Probing Biomolecular Machinery with Simulation Tools

It is now well established that biomolecules undergo conformational fluctuations to perform a variety of cellular functions such as signal transduction, transport, and catalysis. Many experimental techniques such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, small-angle X-ray scattering (SAXS), and single-particle electron microscopy (EM) have indeed provided structural evidence at different resolutions to support the view of multiple functional states of biomolecules. Yet it remains difficult to characterize the vast conformational repertoire of biomolecules via experimental methods alone. Therefore, biophysical theory, modeling, and simulation techniques rooted in statistical mechanics are often useful for a detailed molecular understanding of biomolecular structures. Given the large number of degrees of freedom in biomolecules, conventional simulation approaches remain limited in providing information on conformational statistics, particularly metastable intermediates, at longer time-scales. Such information is often required for targeted therapeutic intervention in various disease states. Therefore, novel approaches are needed for extensive conformational sampling via biomolecular simulations. In this talk, I’ll highlight the theory and applications of temperature-accelerated molecular dynamics (TAMD) in accelerating “slow” conformational changes in biomolecules via examples on enzymes, receptor proteins, and small molecule drugs. I’ll also discuss how TAMD can be combined with state-of-the-art simulation methods to compute key thermodynamic properties such as the free-energy. In general, the simulation methodologies and concepts presented in this talk may have key implications for understanding biomolecular dynamics, enzyme catalysis, and solute transport at the molecular level

Self-assembly behavior of experimentally realizable lobed patchy particles

We report simulation studies on the self-assembly behavior of five different types of lobed patchy particles of different shapes (snowman, dumbbell, trigonal planar, square planar, and tetrahedral). Inspired by an experimental method of synthesizing patchy particles (Wang et al., Nature, 2012, 491, 51–55), we control the lobe size indirectly by gradually varying the seed diameter and study its effect on self-assembled structures at different temperatures. Snowman shaped particles self-assemble only at a lower temperature and form two-dimensional sheets, elongated micelles, and spherical micelles, depending on the seed diameter. Each of the four other lobed particles self-assemble into four distinct morphologies (random aggregates, spherical aggregates, liquid droplets, and crystalline structures) for a given lobe size and temperature. We observed temperature-dependent transitions between two morphologies depending on the type of the lobed particle. The self-assembled structures formed by these four types of particles are porous. We show that their porosities can be tuned by controlling the lobe size and temperature

Self-Assembly of Porous Structures From a Binary Mixture of Lobed Patchy Particles

We report simulation studies on the self-assembly of a binary mixture of snowman and dumbbell shaped lobed particles. Depending on the lobe size and temperature, different types of self-assembled structures (random aggregates, spherical aggregates, liquid droplets, amorphous wire-like structures, amorphous ring structures, crystalline structures) are observed. At lower temperatures, heterogeneous structures are formed for lobed particles of both shapes. At higher temperatures, homogeneous self-assembled structures are formed mainly by the dumbbell shaped particles, while the snowman shaped particles remain in a dissociated state. We also investigated the porosities of self-assembled structures. The pore diameters in self-assemblies increased with an increase in temperature for a given lobe size. The particles having smaller lobes produced structures with larger pores than the particles having larger lobes. We further investigated the effect of σ, a parameter in the surface-shifted Lennard-Jones potential, on the self-assembled morphologies and their porosities. The self-assembled structures formed at a higher σ value are found to produce larger pores than those at a lower σ

Conformational dynamics and energetics of viral RNA recognition by lab-evolved proteins

The conserved and structured elements in viral RNA genomes interact with proteins to regulate various events in the viral life cycle and have become key targets for developing novel therapeutic approaches. We probe physical interactions between lab-evolved proteins and a viral RNA element from the HIV-1 genome. Specifically, we study the role of an arginine-rich loop in recognition of designed proteins by the viral RNA element. We report free energy calculations to quantitatively estimate the protein/RNA binding energetics, focusing on the mutations of arginine residues involved in recognition of the major groove of RNA by proteins

Role of conformational heterogeneity in ligand recognition by viral RNA molecules

Ribonucleic acid (RNA) molecules are known to undergo conformational changes in response to various environmental stimuli including temperature, pH, and ligands. In particular, viral RNA molecules are a key example of conformationally adapting molecules that have evolved to switch between many functional conformations. The transactivation response element (TAR) RNA from the type-1 human immunodeficiency virus (HIV-1) is a viral RNA molecule that is being increasingly explored as a potential therapeutic target due to its role in the viral replication process. In this work, we have studied the dynamics in TAR RNA in apo and liganded states by performing explicit-solvent molecular dynamics (MD) simulations initiated with 27 distinct structures. We determined that the TAR RNA structure is significantly stabilized on ligand binding with especially decreased fluctuations in its two helices. This rigidity is further coupled with the decreased flipping of bulge nucleotides, which were observed to flip more frequently in the absence of ligands. We found that initially-distinct structures of TAR RNA converged to similar conformations on removing ligands. We also report that conformational dynamics in unliganded TAR structures leads to the formation of binding pockets capable of accommodating ligands of various sizes

Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides

Interactions between RNA molecules and proteins are critical to many cellular processes and are implicated in various diseases. The RNA-peptide complexes are good model systems to probe the recognition mechanism of RNA by proteins. In this work, we report studies on the binding-unbinding process of a helical peptide from a viral RNA element using nonequilibrium molecular dynamics simulations. We explored the existence of various dissociation pathways with distinct free-energy profiles that reveal metastable states and distinct barriers to peptide dissociation. We also report the free-energy differences for each of the four pathways to be 96.47 ± 12.63, 96.1 ± 10.95, 91.83 ± 9.81, and 92 ± 11.32 kcal/mol. Based on the free-energy analysis, we further propose the preferred pathway and the mechanism of peptide dissociation. The preferred pathway is characterized by the formation of sequential hydrogen-bonding and salt-bridging interactions between several key arginine amino acids and the viral RNA nucleotides. Specifically, we identified one arginine amino acid (R8) of the peptide to play a significant role in the recognition mechanism of the peptide by the viral RNA molecule

Water Dynamics in a Peptide-appended Pillar[5]arene Artificial Channel in Lipid and Biomimetic Membranes

Peptide-appended Pillar[5]arene (PAP) is an artificial water channel that can be incorporated into lipid and polymeric membranes to achieve high permeability and enhanced selectivity for angstrom-scale separations [Shen et al. Nat. Commun. 9:2294 (2018)]. In comparison to commonly studied rigid carbon nanotubes, PAP channels are conformationally flexible, yet these channels allow a high water permeability [Y. Liu and H. Vashisth Phys. Chem. Chem. Phys. 21:22711 (2019)]. Using molecular dynamics (MD) simulations, we study water dynamics in PAP channels embedded in biological (lipid) and biomimetic (block-copolymer) membranes to probe the effect of the membrane environment on water transport characteristics of PAP channels. We have resolved the free energy surface and local minima for water diffusion within the channel in each type of membrane. We find that water follows single file transport with low free-energy barriers in regions surroundings the central ring of the PAP channel and the single file diffusivity of water correlates with the number of hydrogen bonding sites within the channel, as is known for other sub-nm pore-size synthetic and biological water channels [Horner et al. Sci. Adv. 1:e1400083 (2015)]

All‐atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone‐binding element

Insulin regulates blood glucose levels in higher organisms by binding to and activating insulin receptor (IR), a constitutively homodimeric glycoprotein of the receptor tyrosine kinase (RTK) superfamily. Therapeutic efforts in treating diabetes have been significantly impeded by the absence of structural information on the activated form of the insulin/IR complex. Mutagenesis and photo‐crosslinking experiments and structural information on insulin and apo‐IR strongly suggest that the dual‐chain insulin molecule, unlike the related single‐chain insulin‐like growth factors, binds to IR in a very different conformation than what is displayed in storage forms of the hormone. In particular, hydrophobic residues buried in the core of the folded insulin molecule engage the receptor. There is also the possibility of plasticity in the receptor structure based on these data, which may in part be due to rearrangement of the so‐called CT‐peptide, a tandem hormone‐binding element of IR. These possibilities provide opportunity for large‐scale molecular modeling to contribute to our understanding of this system. Using various atomistic simulation approaches, we have constructed all‐atom structural models of hormone/receptor complexes in the presence of CT in its crystallographic position and a thermodynamically favorable displaced position. In the “displaced‐CT” complex, many more insulin–receptor contacts suggested by experiments are satisfied, and our simulations also suggest that R‐insulin potentially represents the receptor‐bound form of hormone. The results presented in this work have further implications for the design of receptor‐specific agonists/antagonists. Proteins 2013; © 2012 Wiley Periodicals, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/98204/1/PROT_24255_sm_SuppInfo.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/98204/2/24255_ftp.pd

Reaction Coordinate and Thermodynamics of Base Flipping in RNA

Base flipping is a key biophysical event involved in recognition of various ligands by ribonucleic acid (RNA) molecules. However, the mechanism of base flipping in RNA remains poorly understood, in part due to the lack of atomistic details on complex rearrangements in neighboring bases. In this work, we applied transition path sampling (TPS) methods to study base flipping in a double-stranded RNA (dsRNA) molecule that is known to interact with RNA-editing enzymes through this mechanism. We obtained an ensemble of 1000 transition trajectories to describe the base-flipping process. We used the likelihood maximization method to determine the refined reaction coordinate (RC) consisting of two collective variables (CVs), a distance and a dihedral angle between nucleotides that form stacking interactions with the flipping base. The free energy profile projected along the refined RC revealed three minima, two corresponding to the initial and final states and one for a metastable state. We suggest that the metastable state likely represents a wobbled conformation of nucleobases observed in NMR studies that is often characterized as the flipped state. The analyses of reactive trajectories further revealed that the base flipping is coupled to a global conformational change in a stem-loop of dsRNA