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Structural View of Biology


Biomolecular structures allow us to understand the molecular nature of healthy cells and treat the underlying molecular causes of disease. Our cells contain thousands of molecules that must all work in concert to keep us healthy. When any of these molecules fails, or when a poison or pathogenic organism attacks these molecules, it may cause disease. Our bodies have many defenses against disease, and medical science has developed powerful drugs to assist these defenses.

Many diseases are caused by malfunctions of cellular molecules. These malfunctions may be caused by environmental dangers, like pathogens or radiation, or may be the result of genetic errors. Our cells contain many defenses to fight these malfunctions, ranging from the detoxification of poisons to the forced suicide of compromised cells.

Scroll to a Molecule of the Month Feature in this subcategory:

  • ABO Blood Type Glycosyltransferases

    ABO Blood Type Glycosyltransferases

    Researchers have discovered that blood comes in several types, which define groups of people with compatible blood. The ABO system defines one of the major types determining groups of people who can donate blood to each other.

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    Discussed Structures
    Glycosyltransferase A
    Glycosyltransferase A
    Glycosyltransferase B
    Glycosyltransferase B
  • Amyloid-beta Precursor Protein

    Amyloid-beta Precursor Protein

    Like Dr. Jekyll and Mr. Hyde, some seemingly innocent proteins have evil alter egos. The amyloid-beta precursor protein is an important example. It is a large membrane protein that normally plays an essential role in neural growth and repair. However, later in life, a corrupted form can destroy nerve cells, leading to the loss of thought and memory in Alzheimer's disease.

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    Discussed Structures
    amyloid-beta peptide
    amyloid-beta peptide
    amyloid-beta peptide fibril
    amyloid-beta peptide fibril
    beta-secretase and inhibitor
    beta-secretase and inhibitor
  • Carbonic Anhydrase

    Carbonic Anhydrase

    Breathing is a fundamental function in life - ever wondered what really happens when we breathe? The air we breathe in has precious oxygen that fuels the breakdown of sugars and fat in our cells. In our lungs, oxygen diffuses into the blood, binds to hemoglobin and is transported to all the cells of our body (see the Molecule of the Month feature on hemoglobin). Carbon dioxide is a byproduct of sugar and fat breakdown in cells and needs to be removed from our body. Again, blood acts as a transport medium. Carbon dioxide diffuses out of cells and is transported in blood in a few different ways: less than 10% dissolves in the blood plasma, about 20% binds to hemoglobin, while the majority of it (70%) is converted to carbonic acid to be carried to the lungs. An enzyme present in red blood cells, carbonic anhydrase, aids in the conversion of carbon dioxide to carbonic acid and bicarbonate ions. When red blood cells reach the lungs, the same enzyme helps to convert the bicarbonate ions back to carbon dioxide, which we breathe out. Although these reactions can occur even without the enzyme, carbonic anhydrase can increase the rate of these conversions up to a million fold.

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    Discussed Structures
    alpha carbonic anhydrase
    alpha carbonic anhydrase
    beta carbonic anhydrase
    beta carbonic anhydrase
    gamma carbonic anhydrase
    gamma carbonic anhydrase
  • Caspases

    Caspases

    Billions of cells in your body will die in the next hour. This is entirely normal--the human body continually renews itself, removing obsolete or damaged cells and replacing them with healthy new ones. However, your body must do this carefully. If cells are damaged, like when you cut yourself, they may swell and burst, contaminating the surrounding area. The body responds harshly to this type of cell death, inflaming the area by rushing in blood cells to clean up the mess. To avoid this messy problem, your cells are boobytrapped with a method to die cleanly and quickly on demand. When given the signal, the cell will disassemble its own internal structure and fragment itself into small, tidy pieces that are readily consumed by neighboring cells. This process of controlled, antiseptic death is called apoptosis.

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    Discussed Structures
    caspase-1
    caspase-1
    caspase-9
    caspase-9
    caspase-3
    caspase-3
    procaspase-7
    procaspase-7
    caspase-7
    caspase-7
  • Crystallins

    Crystallins

    As you read this Molecule of the Month, the light from the page is being focused in your eyes by a concentrated solution of crystallin proteins. The lenses in your eyes are built of long cells that, early in their development, filled themselves with crystallins and then made the major sacrifice, ejecting their nuclei and mitochondria and leaving only a smooth, transparent solution of protein. We then rely on these proteins to see for the rest of our lives.

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    Discussed Structures
    alphaA crystallin
    alphaA crystallin
    alphaB crystallin
    alphaB crystallin
    beta crystallin
    beta crystallin
    gamma crystallin
    gamma crystallin
    delta crystallin
    delta crystallin
    epsilon crystallin
    epsilon crystallin
    lambda crystallin
    lambda crystallin
  • Glucansucrase

    Glucansucrase

    We brush our teeth twice a day with fluoride toothpaste, use mouthwash, limit sugars in our diet...and we still get cavities. Cavities are caused by bacteria that consume some of the sugar in our diet, ferment it, and then release acids. These acids eat away at the hard minerals in our teeth. It seems like it would be easy to brush these bacteria away, and get rid of them once and for all. However, they have a trick to avoid this.

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    Discussed Structures
    glucansucrase with glucose
    glucansucrase with glucose
    glucansucrase with acarbose
    glucansucrase with acarbose
  • Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)

    Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)

    Cells are great recyclers. They need to be, otherwise we would be faced with an insurmountable need for new molecular building blocks and enough energy to manage them. For instance, new messenger RNA chains are made constantly, transmitting information from the nucleus to build new proteins. Afterwards, these chains are broken down and the components are recycled. A complex set of salvage machinery is used to recycle these components.

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    Discussed Structures
    Human HGPRT
    Human HGPRT
    Malarial HGPRT
    Malarial HGPRT
  • Leptin

    Leptin

    The delivery of nutrients to cells throughout the body is controlled by a complex network of signaling molecules. Some of these signals happen without us really noticing, for instance, when insulin and glucagon control the level of glucose that is delivered through the blood after we eat. The signaling protein leptin, however, has a more apparent effect, acting within the system that makes us hungry when we need food.

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    Discussed Structures
    Leptin
    Leptin
    Leptin receptor
    Leptin receptor
    Neuropeptide Y
    Neuropeptide Y
  • Prions

    Prions

    Prions are proteins that can adopt two different forms, a normal form and a misfolded form. This may not seem unusual, since many proteins are flexible and adopt different shapes. However, prions have another unusual characteristic: the misfolded form of the prion can force normal prions to change into the misfolded shape. In this way, a few misfolded prions can corrupt a whole population of normal prions, converting them one-by-one into the misfolded shape. This can have deadly consequences, as the levels of misfolded proteins build up. For instance, misfolding of the PrP prion causes fatal neural diseases in humans and other mammals. To make things worse, misfolded prions are infectious, so a small dose of misfolded prions can infect and corrupt an entire organism.

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    Discussed Structures
    prion fragment
    prion fragment
    HET-s amyloid fibril
    HET-s amyloid fibril
  • Proton-Gated Urea Channel

    Proton-Gated Urea Channel

    The acid in your stomach helps to digest food, but it also helps protect you from bacterial infection. However, one type of bacteria, Helicobacter pylori, is able to live in the acidic environment of the stomach. It is one of the most common bacterial infections, found worldwide in half of the population. It causes a continued inflammation of the stomach, which leads in some cases to stomach ulcers and stomach cancer.

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    Discussed Structures
    Proton-Gated Urea Channel
    Proton-Gated Urea Channel
    Urease
    Urease
  • Ras Protein

    Ras Protein

    Cells are constantly sending messages, discussing nutrient levels and growth rates with other cells, and also managing the internal needs of the cell. These messages need to be clear and strong, so that they can be heard over the busy bustle inside the crowded cytoplasm. One way to strengthen signals is to link them to a process that is chemically irreversible, like the cleavage of ATP or GTP.

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    Discussed Structures
    Ras with GTP analog
    Ras with GTP analog
    Ras with GDP
    Ras with GDP
  • Superoxide Dismutase

    Superoxide Dismutase

    We can't live without oxygen. Our cells rely on oxygen as the final acceptor of electrons in respiration, allowing us to extract far more energy from food than would be possible without oxygen. But oxygen is also a dangerous compound. Reactive forms of oxygen, such as superoxide (oxygen with an extra electron), leak from the respiratory enzymes and wreak havoc on the cell. This superoxide can then cause mutations in DNA or attack enzymes that make amino acids and other essential molecules. This is a significant problem: one study showed that for every 10,000 electrons transferred down the respiratory pathway in Escherichia coli cells, about 3 electrons end up on superoxide instead of the proper place. To combat this potential danger, most cells make superoxide dismutase (SOD, shown here from PDB entry 2sod), an enzyme that detoxifies superoxide.

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    Discussed Structures
    Cu,Zn superoxide dismutase
    Cu,Zn superoxide dismutase
    Mn superoxide dismutase
    Mn superoxide dismutase
    Fe superoxide dismutase
    Fe superoxide dismutase
    Ni superoxide dismutase
    Ni superoxide dismutase
  • Thymine Dimers

    Thymine Dimers

    Summer is here, and we're all heading outdoors to enjoy the sun. But remember to take your sunscreen, since too much sunlight can damage your cells. Small doses of sunlight are needed to create vitamin D, but larger doses attack your DNA. Ultraviolet light is the major culprit. The most energetic and dangerous wavelengths of UV light, termed UVC, are screened out (at least for now) by the ozone in the upper atmosphere. However, the weaker UV light, termed UVA and UVB, passes through the atmosphere and is powerful enough to cause chemical changes in the DNA.

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    Discussed Structures
    Ultraviolet light can form crosslinks between adjacent bases in DNA, leading to mutations when the DNA is replicated. This crystallographic structure includes a short piece of DNA with two crosslinked thymine bases.
    Ultraviolet light can form crosslinks between adjacent bases in DNA, leading to mutations when the DNA is replicated. This crystallographic structure includes a short piece of DNA with two crosslinked thymine bases.
    Ultraviolet light can form crosslinks between adjacent bases in DNA, leading to mutations when the DNA is replicated. This NMR[BW11] structure includes a short piece of DNA with two crosslinked thymine bases.
    Ultraviolet light can form crosslinks between adjacent bases in DNA, leading to mutations when the DNA is replicated. This NMR[BW11] structure includes a short piece of DNA with two crosslinked thymine bases.
    Ultraviolet light can form crosslinks between adjacent bases in DNA, leading to mutations when the DNA is replicated. This structure includes an enzyme that recognizes thymine dimers and removes them.
    Ultraviolet light can form crosslinks between adjacent bases in DNA, leading to mutations when the DNA is replicated. This structure includes an enzyme that recognizes thymine dimers and removes them.
    Ultraviolet light can form crosslinks between adjacent bases in DNA, leading to mutations when the DNA is replicated. This structure includes an enzyme that recognizes thymine dimers and breaks the crosslink.
    Ultraviolet light can form crosslinks between adjacent bases in DNA, leading to mutations when the DNA is replicated. This structure includes an enzyme that recognizes thymine dimers and breaks the crosslink.
    Ultraviolet light can form crosslinks between adjacent bases in DNA, leading to mutations when the DNA is replicated. This structure includes a special DNA polymerase that is able to read through the damaged DNA.
    Ultraviolet light can form crosslinks between adjacent bases in DNA, leading to mutations when the DNA is replicated. This structure includes a special DNA polymerase that is able to read through the damaged DNA.
  • Vitamin D Receptor

    Vitamin D Receptor

    Vitamins are exotic molecules that are essential for the proper function of cells, but somewhere along the process of evolution, our bodies have lost the ability to make them. So instead, we need to obtain them in our diet, or in a daily multivitamin tablet. These include vitamin A, which is used to build the light sensors in our eyes, a host of B vitamins used to build specialized tools for chemical reactions, and vitamin C, which plays an essential role in construction of collagen. Vitamin D is an exceptional case: our cells can make it, but only if there is enough sunlight.

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    Discussed Structures
    Vitamin D Receptor
    Vitamin D Receptor
    Vitamin D Receptor
    Vitamin D Receptor
    Vitamin D Binding Protein
    Vitamin D Binding Protein
    CYP2R1
    CYP2R1
  • beta-Secretase

    beta-Secretase

    Many of our proteins need to be shaped, folded and trimmed after they are made, to coax them into their proper functional form. A variety of specialized chaperones and proteases perform these tasks. Occasionally, however, these chaperones and proteases make mistakes that can have life-threatening consequences.

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    Discussed Structures
    beta-secretase
    beta-secretase
    beta-secretase and inhibitor
    beta-secretase and inhibitor
  • p53 Tumor Suppressor

    p53 Tumor Suppressor

    Our cells face many dangers, including chemicals, viruses, and ionizing radiation. If cells are damaged in sensitive places by these attackers, the effects can be disastrous. For instance, if key regulatory elements are damaged, the normal controls on cell growth may be blocked and the cell will rapidly multiply and grow into a tumor. p53 tumor suppressor is one of our defenses against this type of damage. p53 tumor suppressor is normally found at low levels, but when DNA damage is sensed, p53 levels rise and initiate protective measures. p53 binds to many regulatory sites in the genome and begins production of proteins that halt cell division until the damage is repaired. Or, if the damage is too severe, p53 initiates the process of programmed cell death, or apoptosis, which directs the cell to commit suicide, permanently removing the damage.

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    Discussed Structures
    p53 tumor suppressor tetramerization domain
    p53 tumor suppressor tetramerization domain
    p53 tumor suppressor DNA-binding domain
    p53 tumor suppressor DNA-binding domain

Please see our usage polices for citation and reprint information. Copies of the illustrations used in these features are available for download as high resolution TIFF images. Please note that the structures used to illustrate each installment are chosen at the discretion of the authors; the features are not intended to represent a historical record. The process behind the creation of this feature is described by the author.