Translocation of non-interacting heteropolymer protein chains in terms of single helical propensity and size.

In this work we present an analytical framework to calculate the average translocation time τ required for an ideal proteinogenic polypeptide chain to cross over a small pore on a membrane. Translocation is considered to proceed as a chain of non-interacting amino acid residues of sequence {Xj} diffuses through the pore against an energy barrier Δℱ, set by chain entropy and unfolding-folding energetics. We analyze the effect of sequence heterogeneity on the dynamics of translocation by means of helical propensity of amino acid residues. In our calculations we use sequences of fifteen well-known proteins that are translocated which span two orders of magnitude in size according to the number of residues N. Results show non-symmetric free energy barriers as a consequence of sequence heterogeneity, such asymmetry in energy may be useful in differentiated directions of translocation. For the fifteen polypeptide chains considered we found conditions when sequence heterogeneity has not a significant effect on the time scale of translocation leading to a scaling law τ ∝ Nν, where ν ∼ 1.6 is an exponent that holds for most ground state energies. We also identify conditions when sequence heterogeneity has a great impact on the time scale of translocation, in consequence, no more scaling laws for τ there exist.

Jump transition observed in translocation time for ideal poly-X proteinogenic chains as a result of competing folding and anchoraging contributions.

In this work we analyze the translocation of homopolymer chains poly-X, where X represents any of the 20 naturally occurring amino acid residues, in terms of size N and single-helical propensity ω. We provide an analytical framework to calculate both the free energy F of translocation and the translocation time τ as a function of chain size N, energies U and ε of the unfolded and folded states, respectively. Our results show that free energy F has a characteristic bell-shaped barrier as function of the percentage of monomers translocated. Inclusion of single-helical propensity ω associated to monomer X and chain's native energy ε in the translocation model increases the energy barrier ΔF up to one order of magnitude as compared with the well-known Gaussian chain model. Computation of the mean first-passage time as function of chain size N shows that the translocation time τ exhibits a significant jump of several orders of magnitude at a critical chain size N. This jump markedly slows down translocation of chains larger than N. Existence of the transition jump of τ has been observed experimentally at least in poly(ethylene oxide) chains [R. P. Choudhury, P. Galvosas, and M. Schönhoff, J. Phys. Chem. B 112, 13245 (2008)]JPCBFK1520-610610.1021/jp804680q. Our results suggest the transition jump of τ as a function of N may be a very well spread feature throughout translocation of poly-X chains.

Steric contribution of macromolecular crowding to the time and activation energy for preprotein translocation across the endoplasmic reticulum membrane.

Protein translocation from the cytosol to the endoplasmic reticulum (ER) or vice versa, an essential process for cell function, includes the transport of preproteins destined to become secretory, luminal, or integral membrane proteins (translocation) or misfolded proteins returned to the cytoplasm to be degraded (retrotranslocation). An important aspect in this process that has not been fully studied is the molecular crowding at both sides of the ER membrane. By using models of polymers crossing a membrane through a pore, in an environment crowded by either static or dynamic spherical agents, we computed the following transport properties: the free energy, the activation energy, the force, and the transport times for translocation and retrotranslocation. Using experimental protein crowding data for the cytoplasm and ER sides, we showed that dynamic crowding, which resembles biological environments where proteins are translocated or retrotranslocated, increases markedly all the physical properties of translocation and retrotranslocation as compared with translocation in a diluted system. By contrast, transport properties in static crowded systems were similar to those in diluted conditions. In the dynamic regime, the effects of crowding were more notorious in the transport times, leading to a huge difference for large chains. We indicate that this difference is the result of the synergy between the free energy and the diffusivity of the translocating chain. That synergy leads to translocation rates similar to experimental measures in diluted systems, which indicates that the effects of crowding can be measured. Our data also indicate that effects of crowding cannot be neglected when studying translocation because protein dynamic crowding has a relevant steric contribution, which changes the properties of translocation.