Jung-Chi Liao, Ph.D.

1. Liao, J.-C., Elting, M.W., Delp, S.L., Spudich, J.A., Bryant, Z. (2008) Probing the reverse directionality and processivity of myosin VI. (in preparation)
2. Parker, D., Liao, J.-C., Spudich, J.A., Delp, S.L. (2008) Mechanical characterization of a myosin V neck. (in preparation)
3. Liao, J.-C., Spudich, J.A., Parker, D., Delp, S.L. (2007) Extending the absorbing boundary method to fit dwell-time distributions of molecular motors with complex kinetic pathways, PNAS, 104, 3171-3176. (pdf)
4. Tang, S.*, Liao, J.-C.* (as a co-first author), Dunn, A.R., Altman, R.B., Spudich, J.A., Schmidt, J.P. (2007) Predicting allosteric communication in myosin via a pathway of conserved residues, Journal of Molecular Biology, 373(5), 1361-1373. (pdf)
5. Zheng, W.*, Liao, J.-C.* (as a co-first author), Doniach, S., Brooks, B.R. (2007) Toward the mechanism of dynamical couplings in Hepatitis C virus NS3 helicase using elastic network model. Proteins, 67, 886-896. (pdf)
6. Adelman, J.L., Jeong, Y.-J., Liao, J.-C., Patel, G., Kim, D.-E., Oster, G., Patel, S. S. (2006) Mechanochemistry of transcription termination factor Rho. Molecular Cell, 22, 611-621. (pdf)
7. Xing, J., Liao, J.-C., Oster, G. (2005) Making ATP, PNAS, 102(46), 16539-16546. (pdf)
8. Liao, J.-C.* (as a co-first author), Jeong, Y.-J.*, Kim, D.-E., Patel, S.S., Oster, G. (2005) Mechanochemistry of T7 DNA helicase. Journal of Molecular Biology, 210(3), 452-475. (pdf)
9. Liao, J.-C., Sun, S., Chandler, D., Oster, G. (2004) The conformational states of Mg-ATP in water. European Biophysics Journal, 33, 29-37. (pdf)
10. Liao, J.-C., Oster, G. (2004) The engines of biomolecular motors. Proceedings of NANO2004, ASME Integrated Nanosystems: Design, Synthesis and Applications, Pasadena, California. (pdf)
11. Liao, J.-C. (2002) A tensioned beam on a spatially varying elastic foundation with a turning point. (pdf)
12. Liao, J.-C. (2002) Vortex-induced vibration of slender structures in unsteady flow. DSpace, hdl.handle.net/1721.1/8331. (pdf)
13. Liao, J.-C., Vandiver, J.K. (2000) Vortex-induced vibration analysis of the Allegheny riser using SHEAR7. STRIDE JIP Document, 2H Offshore Engineering, Ltd. (pdf)
14. Liao, J.-C., Srinivasan, M. A. (1999) Experimental investigation of frictional properties of the human fingerpad. RLE Technical Report, M.I.T., 629, 3-154. (pdf)
15. Srinivasan, M. A., Raju, B. I., De, S., Liao, J.-C., Cysyk, J. P., LaMotte, R. H. (1998) Role of skin biomechanics in mechanoreceptor response. RLE Progress Report, M.I.T., 141, 368-376.

Probing Structural Effects on Directionality of Myosin VI Using Artifiical Lever Arms

Myosin uses ATP chemical energy to perform diverse functions such as muscle contractions, cell division, and vesicle transports. My interests lie in integrating experimental and computational techniques together to understand its mechanics and energy transduction. I have designed myosin VI with artificial lever arms to identify key structural elements of myosin VI dictating its reverse directionality. I implemented computational modeling and molecular dynamics simulation to guide the chimera design. I then used in vitro motility, optical tweezers, total internal reflection fluorescence microscopy to test these designs. The following movies show the actin filaments moved by designed myosins toward the opposite directions. Movies: (a) Myosin VI design with plus-end directed movement (actins moving away from the red Cy5 labels); (b) myosin VI design with minus-end directed movement (actins moving toward the red Cy5 labels). These two designed myosins differ only by 18 amino acids. Field size: 12.8 μm x 6.4 μm

  (a)             (b)

Identifying the Power Stroke Step of Myosin V Using a Novel Dwell-Time Distribution Analysis

The sequence of the mechanochemical steps involving the power stroke and the Pi release remains an open question for myosin. It is difficult to resolve this issue because the power stroke step and the Pi release step occur so rapidly that it is difficult to determine if they are separate steps, and if so, which one occurs first. Laser trap assays, however, can accelerate or decelerate the power stroke step so that the kinetic flux is redistributed, making it possible to distinguish these steps. I have developed a novel computational algorithm that can exactly predict dwell-time distributions of any complex kinetics. Using this new algorithm, I simulated the possible mechanochemical mechanism of one head of myosin V. By fitting the data of dwell-time distributions under different applied forces and nucleotide concentrations, we conclude that the power stroke is neither coupled to the Pi release step nor the ADP release step. Our analysis suggests that the power stroke happens after the Pi release step and before the ADP release step. Figure: (a) The simulation of dwell-time distributions fails to fit to the single molecule measurement when assuming the power stroke step happens during ADP release. (b) The dwell-time distributions fit well to the experiments when assuming the power stroke step occurs after Pi release and before ADP release.

(a)          (b)

Dynamical Coupling of Hepatitis C Virus NS3 Helicase (DNA Translocation by NS3 Helicase using Normal Mode Method)

Hepatitis C virus NS3 helicase is an enzyme that unwinds double-stranded polynucleotides in an ATP-dependent reaction. Despite recent progress, the detailed mechanism of the coupling between ATPase activity and helicase activity remains unclear. Based on an elastic network model (ENM), we apply two computational analysis tools to probe the dynamical mechanism underlying the allosteric coupling between ATP binding and polynucleotide binding in this enzyme. The conformational changes between different crystal structures of NS3 helicase are found to be dominated by the lowest frequency mode (#1) solved from the ENM. This mode corresponds to a hinge motion of the highly flexible domain 2. This motion simultaneously modulates the opening/closing of the domains 1-2 cleft where ATP binds, and the domains 2-3 cleft where the polynucleotide binds.

Kinematics of F1 ATP Synthase (Hydrolysis Cycle Movie by Wang and Oster)

F1 ATP synthase is a rotary motor (see movie above) which synthesizes 3 ATPs per revolution. Kinetic experiments have been carried out under different ADP and Pi concentrations to observe the synthesis rate (Tomashek JJ et al, JBC 2004, 279, 4465-4470). Based on the electrostatic and hydrophobic properties of residues, I have mapped out the residues on the gamma shaft and on the contact residues on the beta subunits. The residues on gamma form a contact groove (shown in green in the figure). This groove guides the movements of beta subunits according to the cyclic pattern shown in the right panel of the figure. This kinematic mechanism allows the accurate control of ATP synthesis during the rotation of the gamma shaft, which plays as a cam shaft in a rotary engine.

Sequential Nucleotide Hydrolysis by the Ring-shaped T7 Helicase (Schematic movie of sequential power strokes)

Bacteriophage T7 helicase is a hexameric motor protein that couples energy from the dTTP hydrolysis cycle to unwind double-stranded DNA by translocating along one of the DNA strands. The experimental studies show that at least 5 subunits are catalytic and, from the arguments of mechanical stresses among different subunits, we conclude that all 6 subunits are catalytic. We propose a 6-state, 6-subunit, sequential kinetic network to describe the system, and rate constants are obtained numerically by an optimization algorithm. The simulation based on this model agrees with experimental results over the entire time trajectories. From kinetic flux analyses, the distribution of multiple kinetic pathways is determined quantitatively. The flux distribution varies with the initial concentrations, so that the main pathways also shift according to the ambient conditions. Three cooperative sequential steps are required for all main pathways. From the kinetic model we also predict the single molecule force-velocity curve, with a stall force of ~ 30 pN. The first figure shows the hexameric ring and a single-stranded DNA in the channel. The mechanical stresses mainly pass through the beta-sheet of each subunit, colored in red in the figure. The second figure shows three required cooperative steps of the DNA translocation cycle. Each cooperative step is the result of mechanical coordinations among subunits and the substrate DNA. The computational results demonstrate multiple pathways of this molecular machine.

Mechanical Mechanisms for the Power Strokes of RecA-like Motor Proteins

The RecA-like protein family is one of 2 major divisions amongst NTP-powered motor proteins. In each subunit of these mechano-enzymes, loops emanating from a central parallel beta-sheet grasp the nucleotide in a network of hydrogen bonds. The progressive formation of these hydrogen bonds between the nucleotide and the P-loop is the mechanism by which the energy in the hydrogen bonds is converted into mechanical work (the 'Binding Zipper'). The stress generated in the catalytic site by the binding transition radiates outward through the subunit to both drive the power stroke, and to coordinate the hydrolysis cycles between the subunits. The figures show how the mechanical transmission propagates for T7 helicase and for F1 ATPase.

Mechanical Properties of Mg-ATP in Water (Simulation Movie)

The conformational equilibria of Mg-ATP in solution is studied using molecular dynamics (MD) augmented with umbrella sampling methods. Free energy comparisons show that the Mg2+ ion is equally likely to coordinate the oxygens of the two end phosphates, or of all three phosphates, as shown in the free energy below. The MD trajectories reveal two major degrees of freedom of the Mg-ATP molecule in solution, and we compute the free energy as a function of these variables, and determine its elastic properties. Comparing the free energy function with several crystallographic structures of ATP analogs as shown in the figure, we find that the crystal structures correspond to states where ATP would be elastically strained.