Describe the Nature, Structure, and Function of Domains in Proteins
Domains
"Within a single subunit [polypeptide chain], contiguous portions of the polypeptide chain frequently fold into compact, local semi-independent units called domains." - Richardson, 1981
In the hierarchial organisation of proteins, domains are found at the highest level of tertiary structure. Since the term was first used by Wetlaufer (1973) a number of definitions exist reflecting author bias, however all of the definitions agree that domains are independently folding compact units. Domains are frequently coded by exons and therefore have specific functionality. Among the many descriptions of protein domains the two most striking and simple are " Protein evolutionary units" and "Basic currency of Proteins".
Domains may be considered to be connected units, which are to varying extents independent in terms of their structure, function and folding behaviour. Each domain can be described by its fold. While some proteins consist of a single domain, others consist of several or many. A number of globular protein chains consist of two or three domains appearing as 'lobes'. In other cases the domains may be of very different nature- for example some proteins located in cell membranes have a globular intracellular or extracellular domain distinct from that which spans the membrane.
Protein domains occur in large polypeptides, (proteins that have more than 200 residues). These proteins have two or more globular clusters which in turn have domains composed of 100-200 amino acids. Thus many domains are structurally independent units that have the characteristics of small globular proteins.
If we examine the detailed structures of many transmembrane proteins, we see that they often have three different domains, two hydrophilic and one hydrophobic .(fig 1&2) A hydrophilic domain (consisting of hydrophilic amino acids) at the N-terminus pokes out in the extracellular medium, a hydrophobic domain in the middle of the amino acid chain, often only 20-30 amino acids long, is threaded through the plasma membrane, and a hydrophilic domain at the C-terminus protrudes into the cytoplasm. The transmembrane domain, because it is made of amino acids having hydrophobic side chains, exists comfortably in the hydrophobic inner layers of the plasma membrane. Because these transmembrane domains anchor many proteins in the lipid bilayer, these proteins are not free-floating and cannot be isolated and purified biochemically without first dissolving away the lipid bilayer with detergents. (Indeed, much of the washing we do in our lives is necessitated by the need to solubilize proteins that are embedded in lipid membranes using detergents!)
The primary structure is the sequence of amino acids that make up a polypeptide chain. 20 different amino acids are found in proteins. The exact order of the amino acids in a specific protein is the primary sequence for that protein. [IMAGE] [IMAGE]Protein secondary structure refers to regular, repeated patterns of folding of the protein backbone. The two most common folding patterns are the alpha helix and the beta sheet.
called an active site. This active site is made by a few of the amino
This occurs when special carrier proteins carry solutes dissolved in the water across the membrane by using active transport. When the concentration gradient can not allow travel from one side of the membrane to the other fast enough for the cell’s nutritional needs, then facilitated diffusion is used. The transport protein is specialized for the solute it is carrying, just as enzymes are specialized for their substrate. The transport protein can be
(A) A monomer showing the central α-helix flanked by N-terminal and C-terminal regions. (B) Dimer of two monomers are coiled coil with a length of 48nm. (C) Assembly of antiparallel dimers forming a staggered tetramer. (D) Two tetramers are linked together. (E) The 10nm-intermediate filament is composed of twisted eight tetramers. Figure adapted from Alberts et al., 2008).
The direction of osmosis depends on the relative concentration of the solutes on the two sides. In osmosis, water can travel in three different ways. If the molecules outside the cell are lower than the concentration in the cytosol, the solution is said to be hypotonic to the cytosol, in this process, water diffuses into the cell until equilibrium is established. If the molecules outside the cell are higher than the concentration in the cytosol, the solution is said to be hypertonic to the cytosol, in this process, water diffuses out of the cell until equilibrium exists. If the molecules outside and inside the cell are equal, the solution is said to be isotonic to the cytosol, in this process, water diffuses into and out of the cell at equal rates, causing no net movement of water. In osmosis the cell is selectively permeable, meaning that it only allows certain substances to be transferred into and out of the cell. In osmosis, the proteins only on the surface are called peripheral proteins, which form carbohydrate chains whose purpose is used like antennae for communication. Embedded in the peripheral proteins are integral
The cell plasma membrane, a bilayer structure composed mainly of phospholipids, is characterized by its fluidity. Membrane fluidity, as well as being affected by lipid and protein composition and temperature (Purdy et al. 2005), is regulated by its cholesterol concentration (Harby 2001, McLaurin 2002). Cholesterol is a special type of lipid, known as a steroid, formed by a polar OH headgroup and a single hydrocarbon tail (Wikipedia 2005, Diwan 2005). Like its fellow membrane lipids, cholesterol arranges itself in the same direction; its polar head is lined up with the polar headgroups of the phospholipid molecules (Spurger 2002). The stiffening and decreasing permeability of the bilayer that results from including cholesterol occurs due to its placement; the short, rigid molecules fit neatly into the gaps between phospholipids left due to the bends in their hydrocarbon tails (Alberts et al. 2004). Increased fluidity of the bilayer is a result of these bends or kinks affecting how closely the phospholipids can pack together (Alberts et al. 2004). Consequently, adding cholesterol molecules into the gaps between them disrupts the close packing of the phospholipids, resulting in the decreased membrane fluidity (Yehuda et al. 2002).
its original shape and shape. Within the phospholipid bi-layer there are proteins, and these. proteins are made up of polypeptide chains which are joined together. by hydrogen, hydrophobic and peptide bonds. Once the temperature has increased above 40°C the molecules vibrate so energetically that these bonds break easily and therefore create holes within the cell wall.
Myoglobin consist of single polypeptide chain that made up of 153 amino acid and ahs a size of 18 kDa. Its three-dimensional structure was first determined by X-ray crystallography by John Kendrew in 1957. Myoglobin is a typical globular protein in that it is a highly folded compact structure with most of the hydrophobic amino acid residues buried in the interior and many of the polar residues on the surface. X-ray crystallography revealed that the single polypeptide chain of myoglobin consist of entirely of eight (labelled A-H) alpha-helical. Within a hydrophobic crevice formed by the folding polypeptide chain is the heme prosthetic group. This nonopolypepetide unit is noncovalently bound to myoglobin and is essential for the biological activity of the protein.
In the secondary structure, the conformations of the proteins or amino acid chain depend on the hydrogen bonding between the molecules. Two main types of secondary structures are α-helices and the ß-sheets. In Cx26, the amino acid sequence forms into a α-helical domains. In the Cx26 protein there is also another secondary structure called 310 helix.
n.d. - n.d. Peptides and Proteins. Proteins. Retrieved July 25, 2008, from http://www.cd http://www.cem.msu.edu/reusch/VirtualText/protein2.htm Ophardt, C. E. (2003).
plasma membranes, meaning animals and plants contain lipids. In this paper I will display and
Each protein is a large complex molecule; these molecules are made up of. of a string of amino acids. There are 20 different amino acids that occur naturally to form proteins and they all have the same basic structure. The. The 20 amino acids the body needs can be linked in.
There are many functions lipids have. One of the main functions lipids are structural components in the cell. Lipids make up approximately 50% of the mass of most cell membranes. The lipids that are found in the cell membrane are called phospholipid. Phospholipid are the predominant lipids of cell membrane. Phospholipids aggregate or self-assemble when mixed with water, but in a different manner than the soaps and detergents. Because of the two pendant alkyl chains in phospholipids and the unusual mixed charges in their head groups, micelle formation is unfavorable relative to a bilayer structure.
A polypeptide chain is a series of amino acids that are joined by the peptide bonds. Each amino acid in a polypeptide chain is called a residue. It also has polarity because its ends are different. The backbone or main chain is the part of the polypeptide chain that is made up of a regularly repeating part and is rich with the potential for hydrogen-bonding. There is also a variable part, which comprises the distinct side chain. Each residue of the chain has a carbonyl group, which is good hydrogen-bond acceptor, and an NH group, which is a good hydrogen-bond donor. The groups interact with the functional groups of the side chains and each other to stabilize structures. Proteins are polypeptide chains that have 500 to 2,000 amino acid residues. Oligopeptides, or peptides, are made up of small numbers of amino acids. Each protein has a precisely defined, unique amino acid sequence, referred to as its primary structure. The amino acid sequences of proteins are determined by the nucleotide sequences of genes because nucleotides in DNA specify a complimentary sequence in RNA, which specifies the amino acid sequence. Amino acid sequences determine the 3D structures of proteins. An alteration in the amino acid sequence can produce disease and abnormal function. All of the different ways
There are four main levels of a protein, which make up its native conformation. The first level, primary structure, is just the basic order of all the amino acids. The amino acids are held together by strong peptide bonds. The next level of protein organization is the secondary structure. This is where the primary structure is repeated folded so that it takes up less space. There are two types of folding, the first of which is beta-pleated sheets, where the primary structure would resemble continuous spikes forming a horizontal strip. The seco...