NEW PROTEIN DISCOVERY

ARTICLE follows my comments.............

Essentially Creationists are saying that these new discoveries supports their fundamental literal interpretation of the Bible.  I believe the OPPOSITE is true.

My Comments.............

These new discoveries are very exciting but the irony is that these discoveries actually lend more support to microevolution.  Most fundamental Creationists do accept microevolution because of the overwhelming evidence revealed in pathogen resistance to antibiotics.  However, the

real issue that separates science from religion is macroevolution and the creation of man. Science claims man evolved from Simian ancestors over a long period of time by Natural Selection. Religion claims God Created man in His Image from the "dust of the Earth."  We can observe evidence of Natural Selection at the "macro" level in the plant and animal Kingdom at various taxonomical levels. However....there is critical scientific evidence that reveals that man DID NOT EVOLVE FROM APES.

New "natural" genetic information that results in new survival traits in a changing "selective" environment occurs from DNA mutation of which 99% are "lethal" and less than 1% of any possible positive mutations occur in germ tissue...the ONLY ones passed on to future generations for Natural Selection to act on. This presents a problem because there simply was not enough "time" in the separation of the Simian and Human evolutionary lines. Therefore there has to be a different mechanism involved to explain the common genome between ape and man.  Ironically....the religious Biblical position that God Created Adam in His Image from the "dust of the Earth" by Intelligent Design DOES explain the science! 

Creationists unfortuneately have an inherent "fear" that science is incompatible with their fundamental interpretation of the Bible and therefore claim a "supernatural" mechanism in Creation. Such a position requires a "blind faith" instead of "informed faith" in  the inerrant and absolute Truth revealed in God's Word.  Blind faith is accepting the fundamental literal interpretation of the Bible.  Informed faith is accepting science as a "gift" of God that reveals God's PERFECT Laws which reveals the absolute Truth revealed in the Bible. In fact..science actually eliminates ALL the alleged "errors" and apparent "fantasy" in the Bible claimed by atheists.

Science historically embraced the Truth and Wisdom revealed in God's Word but unfortuneately following the "Age of Reason" going into the 20th Century, science has totally rejected the Bible's Truth.  The irony is that science HAS discovered the mechanism of how God Created Adam from "the dust of the Earth" by Intelligent Design via RECOMBINANT DNA. DNA is made up of the elements of  carbon, hydrogen, oxygen, nitrogen and phosphorous and those elements certainly qualify as "dust."

If people really understand the God revealed in the "flesh" 2000 years ago in the Incarnation of Yeshua ben Joseph (Jesus The Christ) they would understand what Intelligent Design is and realize that science is NOT incompatible with God's Word...it PROVES its' authenticity! I believe the Creation of Eve from Adam's "rib" seals the argument…….God saw that Adam needed a “helpmate” and He placed Adam in to a “deep sleep”, removed a “rib” and covered it in “flesh and bone”  Creating Eve. When she was presented to Adam he exclaimed….”At last, this is flesh of my ‘flesh and bone of my bone’, I will call her ‘women’ because she comes from man.”   Fantasy?  Fundamental Christians are subject to be labeled with this ridicule……HOWEVER….Truth sets us “free” from ALL illusion……

The science of the Bible………..

The “rib marrow” is an easily accessible and rich source of adult stem cells which are easily reset to an early embryonic state by “induced pluripotency.”  Two IPS cells are involved. The “Y” chromosome of one is replaced by an “X” chromosome from the second cell…..the second cell and the “Y” chromosome are discarded.  The “modified” first cell is easily induced to begin “cleavage” and forms a blastocyst which completes morphogenesis and gestation in a “surrogate” womb. (I suspect “in vitro” although an indigenous female might have been involved)   Nine months later “little baby Eve” is born. I suspect the “deep sleep” was a form of suspension because Eve was a sexually mature young women when she was presented to Adam because he would have been without a “helpmate” for 12 years or so!  (good thing the Y was replaced with an X  too or it would have been “Adam and Steve!”)  There is no question that Eve is a modified “clone” of Adam and the Scripture supports the science and vice versa.  “At last flesh of my flesh and bone of my bone, I will call her ‘women’ because she COMES FROM MAN.”

In Christ Jesus…..David Brown

Collective Motion: A New Level of Design Found in Proteins

Evolution News & Views March 15, 2016 3:06 AM | Permalink

A "previously unidentified mechanism for modulating protein affinity" has come to light. A team of scientists at the Max Planck Institute for Biochemical Chemistry, publishing in the Proceedings of the National Academy of Sciences, has identified new functional roles for collective motions within protein molecules. These motions, referred to as allostery, allow one end of the protein to affect a distant part through what is termed "allosteric communication."

Intermolecular interactions are one of the key mechanisms by which proteins mediate their biological functions. For many proteins, these interactions are enhanced or suppressed by allosteric networks that couple distant regions together. The mechanisms by which these networks function are just starting to be understood, and many of the important details have yet to be uncovered. In particular, the role of intrinsic protein motion and kinetics remains particularly poorly characterized. [Emphasis added.]

This is cutting-edge research. The team studied a common protein named ubiquitin which, as the name implies, is ubiquitous in the cell. It serves as a molecular "tag" on other molecules slated for degradation by the proteasome. As such, it needs to form connections with the proteasome and with a variety of other proteins. What they found is that distant parts of the molecule could affect binding affinity of other parts through motions transmitted throughout the entire molecule.

To determine how this collective motion influences binding and other functions of ubiquitin (e.g., presence of different covalent linkages), we performed an extensive structural bioinformatics survey of known ubiquitin crystal structures. Because the peptide bond conformation was the most recognizable feature of the collective mode, we used its conformation as a "marker" for structural discrimination. The most significant relationship we found was the universal association between the NH-in state and binding to the ubiquitin-specific protease (USP) family of deubiquitinases (Fig. S11). This association has been previously noted and is surprising because the peptide bond is at least 6.8 Å from any USP (Fig. 3A).

By comparing mutants with wild-type forms, the team found several kinds of motion that involve twisting, rocking and stretching. Mutations on a peptide bond between two specific amino acid residues, in particular, had a surprising effect, reducing binding affinity by a factor of 10 (or abolishing it altogether). This suggests low tolerance for mutation.

They found "strong allosteric coupling between opposite sides of the protein" in some cases. "Given the relative subtlety of the expansion and contraction" of allosteric interactions, they found it "surprising" again that two different states could produce large effects. It implies that ubiquitin and its ligand "appear to adapt their conformations mutually to establish a complementary binding interaction" for best fit at the appropriate times.

One mutant showed a two-fold weaker affinity for its particular USP. "Although this change may seem like a moderate effect," they note, "it is actually surprisingly large and highly significant when one considers that it is allosterically triggered by the simple rotation of a solvent-exposed peptide bond on a distal side of the protein."

These motions are so rapid -- on the order of microseconds -- they were not really considered significant until recently. Other motions they mention, like "pincer time" and "tumbling time," occur on different time scales, the former being quicker, the latter being much slower. This may suggest a kind of timing code for different functions.

Their conclusions reveal a significant new area of study: switch-controlled "allosteric communication" in protein molecules:

This study revealed an allosteric switch affecting protein-protein binding through collective protein motion at the microsecond time scale.... Whereas most known microsecond to millisecond time-scale motions involve excursions to excited, lowly populated states, this motion occurs between two ground state ensembles with nearly equal populations (NH-in and NHout). Strikingly, the peptide bond conformation is allosterically coupled through a diverse set of interactions that triggers contraction/ expansion of the entire domain. This type of global domain motion reveals a previously unidentified mechanism for modulating protein affinity. The presence of this allosteric network suggests there may be heretofore undiscovered ways in which macromolecular assemblies and covalent linkages regulate ubiquitin binding. More broadly, this study demonstrates how relatively modest changes in hydrogen bond networks and the protein backbone can bring about distant changes in protein conformation and binding affinity.

We encounter, therefore, a whole new level of specificity in protein architecture. It's not the old picture of an active site surrounded by haphazard amino acid residues. Any change could affect the allosteric communication of the whole protein. Clearly, mutants were less able to take advantage of the benefits of collective motion.

How did an unguided process arrive at a molecular machine that not only grips its substrate and catalyzes a reaction efficiently, but moves with intrinsic twists and stretches to improve the grip? The design specs for proteins just shot up a notch, and along with them, the challenges to Darwinian evolution.