Dynamics of cooperative cargo transport by two elastically coupled kinesin motors.

Intracellular transport is performed often by multiple motor proteins bound to the same cargo. Here, we study theoretically collective transport of the cargo by two kinesin motors. We propose that the motor has only the elastic interaction with the cargo via the linker connecting them and has no interaction with another motor. With parameters values for single motors from the available single-molecule data, we show that at linker's elastic strength [Formula: see text] pN/nm the theoretical data of both velocity and run length of the two-motor assembly under no load are identical to the available experimental data. The run length distribution is single exponential. The single-motor-bound state of the assembly dominates the transport. Both the force dependence of the velocity of the cargo driven by single load-bearing motor and that by two load-bearing motors in the assembly are consistent with the experimental data. The stall force of the assembly is larger than the sum of stall forces of two uncoupled motors. Moreover, we predict that the stall force increases with the increase of K and becomes saturated at large K, with the saturated value being 1.5-fold larger than the sum of stall forces of the two uncoupled motors.

Involvement of G-triplex and G-hairpin in the multi-pathway folding of human telomeric G-quadruplex.

G-quadruplex (G4) can be formed by G-rich DNA sequences that are widely distributed throughout the human genome. Although G-triplex and G-hairpin have been proposed as G4 folding intermediates, their formation still requires further investigation by experiments. Here, we employed single-molecule FRET to characterize the folding dynamics of G4 from human telomeric sequence. First, we observed four states during G4 folding initially assigned to be anti-parallel G4, G-triplex, G-hairpin and unfolded ssDNA. Then we constructed putative intra-strand G-triplex, G-hairpin structures and confirmed their existences in both NaCl and KCl. Further studies revealed those structures are going through dynamic transitions between different states and show relatively weak dependence on cations, unlike G4. Based on those results and molecular dynamics simulations, we proposed a multi-pathway folding mechanism for human telomeric G4. The present work may shed new light on our current understanding about the existence and stability of G4 intermediate states.

Investigating role of conformational changes of microtubule in regulating its binding affinity to kinesin by all-atom molecular dynamics simulation.

Changes of affinity of kinesin head to microtubule regulated by changes in the nucleotide state are essential to processive movement of kinesin on microtubule. Here, using all-atom molecular dynamics simulations we show that besides the nucleotide state, large conformational changes of microtubule-tubulin heterodimers induced by strong interaction with the head in strongly binding state are also indispensable to regulate the affinity of the head to the tubulin. In strongly binding state the high affinity of the head to microtubule arises largely from mutual conformational changes of the microtubule and head induced by the specific interaction between them via an induced-fit mechanism. Moreover, the ADP-head has a much weaker affinity to the local microtubule-tubulin, whose conformation is largely altered by the interaction with the head in strongly binding state, than to other unperturbed tubulins. This indicates that upon Pi release the ADP-head temporarily has a much weaker affinity to the local tubulin than to other tubulins.

Dynamics of bridge helix bending in RNA polymerase II.

One of critical issues for RNA polymerase is how the enzyme translocates along the DNA substrate during transcription elongation cycle. Comparisons of the structure of RNA polymerase II (Pol II) with that of bacterial enzyme have suggested that the transition of the bridge helix (BH) from straight to flipped-out conformations facilitates the translocation of upstream DNA-RNA hybrid. However, the flipped-out conformation of BH in Pol II has not been observed up to now and the detailed mechanism of how the BH facilitating upstream hybrid translocation still remains obscure. Here we use all-atom molecular dynamics simulations to study the transition dynamics of BH in Pol II. Two different flipped-out conformations (termed as F1 and F2) are derived from our simulation trajectories, both of which could contribute to upstream hybrid translocation. In particular, the structure of BH in F2 conformation shows nearly identical to that observed in free bacterial enzyme, showing the existence of the flipped-out conformation in Pol II. Analysis of hydrogen bonds and salt bridge formed intra BH in different conformations indicates that the flipped-out conformations are more unstable than the straight conformation. Moreover, a detailed understanding of how the transition of BH conformations facilitating upstream hybrid translocation is given. Proteins 2017; 85:614-629. © 2016 Wiley Periodicals, Inc.

Optimal numbers of residues in linkers of DNA polymerase I, T7 primase and DNA polymerase IV.

DNA polymerase I (PolI), T7 primase and DNA polymerase IV (Dpo4) have a common feature in their structures that the two main domains are connected by an unstructured polypeptide linker. To perform their specific enzymatic activities, the enzymes are required to rearrange the position and orientation of one domain relative to the other into an active mode. Here, we show that the three enzymes share the same mechanism of the transition from the inert to active modes and use the minimum numbers of residues in their linkers to achieve the most efficient transitions. The transition time to the finally active mode is sensitively dependent on the stretched length of the linker in the finally active mode while is insensitive to the position and orientation in the initially inert state. Moreover, we find that for any enzyme whose two domains are connected by an unstructured flexible linker, the stretched length (L) of the linker in the finally active mode and the optimal number (Nopt) of the residues in the linker satisfy relation L ≈ αNopt, with α = 0.24-0.27 nm being a constant insensitive to the system.