Molecular insight into ion-driven processes requires a precise knowledge of how the energetics, structures, dynamics of ions differ between hydrated and biomolecule-bound states. While first principles quantum mechanical models can yield reliable estimates for relative binding energies, estimates for thermodynamics and ion-binding response are subject to limitations from conformational sampling and system size. In contrast, molecular mechanics models that do not describe many body effects explicitly can technically get past sampling/system-size issues, but suffer severely from accuracy. Polarizable models are being developed as a compromise between accuracy and efficiency, but are they sufficiently reliable to derive causalities? In general, where do we stand in terms of being able to use molecular simulations to understand selective ion binding to biomolecules, and the response of ion binding to biomolecular function? Here I’ll discuss these issues and potential solutions in the context of our work on potassium channels.

Amyloid Beta (Ab) peptides are biomolecules that are capable of forming a rich variety of materials under diverse conditions. Driven by intermolecular forces such as hydrogen bonds, hydrophobic interactions and π-π stacking, they can self-assemble molecule by molecule to produce supramolecular architectures (fibrils). Due to their mechanical rigidity, strength, and elasticity, biomaterials formed by amyloid fibrils can be used for novel Bio-Nano-Med applications. In a combined experimental (deep ultraviolet resonance Raman (DUVRR) spectroscopy and atomic force microscopy (AFM)) and theoretical (molecular dynamics (MD) simulations and stress−strain (SS)) study, the structural and mechanical properties of amyloid beta (Aβ40) fibrils such as β-sheet character, twist, inter-strand distance, and periodicity were found to be in agreement with experimental measurements. Furthermore, Young’s modulus (Y) = 4.2 GPa computed using SS calculations was supported by measured values of 1.79 ± 0.41 and 3.2 ± 0.8 GPa provided by two separate AFM experiments. These results revealed size dependence of structural and material properties of amyloid fibrils and show the utility of such combined experimental and theoretical studies in the design of precisely engineered biomaterials.

Multi-stranded DNA topologies, including quadruplexes, triplexes and duplexes, are present in human telomeric DNA, and provide important insights into pathological mechanisms. Assessing their stability is important for drug discovery and biosensing. With the recent development of Trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS), biomolecular ions can be separated by mass, charge and size in the gas phase as a function of their tridimensional structure, providing insight into conformeric subpopulations and folding pathways on the millisecond timescale not accessible using traditional techniques. In the current research, model oligonucleotides shown to adopt multi-stranded topologies were analyzed using TIMS-MS. Multiple charge states and oligomeric states were observed (e.g., [M+H]⁺, [2M+2H]²⁺, [3M+3H]³⁺ and [4M+4H]⁴⁺). Multiple mobility bands were detected as a function of the charge states, indicating a series of partially-folded DNA geometries. Conformational dynamics were studied as a function of the time after desolvation on the millisecond timescale. These data provide insight into DNA folding mechanisms and oligomeric complex stability, which can be further supported with candidate structure generation.

Internal ionizable residues, despite being inherently incompatible with hydrophobic environments, play major roles in energy transduction and enzyme catalysis. These buried ionizable residues display anomalous experimental pK_a values.  In the present work, we study the pH-dependent conformational reorganizations associated with the ionization of lysine residues in the L25K and L125K  variants of staphylococcal nuclease (SNase). We carried out constant pH replica exchange molecular dynamics simulations (pH-REMD) in explicit solvent using AMBER, implemented to run in GPUs. Our calculations show that the pK_a values of Lys25 and Lys125 are significantly deviated from their pK_a values in bulk water and are in good agreement with experimental values. A study of the water proximity to the lysine residues at different pH indicate that the lysine residues move towards the protein-water interface when protonated and prefer to remain deprotonated when buried in the hydrophobic protein pocket. The root mean square fluctuations display signatures of pH dependent conformational fluctuations in L25K, in contrast to the relatively pH independent conformational changes observed in L125K. The present computational study, besides offering a detailed atomistic understanding of the structural determinants of the shifted pK_a values displayed by internal ionizable residues, aids in bolstering the experimental findings.

Downstream regulatory antagonist modulator also known as K⁺ channel interacting protein 3 (DREAM/KChIP3) is a calcium sensing protein that co-assembles with Kv4 potassium channels in the brain and heart as well as with DNA in the nucleus where it regulates gene expression. The interaction of DREAM/KChIP3 with A-type Kv4 channels and DNA has been shown to regulate neuronal signaling, pain sensing and memory retention. Previous results have shown a Ca²⁺ dependent interaction between DREAM/KChIP3 and Kv4/DNA which involves interactions at the N-terminus. However, the mechanism by which Ca²⁺ binding at the C-terminus of DREAM/KChIP3 induces structural changes at the N-terminus remains unknown. We have identified a highly conserved network of aromatic residues that modulate protein dynamics and the pathways of signal transduction on DREAM/KChIP3. Using molecular dynamics simulations, site directed mutagenesis and fluorescence spectroscopy we provide strong evidence in support of a highly dynamic mechanism of signal transduction and regulation. We have identified that Trp169, Phe171, and Tyr174 at the entering helix of EF-hand 3 function as key amino acids involved in propagation of Ca²⁺ induced structural changes. The observed structural motions provide insight into the mechanism mediating the calcium dependent Kv4 and DNA binding. Together, the work presented here provides the first mechanism of intramolecular signal transduction in a Ca²⁺ binding protein of the NCS family.

Cell membranes provide an efficient mechanism of compartmentalizing cellular contents from the surrounding while allowing selective transportation of essential molecules across the hydrophobic barrier. It is not surprising that many small amphipathic peptides can threaten bacteria by directly interacting with their membrane envelopes. Identifying the interaction mechanism of those small peptides will help us develop antimicrobial compounds with better potency. We are interested in elucidating the impacts of natural and synthesized peptides on physical properties of model lipid membranes. Our main experimental tools include atomic force microscopy, force spectroscopy, Raman spectroscopy, electron paramagnetic spectroscopy, and fluoresce microscopy. The second topic of membrane interaction centers on misfolded protein aggregates. In particular, we have obtained several interesting aspects of membrane perturbation caused by oligomeric and fibrillar aggregates formed by a polyglutamine peptide. Lastly, I will briefly cover how simple lipid mixtures can give rise to the fascinating heterogeneous organization in lipid membranes.