Origin of the Surprising Mechanical Stability of Kinesin's Neck Coiled Coil.

Kinesin-1 is a motor protein moving along a microtubule with its two identical motor heads dimerized by two neck linkers and a coiled-coil stalk. When both motor heads bind the microtubule, an internal strain is built up between the two heads, which is indispensable to ensure proper coordination of the two motor heads during kinesin-1's mechanochemical cycle. The internal strain forms a tensile force along the neck linker that tends to unwind the neck coiled coil (NCC).

Shaft Function of Kinesin-1's α4 Helix in the Processive Movement.

Introduction: Kinesin-1 motor is a molecular walking machine constructed with amino acids. The understanding of how those structural elements play their mechanical roles is the key to the understanding of kinesin-1 mechanism.

Methods: Using molecular dynamics simulations, we investigate the role of a helix structure, α4 (also called switch-II helix), of kinesin-1's motor domain in its processive movement along microtubule.

Mechanical amplification mechanism of kinesin's β-domain.

Conventional kinesin's force generation process always takes place on the leading head and the generated force is transmitted to the trailing head through two neck linkers. To guarantee a strong force to be transmitted to the trailing head so that it can be detached from microtubule surface, the neck linker of the leading head must have a large enough forward displacement, which is proposed to be achieved by the amplifying function of the β-domain. However, the experimental result shows that the forward displacement of the β-domain itself appears too small.

An ab initio molecular dynamics study on hydrogen bonds between water molecules.

The quantitative estimation of the total interaction energy of a molecular system containing hydrogen bonds (H bonds) depends largely on how to identify H bonding. The conventional geometric criteria of H bonding are simple and convenient in application, but a certain amount of non-H bonding cases are also identified as H bonding. In order to investigate the wrong identification, we carry out a systematic calculation on the interaction energy of two water molecules at various orientation angles and distances using ab initio molecular dynamics method with the dispersion correction for the Becke-Lee-Yang-Parr (BLYP) functionals.