January 19, 2010 | David F. Coppedge

Molecular Machines Use Moving Parts

Research papers into the processes of molecular machines continue to reveal moving parts: “fingers” that open and close, ratchets that lock into place, and feet that move along tracks.  Here are a few samples from the voluminous literature that continues to pour from biophysics labs.

  1. DNA Polymerase I:  Scientific papers tend to be reserved in their language, but the authors of a paper in Structure1 couldn’t help themselves: “DNA polymerases are spectacular molecular machines that can accurately copy genetic material with error rates on the order of 1 in 105 bases incorporated, not including the contributions of proofreading exonucleases.”  Their paper went into detail on how the “fingers” and “thumb” of the machine open and close in precise sequence as the machine moves along the DNA strand base by base.  Part of the machine rotates 50° as the machine translocates along the DNA.  These machines copy millions of base pairs of DNA every cell division so that each daughter cell gets an accurate copy.  The research was done on a bacterium that lives in hot springs.
        Pata and Jaeger, who reviewed the paper by Golosov et al in Structure,2 included a diagram showing the “conformational changes” that DNA polymerase I undergoes in its action along the DNA strand.  “After more than fifty years of research, the DNA polymerases responsible for copying the genetic material are some of the most well characterized enzymes in all of biology,” they said.  “Although the polymerases are divided into several different families, they all share a common two metal-ion catalytic mechanism, and most of them are described as having fingers, palm, and thumb domains: the palm contains metal-binding catalytic residues, the thumb contacts DNA duplex, and the fingers form one side of the pocket surrounding the nascent base pair.”  Three phases occur during each step along the DNA chain: the fingers open, the machine moves one base pair as it rotates, then the base in the “palm” is placed into the “pre-insertion site,” while another moving part prevents further movement till the operation is completed.  Then the process repeats – millions of times per operation.
        A paper in PNAS3 on DNA Polymerase I noted that “The remarkable fidelity of most DNA polymerases depends on a series of early steps in the reaction pathway which allow the selection of the correct nucleotide substrate, while excluding all incorrect ones, before the enzyme is committed to the chemical step of nucleotide incorporation.”  Their paper also discussed numerous conformational changes in the operation – some that precede the emplacement of the nucleotide at each step.  They described how the fingers-closing step forms “a snug binding pocket around the nascent base pair.”  They discussed at length how the machine prevents mismatched bases at several stages of the operation.  None of the authors of these three papers used the word evolution.
  2. Virus replicator:  Language of moving parts abounds in an article in PNAS about the machinery a virus uses to replicate itself.4  This little helicase called NS3h undergoes three successive conformational changes as it ratchets along the DNA.  Words found in the paper suggesting moving parts include: stretched spring, torsion, rotation, bending, propel, motion, unwinding, gating, cycle, kinetic steps, motor domains, structural transitions, and ratchet-type unidirectional translocation.  This particular machine works in a virus that causes hepatitis C.  It is part of superfamily SF2 of this kind of machine.  Regarding evolution, the authors only said, “structural comparison of the representative SF1 and SF2 members reveals explicit differences in catalyzing nucleotide hydrolysis and motion (Figs. S6 and S7), reflecting the fact that these helicases have evolved to adopt divergent mechanisms and act in different biological processes.” 
  3. Torsion springs and lever arms:  There’s a molecular machine that detects stretching force when a load is applied.  The keywords for a paper in PNAS5 about one of the myosins include kinetics, torsional motions, lever arm, force-sensitive transition, and more.  “Myosin-Is are molecular motors that link cellular membranes to the actin cytoskeleton, where they play roles in mechano-signal transduction and membrane trafficking,” the paper begins.  “Some myosin-Is are proposed to act as force sensors, dynamically modulating their motile properties in response to changes in tension.”  Why do cells need force sensors?  “Tension sensing by myosin motors is important for numerous cellular processes, including control of force and energy utilization in contracting muscles, transport of cellular cargos, detection of auditory stimuli, and control of cell shape.”  The authors found that alternative splicing of the gene produces isoforms of the motor with lever arms of different lengths, with varying response to force.  This “increases the range of force sensitivities of the proteins translated from the myo1b gene.”  and it “tunes the mechanical properties of myo1b for diverse mechanical challenges, while maintaining the protein’s basal kinetic and cargo-binding properties.”
        How did these myosin machines arise?  They just evolved.  “Myosins have evolved different tension sensitivities tuned for these diverse cellular tasks,” the authors said.  That’s all they had to say about evolution.
  4. Ribosome dynamics:  When transfer-RNAs and messenger-RNAs traverse the ribosome protein-assembly factory with their amino-acid cargos and genetic data readouts, respectively, they undergo several motions as they are transported along.  Researchers writing in PNAS said,6 “Spontaneous formation of the unlocked state of the ribosome is a multistep process.”  Their paper described how the L1 stalks of the ribosome bend, rotate and uncouple – undergoing at least four distinct stalk positions while each tRNA ratchets through the assembly tunnel.  At one stage, for instance, “the L1 stalk domain closes and the 30S subunit undergoes a counterclockwise, ratchet-like rotation” with respect to another domain of the factory.  This is not simple.  “Subunit ratcheting is a complex set of motions that entails the remodeling of numerous bridging contacts found at the subunit interface that are involved in substrate positioning,” they said.

Since the discovery of molecular machines, biochemistry has transformed into biophysics.  The kind of chemistry we learned in school is inadequate for understanding the machinery of the cell.  Interactions between molecules are not simply matters of matching electrons with protons.  Instead, large structural molecules form machines with moving parts.  These parts experience the same kinds of forces and motions that we experience at the macro level: stretching, bending, leverage, spring tension, ratcheting, rotation and translocation.  The same units of force and energy are appropriate for both – except at vastly different levels.

1.  Golosov, Warren, Beese and Karplus, “The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis,” Structure, Volume 18, Issue 1, 83-93, 13 January 2010, 10.1016/j.str.2009.10.014.
2.  Janice D. Pata and Joachim Jaeger, “Molecular Machines and Targeted Molecular Dynamics: DNA in Motion,” Structure, Volume 18, Issue 1, 13 January 2010, Pages 4-6, doi:10.1016/j.str.2009.12.003.
3.  Santoso et al, “Conformational transitions in DNA polymerase I revealed by single-molecule FRET,” Proceedings of the National Academy of Sciences, January 12, 2010, vol. 107, no. 2, pp. 715-720, doi:10.1073/pnas.0910909107.
4.  Gu and Rice, “Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism,” Proceedings of the National Academy of Sciences, January 12, 2010, vol. 107, no. 2, pp. 521-528, doi:10.1073/pnas.0913380107.
5.  Laakso, Lewis, Shuman, and Ostap, “Control of myosin-I force sensing by alternative splicing,” Proceedings of the National Academy of Sciences, January 12, 2010, vol. 107, no. 2, pp. 698-702, doi:10.1073/pnas.0911426107.
6.  Munro, Altman, Tung, Cate, Sanbonmatsu and Blanchard, “Spontaneous formation of the unlocked state of the ribosome is a multistep process,” Proceedings of the National Academy of Sciences, January 12, 2010, vol. 107, no. 2, pp. 709-714, doi:10.1073/pnas.0908597107.

In the major general journals, papers on biochemistry and biophysics appear to vastly exceed other topics.  In the current issue of PNAS, for instance, there are 3 papers on physical sciences, 7 on chemistry (but several overlapping with biochemistry), one on engineering, 1 on environmental science, 1 on geology, 2 on mathematics, 2 on social sciences, 6 on biology, 1 on ecology, 1 on environmental sciences, 2 on evolution, 4 on genetics, 6 on immunology, 6 on medical sciences, 5 on microbiology, 2 on neuroscience, 2 on physiology, 1 on plant biology, 2 on psychology, 1 on “sustainability science,” but 25 on biochemistry/biophysics/cell biology.  This is not atypical.  There may be various reasons for this lopsided publishing on cells, but clearly major discoveries are being made as techniques become refined that allow us to see more clearly into the operations of cellular factories.  The pattern we see repeatedly here is known as the CEH Law: talk of evolution is inversely proportional to the amount of observational detail.  Usually the Darwinspeak is only a casual passing reference without demonstration, like “such-and-such evolved to….” (for the fallacy of using evolved as an active verb, see the 01/17/2010 entry).  The evidence shouts “design!” to the rest of us.
    It has probably not escaped your notice that viruses and disease-causing bacteria contain the same high-tech machinery as the “good” cells.  In fact, many of our worst plagues are caused by organisms employing exquisite molecular machines against us.  This undoubtedly raises philosophical and theological questions.  It’s the long-standing problem of natural evil.
    The Darwinist answer is less than helpful: it says that nothing is evil.  Whatever is, is right; more accurately, whatever is, is.  Everything is in its own struggle for existence.  But why struggle, if existence is meaningless?  We’ve come a long way since the 18th century, when deists, and later atheists, portrayed nature as good and benevolent.  They argued on that basis that we should build our morality on the observation that all creatures seek pleasure and flee pain.  But should do we do it corporately, or individually?  If individually, what if my pleasure involves your pain?  If corporately, what eggs have to be broken to make the omelet?  In hindsight, this has been a disastrous way to build a social contract.  It also begs the question that any objective moral categories can be derived from nature.  One man may see a beautiful sunrise; another a threat of rain.  One may admire the beauty of the Alps; another may say, what a chaotic jumble of rocks.  And it’s doubtful an evolutionary biologist will be dispassionate about natural evil when afflicted with hepatitis C.  The naturalistic position also is incoherent.  One cannot describe it without the Yoda Complex: stepping outside one’s natural skin and pontificating about truth and reality from an imagined exalted plane.
    The Christian position is not devoid of its own problems in specifics, but provides a coherent framework for understanding natural evil.  Unlike deism, which tries to see everything as providentially good, the Judeo-Christian tradition sees nature as fallen from its original goodness.  The deist Rousseau would have us believe that the way to happiness is getting close to nature and letting our natural tendencies guide us.  Notice that he had to invoke his Yoda Complex to say that; he wrote it in books, not while trouncing naked in the forest hunting prey.  He was appealing to concepts and principles he assumed were true.  Like most attractive philosophies, his views contained some half-truths that persist in some modern movements.  But it is doubtful he would look at natural disaster as evidence of a benevolent deity, or the behaviors of many native tribes that subjugate women, disfigure children and cannibalize their enemies, as models for how to build a natural society.
    The Biblical description of the Fall provides enough detail to get us thinking about natural evil from a coherent framework, but leaves some room for differences of opinion.  We are told that evil entered with Satan’s fall and man’s capitulation to the temptation to doubt and disobey God’s word.  We learn that the world was put under a curse because of sin, and that some of the curse included natural pain: thorns, pain in childbirth, difficulty in agriculture.  These changes apparently took place immediately at the hand of God.  The world was judged again by a catastrophic flood because every intent of the thoughts of man’s heart was only evil continually.  Paul tells us that creation groans as if in labor pains, waiting for the consummation (Romans 8).  And we learn from Scripture that God remains merciful and good to His creation, and that His providential care, wisdom and glory is still abundantly evident to all people – not just to believers (Psalm 19, Psalm 104).  Meanwhile, the goal of man’s highest aspirations is to be heaven, not the pleasures of this world.
    Within that framework some additional questions can be asked.  As details come to light about exquisite machinery in viruses and bacteria that cause disease, how are we to interpret them?  Did God design these machines directly to cause pain?  If so, it would be right for him as the Judge of all to execute judgment.  We do not condemn human judges for inflicting pain and even the death penalty when the law demands it.  We are all under the penalty of death for our own sin.  The real wonder is not why the suffering appears random to us, but why God lets us all live as long as we do, when his justice could require instant incineration of the planet.  In some cases, however, the pain may come from God indirectly, from his having relaxed some of his providence on life-forms that were originally intended for good, letting mutations and decay processes operate according to the laws of a cursed creation.  Even evolutionary biologists ponder how toxins arose and how structures might have become modified.  Creationists do not have problems with existing machinery getting co-opted for other uses under selection pressure; it’s the origin of new complex information de novo that is too improbable for evolution to explain.  Perhaps the needle pumps in bacteria and the genetic modification mechanisms in viruses had a good function originally.  The fact that the vast majority of these microbes are beneficial lends credence to the idea; an article on Science Daily said that the same bacterium responsible for stomach ulcers may protect against tuberculosis.  This could indicate that microbes can offset one another and perhaps have gotten out of balance.  Some theologians might wonder if the spiritual forces of Satan’s dominion have limited ability to turn parts of nature against itself – not to exercise creative power, but like the disasters in the Book of Job, to take existing forces of nature (fire, whirlwinds) and turn them against man.  They would be analogous to hackers who take existing computers and networks and turn them into weapons of harm.  This would, of course, be within the permissive will of God.  This short list does not exhaust the possibilities.  The Bible has provided sufficient, but not exhaustive, information to address this question.  He also grants us the power of prayer to seek relief from the natural afflictions of life – though we know physical death cannot be delayed forever.  Undoubtedly if knew every calamity that would befall us and the day of our death, we would be tempted to procrastinate our preparations for meeting our Maker.  The uncertainties of natural disasters should force us to lean on God and be ready at all times to stand before him.
    There is a rich literature on attempted solutions to the problem of natural evil.  Only the Biblical view is coherent: natural evil is contrary to the divine will, but is used by the divine will for purposes that are ultimately good.  Unlike evolutionary, pantheistic, deistic, animistic or mystical solutions, which cannot define good or evil in a consistent or coherent way, (or try to deny good and evil altogether), the Biblical world view gives people the liberty to oppose evil and strive to eliminate pain in this life, while recognizing the goal of mankind is to strive for the kingdom of God, where evil will be vanquished forever.  Medicine and science are, therefore, logical applications of the Biblical world view.

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