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Protein structure
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Interactive diagram of protein structure, using PCNA as an example. (PDB: 1AXC)
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers – specifically polypeptides – formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer may also be called a residue indicating a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond. By convention, a chain under 30 amino acids is often identified as a peptide, rather than a protein.[1] To be able to perform their biological function, proteins fold into one or more specific spatial conformations driven by a number of non-covalent interactions such as hydrogen bonding, ionic interactions, Van der Waals forces, and hydrophobic packing. To understand the functions of proteins at a molecular level, it is often necessary to determine their three-dimensional structure. This is the topic of the scientific field of structural biology, which employs techniques such as X-ray crystallography, NMR spectroscopy, and dual polarisation interferometry to determine the structure of proteins.
Protein structures range in size from tens to several thousand amino acids.[2] By physical size, proteins are classified as nanoparticles, between 1–100 nm. Very large aggregates can be formed from protein subunits. For example, many thousands of actin molecules assemble into a microfilament.
A protein generally undergo reversible structural changes in performing its biological function. The alternative structures of the same protein are referred to as different conformational isomers, or simply, conformations, and transitions between them are called conformational changes.
Contents
1 Levels of protein structure
1.1 Primary structure
1.2 Secondary structure
1.3 Tertiary structure
1.4 Quaternary structure
2 Domains, motifs, and folds in protein structure
2.1 Structural domain
2.2 Structural and sequence motif
2.3 Supersecondary structure
2.4 Protein fold
2.5 Superdomain
3 Protein folding
4 Protein stability
5 Protein structure determination
5.1 Protein Sequence Analysis: Ensembles
6 Protein structure databases
7 Structure classification
8 Computational prediction of protein structure
9 See also
10 References
11 Further reading
12 External links
Levels of protein structure[edit]
There are four distinct levels of protein structure.
Primary structure[edit]
Main article: Protein primary structure
The primary structure of a protein refers to the sequence of amino acids in the polypeptide chain. The primary structure is held together by peptide bonds that are made during the process of protein biosynthesis. The two ends of the polypeptide chain are referred to as the carboxyl terminus (C-terminus) and the amino terminus (N-terminus) based on the nature of the free group on each extremity. Counting of residues always starts at the N-terminal end (NH2-group), which is the end where the amino group is not involved in a peptide bond. The primary structure of a protein is determined by the gene corresponding to the protein. A specific sequence of nucleotides in DNA is transcribed into mRNA, which is read by the ribosome in a process called translation. The sequence of amino acids in insulin was discovered by Frederick Sanger, establishing that proteins have defining amino acid sequences.[3][4] The sequence of a protein is unique to that protein, and defines the structure and function of the protein. The sequence of a protein can be determined by methods such as Edman degradation or tandem mass spectrometry. Often, however, it is read directly from the sequence of the gene using the genetic code. It is strictly recommended to use the words "amino acid residues" when discussing proteins because when a peptide bond is formed, a water molecule is lost, and therefore proteins are made up of amino acid residues. Post-translational modification such as disulfide bond formation, phosphorylations and glycosylations are usually also considered a part of the primary structure, and cannot be read from the gene. For example, insulin is composed of 51 amino acids in 2 chains. One chain has 31 amino acids, and the other has 20 amino acids.
Secondary structure[edit]
An α-helix with hydrogen bonds (yellow dots)
Main article: Protein secondary structure
Secondary structure refers to highly regular local sub-structures on the actual polypeptide backbone chain. Two main types of secondary structure, the α-helix and the β-strand or β-sheets, were suggested in 1951 by Linus Pauling and coworkers.[5] These secondary structures are defined by patterns of hydrogen bonds between the main-chain peptide groups. They have a regular geometry, being constrained to specific values of the dihedral angles ψ and φ on the Ramachandran plot. Both the α-helix and the β-sheet represent a way of saturating all the hydrogen bond donors and acceptors in the peptide backbone. Some parts of the protein are ordered but do not form any regular structures. They should not be confused with random coil, an unfolded polypeptide chain lacking any fixed three-dimensional structure. Several sequential secondary structures may form a "supersecondary unit".[6]
Tertiary structure[edit]
Main article: Protein tertiary structure
Tertiary structure refers to the three-dimensional structure of monomeric and multimeric protein molecules. The α-helixes and β-pleated-sheets are folded into a compact globular structure. The folding is driven by the non-specific hydrophobic interactions, the burial of hydrophobic residues from water, but the structure is stable only when the parts of a protein domain are locked into place by specific tertiary interactions, such as salt bridges, hydrogen bonds, and the tight packing of side chains and disulfide bonds. The disulfide bonds are extremely rare in cytosolic proteins, since the cytosol (intracellular fluid) is generally a reducing environment.
Quaternary structure[edit]
Main article: Protein quaternary structure
Quaternary structure is the three-dimensional structure consisting of the aggregation of two or more individual polypeptide chains (subunits) that operate as a single functional unit (multimer). The resulting multimer is stabilized by the same non-covalent interactions and disulfide bonds as in tertiary structure. There are many possible quaternary structure organisations.[7] Complexes of two or more polypeptides (i.e. multiple subunits) are called multimers. Specifically it would be called a dimer if it contains two subunits, a trimer if it contains three subunits, a tetramer if it contains four subunits, and a pentamer if it contains five subunits. The subunits are frequently related to one another by symmetry operations, such as a 2-fold axis in a dimer. Multimers made up of identical subunits are referred to with a prefix of "homo-" (e.g. a homotetramer) and those made up of different subunits are referred to with a prefix of "hetero-", for example, a heterotetramer, such as the two alpha and two beta chains of hemoglobin.
Domains, motifs, and folds in protein structure[edit]
Protein domains. The two shown protein structures share a common domain (maroon), the PH domain, which is involved in phosphatidylinositol (3,4,5)-trisphosphate binding
Proteins are frequently described as consisting of several structural units. These units include domains, motifs, and folds. Despite the fact that there are about 100,000 different proteins expressed in eukaryotic systems, there are many fewer different domains, structural motifs and folds.
Structural domain[edit]
A structural domain is an element of the protein's overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. Many domains are not unique to the protein products of one gene or one gene family but instead appear in a variety of proteins. Domains often are named and singled out because they figure prominently in the biological function of the protein they belong to; for example, the "calcium-binding domain of calmodulin". Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimera proteins.
Structural and sequence motif[edit]
The structural and sequence motifs refer to short segments of protein three-dimensional structure or amino acid sequence that were found in a large number of different proteins.
Supersecondary structure[edit]
The supersecondary structure refers to a specific combination of secondary structure elements, such as β-α-β units or a helix-turn-helix motif. Some of them may be also referred to as structural motifs.
Protein fold[edit]
A protein fold refers to the general protein architecture, like a helix bundle, β-barrel, Rossman fold or different "folds" provided in the Structural Classification of Proteins database.[8] A related concept is protein topology that refers to the arrangement of contacts within the protein.
Superdomain[edit]
A superdomain consists of two or more nominally unrelated structural domains that are inherited as a single unit and occur in different proteins.[9] An example is provided by the protein tyrosine phosphatase domain and C2 domain pair in PTEN, several tensin proteins, auxilin and proteins in plants and fungi. The PTP-C2 superdomain evidently came into existence prior to the divergence of fungi, plants and animals is therefore likely to be about 1.5 billion years old.
Protein folding[edit]
Main article: Protein folding
As it is translated, polypeptides exit the ribosome as a random coil and folds into its native state.[10][11] Since the fold is determined by a network of interactions between amino acids in the polypeptide, the final structure of the protein chain is determined by its amino acid sequence (Anfinsen's dogma).[12]
Protein stability[edit]
Protein stability depends upon a few factors such as 1) Non-covalent electrostatic interactions 2) Hydrophobic interactions These interaction energies are from the order of 20-40 kJ/mol.[citation needed] Proteins are very sensitive to changing temperatures and a change in temperature may result in unfolding or denaturation. Protein denaturation may result in loss of function, and loss of native state.
X-ray crystallography and calorimetry indicates that there is no general mechanism that describes the effect of temperature change on the functions and structure of proteins. This is due to the fact that proteins do not represent a uniform class of chemical entities from an energetic point of view. The structure and stability of an individual protein depends on the ratio of its polar and non-polar residues. They contribute to the conformational and the net enthalpies of local and non-local interactions.
Taking the weak intermolecular interactions responsible for structural integrity into consideration, it is hard to predict the effects of temperature because there are too many unknown factors contributing to the hypothetical free energy balance and its temperature dependence. Internal salt linkages produce thermal stability, and whether cold temperature results in the destabilization of these linkages is unknown.
In principle, the free energy of stabilization of soluble globular proteins does not exceed 50-100 kJ/mol.[citation needed] The stabilization is based on the equivalent of few hydrogen bonds, ion pairs, or hydrophobic interactions, even though numerous intramolecular interactions results in stabilization. Taking into consideration the large number of hydrogen bonds that take place for the stabilization of secondary structures, and the stabilization of the inner core through hydrophobic interactions, the free energy of stabilization emerges as small difference between large numbers. Therefore, the structure of a native protein is not optimized for the maximum stability.[13]
Protein structure determination[edit]
Examples of protein structures from the PDB
Rate of Protein Structure Determination by Method and Year
Around 90% of the protein structures available in the Protein Data Bank have been determined by X-ray crystallography.[14] This method allows one to measure the three-dimensional (3-D) density distribution of electrons in the protein, in the crystallized state, and thereby infer the 3-D coordinates of all the atoms to be determined to a certain resolution. Roughly 9% of the known protein structures have been obtained by nuclear magnetic resonance (NMR) techniques.[citation needed] For larger protein complexes, cryo-electron microscopy can determine protein structures. The resolution is typically lower than that of X-ray crystallography, or NMR, but the maximum resolution is steadily increasing. This technique is still a particularly valuable for very large protein complexes such as virus coat proteins and amyloid fibers.
General secondary structure composition can be determined via circular dichroism. Vibrational spectroscopy can also be used to characterize the conformation of peptides, polypeptides, and proteins.[15] Two-dimensional infrared spectroscopy has become a valuable method to investigate the structures of flexible peptides and proteins that cannot be studied with other methods.[16][17] A more qualitative picture of protein structure is often obtained by proteolysis, which is also useful to screen for more crystallizable protein samples. Novel implementations of this approach, including fast parallel proteolysis (FASTpp), can probe the structured fraction and its stability without the need for purification.[18] Once a protein's structure has been experimentally determined, further detailed studies can be done computationally, using molecular dynamic simulations of that structure.[19]
Protein Sequence Analysis: Ensembles[edit]
Schematic view of the two main ensemble modeling approaches.[20]
Proteins are often thought of as relatively stable structures that have a set tertiary structure and experience conformational changes as a result of being modified by other proteins or as part of enzymatic activity. However proteins have varying degrees of stability and some of the less stable variants are intrinsically disordered proteins. These proteins exist and function in a relatively 'disordered' state lacking a stable tertiary structure. As a result, they are difficult to describe in a standard protein structure model that was designed for proteins with a fixed tertiary structure. Conformational ensembles have been devised as a way to provide a more accurate and 'dynamic' representation of the conformational state of intrinsically disordered proteins. Conformational ensembles function by attempting to represent the various conformations of intrinsically disordered proteins within an ensemble file (the type found at the Protein Ensemble Database).
Protein ensemble files are a representation of a protein that can be considered to have a flexible structure. Creating these files requires determining which of the various theoretically possible protein conformations actually exist. One approach is to apply computational algorithms to the protein data in order to try to determine the most likely set of conformations for an ensemble file.
There are multiple methods for preparing data for the Protein Ensemble Database that fall into two general methodologies – pool and molecular dynamics (MD) approaches (diagrammed in the figure). The pool based approach uses the protein’s amino acid sequence to create a massive pool of random conformations. This pool is then subjected to more computational processing that creates a set of theoretical parameters for each conformation based on the structure. Conformational subsets from this pool whose average theoretical parameters closely match known experimental data for this protein are selected.[20]
The molecular dynamics approach takes multiple random conformations at a time and subjects all of them to experimental data. Here the experimental data is serving as limitations to be placed on the conformations (e.g. known distances between atoms). Only conformations that manage to remain within the limits set by the experimental data are accepted. This approach often applies large amounts of experimental data to the conformations which is a very computationally demanding task.[20]
Protein
Data Type
Protocol
PED ID
References
Sic1/Cdc4 NMR and SAXS Pool-based PED9AAA [21]
p15 PAF NMR and SAXS Pool-based PED6AAA [22]
MKK7 NMR Pool-based PED5AAB [23]
Beta-synuclein NMR MD-based PED1AAD [24]
P27 KID NMR MD-based PED2AAA [25]
(adapted from image in "Computational approaches for inferring the functions of intrinsically disordered proteins"[20])
Protein structure databases[edit]
Protein structure database is a database that is modeled around the various experimentally determined protein structures. The aim of most protein structure databases is to organize and annotate the protein structures, providing the biological community access to the experimental data in a useful way. Data included in protein structure databases often includes 3D coordinates as well as experimental information, such as unit cell dimensions and angles for x-ray crystallography determined structures. Though most instances, in this case either proteins or a specific structure determinations of a protein, also contain sequence information and some databases even provide means for performing sequence based queries, the primary attribute of a structure database is structural information, whereas sequence databases focus on sequence information, and contain no structural information for the majority of entries. Protein structure databases are critical for many efforts in computational biology such as structure based drug design, both in developing the computational methods used and in providing a large experimental dataset used by some methods to provide insights about the function of a protein.[26]
Structure classification[edit]
Protein structures can be grouped based on their similarity or a common evolutionary origin. The Structural Classification of Proteins database[27] and CATH database[28] provide two different structural classifications of proteins. Shared structure between proteins is considered evidence of evolutionary relatedness between proteins and is used group proteins together into protein superfamilies.[29]
Computational prediction of protein structure[edit]
Main article: Protein structure prediction
The generation of a protein sequence is much easier than the determination of a protein structure. However, the structure of a protein gives much more insight in the function of the protein than its sequence. Therefore, a number of methods for the computational prediction of protein structure from its sequence have been developed.[30] Ab initio prediction methods use just the sequence of the protein. Threading and homology modeling methods can build a 3-D model for a protein of unknown structure from experimental structures of evolutionarily-related proteins, called a protein family.
See also[edit]
3did
Biomolecular structure
Gene structure
Nucleic acid structure
Z-matrix conversion from Torsion angles to Cartesian coordinates
References[edit]
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Further reading[edit]
50 Years of Protein Structure Determination Timeline - HTML Version - National Institute of General Medical Sciences at NIH
External links[edit]
Media related to Protein structures at Wikimedia Commons
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Reuben sandwich
From Wikipedia, the free encyclopedia
Jump to navigation Jump to search
Reuben sandwich
Reuben from Katz's Delicatessen
Type
Sandwich
Course
Main course
Place of origin
United States
Created by
Various claims
Serving temperature
Warm/Hot
Main ingredients
Corned beef
Sauerkraut
Swiss cheese
Rye bread
Russian Dressing
Cookbook: Reuben sandwich Media: Reuben sandwich
The Reuben sandwich is an American hot sandwich composed of corned beef, Swiss cheese, sauerkraut, and Russian dressing, grilled between slices of rye bread.
Contents
1 Possible origins
1.1 Reuben Kulakofsky, Blackstone Hotel: Omaha, Nebraska
1.2 Reuben's Delicatessen: New York City
2 Variations
2.1 Montreal Reuben
2.2 Thousand Island dressing
2.3 Walleye Reuben
2.4 Grouper Reuben
2.5 Reuben egg rolls
2.6 Rachel sandwich
2.7 Vegetarian versions
3 See also
4 References
5 Further reading
Possible origins[edit]
Reuben Kulakofsky, Blackstone Hotel: Omaha, Nebraska[edit]
One origin story holds that Reuben Kulakofsky (his first name sometimes spelled Reubin; his last name sometimes shortened to Kay), a Jewish Lithuanian-born grocer residing in Omaha, Nebraska, was the inventor, perhaps as part of a group effort by members of Kulakofsky's weekly poker game held in the Blackstone Hotel from around 1920 through 1935. The participants, who nicknamed themselves "the committee", included the hotel's owner, Charles Schimmel. The sandwich first gained local fame when Schimmel put it on the Blackstone's lunch menu, and its fame spread when a former employee of the hotel won a national contest with the recipe.[1] In Omaha, March 14 was proclaimed as Reuben Sandwich Day.[2]
Reuben's Delicatessen: New York City[edit]
Another account holds that the Reuben's creator was Arnold Reuben, the German-Jewish owner of the famed Reuben's Delicatessen (1908–2001) in New York City. According to an interview with Craig Claiborne, Arnold Reuben invented the "Reuben Special" around 1914.[3][4] The earliest references in print to the sandwich are New York–based, but that is not conclusive evidence, though the fact that the earliest, in a 1926 issue of Theatre Magazine, references a "Reuben Special", does seem to take its cue from Arnold Reuben's menu.
A variation of the above account is related by Bernard Sobel in his 1953 book, Broadway Heartbeat: Memoirs of a Press Agent. Sobel states that the sandwich was an extemporaneous creation for Marjorie Rambeau inaugurated when the famed Broadway actress visited the Reuben's Delicatessen one night when the cupboards were particularly bare.[5]
Some sources[who?] name the actress in the above account as Annette Seelos, not Marjorie Rambeau, while also noting that the original "Reuben Special" sandwich of 1926 did not contain corned beef or sauerkraut and was not grilled.
Still other versions give credit to Alfred Scheuing, a chef at Reuben's Delicatessen, and say he created the sandwich for Reuben's son, Arnold Jr., in the 1930s.[1]
Variations[edit]
Corned beef Reuben sandwich
Montreal Reuben[edit]
The Montreal Reuben substitutes Montreal-style smoked meat for corned beef.[6]
Thousand Island dressing[edit]
Thousand Island dressing is commonly used as a substitute for Russian dressing.[citation needed]
Walleye Reuben[edit]
The Walleye Reuben is a version of the classic that features the Minnesota state fish, the walleye, Sander vitreus, in place of the corned beef. It is eaten in Minnesota and Ohio.[7][8][9]
Grouper Reuben[edit]
The grouper Reuben is a variation on the standard Reuben sandwich, substituting grouper for the corned beef, and sometimes will substitute coleslaw for the sauerkraut as well. This variation is often a menu item in restaurants in Florida.[10]
Reuben egg rolls[edit]
Reuben egg rolls, sometimes called "Irish egg rolls" or "Reuben balls", use the standard Reuben sandwich filling of corned beef, sauerkraut, and cheese inside a deep-fried egg roll wrapper. Typically served with Thousand Island dressing (instead of Russian dressing) as an appetizer or snack, they originated at Mader's, a German restaurant in Milwaukee, Wisconsin, where chef Dennis Wegner created them for a summer festival in about 1990.[11]
Rachel sandwich[edit]
The Rachel sandwich is a variation on the standard Reuben sandwich, substituting pastrami for the corned beef, and coleslaw for the sauerkraut.[12] Other recipes for the Rachel call for turkey instead of pastrami.[13][14] In some parts of the United States, especially Michigan, this turkey variant is known as a "Georgia Reuben" or "California Reuben", and it may also call for barbecue sauce or French dressing instead of Russian dressing.
Vegetarian versions[edit]
Vegetarian versions, called "veggie reubens", omit the corned beef or substitute vegetarian ingredients for it, including zucchini, cucumbers,[15] wheatmeat,[16] mushrooms,[17] etc.
See also[edit]
Food portal
Sloppy joe (New Jersey)
List of American sandwiches
List of sandwiches
Pastrami on rye
References[edit]
^ Jump up to: a b Rader, Jim. "The Reuben Sandwich". Reuben Realm.
Jump up ^ Griswold, Jennifer. "Today is Proclaimed Reuben Sandwich Day". KMTV. Archived from the original on 2015-03-15.
Jump up ^ Jared Ingersoll (2006). "Toasted Reuben sandwich". Danks Street Depot. Murdoch Books. p. 115. ISBN 9781740455985.
Jump up ^ Craig Claiborne. The New York Times Food Encyclopedia. See also Arnold Reuben interview, American Life Histories: Manuscripts from the Federal Writers' Project, 1936–1940, quoted on What's cooking America site.
Jump up ^ Sobel, Bernard (1953). "Broadway Heartbeat: Memoirs of a Press Agent". New York City: Hermitage House: 233. OCLC 1514676.
Jump up ^ "Montreal Corned Beef Reuben Sandwich", The Gazette
Jump up ^ Minneapolis, Town Ball Tavern 1 Twins Way; MN. "Walleye Reuben @ Town Ball Tavern".
Jump up ^ Otis, Ginger Adams (September 6, 2015). "Ohio proves to be a great destination for a history- and fun-loving family". New York Daily News.
Jump up ^ Deptolla, Carol (May 17, 2012). "Chez Ballpark: What's good to eat at Miller Park". Milwaukee Journal Sentinel. For the homestand against the Minnesota Twins this weekend, look for walleye Reuben sandwiches, for $9.25.
Jump up ^ Calloway, Karin (September 21, 2010). "Takeoff on Reuben sandwich makes tasty meal". The Augusta Chronicle. Retrieved February 2, 2011. In Florida … many restaurants serve a grouper Reuben
Jump up ^ Zeldes, Leah A. (March 10, 2010). "Irish' food in Chicago isn't quite so in Ireland: Who played a role in the reuben egg roll?". Chicago Sun-Times. Archived from the original on April 13, 2010. Retrieved March 15, 2010.
Jump up ^ Mary-Lane Kamberg (2004). "Grilled Reuben sandwich variation: Grilled Rachel sandwich". The I Don't Know How to Cook Book: 300 Great Recipes You Can't Mess Up. Adams Media. p. 42. ISBN 9781593370091.
Jump up ^ Popik, Barry (November 13, 2004). "Reuben Sandwich (and Rachel Sandwich, Celebrity Sandwiches)". The Big Apple. Retrieved November 2, 2013.
Jump up ^ Rombauer, Irma S.; Becker, Marion Rombauer; Becker, Ethan (2006). "Reuben Sandwich". Joy of Cooking (75th Anniversary ed.). Scribner. p. 181. ISBN 978-0-7432-4626-2. For a Rachel, substitute turkey for the corned beef.
Jump up ^ Better Homes and Gardens, Cooking for Two, p. 82
Jump up ^ Joy Nicholson, "Reubenesque", Los Angeles Magazine September, 2001, p. 52
Jump up ^ Cameron Woodworth, Green Cuisine, p. 25
Further reading[edit]
Wikimedia Commons has media related to Reuben sandwiches.
Wikibooks Cookbook has a recipe/module on
Reuben Sandwich
Claiborne, Craig (May 17, 1976). "DE GUSTIBUS; Whence the Reuben? Omaha, It Seems". The New York Times. p. 24 (Family/Style section).
McMorris, Robert (September 11, 1965). "Omaha Saw Invention of Reuben Sandwich". The Omaha Evening World-Herald.
McMorris, Robert (January 31, 1986). "Just When You Thought Reuben's Roots Were Safe". The Omaha World-Herald. p. 2.
McMorris, Robert (July 24, 1989). "This Reuben Explanation Seems Hard to Swallow". The Omaha World-Herald. p. 2.
Weil, Elizabeth (June 7, 2013). "My Grandfather Invented the Reuben Sandwich. Right? The Midnight Lunch Special". The New York Times.
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