Comments on: How to design proteins from scratch http://www.kurzweilai.net/how-to-design-proteins-from-scratch Accelerating Intelligence Sun, 19 May 2013 09:03:12 +0000 hourly 1 http://wordpress.org/?v=3.4.1 By: Dr. X http://www.kurzweilai.net/how-to-design-proteins-from-scratch/comment-page-1#comment-65971 Dr. X Sun, 09 Dec 2012 14:46:32 +0000 http://www.kurzweilai.net/?p=170332#comment-65971 No, this technology allow to design new proteins, proteins that do not exist in nature. On the other hand, if you lack protein or gene that is coding it is "broken", you could be cured by means of gene therapy. There are a lot of vectors that designed to cure such diseases. Unfortunately market is small, and FDA requirements are costly to meet and very bureaucratic. So while we do have technology (gene therapy), a very few therapies progressed to human trials and only one was approved for commercial use so far. Chances are that no one have tried to cure your particular condition. No, this technology allow to design new proteins, proteins that do not exist in nature.

On the other hand, if you lack protein or gene that is coding it is “broken”, you could be cured by means of gene therapy. There are a lot of vectors that designed to cure such diseases. Unfortunately market is small, and FDA requirements are costly to meet and very bureaucratic. So while we do have technology (gene therapy), a very few therapies progressed to human trials and only one was approved for commercial use so far. Chances are that no one have tried to cure your particular condition.

]]> By: pani http://www.kurzweilai.net/how-to-design-proteins-from-scratch/comment-page-1#comment-51146 pani Fri, 09 Nov 2012 16:10:05 +0000 http://www.kurzweilai.net/?p=170332#comment-51146 would this solve the "fold it" puzzles? would this solve the “fold it” puzzles?

]]> By: Phil Osborn http://www.kurzweilai.net/how-to-design-proteins-from-scratch/comment-page-1#comment-50916 Phil Osborn Fri, 09 Nov 2012 03:11:15 +0000 http://www.kurzweilai.net/?p=170332#comment-50916 Another potential application comes from the capability of folding proteins in ways that would never occur in natural biology, hence creating one of a kind structures that would have no chance of replicating, and yet might be fully functional as constituted. This is an important consideration as the dangers of "grey goo," spongiform prions, etc. are known to be very real. Ensuring that a protein or macrostructure of protein elements is immune from natural misuse could be a critical safety factor. If even one crucial element to a nanobot could not be replicated, at least without the proper externally supplied key, that would serve as a safety lock. Binary lock and key components could be based on this technology, such that both would be required for the system to function, or a quick shutdown could be forced in a way that no natural process could duplicate. Another potential application comes from the capability of folding proteins in ways that would never occur in natural biology, hence creating one of a kind structures that would have no chance of replicating, and yet might be fully functional as constituted. This is an important consideration as the dangers of “grey goo,” spongiform prions, etc. are known to be very real. Ensuring that a protein or macrostructure of protein elements is immune from natural misuse could be a critical safety factor. If even one crucial element to a nanobot could not be replicated, at least without the proper externally supplied key, that would serve as a safety lock. Binary lock and key components could be based on this technology, such that both would be required for the system to function, or a quick shutdown could be forced in a way that no natural process could duplicate.

]]> By: Ralph Dratman http://www.kurzweilai.net/how-to-design-proteins-from-scratch/comment-page-1#comment-50766 Ralph Dratman Thu, 08 Nov 2012 21:03:12 +0000 http://www.kurzweilai.net/?p=170332#comment-50766 This breakthrough and its logical extension to many more proteins implies that one could in principle build condensed-matter structures of practically any kind imaginable. Whether the method can scale up to industrial yields is not known, but if that succeeds, we may find ourselves living in a world of far more sophisticated human artifacts than any we have yet seen. This breakthrough and its logical extension to many more proteins implies that one could in principle build condensed-matter structures of practically any kind imaginable. Whether the method can scale up to industrial yields is not known, but if that succeeds, we may find ourselves living in a world of far more sophisticated human artifacts than any we have yet seen.

]]> By: Thomas Zolotor http://www.kurzweilai.net/how-to-design-proteins-from-scratch/comment-page-1#comment-50739 Thomas Zolotor Thu, 08 Nov 2012 20:19:53 +0000 http://www.kurzweilai.net/?p=170332#comment-50739 Amazing!!!! Amazing!!!!

]]> By: melajara http://www.kurzweilai.net/how-to-design-proteins-from-scratch/comment-page-1#comment-50716 melajara Thu, 08 Nov 2012 18:59:38 +0000 http://www.kurzweilai.net/?p=170332#comment-50716 @Neo Proteins, the essential byproduct of DNA transcription, are the fundamental building blocks of all metabolic interactions in living creatures. As for now, we had tools to gauge the content of a protein, its primary and secondary structure but not reliably its 3D shape resulting from the way it folds around itself. But those conformations are essential to know as they are responsible of most of the efficacy of a protein (through binding sites for molecule exchanges, see e.g. here for further explanation: http://www.ncbi.nlm.nih.gov/books/NBK26911/). According to wikipedia (http://en.wikipedia.org/wiki/Protein_folding) : "The correct three-dimensional structure is essential to function, although some parts of functional proteins may remain unfolded. Failure to fold into native structure produces inactive proteins that are usually toxic. Several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrils formed by misfolded proteins. Many allergies are caused by the folding of the proteins, for the immune system does not produce antibodies for certain protein structures". Up to the work announced here, we had to rely on very costly computer simulations to predict from its constituents the actual folding of a protein. This team has devised rules precise enough not only for prediction but for creating the desired folding to promote a given interaction. This is HUGE for synthetic biology but also for pharmacology or medicine. Hope that helps ;-) @Neo
Proteins, the essential byproduct of DNA transcription, are the fundamental building blocks of all metabolic interactions in living creatures.

As for now, we had tools to gauge the content of a protein, its primary and secondary structure but not reliably its 3D shape resulting from the way it folds around itself. But those conformations are essential to know as they are responsible of most of the efficacy of a protein (through binding sites for molecule exchanges, see e.g. here for further explanation: http://www.ncbi.nlm.nih.gov/books/NBK26911/).

According to wikipedia (http://en.wikipedia.org/wiki/Protein_folding) :

“The correct three-dimensional structure is essential to function, although some parts of functional proteins may remain unfolded.
Failure to fold into native structure produces inactive proteins that are usually toxic. Several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrils formed by misfolded proteins. Many allergies are caused by the folding of the proteins, for the immune system does not produce antibodies for certain protein structures”.

Up to the work announced here, we had to rely on very costly computer simulations to predict from its constituents the actual folding of a protein. This team has devised rules precise enough not only for prediction but for creating the desired folding to promote a given interaction.

This is HUGE for synthetic biology but also for pharmacology or medicine.

Hope that helps ;-)

]]> By: Neo http://www.kurzweilai.net/how-to-design-proteins-from-scratch/comment-page-1#comment-50670 Neo Thu, 08 Nov 2012 17:06:56 +0000 http://www.kurzweilai.net/?p=170332#comment-50670 can someone explain what can be done with this breakthrough in the future? (in simple terms) thank you. can someone explain what can be done with this breakthrough in the future? (in simple terms) thank you.

]]> By: David http://www.kurzweilai.net/how-to-design-proteins-from-scratch/comment-page-1#comment-50632 David Thu, 08 Nov 2012 16:06:17 +0000 http://www.kurzweilai.net/?p=170332#comment-50632 Does this mean they could construct a desired protein? I have a condition where my body lacks a protein. Could they conceivably make the protein this way? Thanks! Does this mean they could construct a desired protein? I have a condition where my body lacks a protein. Could they conceivably make the protein this way? Thanks!

]]> By: Ryan Jackson http://www.kurzweilai.net/how-to-design-proteins-from-scratch/comment-page-1#comment-50570 Ryan Jackson Thu, 08 Nov 2012 15:04:12 +0000 http://www.kurzweilai.net/?p=170332#comment-50570 This is truely incredible! Dr. Baker's lab has accomplished this in part by taking advantage of the idle CPU cycles of volunteers across the globe. I have contributed some of my personal computer's spare cycles to this effort and you can too. Google Rosetta@home if you would like to help push this research along by contributing your idle CPU cycles to this great work as well. This is truely incredible! Dr. Baker’s lab has accomplished this in part by taking advantage of the idle CPU cycles of volunteers across the globe. I have contributed some of my personal computer’s spare cycles to this effort and you can too. Google Rosetta@home if you would like to help push this research along by contributing your idle CPU cycles to this great work as well.

]]> By: Bri http://www.kurzweilai.net/how-to-design-proteins-from-scratch/comment-page-1#comment-50552 Bri Thu, 08 Nov 2012 14:43:37 +0000 http://www.kurzweilai.net/?p=170332#comment-50552 This is monumental in the field of biology. It could significantly increase our understanding of how biological systems function and evolve. It opens the door for the creation of novel animate and inanimate structures, tailored to specific needs. An unbelievable breakthrough that will shave years of the need for powerful computers to figure out protien folding. Uncountable other basic rules will become apparent. The ramifications of this research are endless. This is monumental in the field of biology. It could significantly increase our understanding of how biological systems function and evolve. It opens the door for the creation of novel animate and inanimate structures, tailored to specific needs. An unbelievable breakthrough that will shave years of the need for powerful computers to figure out protien folding. Uncountable other basic rules will become apparent. The ramifications of this research are endless.

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