NMR is a non-invasive technique to probe the structure and dynamics of molecules and atoms. The acquired NMR spectrum exhibits features such as shift of resonance frequency, linewidth, and symmetry of lineshape, which are manifestations of perturbations of local magnetic field on the site of the nucleus under surveillance. Combined with theoretical and empirical interpretations, They inform us the electronic and magnetic structure of materials, or geometric constraints between atoms. Information from NMR can be complementary to those from other spectroscopy techniques, such as X-ray diffraction, Electron Microscopy (EM). In some situations, NMR can be the only effective tool applicable. In this lab, we utilize NMR as the major force to characterize the properties of materials, in combination with other spectroscopy methods and theorectical calculations and simulations.

Nano particles of many transition metals are widely used to catalyze chemical reactions. As chemical properties are dominated by the valence electrons, it's conceivable that the enhancement in catalytic performance is associated with the altered band structures due to the unique physical properties of nano particles that approach microscopic scales. However, significant challenges pose against the extraction and interpretation of the relations between the two. We take advantage of the non-invasive nature of NMR to probe the electronic and magnetic properties associated with band structures and identify the effects of the physical properties of such nano particles on enhancements of catalytic behaviors.

Solution NMR has been highly successful in characterization of the structure and dynamics of molecules tumbling in solutions, such as polymers or proteins. However, there are a large group of biomolecules that aggregates into large complexes and precipitate out of the solution, therefore they become "invisible" to solution NMR techniques. Many of these entities are associated with pathogens or diseases that impact human society dearly, examples are capsid shells in viruses, amyloid plaques observed in many neurodegenative disease such Alzheimer disease, or the famous mad-cow disease. It is of great value to resolve the structures and dynamics of such aggregates in order to decipher the assembly mechanism and provide insight to conquer these terrible diseases. Solid state NMR (ssNMR) is one of the few techniques applicable to these subjects. We are actively developing and applying ssNMR methods to study the capsid protein assembly of HIV-1 virus and the prions present in yeast Saccharomyces Cerevisiae. We are also working out innovative models for simulations of self-assembly.

Self-assembly is an intriguing phenomenon exhibited by many chemical and biological systems, for example, prions and virus capsid proteins. Usually, a large number of molecules are involved, and it is impossible to simulate the process with full-atom representations with current computation resources. Coarse-grain modelling are often adopted where simple geometric objects such as spheres or polygons are used. In this case, a boost of simulation speed is achieve at the expense of molecular structures. Insights into basic principles can be obtained with such simplified models. However, it is in general difficult to relate the simulation to experimental observations. Here I designed a novel coarse grain model to capture the overall geometry of the protein molecules, as shown in Figure 1.
Monte Carlo simulation with this model applied successfully to simulate the self-assembly of HIV-1 capsid protein in 2D (Biophys. J. 100, 3035 (2011)). The movie compiled from this work is shown below.

AMPs are short polypeptides capable of disruption of lipid membrane. They are so called “amphipathic molecules”, include both hydrophobic and hydrophilic amino acids, which intend to interact with the charged head groups and long hydrophobic chains of molecules in lipids. Generally speaking, AMPs interact with the lipid bilayers to increase the ion permeability and changes the electrochemical potential across the membrane, thus induce the killing of the cells. In addition, many AMPs also exhibit selectivity of toxicity against bacteria than eukaryotic cells. Therefore, they are promising candidates for antibiotics to open new frontlines in the battle against the bacterial resistance in medicine. More than 800 AMPs have been identified and documented. However, the mechanism of their function and selectivity towards bacteria is still debated. We will use ssNMR to study the structure and dynamics associate with variants of AMPs, and look for clues or answers to this million dollar question.