LIFE SCIENCES

Diabetes reaches epidemic proportions with a major and growing economic impact on the society. An effective treatment requires atomic-level understanding of how insulin acts on cells. Using molecular dynamics simulations, an international team of researchers studied the process of insulin binding to its receptor and the resulting structural changes at atomic scale with cryogenic election microscopy and atomistic MD simulation. The results of these studies were recently published in the Journal of Cell Biology.

Ion channels play a fundamental role in maintaining vital electrochemical gradients across the cell membrane and in enabling electrical signaling across cells. Key characteristics of ion channel function that can be experimentally quantified include ion permeation rates and selectivities. In this project, the functional mechanism of a very important class of ion channels is investigated with the help of molecular dynamics simulations. The computer simulations exhibit a wide range of GLIC states from completely closed to wide open, with conductance and selectivity for the open state in agreement with experimental values. The scientists are now beginning to investigate the intricate opening/closing mechanism in detail to ultimately explain it…

Rapid and accurate calculation of binding free energies is of major concern in drug discovery and personalized medicine. A pan-European research team leveraged the computing power of LRZ’s SuperMUC system to predict the strength of macromolecular binding free energies of ligands to proteins. An in-house developed, highly automated, molecular-simulation-based free energy calculation workflow tool assisted the team in achieving optimal efficiency in its modelling and calculations, resulting in rapid, reliable, accurate and precise predictions of binding free energies.

HIV is one of the most significant global public health threats. The virus evolves rapidly, and multi-drug resistant strains have already emerged. The drugs approved to date target only four HIV proteins. While two novel drug targets, Rev and the capsid protein (CA), have been identified, so far none have reached clinical trials. Scientists leverage the computing power of HPC system SuperMUC to simulate detailed and accurate models of the protein-protein interactions of these targets with the aim to facilitate the design of more effective drugs.

Integral membrane proteins exhibit conformational flexibility at different structural levels and time scales. Our work focusses on the biophysical basis of the interdependence of transmembrane helix dynamics, helix-helix recognition, and helix-lipid interactions. In this context, we try to understand the impacts of these phenomena on biological processes, such as membrane fusion, lipid translocation, and intramembrane proteolysis. Our approach closely connects experimental work and established computational analysis in order to interpret and guide the experiments and to validate the simulations.

Leveraging the computing power of HPC system SuperMUC, researchers of the Technische Universität München investigated the free energy landscape for large-scale conformational changes coupled to the association of biomolecules. It allowed understanding the mechanism of substrate and inhibitor binding to the adenylate kinase (ADK) enzyme and helped to characterize the thermodynamics and kinetics of the propagation of Alzheimer Alzheimer Aβ_9-40 amyloid fibrils.

While some proteins of a biological cell are bound to cellular structures others diffuse freely. Especially in a crowded cellular environment, proteins constantly bump into other proteins which sometimes leads to biologically meaningful contact of the two proteins–the binding partners may either remain bound or a chemical reaction may take place. Performing atomistic molecular dynamics simulations on SuperMUC, bioinformaticists try to unravel the biophysical principles underlying such “specific” biomolecular interactions.

Scientists leverage high performance computing technologies to identify the morphological characteristics of intracranial aneurysms that result in high frequency fluctuations, and assess the role of these fluctuations in aneurysmal wall degradation and consequently aneurysm rupture. Using SuperMUC they performed simulations with up to one billion elements, which allowed the simulation of flow at spatial and temporal resolutions of 8µm and 1µs, while resolving the smallest structures that can develop in a turbulent flow.

Ligand-gated ion channels (LGIC) play a central role in intercellular communication in the central and peripheral nervous systems as well as in non neuronal cells. Understanding their function at an atomic level of detail will be beneficial for the development of drug therapies against a range of diseases including Alzheimer's disease, schizophrenia, pain, and depression. By capitalizing on the increasing availability of high-resolution structures of both pentameric and trimeric LGICs we aim at elucidating the molecular mechanism underlying activation/deactivation by atomistic Molecular Dynamics (MD) simulations, which is essential to rationalize the design of potent allosteric modulators.

A significant part of modern mortality is contributed by strokes, caused by the rupture of intracranial aneurysms (IA). Nearly 4-5% of the world population is reported to be suffering from IA. The deployment of a flow diverter stent in the parent artery of an aneurysm is a novel and minimally invasive treatment procedure, which can cause complete obliteration of the aneurysm by thrombosis.

The process of protein-protein complex formation is of fundamental importance for a better understanding of a variety of biological processes. In a cellular environment the high concentration of surrounding proteins can influence the association process between proteins. Aim of the research project was to simulate the formation of specific and non-specific protein-protein complexes and to investigate the effect of additional protein molecules (crowding) on complex formation in atomic detail. 

Bacterial infections represent the second leading cause of death worldwide. The effectiveness of the available weaponry against these pathogens is progressively lowered by the constant insurgence multidrug-resistant bacterial strains. Antibacterial resistance constitutes nowadays a major concern for human health due to its social implications and economical impact, i.e. loss of human lives and increased mortality, morbidity, hospitalization length and healthcare costs.

Membrane proteins are of great biomedical importance. They account for ~25% of all genes and are involved in diseases ranging from diabetes to cancer. Membrane proteins play a key role in the biology of infection by pathogens, including both bacteria and viruses. They also play an important role in signalling within and between cells. It is therefore not surprising that membrane proteins are major targets for a wide range of drugs and other therapeutic agents. Recently, the number of known structures of membrane proteins has started to increase. Large scale computer simulations allow researchers to study the movements of these proteins in their native membrane environments. 

The mechanisms of interaction between solid excipients and drugs are based on surface chemistry related phenomena. Consequently, understanding the physico-chemical features of surfaces is a fundamental step to describe and predict the strength of these interactions. The results of this analysis can shed light on how the nature of the excipient can affect the properties of a drug formulation. Among silica-based mesoporous materials, MCM-41 (Mobil Composition of Matter) is one of the most studied. In 2001 it was first proposed as a drug delivery system, with ibuprofen as a model drug. 

Detailed knowledge about the structural and dynamical properties of biomolecules is essential for Life Sciences, from fundamental research to medical drug design. Molecular dynamics simulations are a valuable tool that complement experimental results and help to understand them. Molecular mechanics enable simulations of large systems, such as a protein in solution with several ten thousand atoms, up to a microsecond time scale. However, such simulations are by far not accurate enough for tasks like calculating infrared spectra. In contrast, high-level quantum mechanical methods like density functional theory provide the required accuracy, but are computationally limited to much smaller length and time scales.