A protein"s major structure is defined as the amino acid sequence that its polypeptide chain; an additional structure is the neighborhood spatial plan of a polypeptide"s backbone (main chain) atoms; tertiary structure describes the three-dimensional framework of an entire polypeptide chain; and quaternary structure is the three-dimensional arrangement of the subunits in a multisubunit protein. In this series of pages we study the various levels the protein organization. We likewise view structures in numerous ways -- Cα backbone, ball-and-stick, CPK, ribbon, spacefilling -- as well color is provided to to mark different elements of the amino acids, structure, etc. As you traverse despite this module please note these aspects.

You are watching: Match each definition and example to the level of protein structure.

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This module has links to KiNG (Kinemage, following Generation), which screens three-dimensional structures in one animated, interactive format. This "kinemages" (kinetic images) deserve to be rotated, moved, and zooneurosoup.org, and also parts deserve to be surprise or shown. Kinemages were originally applied under the auspices that the Innovative an innovation Fund and also the Protein Society, and the programming and also maintenance space done by David C. Richardson and also Jane S. Richardson.

Reference: "THE KINEMAGE: A device FOR clinical COMMUNICATION" D.C. Richardson and also J.S. Richardson (1992) Protein Science 1: 3-9. Additionally Trends in Biochem. Sci. (1994) 19: 135-8.

Text adjusted from: Demo5_4a.kin

Primary structure (1˚)

The main structure that a peptide or protein is the direct sequence the its amino mountain (AAs). By convention, the major structure that a protein is read and written indigenous the amino-terminal (N) to the carboxyl-terminal (C) end. Every amino mountain is associated to the following by a peptide bond.

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Secondary structure (2˚) -- Alpha Helices

While major structure describes the succession of amino acids developing a peptide chain, secondary structure refers to the local setup of the chain in space. Several common second structures have actually been established in proteins. These will be described in the complying with sections and also visualized making use of the KiNG software pointed out previously.

To pack the KiNG Java Applet, simply click here. Top top loading this page, the KiNG Java Applet should instantly spawn. If friend need details on using King, please float here.

The Alpha Helix

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an alpha helix is an facet of secondary structure in i m sorry the amino acid chain is arranged in a spiral. The kinemage linked over shows an separation, personal, instance alpha helix, viewed from the N-terminal finish to resemble the "helical wheel" (see number below). The O and also N atoms of the helix main chain are shown as red and blue balls, respectively. The non-integral, 3.6-residue-per-turn repeat of the alpha helix method that the Cα"s of succeeding turns are about halfway offset, offering the main chain a distinctive 7-pointed star appearance in end view. Notice that the Cα-Cβ bonds execute not allude out radially from the helix axis however "pinwheel" follow me the heat of one of the adjacent peptides, offering the side chains one asymmetrical start.

The hydrophobic next chains are displayed in seagreen, polar ones in skyblue, and charged ones in red. These can be rotate on by clicking the checkbox labeling "side ch". Currently TURN ON and also OFF the various screen groups and sets, by clicking in the proper button box.

When you clicked the various sidechain species on, what did girlfriend observe? walk you notification that the helix has actually one next with largely polar residues, and also the other with largely hydrophobic residues?. This is a common globular-protein helix; in its native configuration, the polar residues would confront the solvent when the hydrophobic residues would confront the protein interior. In the view food selection in KiNG, pick View2 or View3 come see much more of the structure.

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The figure to the left reflects a helical wheel depiction of one amino acid sequence, as if looking under the axis of an alpha helix that is perpendicular to the page. The amino mountain residues space numbered from nearest to most distant and are arranged as an ideal alpha helix v 3.6 residual water per complete turn. This number is a snaphot the a Java Applet composed by Edward K. O"Neil and Charles M. Grisham (University that Virginia in Charlottesville, Virginia).

In KiNG, pick View4 because that a close-up native the side, v the helical hydrogen binding (H-bonds) in brown. Turn on "Hbonds" on the switch panel, to see the H-bonds in brown. Click backbone atom at either end of one of the H-bonds, come verify that the alpha-helical H-bond pattern does without doubt go indigenous a donor NH at residue ns to an agree O at residue i-4 (as shown in the figure to the right). Check to watch if this alpha helix has 3.6 residues every turn. If you were to mesure, the climb of a full turn is 5.4 Angstroms (Â).

Alpha helices are practically all right-handed. To watch that this one is righthanded, host your best hand v the ignorance pointing up and the finger loosely curled; do the efforts to match the spiral the the helix, move progressively along the direction your thumb points and curl follow me the heat of her fingers, together though tightening a screw. Once that movement matches the backbone spiral if done with the ideal hand, then the helix is righthanded.

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To measure up phi,psi angle for the KiNG example helix, rotate on "Measure edge & dihedral" ~ above the "Tools" pulldown menu. Begin by clicking a carbonyl C atom close to the top, climate the next N, then the Cα, and then a C again; at that allude the details line will show a dihedral angle that is the phi angle of the main N-Cα bond of those 4 atoms. For a righthanded alpha-helix, it should be in the selection of -50 come -80 degrees. Click the next N and also you will obtain the psi angle, which have to be between -25 and -60 degrees. Proceed down the helix backbone, gaining omega (near 180 degrees), phi, psi, etc. This helical phi,psi values are in the well-populated area in the lower left of the Ramachandran plot (shown on the right).

In summary, the appropriate alpha helix has actually the following properties:

It completes one revolve every 3.6 residues;It rises about 5.4 Â v each turn;It is a right-handed helix;It is hosted together through hydrogen bonds in between the C=O the residue i and the NH the residue i+4;It is typically slightly curved.

Some general properties the alpha-helices:

An typical alpha-helix is 10 residues long (15 Â in length), return alpha-helices can selection between 4 to 40 residues in length in a conventional globular protein.All residues participating in one alpha-helix have comparable (phi,psi) angles. These angles, which are roughly -60 and also -50, are from the bottom left quadrant of the Ramachandran plot.Some amino mountain are wanted in one alpha-helix. Residual water such as Ala, Glu, Leu and also Met have actually a high tendency to get involved in a helix , while residues such as Pro and Gly have a tiny such tendency. Of distinct interest is Proline, which can not fit into a helix, and also introduces a kink.The helix has an in its entirety dipole moment, which is a vector sum of the to adjust dipole moments of the separation, personal, instance peptide bonds. The confident pole is at the N-terminus and the an adverse pole is in ~ the C-terminus. Periodically this dipole has actually a practical role.

Some text adjusted from: Kinemage complement to Branden & Tooze "Introduction come Protein Structure", chapter 2 - MOTIFS the PROTEIN structure by woman S. And also David C. Richardson.

Secondary framework (2˚) -- Beta Strands

A beta strand is an aspect of an additional structure in i m sorry the protein chain is practically linear. Adjacent beta strands can hydrogen bond to kind a beta sheet (also referred to as a beta pleated sheet). The participating beta strands space not consistent in the major sequence, and also do not also have to it is in close to each various other in the sequence, i.e. The strands creating a beta sheet can be separated in primary structure by long sequences of amino mountain that room not part of the sheet. About a 4 minutes 1 of all residues in a usual protein are in beta strands, despite this different greatly in between proteins

To see a beta sheet in the KiNG Java Applet, click here. Kinemage 1 reflects the 6-stranded parallel beta sheet from domain 1 of lactate dehydrogenase (file 1LDM). This doubly-wound parallel beta paper is the most typical folding pattern uncovered in recognized protein structures. This "fold" is also known as the "nucleotide-binding domain", due to the fact that most examples bind a mononucleotide (such together FMN) or a dinucleotide (such together NAD) close to the center of one end of the beta sheet. Lactate dehydrogenase is the classic, first-seen instance of this form of structure and also has the many frequently-observed topology of beta connections.

Notice the the H-bonds in this parallel shet are slanted in alternate directions, fairly than perpendicular to the strands as we will see in antiparallel sheets. Drag ideal or left to better see the the sheet as a totality twists. This twist is usually described by the twist in orientation that the peptide airplane (or H-bond plane) together one progresses along the strand; by this an interpretation beta paper twist is constantly right-handed, although by varying amounts. Click atoms follow me a strand to tell its direction from the residue numbers, and also satisfy yourself the all 6 strands are certainly parallel. The strand labels show strand succession order. Keep in mind that most sequential bag are next to each other, and also that the chain beginning in the middle, moves to one edge, skips earlier to the middle and also then moves the end to the other edge.There are three possible ways to type a beta sheet from beta strands, questioned below.

Types the Beta Sheets it was observed in Proteins

1) Parallel beta paper - every bonded strands have actually the very same N come C direction. Together a result they have to be be separated by lengthy sequence stretches. The hydrogen bonds are equally distanced.

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The number to the left shows a three-stranded parallel beta paper from the protein thioredoxin. The 3 parallel strands are shown in both cartoon style (left) and in stick type containing backbone atom N, CA, C, and O" (right). Hydrogen binding are established by arrows connecting the donor nitrogen and also acceptor oxygens. Strands space numbered follow to their relative position in the polypeptide sequence.

2) Antiparallel beta sheet - The beta strands operation in alternating directions and therefore can be rather close top top the primary sequence. The distance in between successive hydrogen binding alternates between much shorter and longer.

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The figure to the right shows a three-stranded antiparallel beta sheet from thioredoxin. The 3 antiparallel strands are shown in both cartoon format (left) and in stick type containing backbone atom N, CA, C, and also O" (right). Hydrogen binding are figured out by arrows connecting the donor nitrogen and also acceptor oxygens. Strands are numbered according to your relative place in the polypeptide sequence.

3) combined beta paper - a mixture the parallel and also antiparallel hydrogen bonding. Around 20% of every beta sheets are mixed.

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Hydrogen bond patterns in a combined beta paper (figure to the left). Right here a four-stranded beta paper containing 3 antiparallel strands and one parallel strand is attracted schematically. Hydrogen bonds between antiparallel strands are indicated with red lines, those between parallel strands with green lines.

Some the the main functions of beta sheets include:

The extended conformation in a beta strand is about 3.5 Â per residue, and also beta strands have the right to be expanded as lot as 35 Â in length.The as whole geometry the a sheet is not planar but rather is pleated, with alternative Cα carbons above and below the average aircraft of the sheet.Due come the chirality the the amino mountain (L amino acids) every beta strands have actually a right-handed twist, conversely, a beta sheet has actually an as whole left-handed twist.Since the strands do not have to be surrounding on the succession there are many possible ways to arrange strands in a sheet, this arrangements are called topologies and also can be fairly complicated.

Turn top top the side chains in KiNG to research their arrangment. Follow me a given strand the sidechains alternative between one next of the paper (gold) and the other (sea or sky). On nearby strands the alternation is in register, so the the side chains kind rows that room in fairly close contact. Top top parallel beta sheet, the geometry is such that sidechains through branched beta-carbons (Val, Ile, or Thr) make quite favorable call along a row; since these positions space usually buried and also hydrophobic, the result is the Val and Ile room the dominant residues found in this positions. The leaf strands, or the really ends the a offered strand, can be exposed to solvent and also often have actually significantly more hydrophilic residual water (as, because that instance, in row 0 here, or the Ser on strand 3).

Some text adjusted from: "The Protein Tourist: DOUBLY-WOUND PARALLEL ALPHA/BETA PROTEINS, OR NUCLEOTIDE-BINDING DOMAINS" through J.S. Richardson and D.C. Richardson.

Secondary structure (2˚) -- Beta Turns and also Random Coils

The Beta Turn

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Turns generally occur as soon as the protein chain demands to adjust direction in bespeak to attach two other elements of secondary structure. The most common is the beta turn, in i beg your pardon the change of direction is executed in the space of 4 residues. Some frequently observed features of beta turns space a hydrogen bond between the C=O the residue i and also the N-H the residue i+3 (i.e, in between the an initial and the 4th residue that the turn) and a solid tendency come involve glycine and/or proline. You will sometimes hear the phrase "beta hairpin" which deserve to be supplied to explain a beta rotate joining two anti-parallel beta strands together. Beta turns room subdivided right into numerous varieties on the basis of the details of their geometry.

Gamma turns are three-residue turns which often incorporate a hydrogen bond between the C=O of residue i and the N-H of residue i+2.

Random Coil

Some areas of the protein chain perform not form regular an additional structure and also are not identified by any regular hydrogen bonding pattern. These areas are known as arbitrarily coils and also are found in two locations in proteins:

Terminal eight - both in ~ the N-terminus and also the C-terminus the the protein;Loops - Loops room unstructured regions found between regular secondary structure elements.

Random coils can be 4 come 20 residues long, although many loops room not longer than 12 residues. Most loops are exposed come the solvent and are have actually polar or fee side-chains. In some instances loops have a useful role, however in many instances they do not. Together a result, loop regions are frequently poorly conserved (i.e. Much more prone come change) during evolution.

Some text adapted from: "EXERCISE 3. PROTEIN secondary STRUCTURES" through Kim M. Gernert and Kim M. Kitzler.

Propensity of AAs to kind Secondary Structures

As we have learned, the bespeak of the AAs is the primary structure and also all residues in a polypeptide chain have actually the very same main-chain atoms. What vary room the next chains (R groups). Carry out the particular AAs current dictate the second structure? As presented in the figure, all amino acids have the right to be found in all second structure elements, yet some are more or less usual in details elements. Pro and Gly, for isntance, aren"t great in helices but are favored in beta-turns. If we take this a action further and also ask whether 2, 3, or 4 amino mountain combinations dictate an additional structure we discover a stronger correlation, but still not solid enough to reliably suspect tertiary structure.

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Tertiary (3˚) Structure

Proteins are numerous in every organisms and are basic to life. The diversity the protein framework underlies the very huge range of their functions: enzyme (biological catalysts), storage, transport, messengers, antibodies, regulation, and structural proteins.

Proteins are linear heteropolymers of solved length; i.e. A single type of protein constantly has the exact same number and composition of AAs, however different protein may have 100 to much more than 1000 AAs. There is thus a an excellent diversity of possible protein sequences. The direct chains fold into particular three-dimensional conformations, which are identified by the succession of amino acids and therefore are additionally extremely diverse, varying from fully fibrous to globular. Covalent disulfide bonds have the right to be introduced between cysteine residues placed in nearby proximity in 3D space -- this gives rigidity because that the result 3D structure. Ribbon diagrams favor the one shown here space a common method to visualize proteins.

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Protein structures deserve to be identified to an atom level through X-ray diffraction and neutron-diffraction researches of crystallized proteins, and much more recently by nuclear magnetic resonance (NMR) spectroscopy of protein in solution. The frameworks of many proteins, however, continue to be undetermined.

To view an instance of tertiary structure in KiNG, click here. This is ribonuclease A, an enzyme responsible because that the destruction of RNA. The picture depicts every atoms of one fifty percent of the molecule (cyan for side chains, brown because that hydrogen atoms) and just key chain and also side chains because that the various other half. The alternate view reflects main-chain atoms and also H-bonds (purple). Click "Animate" to cycle between the views.

Although hydrogens constitute about half the atom in a protein, they space seldom presented explicitly since they are hard to detect with x-ray crystallography (due to low electron density) and they very much complicated the picture. This ribonuclease picture is a joint x-ray/neutron diffraction structure, because that which hydrogens are constantly included. Also without H atoms, one all-atom check out is as well crowded come be really useful however is a great way to evaluate where simplified versions start from.

Some text adjusted from: Kinemage complement to Branden & Tooze "Introduction to Protein Structure", thing 2 - MOTIFS the PROTEIN STRUCTURE, woman S. And David C. Richardson.

Protein Folding

Protein urgent is the physical process by which a linear polypeptide folds into its characteristic and also functional three-dimensional structure. Urgently of a polypeptide chain is strongly influenced by the solubility the the AA R-groups in water. Every protein exists together an unravelled polypeptide or arbitrarily coil when analyzed from a succession of mRNA come a straight chain that amino acids. This polypeptide lacks any stable (long-lasting) three-dimensional framework (the left hand side of the neighboring figure). Amino acids interact with each various other to develop a well-defined three-dimensional structure, the folded protein (the best hand side of the figure), well-known as the indigenous state. All the info for the aboriginal fold shows up therefore to be contained within the primary structure (Anfinsen got the Nobel Prize for this), and proteins are self-folding (although in vivo, polypeptide folding is regularly assisted additional molecules recognized as molecular chaperones).

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Minimizing the variety of hydrophobic side-chains exposed come water (the hydrophobic effect) is vital driving force behind the urgent process. Intramolecular hydrogen bonds also contribute come protein security (think of their prominence in secondary structures). Ionic interactions (attraction in between unlike electric charges of ionized R-groups) additionally contribute come the stability of tertiary structures. Disulfide bridges (covalent bonds) between neighboring cysteine residues can additionally stabilize three-dimensional structures. Keep in mind that disulfide bonds are rarely observed in intracellular proteins due to the fact that of the reduce intracellular environment.

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The exactly 3D framework of a protein is crucial to its function, return some parts of functional proteins might remain unfolded. Failure to wrinkles into native structure generally produces inactive proteins, yet in part instances misfolded proteins have modified or toxic use (think prions & amyloid fibrils). Regular with their functional importance, three-dimensional frameworks of protein are an ext conserved throughout evolution time than room the major amino-acid sequences.

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