| --- Log opened Thu Jul 21 00:00:03 2016 | ||
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| nmz787_i | .wik F. W. Aston | 00:38 |
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| yoleaux | nmz787_i: Sorry, that command (.wik) crashed. | 00:38 |
| kanzure | since ribosome is a ribozyme, we can copy-paste most of the catalytic domains from ribozyme rna polymerase and turn that into a giant polymerase. | 00:38 |
| kanzure | and synthetases have been fairly well engineered | 00:39 |
| nmz787_i | .wik Francis William Aston | 00:39 |
| yoleaux | "Francis William Aston FRS (1 September 1877 – 20 November 1945) was an English chemist and physicist who won the 1922 Nobel Prize in Chemistry for his discovery, by means of his mass spectrograph, of isotopes, in a large number of non-radioactive elements, and for his enunciation of the whole number rule. He was a fellow of the Royal …" — https://en.wikipedia.org/wiki/Francis_William_Aston | 00:39 |
| kanzure | the same azobenzene amino acid can be reused in multiple places inside the same target protein, so optical illumination can cause multiple simultaneous changes | 00:41 |
| nmz787_i | kanzure: you think catalysis of aminos and/or handling them will be so similar? | 00:41 |
| kanzure | you would have to replace the catalytic domains | 00:41 |
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| nmz787_i | but holding aminos must be somewhat different too | 00:42 |
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| nmz787_i | so now you have to replace the binding domains too | 00:42 |
| nmz787_i | what is left? | 00:42 |
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| kanzure | synthetases. which are already well-studied well-engineered objects. | 00:44 |
| nmz787_i | kanzure: is your comment because the azobenzene amino needs a non-standard ribosome ? | 00:44 |
| nmz787_i | kanzure: synthetase is part of a ribosome? | 00:44 |
| kanzure | synthetases bring amino acids to the ribosome | 00:45 |
| kanzure | but they have been hacked to bring many other things | 00:45 |
| nmz787_i | ah | 00:45 |
| nmz787_i | hmm, that phenylazophenylalanine doesn't seem to be available on first-page google results | 00:45 |
| kanzure | and they are much bigger than a single nucleotide, which is nice | 00:45 |
| nmz787_i | hmm, so the azobenzene is basically the amino side-chain | 00:48 |
| kanzure | yes the goal is to pick some residues to replace with that | 00:48 |
| nmz787_i | well I guess I'd been incorrectly thinking it might have been mid-link | 00:49 |
| nmz787_i | but that isn't how peptide chains are formed | 00:49 |
| nmz787_i | mid-link meaning the chain would twist itself...with the sidechain it would need to twist and push on some other part of the molecule (peptide) | 00:50 |
| nmz787_i | is there a python API to gromacs :) | 00:50 |
| kanzure | nanoengineer had one | 00:51 |
| nmz787_i | hmm, seems to be something | 00:51 |
| kanzure | if not, it's trivial to write some bindings | 00:51 |
| nmz787_i | if you swapped an amino in a PDB... making it 'too close' for room-temperature conditions... and put that into gromacs... might it reconfigure into a 'comfortable' energetic/molecular state? | 00:54 |
| nmz787_i | hmm, I am looking for the inverse I think: http://bionano.physics.illinois.edu/nanoengineer2pdb | 00:57 |
| nmz787_i | .title | 00:57 |
| yoleaux | Converting NanoEngineer-1 DNA structure design (MMP file) to all-atom PDB file | The Aksimentiev Group | 00:57 |
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| nmz787_i | well, I see a lot of pdb files in the nanoengineer repo | 00:57 |
| nmz787_i | so I guess they are supported by default | 00:57 |
| nmz787_i | hmm, this seems to exist too? http://brlcad.org/coverage/brlcad/src/proc-db/pdb-g.c.gcov.html | 00:59 |
| nmz787_i | .title https://web.archive.org/web/20020202141648/http://antas.agraria.uniss.it/software.html | 01:00 |
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| chris_99 | https://adeshpande3.github.io/adeshpande3.github.io/A-Beginner%27s-Guide-To-Understanding-Convolutional-Neural-Networks/ | 01:18 |
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| kanzure | erqierjaoifdjqoifjqoiqouiaofdajdioq | 07:04 |
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| ybit_ | https://theconversation.com/all-you-need-for-quantum-computing-at-room-temperature-is-some-mothballs-62549 | 08:55 |
| ybit_ | http://www.nature.com/ncomms/2016/160718/ncomms12232/full/ncomms12232.html | 08:55 |
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| kanzure | .title http://www.nature.com/ncomms/2016/160718/ncomms12232/full/ncomms12232.html | 09:16 |
| yoleaux | Room temperature manipulation of long lifetime spins in metallic-like carbon nanospheres : Nature Communications : Nature Research | 09:16 |
| kanzure | anselm complaining about dna storage ideas https://news.ycombinator.com/item?id=8999919 | 09:21 |
| kanzure | "If we get a little scifi, and assume we build programmable polymerases and get nanopore (direct read) sequencing. Even then, physics limits you to something like 1000 read/writes per sec per pore/polymerase. Instrumenting to these will probably limit per-feature size to being larger than 100micron on a fabricated chip, giving us an ultimate read/write limit around: (2cm/100um)^2 x 1000 bit/sec = 40Mbit/sec for a giant 2cmx2cm chip. With ... | 09:22 |
| kanzure | ... the necessary error-correction and redundancy, it's probably going to cap out around 1Mbit/sec at best. Those 700TB take about 2months to read/write at these rates, and we'll have much-better solid state storage technologies by the time we figure out how to all that with DNA." | 09:22 |
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| kanzure | here's a bunch of polymerases, nucleotidyl transferases, primases, and poly(A) polymerases in the form of pdb files http://diyhpl.us/~bryan/papers2/polymerase/polymerases.pdb.tar.xz (41 MB) | 09:26 |
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| kanzure | dna polymerase mu and TdT seem to be functionally similar | 09:46 |
| kanzure | "Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region" http://nar.oxfordjournals.org/content/early/2009/06/05/nar.gkp460.short | 09:49 |
| kanzure | "... a deletion of the entire Loop1 as in pol λ does confer a limited template-dependent polymerase behavior to Tdt while a chimera bearing an extended pol μ Loop1 reproduces pol μ behavior" | 09:49 |
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| kanzure | "standard tailing protocols" | 10:22 |
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| CaptHindsight | http://www.glenresearch.com/ProductFiles/Product.php?item=10-5800 Azobenzene Phosphoramidite | 11:15 |
| CaptHindsight | 0.25g $550.00 | 11:16 |
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| kanzure | yep | 11:23 |
| kanzure | it's useful | 11:23 |
| kanzure | but also, i'm really excited about those azobenzene amino acids. v. useful for protein conformational changes. | 11:24 |
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| CaptHindsight | http://www.glenresearch.com/Catalog/catalog.php?page=droligo#p18 price drop | 11:30 |
| CaptHindsight | when I looked a few months ago there was a slew of cappers, decappers , linkers etc | 11:31 |
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| CaptHindsight | you just need to decide how you are going to build your synthesizer | 11:32 |
| CaptHindsight | and find someone to build it for you | 11:32 |
| kanzure | don't forget the ligation part. it's just dna hybridization array stuff without ligation and conjugation. | 11:33 |
| kanzure | *stuff if you go without ligation and conjugation. | 11:33 |
| CaptHindsight | it's all out there | 11:35 |
| kanzure | here is a good chapter on "Catalytic mechanism of DNA polymerases" from 2010, http://www.bc.sinica.edu.tw/MDTsai/2010/CNPII%20349-383.pdf | 11:35 |
| CaptHindsight | take your pick | 11:35 |
| kanzure | page 372 (page 25) has a section on molecular dynamics simulations | 11:36 |
| kanzure | CaptHindsight: hm? | 11:36 |
| CaptHindsight | I keep telling you but you you made some comment about "hand waving" which I assumed to be projection | 11:37 |
| kanzure | CaptHindsight: there's no good option yet for dna ligation on an inkjet bed, i proposed one method using reservoire flow (which it turns out that twist biosciences is also using at the moment), and EWOD, and micropipetting (which does not scale well for large amounts of DNA) | 11:37 |
| kanzure | and EWOD might require oil-water emulsion techniques | 11:37 |
| CaptHindsight | who cares if twist biosciences is using it? | 11:38 |
| CaptHindsight | it's not likely for the FDA to approve anything open source | 11:39 |
| kanzure | validation is super important | 11:39 |
| CaptHindsight | from whom? | 11:39 |
| kanzure | if someone tried for years and spent zillions, and it didn't work, then you should avoid it. if they have validated the method, then that's a good signal. | 11:39 |
| CaptHindsight | or they hired idiots | 11:40 |
| CaptHindsight | most often what I discover | 11:40 |
| CaptHindsight | but there's plenty of working chemistry out there | 11:41 |
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| chris_99 | CaptHindsight, i just found myself a robot arm http://www.ebay.co.uk/itm/Sintron-Mini-Industrial-Robotic-Arm-Kit-DIY-Robot-Toy-Servos-Joystick-UNO-R3-/151832587078 ;) | 11:50 |
| chris_99 | could be a fun toy for my desk | 11:51 |
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| CaptHindsight | hobby servos | 11:54 |
| CaptHindsight | not closed loop but fun | 11:55 |
| chris_99 | ah, do hobby servos not have an encoder on? | 11:55 |
| chris_99 | i thought servo means, there is always a feedback loop | 11:56 |
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| CaptHindsight | https://www.princeton.edu/~mae412/TEXT/NTRAK2002/292-302.pdf | 12:03 |
| CaptHindsight | the feedback is just inside the motor | 12:04 |
| CaptHindsight | the controller just outputs PWM | 12:04 |
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| chris_99 | oh interesting | 12:38 |
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| CaptHindsight | chris_99: if you really want to play here's a $25K arm for ~$1k http://www.ebay.com/itm/Staubli-RX60-Robot-Arm-With-Base-/201628876886 | 12:51 |
| chris_99 | now that looks more like it | 12:52 |
| chris_99 | i'm in the UK alas, i've seen some for like £400 before | 12:53 |
| chris_99 | though | 12:53 |
| CaptHindsight | ^^ they have ~10um repeatability | 12:53 |
| CaptHindsight | so goof for tissue engineering | 12:53 |
| chris_99 | 10um?!!!! | 12:53 |
| CaptHindsight | goof/good | 12:53 |
| chris_99 | thats amazing | 12:53 |
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| CaptHindsight | http://www.staubli.com/en/robotics/6-axis-scara-industrial-robot/low-payload-6-axis-scara-robot/6-axis-industrial-robot-tx60/ | 12:54 |
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| CaptHindsight | they spec them at 20um at full load and at top speed, but they can hold much better | 12:55 |
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| kanzure | how is it that there are aptamers that bind in picomolar concentration, how does that work.. | 14:05 |
| kanzure | hrm i should ping genehacker at some point | 14:10 |
| btcdrak | probably off topic but http://www.theverge.com/2016/7/21/12247370/police-fingerprint-3D-printing-unlock-phone-murder | 14:12 |
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| kanzure | parahsailin points out that azobenzene switching time might be too slow for our purposes | 14:36 |
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| kanzure | we need a good rational protein design conspiracy theory or two... if this was working, do you think anyone would really want to tell everyone that "hey protein design works"? | 14:42 |
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| kanzure | re: restriction of protein engineering to only those spiral shapes or whatever. i think that needs to be double checked. i think some of the protein folding is solved for. so we should find some good chases in existing proteins. then paste catalytic protein domains to that, run selection experiments and get improved proteins with known-simulatable backbones and folding. and next most of biology should be replaced with only those ... | 15:00 |
| kanzure | ... structures, since it's more convenient for us to work with. | 15:00 |
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| kanzure | i think foldit is assuming that all protein folding predictions can be solved by trying to predict and score the lowest minimum energy configuration or something | 15:43 |
| kanzure | so they are assuming that all proteins fold in this way | 15:43 |
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| kanzure | http://foldit.wikia.com/wiki/Research_Chat_Room | 16:07 |
| kanzure | .wik intrinsically unstructured proteins | 16:12 |
| yoleaux | "An intrinsically disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure. IDPs cover a spectrum of states from fully unstructured to partially structured and include random coils, (pre-)molten globules, and large multi-domain proteins connected by flexible linkers." — https://en.wikipedia.org/wiki/Intrinsically_unstructured_proteins | 16:12 |
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| kanzure | slide 8 is pretty interesting (simulation vs experiment for protein folding) http://web.stanford.edu/class/cs279/lectures/lecture5.pdf | 16:15 |
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| kanzure | "Even sequences with 15% sequence identity usually have similar structures. • Also, there only appear to be 1,000–10,000 naturally occurring protein folds." | 16:17 |
| andyphoneshi | kanzure 1000-10000 types (and many per protein) or only that many protein shapes total? | 16:18 |
| kanzure | http://www.sbg.bio.ic.ac.uk/phyre2/html/flibview.cgi?pdb=c5b42A_ | 16:20 |
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| kanzure | andyphoneshi: not sure | 16:20 |
| andyphoneshi | Heh, the latter would be awesome, the former is pretty forboding | 16:21 |
| kanzure | i am a little skeptical about the "just find the most energy minimizing shape" goal... there doesn't seem to be any study showing this is a good assumption. | 16:21 |
| andyphoneshi | ..this in general is a good physical assumption, you can derive tons of chemistry from it | 16:21 |
| kanzure | fold.it has a heuristic scoring function for energy minimization, so it appears to me that they should just try to randomly generate answers and then score them. what's the big deal? it's not even running molecular dynamics. | 16:22 |
| andyphoneshi | mm ok that'll miss local minima ofc | 16:22 |
| kanzure | it's "find the closest local minima and fall down the energy slope"? | 16:22 |
| andyphoneshi | I would expect that | 16:23 |
| andyphoneshi | based on the parts of science I have any familiarity with (not biochem :p) | 16:23 |
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| kanzure | "Uses a large database of 3-residue and 9-residue fragments, taken from structures in the PDB" | 16:26 |
| kanzure | (rosetta) | 16:26 |
| maaku | what local analysis misses is that as the protien folds in on itself, the energy minima change | 16:27 |
| kanzure | ouch.. so basically they are doing find-and-replace for chunks of residues at a time, then updating their free energy minimizing calculations for the rest of the residues in the protein to determine if that (found) shape wokrs. | 16:27 |
| maaku | with naturally occuring genes at least there's a lot of non-intuitive folds because of this effect | 16:27 |
| maaku | easy to engineer around that with designed proteins though | 16:27 |
| kanzure | yeah i am still interested in finding a subset of proteins and amino acid residues that we can say are simpler to simulate and fold | 16:28 |
| kanzure | if the spiral or helical proteins are easier, then fine, let's slap on some catalytic domains and then optimize them through some rounds of selection, and replace all of biology with those proteins instead of whatever nasty folds we're currently using | 16:28 |
| maaku | kanzure: I suspect the key point will be designing DNA origami like interconnects between active sites | 16:29 |
| maaku | right ok what you just said :) | 16:29 |
| kanzure | it is not clear to me if there's a subset of amino acids that are easier to fold and calculate energy for.. | 16:31 |
| andyphoneshi | Presumably the ones we have are in some strong sense the simplest .. since we hit them by chance first | 16:31 |
| kanzure | well one guess would be something like "find amino acids that are mostly inert" | 16:32 |
| kanzure | "How do small single-domain proteins fold?" http://www.sciencedirect.com/science/article/pii/S1359027898000339 | 16:42 |
| maaku | andyphoneshi: or easier to create by natural process, which means more existing by default | 16:42 |
| maaku | probably lots of astrobiology research relevant to this question | 16:43 |
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| kanzure | hm even the alpha helix stuff seems to have weird folding properties | 17:24 |
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| kanzure | "Rational design of α-helical tandem repeat proteins with closed architectures" http://www.nature.com/nature/journal/v528/n7583/abs/nature16191.html | 18:00 |
| kanzure | "Exploring the repeat protein universe through computational protein design" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4845728/ | 18:15 |
| kanzure | "linear repeat protein" | 18:21 |
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| CaptHindsight | kanzure: I've been watching genetic engineering since the early 80's but just recently decided to get involved since it's taking so damn long. | 18:50 |
| CaptHindsight | so far I don't see any conspiracy other than publicized connections between presidents, congress and drug co's, I mostly see idiots with accountants that manage to show millions spent on R&D that could cost a few % of what they say they spend | 18:52 |
| kanzure | no no, i mean protein design not genetic engineering | 18:52 |
| kanzure | protein design is commonly said to be hard due to protein folding-- but often that's handwaving because discussion of the actual problems don't occur afterwards. | 18:53 |
| kanzure | using a constrained set of amino acids and other techniques, like highly repetitive sequences of amino acids, you can predict with high accuracy the shape of the resulting protein | 18:53 |
| kanzure | while that's still "hard to simulate" at an atomistic level, you don't have to simulate it at all because you already know the result ahead of simulation time | 18:55 |
| kanzure | http://diyhpl.us/~bryan/papers2/bio/protein-engineering/ | 18:56 |
| CaptHindsight | an extension of polymer chemistry | 18:58 |
| CaptHindsight | with an emphasis on folding | 19:04 |
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| nmz787 | welp, basically a no-go on SERS single-nucleotide | 20:39 |
| nmz787 | glad I was inspired to get into crazy high-performance analog though | 20:39 |
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| kanzure | why's that? | 21:45 |
| nmz787 | doesn't perform as hoped/proposed | 21:48 |
| nmz787 | noise | 21:48 |
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