Stretching biomolecules

RNA & Protein folding

Molecular Motors

Single molecule force spectroscopy

Deciphering the energy landscape of biomolecules

Polymer Physics


Molecular Motors

Internal strain regulates the nucleotide binding site of the kinesin leading head (PNAS '07)
In the presence of ATP, kinesin proceeds along the protofilament of microtubule by alternated binding of two motor domains on the tubulin binding sites. Because the processivity of kinesin is much higher than other motor proteins, it has been speculated that there exists a mechanism for allosteric regulation between the two monomers. Recent experiments suggest that ATP binding to the leading head (L) domain in kinesin rearward strain built on the neck-linker. We test this hypothesis by explicitly modeling a C{alpha}-based kinesin structure whose motor domains are bound on the tubulin binding sites.
The equilibrium structures of kinesin on the microtubule show disordered and ordered neck-linker configurations for the L and trailing head, respectively. The comparison of the structures between the two heads shows that several native contacts present at the nucleotide binding site in the L are less intact than those in the binding site of the rear head. The network of native contacts obtained from this comparison provides the internal tension propagation pathway, which leads to the disruption of the nucleotide binding site in the L. Also, using an argument based on polymer theory, we estimate the internal tension built on the neck-linker to be f {approx}12-15 pN. Both of these conclusions support the experimental hypothesis.

Mechanical control of the directional stepping dynamics of the kinesin motor (PNAS '07)

Among the multiple steps constituting the kinesin mechanochemical cycle, one of the most interesting events is observed when kinesins move an 8-nm step from one microtubule (MT)-binding site to another. The stepping motion that occurs within a relatively short time scale ({approx}100 microsec) is, however, beyond the resolution of current experiments. Therefore, a basic understanding to the real-time dynamics within the 8-nm step is still lacking. For instance, the rate of power stroke (or conformational change) that leads to the undocked-to-docked transition of neck-linker is not known, and the existence of a substep during the 8-nm step still remains a controversial issue in the kinesin community. By using explicit structures of the kinesin dimer and the MT consisting of 13 protofilaments, we study the stepping dynamics with varying rates of power stroke (kp). We estimate that kFormula lsim20 microsec to avoid a substep in an averaged time trace. For a slow power stroke with kFormula > 20 microsec, the averaged time trace shows a substep that implies the existence of a transient intermediate, which is reminiscent of a recent single-molecule experiment at high resolution. We identify the intermediate as a conformation in which the tethered head is trapped in the sideway binding site of the neighboring protofilament. We also find a partial unfolding (cracking) of the binding motifs occurring at the transition state ensemble along the pathways before binding between the kinesin and MT.

Dynamics of allosteric transitions in GroEL (PNAS '06)
The chaperonin GroEL-GroES,
a machine that helps proteins to fold, cycles through a number of allosteric states, the T state, with high affinity for substrate proteins, the ATP-bound R state, and the R'' (GroEL-ADP-GroES) complex. Here, we use a self-organized polymer model for the GroEL allosteric states and a general structure-based technique to simulate the dynamics of allosteric transitions in two subunits of GroEL and the heptamer. The T -> R transition, in which the apical domains undergo counterclockwise motion, is mediated by a multiple salt-bridge switch mechanism, in which a series of salt-bridges break and form. The initial event in the R -> R'' transition, during which GroEL rotates clockwise, involves a spectacular outside-in movement of helices K and L that results in K80-D359 salt-bridge formation. In both the transitions there is considerable heterogeneity in the transition pathways. The transition state ensembles (TSEs) connecting the T, R, and R'' states are broad with the TSE for the T -> R transition being more plastic than the R -> R'' TSE.

Contact Information : Changbong Hyeon, Professor, School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
+82-2-958-3810 (tel)

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