What Is Protein?

A protein is a long train of amino acids linked together. Proteins have different functions; they can provide structure (ligaments, fingernails, hair), help in digestion (stomach enzymes), aid in movement (muscles), and play a part in our ability to see (the lens of our eyes is pure crytalline protein).

Protein is a long chain molecule made up of amino acids joined by peptide bonds. Protein forms the structural material of bodily tissues.

Proteins, the principal constituents of the protoplasm of all cells, are of high molecular weight and consist essentially of combinations of a amino acids in peptide linkages.

Twenty different amino acids are commonly found in proteins and each protein has a unique, genetically defined amino acid sequence which determines its specific shape and function.

They serve as enzymes, structural elements, hormones, immunoglobulins, etc. And are involved in oxygen transport, muscle contraction, electron transport and other activities throughout the body and in photosynthesis.

Origin: Gr. Protos = first

The most important function of protein is to build up, keep up, and replace the tissues in your body. Your muscles, your organs, and some of your hormones are made up mostly of protein.

Protein also makes antibodies and hemoglobin (responsible for delivering oxygen to your blood cells).

Our body is able to produce 14 of the 20 amino acids. We have to get the remaining amino acids from the foods we eat.

fish. But proteins are complex and have many different functions within the human body.

Proteins form the major components of muscles, skin, tendons, blood vessels, hair, and cores of bones and teeth. They help you grow, heal wounds, and make up collagen - the connective tissue that gives your body its shape.

Other proteins, called enzymes, help generate energy in your body. Proteins called hormones act as internal “project managers”, ensuring your body runs itself properly. Insulin and glucagons, for example, are the hormones that control blood sugar levels. And proteins called antibodies are important components of your immune system, warding off foreign particles like bacteria.

Without protein, life would be impossible. Practically every cell in your body spends considerable time and energy manufacturing various kinds of proteins. Every imaginable part and function of your body has protein involved in some way, from the enzymes that are critical to the digestion of foods to the fibers that plug leaky blood vessels. But before you get carried away with putting protein on a nutritional pedestal, it can also be said that life would be impossible without sugars (carbohydrates) and fats (lipids).

Protein is simply a name for a nutritional family. We could just as easily have said this is a photo of the Jones or Smith family. To pick out their distinctive family characteristics we need to look closer. Do they all have large noses, blue eyes, and freckles? Just as human families have one trait in common with all othersthey are all members of the human speciesso do proteins. The principal trait for all proteins, large or small, is that they are composed of amino acids.

With about 20 different kinds available, every cell of your body can choose from the pool of amino acids to construct specific proteins to meet very diverse needs of human physiology. For example, there are boats to shuttle oxygen around (hemoglobin), taxis for small fats (LDL), and ballistic missiles to destroy invaders (immunoglobulins). Put two amino acids together and you get a dipeptide (di = "two"); put three amino acids together and the result is a tripeptide (tri = "three"); finally, a complex construction of many amino acids makes a polypeptide (poly = "many"). Human insulin, for instance, which is responsible for getting glucose into the muscles, is composed of 51 amino acids in two short polypeptide chains.

As the digestive process kicks into high gear, "intelligent" receptors on the large intestinal surfaces have to decide which amino acid, dipeptide, or tripeptide to absorb, and which will have to wait. This competition among the amino acids for absorption is not a big deal, since the body's receptors "know" which amino acids are needed most of the time. However, if your intestinal tract is flooded with amino acid supplements, the absorptive cells cannot deal with these refined and readily available amino acids all at once. Inevitably, the "pushier" amino acids, or the ones in greatest concentration, leave the receptors no choice but to take them in first.

The constant construction of new proteins, along with the destruction and elimination of old proteins, means that a continual supply of amino acids must be made available via nutrition to maintain a healthy balance. Different foods provide essential amino acids in varying proportions.

We now have clear evidence that even if a diet is derived exclusively from the vegetable kingdom, it can provide all the necessary amino acids for optimal health. It is generally sufficient simply to have a consistent supply of a variety of vegetables, legumes, and grains throughout the week.

Protein is one of the three macronutrients commonly identified as a dietary requirement. It represents nitrogen-containing compounds for which amino acids are the basic structural units.

Amino acids are small organic compounds containing at least one amino group and an organic acid group. The differences between amino acids lies in the differences between the amino acid side proteins are the most abundant organic compound of the body. More than fat, usually. Much more than carbohydrate. About 65% of the total body protein lies in the skeletal muscles.

Proteins function primarily in the growth and repair of body tissue. Just about every cell in our body has a protein component, and we are unable to synthesize new cells without the requisite building blocks. Hair, nails, skin contain protein. Blood contains plasma proteins; hemoglobin has a protein component. Proteins are components of some antibodies. Many hormones are proteins (like insulin). In fact, the protein content of the average cell is 16% of its total mass.

There are more than 50,000 different proteins in our bodies. These are all made from about 22 different amino acids. Our bodies can synthesize 14 of these 22 amino acids, we cannot make 8 of them, and these 8 must come from food. These 8 are called the essential amino acids. Sometimes we cannot synthesize other amino acids and therefore they too must come from diet.

Protein is a large, complex molecule composed of amino acids. The sequence of the amino acids, and thus the function of the protein, is determined by the sequence of the base pairs in the gene that encodes it. Proteins are essential to the structure, function, and regulation of the body. Examples are hormones, enzymes, and antibodies. Many bodybuilders use Protein to help build muscle in the body.

A protein is a complex, high molecular weight organic compound that consists of amino acids joined by peptide bonds. Proteins are essential to the structure and function of all living cells and viruses. Many proteins are enzymes or subunits of enzymes. Other proteins play structural or mechanical roles, such as those that form the struts and joints of the cytoskeleton. Still more functions filled by proteins include immune response and the storage and transport of various ligands. In nutrition, proteins serve as the source of amino acids for organisms that do not synthesize those amino acids natively.

Proteins are one of the classes of bio-macromolecules, alongside polysaccharides and nucleic acids, that make up the primary constituents of living things. They are amongst the most actively studied molecule in biochemistry and were discovered by Jöns Jacob Berzelius, in 1838.

Proteins are amino acid chains, made up from 20 different L-α-amino acids, also referred to as residues, that fold into unique three-dimensional protein structures. The shape into a which a protein naturally folds is known as its native state, which is determined by its sequence of amino acids. Below about 40 residues the term peptide is frequently used. A certain number of residues is necessary to perform a particular biochemical function, and around 40-50 residues appears to be the lower limit for a functional domain size. Protein sizes range from this lower limit to several hundred residues in multi-functional proteins. Very large aggregates can be formed from protein subunits, for example many thousand actin molecules assemble into a an actin filament. Large protein complexes with RNA are found in the ribosome particles, which are in fact 'ribozymes'.

 Biochemists refer to four distinct aspects of a protein's structure:

Primary structure: the amino acid sequence Secondary structure: highly patterned sub-structures--alpha helix and beta sheet--or segments of chain that assume no stable shape. Secondary structures are locally defined, meaning that there can be many different secondary motifs present in one single protein molecule Tertiary structure: the overall shape of a single protein molecule; the spatial relationship of the secondary structural motifs to one another Quaternary structure: the shape or structure that results from the union of more than one protein molecule, usually called subunit proteins subunits in this context, which function as part of the larger assembly or protein complex. In addition to these levels of structure, proteins may shift between several similar structures in performing of their biological function. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as "conformations," and transitions between them are called conformational changes.

The primary structure is held together by covalent peptide bonds, which are made during the process of translation. The secondary structures are held together by hydrogen bonds. The tertiary structure is held together primarily by hydrophobic interactions but hydrogen bonds, ionic interactions, and disulfide bonds are usually involved too.

The two ends of the amino acid chain are referred to as the carboxy terminus (C-terminus) and the amino terminus (N-terminus) based on the nature of the free group on each extremity.

Two amino acids are combined in a condensation reaction. Notice that the peptide bond is in fact planar due to the delocalization of the electrons. The sequence of the different amino acids is considered the primary structure of the peptide or protein. Counting of residues always starts at the N-terminal end (NH2-group).

Proteins are involved in practically every function performed by a cell, including regulation of cellular functions such as signal transduction and metabolism. For example, protein catabolism requires only a few enzymes termed proteases.

Various molecules and ions are able to bind to specific sites on proteins. These sites are called binding sites. They exhibit chemical specificity. The particle that binds is called a ligand. The strength of ligand-protein binding is a property of the binding site known as affinity.

Since proteins are involved in practically every function performed by a cell, the mechanisms for controlling these functions therefore depend on controlling protein activity. Regulation can involve a protein's shape or concentration. Some forms of regulation include:

Allosteric modulation: When the binding of a ligand at one site on a protein affects the binding of ligand at another site. Covalent modulation: When the covalent modification of a protein affects the binding of a ligand or some other aspect of a the protein's function.

Proteins are generally large molecules, having molecular masses of up to 3,000,000 (the muscle protein titin has a single amino acid chain 27,000 subunits long). Such long chains of amino acids are almost universally referred to as proteins, but shorter strings of amino acids are referred to as "polypeptides," "peptides" or very rarely "oligopeptides". The dividing line is somewhat undefined, although a polypeptide may be less likely to have tertiary structure and may be more likely to act as a hormone (like insulin) rather than as an enzyme or structural element.

Proteins are generally classified as soluble, filamentous or membrane-associated (see integral membrane protein). Nearly all the biological catalysts known as enzymes are proteins. (Certain RNA sequences were shown in the late 20th century to have catalytic properties as well.) Membrane-associated exchangers and ion channels, which move their substrates from place to place but do not change them; receptors, which do not modify their substrates but may simply shift shape upon binding them; and antibodies, which appear to do nothing more than bind, all are proteins as well. h. The filamentous material that makes up the cytoskeleton of cells and much of the structure of animals is also protein: microtubules, actin, intermediate filaments, collagen and keratin are components of skin, hair, and cartilage. Another class are the motor proteins such as myosin, kinesin, and dynein. Muscles are composed largely of the proteins myosin and actin.

Proteins can be picky about the environment in which they are found. They may only exist in their active, or native state, in a small range of pH values and under solution conditions with a minimum quantity of electrolytes, as many proteins will not remain in solution in distilled water. A protein that loses its native state is said to be denatured. Denatured proteins generally have no secondary structure other than random coil. A protein in its native state is often described as folded.

One of the more striking discoveries of the 20th century was that the native and denatured states in many proteins were interconvertible, that by careful control of solution conditions (by for example, dialyzing away a denaturing chemical), a denatured protein could be converted to native form. The issue of how proteins arrive at their native state is an important area of biochemical study, called the study of protein folding.

Through genetic engineering, researchers can alter the sequence and hence the structure, "targeting", susceptibility to regulation and other properties of a protein. The genetic sequences of different proteins may be spliced together to create "chimeric" proteins that possess properties of both. This form of tinkering represents one of the chief tools of cell and molecular biologists to change and to probe the workings of cells. Another area of protein research attempts to engineer proteins with entirely new properties or functions, a field known as protein engineering.

In terms of human nutritional needs, proteins come in two forms: complete proteins contain all eight of the amino acids (Threonine, Valine, Tryptophan, Isoleucine, Leucine, Lysine, Phenylalanine, and Methionine) that humans cannot produce themselves, while incomplete proteins lack or contain only a very small proportion of one or more. Humans' bodies can make use of all the amino acids they extract from food for synthesizing new proteins, but the inessential ones themselves need not be supplied by the diet, because our cells can make them ourselves. When protein is listed on a nutrition label it only refers to the amount of complete proteins in the food, though the food may be very strong in a subset of the essential amino acids. Animal-derived foods contain all of those amino acids, while plants are typically stronger in some acids than others. Complete proteins can be made in an all vegan diet by eating a sufficient variety of foods and by getting enough calories. It was once thought that in order to get the complete proteins vegans needed to do protein combining by getting all amino acids in the same meal (the most common example is eating beans with rice) but nutritionists now know that the benefits of protein combining can be achieved over the longer period of the day. Ovo-lacto vegetarians usually do not have this problem, since egg's white and cow's milk contain all essential amino acids. g, c. Peanuts, soy milk, nuts, seeds, green peas, Legumes, the alga spirulina and some grains are some of the richest sources of plant protein.

All eight essential amino acids must be part of one diet in order to survive and are needed in a fixed ratio. A shortage on any one of these amino acids will constrain the body's ability to make the proteins it needs to function.

Different foods contain different ratios of the essential amino acids. By mixing foods that are rich in some amino acids with foods that are rich in others, one can acquire all the needed amino acids in sufficient quantities. Omnivores typically eat a sufficient variety of foods that this is not an issue, however, vegetarians and especially vegans should be careful to eat appropriate combinations of foods (e.g. nuts and green vegetables) so as to get all the essential amino acids in sufficient quantities that the body may produce all the proteins that it needs.

Protein deficiency can lead to symptoms such as fatigue, insulin resistance, hair loss, loss of hair pigment (hair that should be black becomes reddish), loss of muscle mass (proteins repair muscle tissue), low body temperature, and hormonal irregularities. Severe protein deficiency is fatal.

Excess protein can cause problems as well, such as causing the immune system to overreact, liver dysfunction from increased toxic residues, possibly bone loss due to increased acidity in the blood, and foundering (foot problems) in horses.

Proteins can often figure in allergies and allergic reactions to certain foods. This is because the structure of each form of protein is slightly different, and some may trigger a response from the immune system while others are perfectly safe. Many people are allergic to casein, the protein in milk; gluten, the protein in wheat and other grains; the particular proteins found in peanuts; or those in shellfish or other seafoods. It is extremely unusual for the same person to adversely react to more than two different types of proteins.

A denatured protein is one which has lost its functional shape. Denaturing of Proteins is typically done by a change in pH (such as stomach acid) agitation, etc. An example of a protein that requires a special shape to function is Hemoglobin.

Peptides are the family of molecules formed from the linking, in a defined order, of various amino acids. The link between one amino acid residue and the next is an amide bond, and is sometimes referred to as a peptide bond. An amide bond is somewhat shorter than a typical carbon-nitrogen single bond, and has a partial double-bond character, because the participating carbon molecule is doubly bonded to an oxygen molecule and the nitrogen has a lone pair of electrons available for bonding.

Peptides (like proteins) occur in nature and are responsible for a wide array of functions, many of which are not yet understood. Antimicrobial peptides generally disrupt the membranes of a target cell, causing lysis of the cell. How this occurs, and what determines the activity and selectivity of these peptides, is currently only known approximately. Peptides differ from proteins, which are also long chains of amino acids, by virtue of their size. Traditionally, those peptide chains that are short enough to make synthetically from the constituent amino acids are called peptides rather than proteins. The dividing line is at approximately 50 amino acids in length, since naturally-occurring proteins tend, at their smallest, to be hundreds of residues long. So, in essence, a peptide is a small protein. Peptidomimetics (such as peptoids and β-peptides) are molecules related to peptides, but with different properties. g, a. Prions - short for proteinaceous infectious particle - are infectious self-reproducing protein structures. Though their exact mechanisms of action and reproduction are still unknown, it is now commonly accepted that they are responsible for a number of previously known but little-understood diseases generally classified under transmissible spongiform encephalopathy (TSEs) diseases, including scrapie (a disease of sheep), kuru (found in members of the cannibalistic Foré tribe in Papua New Guinea), and bovine spongiform encephalopathy (mad cow disease). These diseases affect the structure of brain tissue and are all fatal and untreatable.

Prions were first hypothesized in 1982 by Stanley B. Prusiner of UCSF, who was awarded the Nobel Prize in physiology or medicine in 1997 for the discovery. Prusiner formed the word "prion" from a combination of the words "proteinaceous infectious particle".

Prior to Prusiner's insight, all known pathogens (bacteria, viruses, etc.) contained nucleic acids, which enable reproduction. The prion hypothesis was developed to explain why the mysterious infectious agent causing Creutzfeldt-Jakob disease resisted ultraviolet radiation (which breaks down nucleic acids) but responded to agents that disrupt proteins. This hypothesis was originally highly controversial, because it seemed to contradict the "central dogma of modern biology," which asserts that all living organisms use nucleic acids to reproduce. Prusiner's idea that a protein containing no DNA could reproduce itself was initially met with skepticism, but evidence has steadily accumulated in support of the hypothesis, and it is now widely accepted. Rather than contradicting the central role of DNA, however, the prion hypothesis suggests a special and possibly exceptional case in which merely changing the shape of a protein (without changing its amino acid sequence) can alter its biological properties. The actual reproduction of the protein is still carried out by the ribosome, while the infectious form of the prion protein only transfers the pathological conformation to the prions synthesized by the cell.

A breakthrough occurred when researchers discovered that the infectious agent consisted mainly of a specific protein, which Prusiner called PrP (an abbreviation for "prion protein"). This protein is found in the membranes of normal cells (its precise function is not known), but an altered shape distinguished the infectious agent. The normal one is called PrPC, while the infectious one is called PrPSC (the 'C' refers to 'cellular' PrP, while the 'SC' refers to 'scrapie', a prion disease occurring in sheep). It is hypothesized that the distorted protein somehow induces normal PrP structure to also become distorted, producing a chain reaction that both propagates the disease and generates new infectious material. k, a, f.. Since the original hypothesis was proposed, a gene for the PrP protein has been isolated (the PRNP gene), several mutations that cause the variant shape have been identified and successfully cloned, and studies using genetically altered mice have bolstered the prion hypothesis. The evidence in support of the hypothesis is quite strong now, but not incontrovertible.

In Prusiner's second Scientific American article, he proposed a mechanism for prion propagation that does not require direct action of a prion protein on a normal protein. The suggestion there is that both N, the normal protein, and P, the prion protein, are a product of a post-translational metabolic pathway that forks, leading to either N or P. The presence of P has a negative feedback effect on the fork yielding N, so that P causes less and less N to be made, and more and more P. (For the Creutzfeld-Jakob prion PrP, N corresponds to PrPC, and P corresponds to PrPSC.)

Prions appear to be most infectious when in direct contact with affected tissues. For example, Creutzfeldt-Jakob disease has been transmitted to patients taking injections of growth hormone harvested from human pituitary glands, and from instruments used for brain surgery (prions can survive the "autoclave" sterilization process used for most surgical instruments). It is also believed that dietary consumption of affected animals can cause prions to accumulate slowly, especially when cannibalism or similar practices allow the proteins to accumulate over more than one generation. Laws in developed countries now proscribe the use of rendered ruminant proteins in ruminant feed as a precaution against the spread of prion infection in cattle and other ruminants.

The reason prions are not detected by the immune system is that their "safe" form is already present from birth in the body. The only distinction the "dangerous" prions have is that they are folded slightly differently. Prions infect the nerve lining of neural cells, forming an aggregate which ultimately destroys nerve cells. Depending on the area of the brain which they infect the symptoms can be different. For example, infecting the cerebellum causes impairment of movement. Infecting the cerebral cortex results in a decrease in memory and mental agility.

Not all prions are dangerous; in fact, prion-like proteins are found naturally in many (perhaps all) plants and animals. Because of this, scientists reasoned that such proteins could give some sort of evolutionary advantage to their host. This was suggested to be the case in a type of fungus (Podospora anserina). Genetically compatible colonies of this fungus can merge together and share cellular contents such as nutrients and cytoplasm. A natural system of protective "incompatibility" proteins exists to prevent promiscuous sharing between unrelated colonies. One such protein, called HET-S, adopts a prion-like form in order to function properly. e, i. The prion form of HET-S spreads rapidly throughout the cellular network of a colony and can convert the non-prion form of the protein to a prion state after compatible colonies have merged. However, when an incompatible colony tries to merge with a prion-containing colony, the prion causes the "invader" cells to die, insuring that only related colonies obtain the benefit of sharing resources.

Since 1965, researchers working with the yeast Saccharomyces cerevisiae under the guidance of Brian S. Cox had been characterizing a genetic trait with a strange form of inheritance, which they referred to as the [PSI+] element. In 1994, Reed Wickner proposed that [PSI+] and another heritable element, [URE3], were both prions. It was soon noticed that heat shock proteins (which help other proteins fold properly) were intimately tied to the inheritance and transmission of [PSI+] and other yeast prions. Researchers studied how the amino acid sequence contributed to the ability of the PSI protein (Sup35p) to convert between its prion and non-prion state. In certain situations, cells infected with [PSI+] actually fare better than their prion-free siblings; this finding suggests that, in some proteins, the ability to adopt a prion form may result from positive evolutionary selection.

Prions may also be thought of as "'auto-chaperone" proteins. Chaperones are proteins that help fold other proteins into their functional conformations. Since prion proteins act on other molecules of their own kind, they can be considered as self-specific examples of a more general type of chaperone activity.

A typical yeast prion proteins contain a region (protein domain) with many repeats of the amino acids glutamine (Q) and asparagine (N); these Q/N-rich domains form the core of the prion's structure. Ordinarily, prion domains are flexible and lack a defined structure. When they convert to the prion state, several molecules of a particular protein come together to form a highly structured amyloid fiber. The end of the fiber acts as a template for the addition of free protein molecules, causing the fiber to grow. Small differences in the amino acid sequence of prion-forming regions lead to distinct structural features on the surface of prion fibers. d, g, h,. As a result, only free protein molecules that are identical in amino acid sequence to the prion protein can be recruited into the growing fiber. This "specificity" phenomenon may explain why transmission of prion diseases from one species to another (such as from sheep to cows or from cows to humans) is a rare event.

The mammalian prion protein (PrP) does not at all resemble the prion proteins of yeast in its amino acid sequence. Nonetheless, the basic structural features (formation of amyloid fibers and a highly specific barrier to transmission between species) are shared between mammalian and yeast prions. The prion variant responsible for mad cow disease has the remarkable ability to bypass the species barrier to transmission. The accompanying figure shows a model of two conformations of PrP; on the left is the normal, alpha helical form, while on the right is the prion form. Note the increased beta sheet content (green arrows) in the prion version of the molecule.

The neuropathology of the human prion diseases (CJD, GSS, and kuru) is characterised by 4 features: spongiform change, neuronal loss, astrocytosis and amyloid plaque formation. These features are shared with prion diseases in animals, and the recognition of these similarities prompted the first attempts to transmit a human prion disease (kuru) to a primate in 1966, followed by CJD in 1968 and GSS in 1981.

These neuropathological features have formed the basis of the histological diagnosis of human prion diseases for many years, although it was recognised that these changes are enormously variable both from case to case and within the central nervous system in individual cases.

Early neuropathological reports on human prion diseases suffered from a confusion of nomenclature, in which the significance of the diagnostic feature of spongiform change was occasionally overlooked. The subsequent demonstration that human prion diseases were transmissible reinforced the importance of spongiform change as a diagnostic feature, reflected in the use of the term "spongiform encephalopathy" for this group of disorders.

Proteinoids are protein-like molecules formed inorganically from amino acids. Some theories of abiogenesis propose that proteinoids were a precursor to the first living cells.

The inorganic polymerization of amino acids into proteins through the formation of peptide bonds was thought to occur only at temperatures over 140°C. However, the biochemist S. W. Fox and his co-workers discovered that phosphoric acid acted as a catalyst for this reaction. They were able to form protein-like chains from a mixture of 18 common amino acids at only 70°C in the presence of phosphoric acid, and dubbed these protein-like chains protenoids. Fox later found proteinoids similar to those he had created in his laboratory in lava and cinders from Hawaiian volcanic vents and determined that the amino acids present polymerized due to the heat of escaping gases and lava. l, c, k. Other catalysts have since been found; one of them, amidinium carbodiimide, is formed in primitive Earth experiments and is effective in dilute aqueous solutions.

When present in certain concentrations in aqueous solutions, proteinoids form small structures called microspheres or protocells. This is due to the fact that some of the amino acids incorporated into proteinoid chains are more hydrophobic than others, and so proteinoids cluster together like droplets of oil in water.

Protein structure prediction is one of the most significant tasks tackled in computational structural biology. It has the aim of determining the three-dimensional structure of proteins from their amino acid sequences. In more formal terms, this is the prediction of protein tertiary structure from primary structure. Given the usefulness of known protein structures in such valuable tasks as rational drug design, this is a highly active field of research.

Every two years, the performance of current methods is assessed in the CASP experiment.

The practical role of protein structure prediction is now more important than ever. Massive amounts of protein sequence data may be derived from modern large-scale DNA sequencing efforts of, for example, the Human Genome Project. The output of experimentally determined protein structures, typically by time-consuming and relatively expensive X-ray crystallography or NMR spectroscopy, is lagging far behind the output of protein sequences.

A number of factors exist that make protein structure prediction a very difficult task, including:

The number of possible structures that proteins may possess is extremely large, as highlighted by the Levinthal paradox. The physical basis of protein structural stability is not fully understood. The primary sequence may not fully specify the tertiary structure. For example, proteins known as chaperonins have the ability to induce proteins to fold in specific ways. Direct simulation of protein folding via methods such as molecular dynamics is not generally tractable for both practical and theoretical reasons. k, g, d, e. However, the distributed computing project, Folding at home, is tackling such simulation difficulties. Despite the above hinderances, much progress is being made by the many research groups that are interested in the task. Prediction of structures for small proteins is now a perfectly realistic goal. A wide range of approaches are routinely applied for such predictions. These approaches may be classified into two broad classes; de novo modelling and comparative modelling.

De novo- or ab initio- protein modelling methods seek to build three-dimensional protein models "from scratch". There are many possible procedures that either attempt to mimic protein folding or apply some stochastic method to search possible solutions (i.e. global optimization of a suitable energy function). These procedures tend to require vast computational resources, and have thus only been carried out for tiny proteins. To attempt to predict protein structure de novo for larger proteins, we will need better algorithms and larger computational resources like those afforded by either powerful supercomputers (such as Blue Gene) or distributed computing (see Human Proteome Folding Project). Although these computational barriers are vast the potential benifits of structural genomics (by predicted or experimental methods) make de novo structure prediction an active research field.

Comparative protein modelling uses previously solved structures as starting points, or templates. These methods may also be split into two groups:

Homology modelling is based on the reasonable assumption that two homologous proteins will share very similar structures. Given the amino acid sequence of a unknown structure and the solved structure of a homologous protein, each amino acid in the solved structure is mutated, computationally, into the corresponding amino acid from the unknown structure. Protein threading scans the amino acid sequence of an unknown structure against a database of solved structures. In each case, a scoring function is used to assess the compatibility of the sequence to the structure, thus yielding possible three-dimensional models.

Protein targeting includes the mechanisms by which a biological cell transports proteins to the appropriate organelle for insertion into a membrane or secretion to the outside.

In 1970, Günter Blobel conducted experiments on the translocation of proteins across membranes. He was awarded the 1999 Nobel prize for his findings. He discovered that many proteins have a signal sequence, that is, a short amino acid sequence at one end that functions like a postal code for the target organelle. The translation of mRNA into protein by a ribosome takes place within the cytosol. If the synthesized proteins "belong" in a different organelle, they can be transported there in either of two ways, depending on the protein.

Cotranslational translocation The N-terminal signal sequence of the protein is recognized by a signal recognition particle (SRP) while the protein is still being synthesized on the ribosome. The synthesis pauses while the ribosome-protein complex is transferred to an SRP receptor on the endoplasmic reticulum (ER, which is a membrane-bound organelle). There, the nascent protein is inserted into a protein channel that passes through the ER membrane. Within the ER, the protein is first covered by a chaperone protein to protect it from the high concentration of other proteins in the ER, giving it time to fold correctly. h, h, d, h. Once folded, the protein is modified as needed (for example, by glycosylation), then transported into the Golgi apparatus for further processing and sorting. From there, it goes to its target organelle. Upon translocation into that organelle, the signal sequence is removed.

Posttranslational translocation Even though most proteins are cotranslationally translocated, some are translated in the cytosol and later transported to their destination. This occurs for proteins that go to a mitochondrion, a chloroplast, or a peroxisome (proteins that go to the latter have their signal sequence at the C terminus). Also, proteins targeted for the nucleus are translocated post-translation. They pass through the nuclear envelope via nuclear pores.

Transmembrane proteins The amino acid chain of transmembrane proteins, which often are transmembrane receptors, passes through a membrane one or several times. They are inserted into the membrane by translocation, until the process is interrupted by a stop-transfer sequence, also called a membrane anchor sequence.

Sorting of proteins to mitochondria Most mitochondrial proteins are synthesized as cytosolic precursors containing uptake peptide signals.

Mitochondrial matrix targeting sequences are rich in positively charged amino acids and hydroxylated ones.

Proteins are targeted to submitochondrial compartments by multiple signals and several pathways.

Targeting to the outer membrane, intermembrane space, and inner membrane often requires another signal sequence in addition to the matrix targeting sequence.

Cytosolic chaperones deliver proteins to chanel linked receptors in the mitochondrial membrane.

Sorting of proteins to peroxisomes All peroxisomal proteins are encoded by nuclear genes.

The signal for uptake into the peroxisomal matrix is SKL (serine-lysine-leucine).

Diseases Peroxisomal protein transport is defective in the following genetic diseases:

Zellweger syndrome. Adrenoleukodystrophy (ADR). Receptor-mediated endocytosis Several molecules that attach to special receptors called coated pits on the outside of cells cause the cell to perform endocytosis, an invagination of the plasma membrane to incorporate the molecule and associated structures into endosomes. This mechanism is used for three main purposes:

Uptake of essential metabolites, for example, LDL. Uptake of some hormones and growth factors, for example, epidermal growth factor and nerve growth factor. Uptake of proteins that are to be destroyed, for example, antigens in phagocytotic cells like macrophages. Receptor-mediated endocytosis can also be "abused":

Some viruses, for example, the Semliki forest virus, enter the cell through this mechanism. Cholera and diphtheria toxins also enter the cell this way. Protein destruction Defective proteins are occasionally produced, or they may be damaged later, for example, by oxidative stress. Damaged proteins can be recycled. Proteins can have very different half lives, mainly depending on their N-terminal amino acid residue. The recycling mechanism is mediated by ubiquitin.

Protein targeting in bacteria Bacteria do not have organelles they can send proteins to, but some proteins are incorporated into the plasma membrane or secreted into the environment. The basic mechanism is similar to the eukaryotic one. b, g, b, l. A secretory pathway is a term used to describe different methods that cells use to transport material from the Golgi apparatus to the outside. There are two different pathways: constitutive and regulated.

Constitutive In constitutive secretion, proteins are packaged in vesicles in the Golgi apparatus and are secreted immediately via exocytosis, all around the cell. They secrete continuously and unlike the regulated pathway, no external signal is needed to stimulate the process. Cells that secrete constitutively have many Golgi apparatus scattered throughout the cytoplasm. Fibroblasts, osteoblasts and chondrocytes are some of the many cells that use this pathway.

Regulated In regulated secretion, proteins are packaged as described in the constitutive pathway, but they are only secreted in response to a specific signal, such as neural or hormonal stimulation. Cells that use the regulated secretory pathway are usually apical or polarized. The Golgi apparatus are found in a supranuclear position (between the nucleus and the secretory surface). Example cells that use regulated pathway are: goblet cells (secrete mucus), beta cells of the pancreas (secrete insulin) and odontoblasts (secrete dentin).

The term proteome was first used in 1995 and has been applied to several different types of biological systems. A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation. It can also be useful to consider an organism's complete proteome. The complete proteome for an organism can be conceptualized as the complete set of proteins from all of the various cellular proteomes. This is very roughly the protein equivalent of the genome. The term "proteome" has also been used to refer to the collection of proteins in certain sub-cellular biological systems. For example, all of the proteins in a virus can be called a viral proteome.

The proteome is larger than the genome, expecially in eukaryotes, in the sense there are more proteins than genes. This is due to alternative splicing of genes and post-translational modifications like glycosylation or phosphorylation.

Moreover the proteome has at least two levels of complexity lacking in the genome. When the genome is defined by the sequence of nucleotides, the proteome cannot be limited to the sum of the sequences of the proteins present. Knowledge of the proteome requires knowledge of (1) the structure of the proteins in the proteome and (2) the functional interaction between the proteins.

Proteomics, the study of the proteome, has largely been practiced through the separation of proteins by two dimensional gel electrophoresis. In the first dimension, the proteins are separated by isoelectric focusing, which resolves proteins on the basis of charge. In the second dimension, proteins are separated by molecular weight using SDS-PAGE. The gel is dyed with Coomassie Blue or silver to visualize the proteins. Spots on the gel are proteins that have migrated to specific locations.

The mass spectrometer has augmented proteomics. Mass mapping identifies a protein by cleaving it into short peptides and then deduces the protein's identity by matching the observed peptide masses against a sequence database. Tandem mass spectrometry, on the other hand, can get sequence information from individual peptides by isolating them, colliding them with a nonreactive gas, and then cataloging the fragment ions produced.

Proteomics is the large-scale study of proteins, particularly their structures and functions. This term was coined to make an analogy with genomics, and is often viewed as the "next step", but proteomics is much more complicated than genomics. a, h, c, c. Most importantly, while the genome is a rather constant entity, the proteome is constantly changing through its biochemical interactions with the genome. One organism will have radically different protein expression in different parts of its body and in different stages of its life cycle.

The entirety of proteins in existence in an organism throughout its life cycle, or on a smaller scale the entirety of proteins found in a particular cell type under a particular type of stimulation, are referred to as the proteome of the organism or cell type respectively.

With completion of a rough draft of the human genome, many researchers are now looking at how genes and proteins interact to form other proteins. A surprising finding of the Human Genome Project is that there are far fewer genes that code for proteins in the human genome than there are proteins in the human proteome (~22,000 genes vs ~200,000 proteins). The large increase in protein diversity is thought to be due to post-translational modification of proteins.

To catalogue all human proteins and ascertain their functions and interactions presents a daunting challenge for scientists. An international collaboration to achieve these goals is being co-ordinated by the Human Proteome Organisation (HUPO (http://www.hupo.org)).

Key technologies for proteomics: 1-D electrophoresis and 2-D electrophoresis are for the separation and visualisation of proteins. To identify and characterise proteins mass spectrometry, X-ray crystallography, and NMR are used. To characterise protein-protein interactions, a number of chromatography techniques are used especially affinity chromatography. Protein expression systems like the yeast two-hybrid and fluorescence resonance energy transfer (FRET) can also be used to characterise protein-protein interactions.

A ribosome is an organelle composed of rRNA (synthesized in the nucleolus) and ribosomal proteins. It translates mRNA into a polypeptide chain (e.g., a protein). It can be thought of as a factory that builds a protein from a set of genetic instructions. Ribosomes can float freely in the cytoplasm (the internal fluid of the cell) or bind to another organelle called the endoplasmic reticulum. Since ribosomes are ribozymes, it is thought that they might be remnants of the RNA world.

Ribosomes consist of two subunits that fit together and work as one to translate the mRNA into a polypeptide chain during protein synthesis. Each subunit consists of one or two very large RNA molecules (known as ribosomal RNA or rRNA) and multiple smaller protein molecules. k, b, e. Experiments have shown that the rRNA are the crucial components in protein synthesis, and that one aspect of the process, peptide transfer, can occur in the presence of rRNA alone, albeit at a slower rate. This suggests that the protein components of ribosomes act as a scaffold that may enhance the ability of rRNA to synthesise protein.

The structure and function of ribosomes, and their attendant molecules, known as the translational apparatus, has been of ongoing research interest since the mid 20th century on through the early 21st century. A triennial conference is held to discuss the ribosome. In 1999, the conference was held in Elsinore, Denmark.

Proteins are highly complex molecules comprised of linked amino acids. Amino acids are simple compounds containing carbon, hydrogen, oxygen, nitrogen and occasionally sulphur. There are about 20 different amino acids commonly found in plant and animal proteins. Amino acids link together to form chains called peptides. A typical protein may contain 500 or more amino acids. Each protein has it's own unique number and sequence of amino acids which determines it's particular structure and function. Proteins are broken down into their constituent amino acids during digestion which are then absorbed and used to make new proteins in the body. Certain amino acids can be made by the human body. However, the essential amino acids cannot be made and so they must be supplied in the diet. The eight essential amino acids required by humans are: leucine, isoleucine, valine, threonine, methionine, phenylalanine, tryptophan, and lysine. For children, histidine is also considered to be an essential amino acid.

Proteins are essential for growth and repair. They play a crucial role in virtually all biological processes in the body. All enzymes are proteins and are vital for the body's metabolism. Muscle contraction, immune protection, and the transmission of nerve impulses are all dependent on proteins. Proteins in skin and bone provide structural support. Many hormones are proteins. Protein can also provide a source of energy. Generally the body uses carbohydrate and fat for energy but when there is excess dietary protein or inadequate dietary fat and carbohydrate, protein is used. Excess protein may also be converted to fat and stored.

Translation is the RNA directed synthesis of polypeptides. This process requires all three classes of RNA. Although the chemistry of peptide bond formation is relatively simple, the processes leading to the ability to form a peptide bond are exceedingly complex. The template for correct addition of individual amino acids is the mRNA, yet both tRNAs and rRNAs are involved in the process. The tRNAs carry activated amino acids into the ribosome which is composed of rRNA and ribosomal proteins. The ribosome is associated with the mRNA ensuring correct access of activated tRNAs and containing the necessary enzymatic activities to catalyze peptide bond formation.

Are Plant Proteins Second Class Citizens? No, certainly not! Nutritionists once believed that plant proteins were of a poorer quality than animal proteins. And even now plant proteins are sometimes called 'second class' proteins whilst animal proteins are elevated to the 'first class' department. This belief centred on early research on the poor laboratory rat which showed that giving extra amino acids of weanling rats reared on a plant-protein diet improved their growth. The same was assumed to be true for humans. However, the parameters of the experiments were set in such a way that differences in the quality of plant and animal proteins were exaggerated. Also, rats and humans have different nutritional requirements, since weanling rats grow at a much faster rate, relatively, than human infants and therefore need more protein. A comparison of rat and human milk makes the difference quite clear: protein comprises only 7% of the calorie content of human milk, while rat milk contains 20% protein. If weanling rats were fed only human milk, they would not thrive. These tests over-estimated the value of some animal proteins while under-estimating the value of some vegetable proteins and The World Health Organisation has now abandoned this inadequate method of assessing the value of proteins to the human body.

Protein Combining - Is It Necessary? No, it really isn't necessary! Research on laboratory rats also led to the misleading theory of protein combining. [2] Protein combining has unfortunately gained momentum over the years. It was based on the idea that complementary protein foods with different limiting amino acids, such as beans and grains, should be eaten at each meal in order to enhance the availability of amino acids.

Proteins in foods have a distinctive pattern, being higher in some amino acids and lower in others. For many years the quality of a protein reflected its amino acid pattern and was measured against the protein in a hen's egg which counted as 100%. By this method, in each protein the amino acid furthest below the standard reference is known as the limiting amino acid. This is not necessarily the one present in the lowest absolute amount but the one present in the lowest proportion compared to protein in a hen's egg! In most grains and seeds, the limiting amino acid is lysine, while in most pulses it is methionine. Tryptophan is the limiting amino acid in corn (maize), and in beef it is methionine. Although each food has a limiting amino acid, most foods have all amino acids in adequate amounts for human health.

Even vegetarians are sometimes advised to combine vegetable proteins with dairy foods. This advice is now very old fashioned. Protein combining may reduce the amount of protein required to keep the body in positive protein balance but several human studies have indicated that this is neither necessary nor even always the case. Diets based solely on plant foods easily supply the recommended amounts of all the indispensable amino acids, and protein combining at each meal is unnecessary. Soya protein is actually equivalent in biological value to animal protein.

Protein - Too Much of a Good Thing? Studies show that vegan diets provide the ideal amounts of protein recommended by the World Health Organisation and by the UK's Department of Health. On the other hand, many omnivores eat more protein than guidelines recommend and this may have disadvantages for their health. Excessive protein consumption may be associated with health risks. Kidney function can be compromised by too much protein in older people and in patients with kidney disease; also, a high protein intake may adversely affect calcium balance and contribute to mineral loss from bone. The Office of Population Censuses and Surveys 1990 survey of British adults [3] showed that average protein intakes are 84g/day for men and 64g/day for women which are higher than recommended,

Different types of dietary protein may have differing effects on cholesterol and fats in the bloodstream. Greater hormonal responses resulted in a meal derived from casein (milk) than from soya beans. This suggests that milk protein leads to higher levels of cholesterol and fats in the blood. These, in turn, are risk factors for coronary heart disease.

A survey of 620 women in Singapore revealed that, among pre-menopausal women, those who regularly ate soya protein and soya products in general had about half the normal risk of developing breast cancer. In contrast, the consumption of red meat and animal protein was linked with an increased risk of breast cancer in pre-menopausal women.

Diets rich in meat protein lead to more uric acid in the urine, and a general increase in urine acidity. because of the acidity, the uric acid does not easily dissolve and can form into kidney stones.

Protein is a part of every cell of your body. It is a major structural component of all cells: skin, hair, nails and bone. It is the necessary raw material from which your body makes the enzymes critical for functioning, from digestion to reproduction. It is necessary for the production of neurotransmitters which affect your mind and mood. Protein (with fat) is the base material of the immune system. Without protein there is no life. You cannot make protein. It must be consumed every day in sufficient quantities to replace daily losses.

Protein foods also contain fat and/or carbohydrate. Beans and grains are protein/carbohydrate (glycoproteins) combinations. Because these glycoproteins are lectins do make sure to read the lectin review . Meat, fish, poultry and eggs are protein/fat combos as are nuts and seeds. When choosing proteins keep the fat/protein ratio in mind and be a label reader. Use a food value table when necessary until you get used to estimating. Meat, as wild game, tends to be lean and contain significant amounts of omega-3 polyunsaturated fatty acids. Nuts and seeds and some fish are high in fat but these fats are easily used by the body for energy and the manufacture of other essential substances. The type of fat in natural protein, from animals and fish NOT fed grain, is higher in the omega 3 fatty acids which are precursors to the anti-inflammatory prostaglandins. Avoid high fat grain fed meats and farmed fish.

High protein foods may be 'chewy' and 'dry'. An easy way to guesstimate fat content is by texture. Fat gives a creamy or juicy texture. Proteins are naturally dry and chewy when cooked by methods other than boiling or slow roasting. Fats become more liquid with heat. Proteins become drier and tougher. Use moisture to keep low fat protein foods palatable. Salsa works as does cooking in a small amount of wine and/or water. Using proteins in soups and stews, steaming and slow cooking keep proteins moist and tender, making them more digestible. Do not overcook proteins.

Bacon, hot dogs, 'lunch meats' and such would not be considered good sources of protein. They are high fat, high salt, chemically-preserved foods.

Vegetarians and even 'raw food' vegans can get sufficient protein but they must consume much larger quantities of food to get adequate amounts.

Total grams per ounce and the essentiality of the amino acids in the protein equal the quality or value of the protein source. Beans and rice are fine. Just count the grams. Early in protein research there was some concern about needing to combine proteins so that all essential proteins were available at each meal. Later research has determined that this is not necessary. While all essential amino acids are needed they do not have to been eaten together. A 'real food' diet with variable protein sources will usually cover all essential amino acids.

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