On the Origin of Protein Folds

5 Replies to “On the Origin of Protein Folds”

1. 1
   gpuccio says:

   September 7, 2012 at 2:38 pm

   Jonathan:

   This is indeed the real stuff we should discuss here!

   Thank you for your contribution 🙂
2. 2
   bornagain77 says:

   September 7, 2012 at 2:43 pm

   Thanks Jonathan, nice summary. I file your well done article right next to Dr. Axe’s article. Of related interest: Here are some other notes on protein folding that I recently came across:

   Computers trying the ‘solve’ protein folding give another compelling piece of evidence for the Intelligent Design of life;

   In the year 2000 IBM announced the development of a new super-computer, called Blue Gene, which was 500 times faster than any supercomputer built up until that time. It took 4-5 years to build. Blue Gene stands about six feet high, and occupies a floor space of 40 feet by 40 feet. It cost $100 million to build. It was built specifically to better enable computer simulations of molecular biology. The computer performs one quadrillion (one million billion) computations per second. Despite its speed, it was estimated to take one entire year for it to analyze the mechanism by which JUST ONE “simple” protein will fold onto itself from its one-dimensional starting point to its final three-dimensional shape.

   “Blue Gene’s final product, due in four or five years, will be able to “fold” a protein made of 300 amino acids, but that job will take an entire year of full-time computing.” Paul Horn, senior vice president of IBM research, September 21, 2000
   http://www.news.com/2100-1001-233954.html

   Networking a few hundred thousand computers together has reduced the time to a few weeks for simulating the folding of a single protein molecule:

   A Few Hundred Thousand Computers vs. A Single Protein Molecule – video
   http://www.metacafe.com/watch/4018233

   As well, despite some very optimistic claims, it seems future ‘quantum computers’ will not fair much better in finding functional proteins in sequence space than even a idealized ‘material’ supercomputer of today can do because protein folding is ‘NP complete’:

   The Limits of Quantum Computers – Scott Aaronson – 2007
   Excerpt: In the popular imagination, quantum computers would be almost magical devices, able to “solve impossible problems in an instant” by trying exponentially many solutions in parallel. In this talk, I’ll describe four results in quantum computing theory that directly challenge this view.,,, Second I’ll show that in the “black box” or “oracle” model that we know how to analyze, quantum computers could not solve NP-complete problems in polynomial time, even with the help of nonuniform “quantum advice states”,,,
   http://www.springerlink.com/co.....330115207/

   Here is Scott Aaronson’s blog in which refutes recent claims that P=NP (Of note: if P were found to equal NP, then a million dollar prize would be awarded to the mathematician who provided the proof that NP problems could be solved in polynomial time):

   Shtetl-Optimized
   Excerpt: Quantum computers are not known to be able to solve NP-complete problems in polynomial time.
   http://scottaaronson.com/blog/?p=456

   Protein folding is found to be a ‘intractable NP-complete problem’ by several different methods. Thus protein folding will not be able to take advantage of any advances in speed that quantum computation may offer to any other problems of computation that may be solved in polynomial time:

   Combinatorial Algorithms for Protein Folding in Lattice
   Models: A Survey of Mathematical Results – 2009
   Excerpt: Protein Folding: Computational Complexity
   4.1
   NP-completeness: from 10^300 to 2 Amino Acid Types
   4.2
   NP-completeness: Protein Folding in Ad-Hoc Models
   4.3
   NP-completeness: Protein Folding in the HP-Model
   http://www.cs.brown.edu/~sorin.....survey.pdf

   Confronting Science’s Logical Limits – John L. Casti – 1996
   Excerpt: in 1993 Aviezri S. Fraenkel of the University of Pennsylvania showed that the mathematical formulation of the protein-folding problem is computationally “hard” in the same way that the traveling-salesman problem is hard.
   http://www.cs.virginia.edu/~ro.....Limits.pdf

   Interestingly, while there are some (perhaps many?) complex protein folding problems found by scientists that have refused to be solved by the brute number crunching power of super-computers (NP-Complete), ‘surprisingly’, these problems have been solved by the addition of ‘human intuition’ (Godel would be pleased);

   So Much For Random Searches – PaV – September 2011
   Excerpt: There’s an article in Discover Magazine about how gamers have been able to solve a problem in HIV research in only three weeks (!) that had remained outside of researcher’s powerful computer tools for years. This, until now, unsolvable problem gets solved because: “They used a wide range of strategies, they could pick the best places to begin, and they were better at long-term planning. Human intuition trumped mechanical number-crunching.” Here’s what intelligent agents were able to do within the search space of possible solutions:,,, “until now, scientists have only been able to discern the structure of the two halves together. They have spent more than ten years trying to solve structure of a single isolated half, without any success. The Foldit players had no such problems. They came up with several answers, one of which was almost close to perfect. In a few days, Khatib had refined their solution to deduce the protein’s final structure, and he has already spotted features that could make attractive targets for new drugs.” Thus,,
   Random search by powerful computer: 10 years and No Success
   Intelligent Agents guiding powerful computing: 3 weeks and Success.
   http://www.uncommondescent.com.....-searches/

   Another factor severely complicating man’s ability to properly mimic protein folding is that, much contrary to evolutionary thought, many proteins fold differently in different ‘contextual’ situations:

   The Gene Myth, Part II – August 2010
   Excerpt: the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous influence over their functions.
   http://darwins-god.blogspot.co.....rt-ii.html
3. 3
   bornagain77 says:

   September 7, 2012 at 2:49 pm

   Also of interest to the extreme difficultly man has in computing the folding of a protein within any reasonable amount of time, it seems that water itself, (H2O), was ‘designed’ with protein folding in mind:

   Protein Folding: One Picture Per Millisecond Illuminates The Process – 2008
   Excerpt: The RUB-chemists initiated the folding process and then monitored the course of events. It turned out that within less than ten milliseconds, the motions of the water network were altered as well as the protein itself being restructured. “These two processes practically take place simultaneously“, Prof. Havenith-Newen states, “they are strongly correlated.“ These observations support the yet controversial suggestion that water plays a fundamental role in protein folding, and thus in protein function, and does not stay passive.
   http://www.sciencedaily.com/re.....075610.htm

   Water Is ‘Designer Fluid’ That Helps Proteins Change Shape – 2008
   Excerpt: “When bound to proteins, water molecules participate in a carefully choreographed ballet that permits the proteins to fold into their functional, native states. This delicate dance is essential to life.”
   http://www.sciencedaily.com/re.....113314.htm

   Finding water to play a ‘fundamental role’ in protein folding ties biological life, once again, directly to the extreme fine tuning for the foundational universal constants noted in the anthropic principle. i.e. It appears once again, in the words of Hoyle, “a super intellect has “monkeyed” with the physics as well as the chemistry and biology, and there are no blind forces worth speaking about in nature.” :

   Water’s remarkable capabilities – December 2010 – Peer Reviewed
   Excerpt: All these traits are contained in a simple molecule of only three atoms. One of the most difficult tasks for an engineer is to design for multiple criteria at once. … Satisfying all these criteria in one simple design is an engineering marvel. Also, the design process goes very deep since many characteristics would necessarily be changed if one were to alter fundamental physical properties such as the strong nuclear force or the size of the electron.
   http://www.evolutionnews.org/2.....42211.html

   Here is a list of many of the anomalous life enabling properties that have been found for water:

   Anomalous life enabling properties of water
   http://www.lsbu.ac.uk/water/anmlies.html

   A even deeper level of the design of water is noted here:

   Water’s quantum weirdness makes life possible – October 2011
   Excerpt: WATER’S life-giving properties exist on a knife-edge. It turns out that life as we know it relies on a fortuitous, but incredibly delicate, balance of quantum forces.,,, They found that the hydrogen-oxygen bonds were slightly longer than the deuterium-oxygen ones, which is what you would expect if quantum uncertainty was affecting water’s structure. “No one has ever really measured that before,” says Benmore.
   We are used to the idea that the cosmos’s physical constants are fine-tuned for life. Now it seems water’s quantum forces can be added to this “just right” list.
   http://www.newscientist.com/ar.....sible.html

   Also of note, ENV just posted a article on protein folding:

   (How do) Chaperone Proteins Know (how to fold other proteins properly)? – September 2012
   Excerpt: Here are some of the neat features of Trigger Factor:
   *Trigger Factor actually constrains protein folding more than the ribosome does. It doesn’t just “get in the way” like the ribosome. It also regulates the folding.
   *Trigger Factor’s function is specific to the particular region of the amino acid chain. It does not just perform one function no matter what the composition of the amino acid chain. It changes based on the region of the chain it is working with.
   *Trigger Factor also changes its activity based on where the protein is in the translation process.
   *Trigger Factor’s process depends on how the amino acid chain is bound to the ribosome, and can even unfold parts of the chain that were misfolded in the translation process.

   An additional factor that regulates when amino acid chains fold into proteins is its distance from the ribosome (the place where the amino acid chain is made). The closer the chain is to the ribosome, the less room it has to fold into a three-dimensional protein. Trigger Factor works with this spatial hindrance, making an interesting and complex regulation system.
   Trigger Factor is only called into the game once the amino acid chain is a certain length (around 100 amino acids long) and when the chain has certain features, such as hydrophobicity. As the authors state it, Trigger Factor keeps the protein from folding into its three-dimensional structure until the amino acid chain has all of the information it needs to fold properly:
   In summary, we show that the ribosome and TF each uniquely affect the folding landscape of nascent polypeptides to prevent or reverse early misfolds as long as important folding information is still missing and the nascent chain is not released from the ribosome.
   So we have a protein that is able to perform various functions that inhibit or slow protein folding until the amino acid has the right chemical information for folding to occur.
   This does not solve the riddle about proteins being made from proteins (otherwise known as the chicken-and-the-egg problem). It actually adds another twist to the riddle: How does one protein know how much information a completely different protein needs to fold into a three dimensional structure? How does a protein evolve the ability to “know” how to respond to specific translational circumstances as Trigger Factor does?
   http://www.evolutionnews.org/2.....63951.html

   Also of note:

   Proteins Fold Who Knows How – July 2010
   Excerpt: New work published in Cell shows that this “chaperone” device speeds up the proper folding of the polypeptide when it otherwise might get stuck on a “kinetic trap.” A German team likened the assistance to narrowing the entropic funnel. “The capacity to rescue proteins from such folding traps may explain the uniquely essential role of chaperonin cages within the cellular chaperone network,” they said. GroEL+GroES therefore “rescues” protein that otherwise might misfold and cause damage to the cell.,,, “In contrast to all other components of this chaperone network, the chaperonin, GroEL, and its cofactor, GroES, are uniquely essential, forming a specialized nano-compartment for single protein molecules to fold in isolation.”
   http://www.creationsafaris.com.....#20100709a

   Nature Review Article Yields Unpleasant Data For Darwinism – August 2011
   Excerpt: The number of possible shapes that a protein can fold into is very high and folding reactions are very complex, involving the co-operation of many weak, non-covalent interactions. A high percentage of proteins do not fold automatically into the required shape and are at risk of aberrant folding and aggregation. As the abstract to this paper states: “To avoid these dangers, cells invest in a complex network of molecular chaperones, which are ingenious mechanisms to prevent aggregation and promote efficient folding.”
   http://www.uncommondescent.com.....darwinism/

   Verse and music:

   Psalm 139:13-14
   For you created my inmost being; you knit me together in my mother’s womb. I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well.

   Steven Curtis Chapman – Lord of the Dance (Live)
   http://www.youtube.com/watch?v=hDXbvMcMbU0
4. 4
   Axel says:

   September 7, 2012 at 5:14 pm

   Ah, but you’re all forgetting that evolution is full of suprises, so they’ll choose to ignore all of its significance, taking the math and the logic in their anti-science stride, and stumble on, unperturbed by any deliberative response.

   However, who can doubt that they would have a fit with their leg up, to borrow a curious Australian locution, on reading the article below?

   http://www.catholicjournal.us/.....ast-supper
5. 5
   PaV says:

   September 10, 2012 at 11:17 am

   Plato had a very jaundiced view of artists since he felt that they could easily distort reality. Hollywood daily confirms his cynicism.

   When it comes to evolution, nothing is more distorted than the common view of fitness landscapes. Kaufman, who started out so optimistic that he could show how evolution is understandable in terms of these landscapes, in the end had to admit that his project was simply not doable.

   What we see as the accepted view of fitness landscapes—one which is found in Johnathan M’s paper—is a complete distortion. They show a slope slowly increasing up to a peak. But the reality is that they are, in terms of configuration space, nothing but single lines—i.e., sheer cliffs. And, sheer cliffs 360 degrees around. Dawkins attempts to confuse the issue by suggesting that “Mount Improbable” can be climbed from behind, a view that is blocked from us but that is ‘seen’ by evolution. This is a distortion. This is nothing but fantasy.

   The Darwinists can run, but they can’t hide. And eventually molecular biologists will make this painfully clear to them. Time is ID’s ally. Time is Darwin’s “Grim Reaper.”