Patent Document ID: 10013525
Application ID: 14301070
Patent Status: 1

Claim One:
1. A computer-based method to provide a protein sequence with a desired translocon-associated biogenesis feature, comprising: i) establishing a desired translocon-associated biogenesis feature of a protein sequence, the desired translocon-associated biogenesis feature selected from a) desired protein topology, b) desired partitioning between protein integration and protein secretion and c) desired protein expression level; ii) providing the protein or protein sequence with a set of translocon-associated biogenesis feature determinants; iii) simulating, in a coordinate system with at least two spatial dimensions by a computer, one or more trajectories of the protein sequence with the set of translocon-associated biogenesis feature determinants, the one or more trajectories being simulation trajectories, the one or more trajectories determining an translocon-associated biogenesis feature of the protein sequence with the translocon-associated biogenesis feature determinants, wherein the simulating comprises projecting protein nascent chain dynamics onto a plane that intersects a translocon channel axis and bisects translocon lateral gate helices when the at least two spatial dimensions are two spatial dimensions, and the simulating comprises modeling the protein nascent chain dynamics in the at least two spatial dimensions when the at least two spatial dimensions are more than two spatial dimensions, wherein the simulating operates in timesteps on the order of 100 nanoseconds over a span of 3 to 100 seconds; iv) comparing the translocon-associated biogenesis feature of the protein sequence with the desired translocon-associated biogenesis feature of the protein sequence; v) if the initial translocon-associated biogenesis feature of the protein sequence is different from the desired translocon-associated biogenesis feature of the protein sequence, modifying the set of translocon-associated biogenesis feature determinants, thus providing the protein sequence with a modified set of translocon-associated biogenesis feature determinants; and vi) repeating steps iii)-v) with the modified set of translocon associated biogenesis feature determinants in place of the set of translocon associated biogenesis feature determinants, thereby modifying the one or more trajectories and resulting in a modified set of translocon associated biogenesis features, until the desired translocon-associated biogenesis feature is obtained, thus obtaining a set of translocon-associated biogenesis feature determinants suitable to be used for production of a protein or plasmid with the desired translocon-associated biogenesis feature.