"Making drug discovery a click"

Lab News

2016-09-30   16th International Symposium on Mathematical and Computational Biology "BIOMAT 2016", take place at Chern Institute of Mathematics, Nankai University, Tianjin, People's Republic of China - 30th October - 05th November 2016

2016-09-30   Lecture notes for the summer school "Topological aspects of condensed matter physics"

Newest computer resources at FEFU


Antti Niemi together with our group members and collaborators from China and Russia welcome the newest addition to a supercomputer at the Department of Biomedicine of Far Eastern Federal University in Vladivostok. The computer, a mix of CPU and GPU processors, was specially designed and built by T-Platform for our research collaboration, to develop protein analysis tools. In the future it will host the Propro platform, now available in a demo version at https://188.162.234.56/propro/index.php


Fold It!

"The problem of life is among fundamental problems in theoretical physics"


— P.A.M. Dirac (1931)



The Nobel Prize of Physics in 2016 is a manifestation of an ongoing revolution at the interface where classical meets quantum, when "Few" becomes "Many". Entirely new states of matter and exotic physics phenomena such as graphene and topological insulators give us great promise for future advances in high tech and biomedicine. The discoveries challenge our understanding of the physical world, with old paradigms replacing new. These new material circumstances are commonly emergent, appearing when individual atomic level constituents self-organise and start acting collectively in unexpected fashions. Frequently the concept of a broken symmetry in combination with topology, geometry and other tools of mathematical physics have a central role when we search for theoretical descriptions.


Life is the most curious and challenging organisational state of a material system. The size and structure of a protein parallels many nanomaterials where emergent exotic self-organisation can be found. However, thus far there have been very few attempts to identify new organisational states in the case of nanoscale biomaterials. At the same time the biological function of a protein is known to depend critically on its three dimensional shape. A wrong fold is a common cause for a protein to lose its function and a misfolded protein can be dangerous and even fatal to a biological organism. In our research group we aim to identify the presence of emergent self-organisation in proteins, the goal is to describe life processes as physical phenomena.


In the present understanding of a protein, classical already meets quantum. All-atom molecular dynamics (MD) solves discretised Newton's equation with both Pauli repulsion and van der Waals attraction accounted for in the Lennard-Jones potential. Many colleagues trust that MD is the answer to the protein folding problem, all one needs is a powerful enough computer. We have full respect to this point of view, we use MD extensively in our research so we know its power. But with our background in Physics,we are also aware of the limitations of such a Landau liquid-like approach: The Physics Nobel Prize 2016 is a manifestation that a Landau Liquid approach often fails to capture and describe emergent collective phenomena and self-organisation in a material system.


Our ambition is to pave a road beyond a Landau liquid level description of proteins, our goals is to explain how new organisational states appear in live matter. We use theoretical tools that have repeatedly proven their correctness in nanoscale scenarios: The general framework devised by Kadanoff, Wilson, the winners of 2016 Nobel Prize in Physics and many others, proposes us a way to try and explain how large scale structure emerges in live matter. Our stated goal is to show how a protein self-organises itself from an incoherently acting group of individual atoms into a collectively acting living entity. Fundamentally proteins are like any other materials, the research of our group during the last 5-6 years provides a strong proof-of-concept that proteins behave like all other nanoscale materials.


The key to success in understanding how structural self-organisation takes place in a protein, like in any material system, is the choice of correct order parameters. Our research relates protein dynamics to a variant of the discrete nonlinear Schroedinger (DNLS) equation, which is the paradigm Hamiltonian that supports solitons. A soliton is an ubiquitous and widely studied object that can be materialized in a variety of practical and theoretical scenarios. Solitons explain the formation of the morning glory cloud in atmosphere, the Meissner effect in superconductors and dislocations in liquid crystals. Solitons model hadronic particles, cosmic strings and magnetic monopoles in high energy physics. Solitons are already deployed to conduct electricity in linearly conjugated organic polymers, though simpler than protein, such as polyacetylene. Research by our group has systematically built the case that a dark multi-soliton solution of the DNLS equation can model proteins and their near-equilibrium dynamics, often with sub-atomic precision.


We have simulated many biochemically important proteins, we have explained the way how a myoglobin folds and why certain diabetes-II and Alzheimer disease related intrinsically unstructured proteins can never become settled. We have identified solitons in all-atom MD simulations and we have studied their dynamical properties using coarse-grained techniques. We have made definite predictions for experimentalists to try and test using methods from NMR to circular dichroism and small-to-wide angle X-ray scattering. We know that we have a methodology that works. We hope to make an impact. We now aim to describe the large time scale properties of various biomedical important proteins from rhodopsin and neuropsin to amylin and myc. How proteins transport signals and how protein structure progresses when temperature, acidity and other environmental factors change. We are keen for collaboration, at the level of both fundamental and applied research and development. Maybe there is a way for our and your interests to overlap.


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