Thursday, April 26, 2012

The Role of Protein Structure in Health and Disease

Proteins are a necessary part of the human diet.  When proteins are digested they are broken down into their building blocks – amino acids.  The body then reassembles these amino acids to produce the proteins required by the organism to live.  Proteins play essential roles in all living things, including humans.  These roles can be included into two major types – structural and metabolic.  Structural proteins maintain the shape and form of the both the individual cells of the body and the whole organism and are essentially responsible for locomotion.  As an example,  collagen is an essential ingredient of the connective tissue and is the most abundant protein found in the body.  In addition, the movement of muscle is due to a fundamental property intrinsic to the structure of muscle proteins – actin and myosin. 

A specialized class of proteins called enzymes is responsible for all the metabolic reactions that make life possible.  There are thousands of different types of enzymes; each responsible for a particular chemical reaction.  The scientific discipline that studies these reactions is referred to as Biochemistry.  An example of a protein that plays a critical role in respiration is hemoglobin.  The structure of this protein is exquisitely designed to react with molecular oxygen that is delivered to the lungs from the air.  This protein, like all proteins, is synthesized from the blueprints that are embedded in the gene responsible for its structure.  There is an axiom in biology that states that one gene has the information for the structure of one protein – this axiom basically still holds true.  Because the structural information for a protein lies in the gene that is responsible for it, a change in a gene – a mutation – can adversely impact protein structure.  Such a change would, therefore, be hereditary.  Sickle Cell Anemia is a disease in which a mutation in the gene that contains the information for the structure of hemoglobin results in a change in the protein's structure that adversely impacts it function.

The techniques devised by molecular biologists and biochemists over the years have helped elucidate the detailed relationships between the structure of proteins and their specific functions.  For example, as a result of these efforts, a relationship has been clearly demonstrated between the amino acid glutamine and protein structure.  Studies have shown that when there are sufficient repeats of this amino acid – a number of glutamines linked side by side in the protein chain - they may cause a significant change in the overall shape of the protein resulting in protein aggregation.   Protein aggregation can adversely affect protein or enzymatic function.   The evidence indicates that when these glutamine repeats become extensive in the protein huntingtin and other proteins found in neurological tissues, the result can be neurodegenerative disease.  The gene that contains the information for the structure of huntingtin is called the Huntington gene (HTT) and is strongly implicated in Huntington disease – a devastating neurological illness.

In conclusion, the examples cited above clearly demonstrate the essential role that proteins play in the human body and the implications for human health when protein structure has been changed due to a genetic aberration.   Linus Pauling, the famous Nobel Prize – winning chemist, described diseases like Sickle Cell Anemia and Huntington disease as "molecular diseases" for the reason that the underlying cause can be traced to an adverse change on the molecular level.

Monday, April 16, 2012

The Hygiene Hypothesis

There are currently many products on the market that claim to be effective household antibacterial agents that are purported to have health benefits by preventing exposure to infectious agents.  Although this may have value to some extent, these claims may, in fact, be misleading in relation to overall public health.

There is a growing body of scientific evidence that strongly suggests that normal human exposure to the microorganisms that pervade the natural environment may be of value to human health by helping to fine tune the human immune system and thereby prevent the unset of the types of immunological overreactions that are typified by asthma and some autoimmune diseases (an autoimmune disease is a condition that is a result of the human immune system attacking its own tissues).  This concept is referred to as the Hygiene Hypothesis.  According to this hypothesis, it is vital that the human immune system be normally exposed at a young age to the microbes that are so ubiquitous in the environment.  Without these kinds of interactions, it is posited that later in life the immune system would be prone to behave in such a way as to result in inflammatory and autoimmune reactions such as allergies, asthma, inflammatory bowel disease (IBS) and multiple sclerosis (MS).  Epidemiological studies have clearly shown that children growing up on farms are considerably less likely to suffer from allergies and asthma as compared to their urban counterparts.  This correlation, however, does not constitute proof given that there are many other variables involved.

The Hygiene Hypothesis has been given further credence as a result of the findings of Dr. Richard Blumberg, an immunologist, from the Brigham and Women's Hospital in Boston.  Blumberg and his colleagues studied mice raised in germ free cages and fed germ free food.  These mice are more susceptible to asthma and colitis - an inflammatory condition of the gut.  On exhaustive examination, they discovered that these animals had elevated levels of a rare immunological cell type - so-called invariant natural killer T cells (iNKT) in the lungs and the intestines.  These cells have been shown to trigger inflammatory responses following exposure to microbes or antigens – molecules that can trigger the immune response – produced by the body.  It should be noted here that the mouse animal model has been proven to be a good one; since, there is a very close correspondence between mouse and human immunology.  In addition, mice that had been genetically altered to lack iNKT cells do not exhibit colitis even when raised in a germ free environment.  Furthermore, when germ-free mice are transferred to a normal environment at an early age, they show a normal distribution of iNKT cells.

These are very interesting findings that show a mechanistic rationale for the Hygiene Hypothesis.  Hopefully, this kind of information will help individuals make more informed decisions regarding the use of anti-bacterial agents in the home. 

Thursday, April 5, 2012

Climate Change

The term Global Warming that is often associated with the cumulative impact of the buildup of greenhouse gases in the atmosphere does not accurately describe the nature of the consequences of this change in climatic conditions arising from human activity.  The more appropriate term is Climate Change.  The reason for this distinction is that the near term effect of this phenomenon is not necessarily warming on all parts of the globe.  However, dramatic changes in climate including temperature are predictable within this model. 
Our first order of business is to examine the science that is the underpinnings of Global Warming.  This necessitates an examination of the earth’s atmosphere.  The major components of the Earth’s Atmosphere are shown in the following table.

Percentage (%)
Parts per Million (ppm)
Nitrogen (N2)
Oxygen (O2)
*Carbon Dioxide (CO2)
*Methane (CH4)
*Water Vapor (H2O)
*Nitrous Oxide (N2O)
*Chlorofluorohydrocarbons (CFC)
Table 1 – Major constituents of the earth’s atmosphere are reported in percentage and parts per million (ppm) where * indicates the greenhouse gases.

Chart 1 – Pie chart showing distribution of major components in the atmosphere and the greenhouse gases (*)
The current level of CO2 in the atmosphere is 390ppm (as shown below in Chart 2).  CO2 is a by-product of respiration of all living things on the planet.  However, this is normally balanced by the uptake of CO2 by the world’s oceans and by green plants that are capable of photosynthesis – these interactions are collectively referred to as the carbon cycle.  In this regard, CO2 is the carbon source for all of life. 
Human activity since the dawn of the machine and the use of oil (hydrocarbon) as a cheap and plentiful source of energy has resulted in a continuous upward climb of this gas in the atmosphere.  The reason for this is that when fossil fuels are burned for energy, the by-products are CO2 and water.
The following chart shows the increase in the concentration of CO2 in the atmosphere over time.

Chart 2 – Concentration of CO2 in the Atmosphere over Time where 1790 represents the beginning of the industrial age – the steam engine was invented in 1775. 

The following chart shows these values as a change in percentage of CO2 per year.

Chart 3 – Change in Percentage of CO2 per Year.

As can clearly be seen from this representation, the increase of CO2 in recent times correlates well with the introduction of industrialization to human societies.   This change might not seem dramatic, but a doubling of the concentration of CO2 from pre-industrial levels is expected to increase the average global temperature by 2.5 degrees C.  From the data shown in Chart 3 it can be estimated that if the current rate of increase remains constant (0.63%/year) this doubling would be reached in approximately 100 years.  This is an extremely significant increase with horrendous implications for the earth’s climate.  Given the current political and economic situation throughout the world, it is unlikely that this increase in the rate of CO2 accumulation will remain static; unless more sustainable sources of energy are actively pursued.  In addition, even if the human production of this gas were to halt today, it would take a few hundred years for the current levels to decrease significantly.
CO2 is referred to as a greenhouse gas based on its molecular structure.  This gas has the ability to absorb heat and retain it much like the glass of a greenhouse allows heat from sunlight to pass freely through it from the outside but prevents some of it from leaving.  Therefore, some of the heat that would normally be reflected back from the earth’s surface and dissipate into space is retained.  The net effect is a general increase in temperature at the lower part of the atmosphere.  The science regarding this property of CO2 is irrefutable.   CO2 is not the only greenhouse gas in the atmosphere; the others as Table 1 demonstrates are water vapor, methane, nitrous oxide and chlorofluorohydrocarbons (CFC).  Increases in CO2, methane and CFC - synthetic compounds that used to be used widely in refrigerants - are a direct consequence of human activity; whereas, the amount of water vapor in the air is not.
There are predominantly two different processes through which heat is transferred throughout the atmosphere.  One is through radiant energy as mentioned earlier and the other is through what is referred to as convection.  In this process as air is heated near the surface of the earth it rises as it becomes less dense and is replaced by the colder and denser air from above.   This process is continuous with the net effect of transferring heat from the surface to higher reaches of the atmosphere.   It is the greenhouse gases that trap some of the heat, effectively warming the air in the lower atmosphere.
The planet Venus is a striking example of the ultimate impact of CO2 on temperature.   Scientific probes of the planet have shown that it has an atmosphere very high in CO2, a dense cloud cover and a surface temperature of over 500 degrees C.  Although Venus is considerably closer to the sun than the earth, the thick and nearly impermeable cloud cover would be expected to cool the planet considerably.  However, the exceedingly high concentration of CO2 in the Venetian atmosphere would explain most the heat trapped at the planet’s surface.
There are additional processes contributing to climate change that are important to consider in addition to the direct greenhouse effect.  These are:
·         The impact that increased CO2 concentrations has on the oceans including increasing ocean temperature.  This gas dissolves to some extent in water and increased concentrations of dissolved CO2 increases the acidity of the oceans.  This has a significant impact on marine life and ocean-based ecological systems.
·         Increased surface temperature in the northern climes can lead to the enhanced release of methane into the atmosphere from melting permafrost.  Methane is not only a potent greenhouse gas, it also possesses toxic properties.
·         An increase in the frequency and intensity of extreme weather conditions.
·         Increased melting of land-based ice in the form of glaciers and especially in regards to Iceland and Antarctica.  This can have powerful implications in regards to sea-level rise.  As a matter of fact, it has been estimated that should all of Greenland’s ice melt, it would cause a rise of sea level by about twenty-five feet.
Climate change is a very real phenomenon and, in my opinion, is the greatest challenge faced by all of humanity.  The manner in which this issue is addressed will have serious repercussions for the future of the human race.

Tuesday, April 3, 2012

How the Botulinum Neurotoxin Survives the Digestive System

The botulinum neurotoxin is such a potent and deadly toxin that the U.S. Centers for Disease Control (CDC) lists it as a category A bioterrorism agent.   Some of its additional characteristic properties are that is highly selective and has a long duration of activity.  This has made it possible for this agent to be used therapeutically, at controlled doses, for focal dystonias, wound healing and used cosmetically to decrease the evidence of wrinkling of the skin associated with aging.
Botulinum neurotoxin is produced by the Clostridium botulinum bacteria – a Gram-positive, spore-forming microorganism that requires an environment lacking in oxygen to grow.  Individuals can be exposed to this deadly toxin either through ingestion or inhalation.  Certain vegetables when improperly canned are notorious for providing the right environment for the growth of the botulinum bacteria and, therefore, the production of botulinum neurotoxin. 
Once an individual has been exposed to this deadly toxin, it finds its way into the bloodstream and attacks the nervous system, resulting in muscle paralysis and autonomic dysfunction.  It is the latter capability that can prove fatal; since, the autonomic nervous system controls such basic functions as breathing and maintaining the rhythm of the heart.  It has long been known that botulinum neurotoxin's mode of action is through the proteolysis – breakdown of proteins – of a key protein involved in the release of acetylcholine from nerve terminals.  Acetylcholine is an essential neurotransmitter in a significant category of cells in the human nervous system.
Structurally, botulinum neurotoxin is a protein.  This poses an interesting question: given its protein structure how is it able to survive the onslaught of the digestive system when it is ingested?  There must be some mechanism that explains how it can survive the acidity of the stomach and the digestive proteolytic enzymes of the stomach and small intestine.
The answer to this question has recently been resolved through the efforts of Dr. Shenyan Gu and his colleagues at the Center for Neuroscience, Aging and Stem Cell Research at the Sanford-Burnham Medical Research Institute in La Jolla California.  They discovered through exhaustive studies of the structure of the intact bioactive toxin that it exists as a complex with four additional proteins associated with botulinum neurotoxin.  One of these associated proteins, referred to as nontoxic non-hemagglutinin (NTNHA), is responsible for protecting the primary toxin from the acidity found in the stomach and for its protection from the proteolytic activity of trypsin produced by the stomach.
This finding not only helps elucidate the complete mechanism of action of botulinum neurotoxin but also suggests that inhibitors could be designed to weaken the necessary interaction between the toxin and its associated proteins early in the intoxication phase of the infection.