Protein Diffusion on Charged Biopolymers: DNA versus Microtubule

Abstract

Protein diffusion in lower-dimensional spaces is used for various cellular functions. For example, sliding on DNA is essential for proteins searching for their target sites, and protein diffusion on microtubules is important for proper cell division and neuronal development. On the one hand, these linear diffusion processes are mediated by long-range electrostatic interactions between positively charged proteins and negatively charged biopolymers and have similar characteristic diffusion coefficients. On the other hand, DNA and microtubules have different structural properties. Here, using computational approaches, we studied the mechanism of protein diffusion along DNA and microtubules by exploring the diffusion of both protein types on both biopolymers. We found that DNA-binding and microtubule-binding proteins can diffuse on each other's substrates; however, the adopted diffusion mechanism depends on the molecular properties of the diffusing proteins and the biopolymers. On the protein side, only DNA-binding proteins can perform rotation-coupled diffusion along DNA, with this being due to their higher net charge and its spatial organization at the DNA recognition helix. By contrast, the lower net charge on microtubule-binding proteins enables them to diffuse more quickly than DNA-binding proteins on both biopolymers. On the biopolymer side, microtubules possess intrinsically disordered, negatively charged C-terminal tails that interact with microtubule-binding proteins, thus supporting their diffusion. Thus, although both DNA-binding and microtubule-binding proteins can diffuse on the negatively charged biopolymers, the unique molecular features of the biopolymers and of their natural substrates are essential for function.

Prerecognition Diffusion Mechanism of Human DNA Mismatch Repair Proteins along DNA: Msh2-Msh3 versus Msh2-Msh6

“… 30 , 34 , 44 In particular, they successfully predicted the mechanism of linear diffusion and particularly the existence of coupling between translation and rotation. 30 , 32 , 33 , 37 The coarse-grained simulations showed, in a manner consistent with experiments, how changing the asymmetry of the affinity of multidomain proteins to DNA affects the search kinetics. 43 , 46 − 48 The consequence of mutating charged residues for the diffusion coefficients 49 and for the rate of conversion from nonspecific to specific binding mode is also described by the coarse-grained model; 50 nonetheless, a more elaborate model that includes conformational changes of both the protein and the DNA is required to address further aspects of this process.…”

“…We note that various transcription factors and enzymes, either monomeric, dimeric, tetrameric, or multidomain, show diffusion along nonspecific DNA with a diffusion coefficient on the order of 0.01–1 μm/s 2 . 30 , 32 , 34 , 37 , 43 , 44 , 52 Therefore, we hypothesize that the initial search structures of Msh2-Msh6 and Msh2-Msh3 are far more open than in model A to allow sliding along DNA. To build probable conformations of Msh2-Msh6 and Msh2-Msh3 capable of sliding on DNA and characterize their diffusion, we used an ENM-based algorithm to reveal the low-frequency collective modes (normal modes) of the individual monomers (Msh2, Msh3, and Msh6) to predict conformational changes that would create gaps in the dimer.…”

“…Furthermore, the sliding dynamics observed for MBD23 and MBD26 indicates that their electrostatic potential and geometry of the interface with DNA are similar to those of other DNA-binding proteins and support the rotation-coupled translation dynamics along DNA. 32 While many DNA-binding proteins follow rotation-coupled translation diffusion along DNA, it is not a universal feature and some DNA-binding proteins 33 , 37 , 56 (as well as other positively charged proteins 32 ) follow diffusion where the translation along the DNA is uncoupled from rotation. Using the APBS plug-in to PyMOL, we see greater positive electrostatic potential associated with the DNA binding area of MBD6 relative to that of MBD3.…”

What Are the Molecular Requirements for Protein Sliding along DNA?

“…To further elucidate the role of electrostatics in linear diffusion and particularly its role at the onset of coupling between rotation and translation during diffusion along DNA, we studied the diffusion of proteins that normally interact electrostatically with microtubules (rather than DNA). Such an investigation can be valuable, given that microtubules are another negatively charged biopolymer 67 and that the linear diffusion coefficients for microtubule-binding proteins sliding along microtubules are similar to the corresponding coefficients for DBPs sliding along DNA, that is, in the range 0.001–1 μm 2 /s depending on the protein’s dimensions. 67 …”

“…Such an investigation can be valuable, given that microtubules are another negatively charged biopolymer 67 and that the linear diffusion coefficients for microtubule-binding proteins sliding along microtubules are similar to the corresponding coefficients for DBPs sliding along DNA, that is, in the range 0.001–1 μm 2 /s depending on the protein’s dimensions. 67 …”