Pathway Assembly Tools

Several common pathway assembly tools have been developed recently to tackle the goals described above. The Gibson assembly technology is based on the two-step thermocycler method which was used to synthesize a complete genome [27]. 

The above bioinformatic tools provide methods of determining differences or similarities in datasets. The next step is to incorporate metabolomic data with other expression information, including mRNA and proteins, to infer gene function. To accomplish this, metabolomic data sets must be integrated and correlated in a global maimer with genetic and enzymatic data, pathways assembled into systems, and... 

As scientists and engineers, natural self-assembly processes represent a tremendous resource, which we can use to create our own miniature materials and devices. Our endeavors are informed by hundreds of years of curiosity-driven research interested in the natural world. Our toolbox is further expanded by modem synthetic chemistry which extends beyond the realm of natural molecules. We can also create artificial environments to control and direct assembly and use computer-based tools and simulations to model and predict self-assembly pathways and their resulting protein structures. Many researchers believe we can use these modern tools to simplify, improve, and refine assembly processes. We have much to do in order to reach this ambitious goal but the next 10 years are likely to be filled with exciting discoveries and advances as self-assembling polypeptide materials move from the laboratory to the clinic or the manufacturing assembly line. 

The reconstitution of bacterial ribosomal subunits from the separated rRNAs and proteins, first announced in 1968, provides a potent tool to investigate such essential aspects of ribosome structure and evolution as the subunits assembly pathway [92,93], the locations and neighbourhoods of the subunit proteins [94,95], the roles of the individual proteins in both assembly and function [92,93,96], and the degree of exchangeability of ribosomal components both within and across domain boundaries [97,98]. 

Theoretical studies of the properties of the individual components of nanocat-alytic systems (including metal nanoclusters, finite or extended supporting substrates, and molecular reactants and products), and of their assemblies (that is, a metal cluster anchored to the surface of a solid support material with molecular reactants adsorbed on either the cluster, the support surface, or both), employ an arsenal of diverse theoretical methodologies and techniques for a recent perspective article about computations in materials science and condensed matter studies [254], These theoretical tools include quantum mechanical electronic structure calculations coupled with structural optimizations (that is, determination of equilibrium, ground state nuclear configurations), searches for reaction pathways and microscopic reaction mechanisms, ab initio investigations of the dynamics of adsorption and reactive processes, statistical mechanical techniques (quantum, semiclassical, and classical) for determination of reaction rates, and evaluation of probabilities for reactive encounters between adsorbed reactants using kinetic equation for multiparticle adsorption, surface diffusion, and collisions between mobile adsorbed species, as well as explorations of spatiotemporal distributions of reactants and products. 

---