug action on organisms.

PuTTY

Tagged with:

Categorised as: Conferences and Meetings, Hot Science, Life of Chris, Open Science, Scientific Culture