"Spicy world of NanoScience" since 2007
Functional copolymers such as the proteins are called "mechanomers" here, distinguishing such naturally-occurring mechanomers as "biopolymers" where convenient; the science of mechanomers is called "mechanomerics"; and applied mechanomerics is called "mechanomeric engineering", including "mechanomeric medicine".
Mechanomeric engineering requires some technique for developing mechanomers to perform desired functions, such as enzymes and molecular machines.
And just as proteins are developed in nature by variation of amino acid order—and therefore of conformation (coiled structure), and therefore of shape, mechanical properties and surface structure, and therefore of function—followed by selection, so too artificial mechanomers can be developed by selecting those performing desired functions from among random mechanomers, mechanomers with random monomer orders, and therefore random conformations, and therefore random shapes, mechanical properties and surface structures, and therefore random functions, in what is called here "mechanomeric selection (MeSe)".
The background to, critical argument for, procedures in referred to below, and some applications of mechanomeric selection are described in the report “Enzymes and Molecular Machines Can Be Selected from Random Copolym....
The present series of short reports describes a sequence of experiments including those procedures and groups thereof sufficient to establish mechanomeric selection on a firm foundation, starting with fundamental experiments and ending with several small but significant applications.
Those experiments and procedures and groups thereof number about forty, and fall naturally into seven phases, each of which shall be addressed in its own part of this series of eight short reports, as follows:
“Part 1: Introduction.” This very report.
"Part 2: Phase I: First Experiments: Incidences of Random Protein Well-Conformedness and Function.” The first phase of mechanomeric-selective research and developmental experiments, procedures and groups thereof described here assesses the incidences of well-conformedness and simple function in random protein stocks. But it begins with four sets of decisions with consequences for all remaining phases, about what industrial organic chemistry reactions; indicators and indicating reactions; the two mechanomer classes to be at least originally employed in mechanomeric selection and the corresponding polymerization reactions and monomers; and those monomers’ prosthetic groups. It chemically synthesizes and thermally tempers random proteins bearing those prosthetic groups. It weighs, assesses the numbers using osmosis, and calculates the average weights, lengths and gram numbers, of those proteins. It uses affinity chromatography using media bearing those prosthetic groups to assess the incidence of well-conformedness among those proteins. And it assesses the incidences of catalyses of those reactions among those proteins in so many assessments of the incidence of such simplest function among random mechanomers.
“Part 3: Phase II: Early Mechanomeric Selection: Mechanomerogenesis.” The second phase of mechanomeric-selective research and developmental experiments, procedures and groups thereof performs the fundamental early mechanomeric-selective procedure of mechanomerogenesis, allowing the self-selection or autoevolution of replicases. It chemically synthesizes test-mechanomers to be used in testing the functionality of the replicases resulting from mechanomerogenesis. It chemically synthesizes and thermally tempers random mechanomers of those classes; weighs, assesses the numbers using osmosis, and calculates the average weights, lengths and gram numbers of those mechanomers; uses affinity chromatography to assess the incidence of well-conformedness, and assesses the incidences of catalyses of the industrial and indicating reactions selected in the first phase, among those random mechanomers, all just as was done in the first phase with random proteins. It performs mechanomerogenesis. It assesses the functions of the replicases produced by mechanomerogenesis. And it assesses the incidences of direct replicability among random mechanomers of the classes used.
“Part 4: Phase III: Early Mechanomeric Selection: Merases” The third phase of mechanomeric-selective developmental experiments, procedures and groups thereof utilizes the replicases selected in the second phase to select the “merases”—polymerases, ligases and other enzymes—useful for mechanomeric selection itself, using affine-chromatographic and spectroscopic techniques to characterize and assess their functions.
“Part 5: Phase IV: Mechanomeric Indication.” The fourth phase of mechanomeric-selective developmental experiments, procedures and groups thereof selects various “indicases” conditionally and “chromases” unconditionally catalyzing the indicating reactions selected in the first phase. It begins with decisions with consequences for all remaining phases, about what species of viruses and bacteria and types of human cells are to be used in these phases. It selects indicases catalyzing those reactions only when complexed with and thus indicating the presences of those viruses and bacteria and cells. It then selects simpler chromases unconditionally catalyzing those indicating reactions and “conditional chromase inhibitors” which complexed with those chromases inhibit their catalyses but dissociate upon complexing with those viruses and bacteria and cells, affording more readily-selected equivalents to those indicases.
“Part 6: Phase V: Mechanomeric Cytotechnology.” The fifth phase of mechanomeric-selective developmental experiments, procedures and groups thereof selects “cytomers” or cell-affecting mechanomers needed for mechanomeric cytotechnology. “Cytoindicators” indicating viruses and bacteria of selected species and human cells of selected types were selected in the previous phase. The fifth phase selects “clastomers” killing only bacteria of those species and human cells of those types; “cytochelates” which bound to media allow very specific separations of chemicals, mechanomers, viruses, bacteria and human cells; “cytodifferentiators” inducing human cells of some easily-obtained and/or –cultured type (selected in the previous phase) to differentiate into cells of those types; and "blastomers” (growth hormones) inducing cells of those types to reproduce, all together allowing the beginning of the construction of the “cytopalettes” of cultures of cells of different types from different species (target, differential, key, representative and endangered) needed for functional and toxicity testing of mechanomers intended for medical or environmental use, some of which cultures themselves will have medical uses examined in the next phase.
“Part 7: Phase VI: Early Applications: Mechanomeric Medicine.” The sixth phase of mechanomeric-selective developmental experiments, procedures and groups thereof examines the medical uses of the cytomers and cytopalettes selected, produced and foreshadowed in the previous phase. It uses those cytomers to produce such cytopalette, and then uses that cytopalette to select mechanomeric antibiotics toxic to a pathogenic bacterium but not human cells or bacteria of other species, mechanomeric antivirals protecting cultures from viruses, and mechanomeric antineoplastics toxic to cancer cells but not to their parent or other human tissues or commensal bacteria.
“Part 8: Phase VII: Early Applications: Mechanomeric Engineering.” The seventh phase of mechanomeric-selective developmental experiments, procedures and groups thereof chooses the reactions and reactants and then selects the enzymes needed to chemically synthesize diamond, and to photosynthesize octane and glucose.
It is not suggested that mechanomeric-selective research and development must follow the above path in every step of the way, but something very closely approximating the sequence from the second through fourth phases described seems unavoidable.
Plainly, such program is as massive as it is ambitious and promising, and not only needs to but should be carried out at every phase by multiple laboratories, openly cross-checking results and sharing technical problems and solutions.
Any and all points may be altered or refined in the course of writing this series of reports (not least nomenclatural—e.g., “conditional chromase inhibitor” is very clumsy)—which is a work in progress, so it behooves those interested to check back occasionally not only for the later parts as they are finished but for such revisions, which will be explicitly indicated in the course, although all such apparatus will be discarded upon the finishing, of the series.
Warning: Finally, even with the precautions with regard to mechanomer and mechanomeric monomer and polymerization reaction classes referred to in the report cited above and in Part 3 of this series of reports, all random mechanomer stocks should be treated as if they are Biosafety Level 4 pathogens: As the cited reports assert, nucleic acids should not be mechanomerically selected, to prevent unwanted genomic introductions; mechanomer classes mechanomers of which are to be selected should not use naturally-existing monomers, to prevent naturalizations of replicative systems; and mechanomer classes mechanomers of which are to be selected should be non-toxic and biodegradable; but even such safety precautions should not be considered adequate at the outset at least of mechanomeric selection, and all random mechanomer stocks should be treated as if they are Biosafety Level 4 pathogens, and all procedures involving such stocks carried out in the appropriate facilities, until experience, experiment and analysis prove such precaution unnecessary and lesser precautions adequate.
(Mirrored at my MeSeBlog.)