Knowledge of the mechanism of association and dissociation of macromolecules is important for many biological structures and processes. Among the examples are the binding and dissociation of substrates of enzyme reactions, the recognition of ligands by their receptors or of DNA sequences by the DNA binding domains of regulatory proteins. These processes have in common a transition from one equilibrium state to another which often is a rare event on the time scale of molecular dynamics simulations of a few hundreds of picoseconds. Conventional computational methods for the sampling of barrier-crossing events increase the probability of unlikely configurations. Once such configurations have been sampled their actual occurence can be determined through the known relation between old and new probabilities. A methodologically related avenue to characterize rare events through molecular dynamics simulation is the addition of external forces which reduce the energy barriers. This approach has the advantage that it corresponds closely to micromanipulation through atomic force microscopy or optical tweezers.

The external force techniques can be applied to study many processes, including dissociation of avidin-biotin complex, dissociation of retinal from bacteriorhodopsin, stretching of DNA, etc. The molecular dynamics program NAMD, developed in the group, is capable of performing several different kinds of SMD, including rotation or translation of one or more atoms. The group's molecular graphics program VMD provides a powerful means of visualizing these simulations, and through the Interactive Molecular Dynamics (IMD) interface can even allow SMD simulations to be performed in real time.

Interactive Molecular Dynamics and GlpF

Interactive Molecular Dynamics allows us to pull sugar molecules by hand through a simulation of the glycerol channel GlpF. As we push the virtual molecules around, we feel them in our hands as if they were real. We use this technique to explore features of the channel and gain new insights into the way it functions.


Energy Conversion in F0-ATPase

ATP synthase overview Adenosine triphosphate (ATP) is the primary energy "currency" in most living organisms. ATP synthase is a large (about 100,000 atoms) protein, which includes a transmembrane F0 unit coupled to a solvent-exposed F1 unit via a central stalk gamma. The F0 unit utilizes a transmembrane electrochemical potential (proton motive force), converting it into the mechanical energy of the stalk rotation. The rotation leads to cyclic conformational changes in the catalytic sites in the F1 unit, thereby driving ATP synthesis. We seek to identify and explore the chain of the elementary chemical (proton transfer) and mechanical (domain motion) events involved in the process of converting the electrochemical energy of the transmembrane proton gradient into the mechanical energy of the c subunit oligomer rotation.

Torque Application to ATP Synthase Central Stalk

ATP synthase is a large multi-protein complex which includes a transmembrane Fo unit coupled to a solvent-exposed F1 unit via a central stalk. The stalk rotates within the surrounding subunits of F1, leading to cyclic conformational changes in the three catalytic sites in F1 and, thereby, to ATP synthesis. We use steered molecular dynamics to apply a torque to the central stalk in order to understand the cooperative interactions that underlie this mechanism.

Avidin-Biotin Complex

Molecular dynamics simulations induce, over periods of 40 ps to 500 ps, the unbinding of biotin from avidin by means of external harmonic forces with force constants close to those of AFM cantilevers. The applied forces are sufficiently large to reduce the overall binding energy enough to yield unbinding within the measurement time. Avidin


PLA2 We are applying the steered molecular dynamics method to investigate the action of human synovial protein phospholipase A2 (PLA2) at the lipid water interface. Our hypothesis is that prior to extruding the phospholipid, PLA2 must form the tightly bound complex, while the loosely bound complex should not lead to catalysis.

Retinal's binding pathway in bR

Formation of bacteriorhodopsin (bR) from the apoprotein and retinal has been studied experimentally, but the actual pathway, including the site of retinal entry, is little understood. Molecular dynamics simulations provide a surprisingly clear prediction. bR-retinal

Ligand Binding Domain of Retinoic Acid

RAR Binding of the hormone to the retinoic acid receptor induces conformational changes that control and influence gene expression. In order to understand the functional role of the hormone one must understand the binding mechanism by which the hormone induces conformational changes. We studied the forced unbinding of the retinoic acid hormone from its receptor by applying an external force on the hormone.

Mechanical proteins

The giant muscle protein titin, also known as connectin, is a roughly 30,000 amino acid long filament which plays a number of important roles in muscle contraction and elasticity. To examine in atomic detail the dynamics and structure-function relationships of this behavior, SMD simulations of force-induced titin Ig domain unfolding were performed. titin

Antibody / Antigen Interactions

antibody-antigen Catalytic antibodies are able to bind their antigen and to perform chemical reaction such as esterification or hydrolysis of the hapten. We use SMD to unbind the hapten and check the differences in unbinding for the wild-type and mutant structures.

Cytochrome bc1 complex

SMD simulations provide insight into how the bc1 complex performs its function of separating electrons and protons across a membrane. bc1

KcsA potassium channel

kcsa One of the best tools for making the connection between the structure and function of ion channels is molecular dynamics~(MD) simulation, which allows one to foll ow conformational changes in the structure, and movement of K+ ions across the potassium channel. The difficulty in simulating the passing of K+ or Na+ ions through the channel can be overcome by using SMD.