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WALP Peptide
WALP peptides are a class of synthesized, membrane-spanning α-helices composed of tryptophan (W), alanine (A), and leucine (L) amino acids. They are designed to study properties of proteins in lipid membranes such as orientation, extent of insertion, and hydrophobic mismatch. Significance The transmembrane region of many integral membrane proteins consists of one or more alpha helices. The orientations and interactions of these helices directly affect cell signaling and molecular transport across the bilayer. The hydrophobic environment of the phospholipid tails in turn modulates the position and structure of such domains and thus may influence protein function. Conversely, the bilayer itself can (locally) change the thickness of its hydrocarbon region to interact optimally with hydrophobic regions of a transmembrane protein (a.k.a. hydrophobic matching). WALPs provide an effective model for studying such interactions because of their systematic design of a core of hydrophobic, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Alpha Helix
The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues earlier along the protein sequence. The alpha helix is also called a classic Pauling–Corey–Branson α-helix. The name 3.613-helix is also used for this type of helix, denoting the average number of residues per helical turn, with 13 atoms being involved in the ring formed by the hydrogen bond. Among types of local structure in proteins, the α-helix is the most extreme and the most predictable from sequence, as well as the most prevalent. Discovery In the early 1930s, William Astbury showed that there were drastic changes in the X-ray fiber diffraction of moist wool or hair fibers upon significant stretching. The data suggested that the unstretched fibers had a coiled molecular structure with a characteristic repeat of ≈. Astb ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tryptophan
Tryptophan (symbol Trp or W) is an α-amino acid that is used in the biosynthesis of proteins. Tryptophan contains an α-amino group, an α- carboxylic acid group, and a side chain indole, making it a polar molecule with a non-polar aromatic beta carbon substituent. It is essential in humans, meaning that the body cannot synthesize it and it must be obtained from the diet. Tryptophan is also a precursor to the neurotransmitter serotonin, the hormone melatonin, and vitamin B3. It is encoded by the codon UGG. Like other amino acids, tryptophan is a zwitterion at physiological pH where the amino group is protonated (–; pKa = 9.39) and the carboxylic acid is deprotonated ( –COO−; pKa = 2.38). Humans and many animals cannot synthesize tryptophan: they need to obtain it through their diet, making it an essential amino acid. Function Amino acids, including tryptophan, are used as building blocks in protein biosynthesis, and proteins are required to sustain life. Man ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Alanine
Alanine (symbol Ala or A), or α-alanine, is an α-amino acid that is used in the biosynthesis of proteins. It contains an amine group and a carboxylic acid group, both attached to the central carbon atom which also carries a methyl group side chain. Consequently, its IUPAC systematic name is 2-aminopropanoic acid, and it is classified as a nonpolar, aliphatic α-amino acid. Under biological conditions, it exists in its zwitterionic form with its amine group protonated (as −NH3+) and its carboxyl group deprotonated (as −CO2−). It is non-essential to humans as it can be synthesised metabolically and does not need to be present in the diet. It is encoded by all codons starting with GC (GCU, GCC, GCA, and GCG). The L-isomer of alanine (left-handed) is the one that is incorporated into proteins. L-alanine is second only to leucine in rate of occurrence, accounting for 7.8% of the primary structure in a sample of 1,150 proteins. The right-handed form, D-alanine, occurs in p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Leucine
Leucine (symbol Leu or L) is an essential amino acid that is used in the biosynthesis of proteins. Leucine is an α-amino acid, meaning it contains an α-amino group (which is in the protonated −NH3+ form under biological conditions), an α- carboxylic acid group (which is in the deprotonated −COO− form under biological conditions), and a side chain isobutyl group, making it a non-polar aliphatic amino acid. It is essential in humans, meaning the body cannot synthesize it: it must be obtained from the diet. Human dietary sources are foods that contain protein, such as meats, dairy products, soy products, and beans and other legumes. It is encoded by the codons UUA, UUG, CUU, CUC, CUA, and CUG. Like valine and isoleucine, leucine is a branched-chain amino acid. The primary metabolic end products of leucine metabolism are acetyl-CoA and acetoacetate; consequently, it is one of the two exclusively ketogenic amino acids, with lysine being the other. It is the most import ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrophobic Mismatch
Hydrophobic mismatch is the difference between the thicknesses of hydrophobic regions of a transmembrane protein and of the biological membrane it spans. In order to avoid unfavorable exposure of hydrophobic surfaces to water, the hydrophobic regions of transmembrane proteins are expected to have approximately the same thickness as the hydrophobic (lipid acyl chain) region of the surrounding lipid bilayer. Nevertheless, the same membrane protein can be encountered in bilayers of different thickness. In eukaryotic cells, the plasma membrane is thicker than the membranes of the endoplasmic reticulum. Yet all proteins that are abundant in the plasma membrane are initially integrated into the endoplasmic reticulum upon synthesis on ribosomes. Transmembrane peptides or proteins and surrounding lipids can adapt to the hydrophobic mismatch by different means. Possible adaptations to mismatch In order to avoid unfavorable exposure of hydrophobic surfaces to a hydrophilic environment, b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transmembrane
A transmembrane protein (TP) is a type of integral membrane protein that spans the entirety of the cell membrane. Many transmembrane proteins function as gateways to permit the transport of specific substances across the membrane. They frequently undergo significant conformational changes to move a substance through the membrane. They are usually highly hydrophobic and aggregate and precipitate in water. They require detergents or nonpolar solvents for extraction, although some of them (beta-barrels) can be also extracted using denaturing agents. The peptide sequence that spans the membrane, or the transmembrane segment, is largely hydrophobic and can be visualized using the hydropathy plot. Depending on the number of transmembrane segments, transmembrane proteins can be classified as single-span (or bitopic) or multi-span (polytopic). Some other integral membrane proteins are called monotopic, meaning that they are also permanently attached to the membrane, but do not pass ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Biology
Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has foundations in applied mathematics, chemistry, and genetics. It differs from biological computing, a subfield of computer engineering which uses bioengineering to build computers. History Bioinformatics, the analysis of informatics processes in biological systems, began in the early 1970s. At this time, research in artificial intelligence was using network models of the human brain in order to generate new algorithms. This use of biological data pushed biological researchers to use computers to evaluate and compare large data sets in their own field. By 1982, researchers shared information via punch cards. The amount of data grew exponentially by the end of the 1980s, requiring new computational methods for quickly interpreting ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Peptides
Peptides (, ) are short chains of amino acids linked by peptide bonds. Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. A polypeptide is a longer, continuous, unbranched peptide chain. Hence, peptides fall under the broad chemical classes of biological polymers and oligomers, alongside nucleic acids, oligosaccharides, polysaccharides, and others. A polypeptide that contains more than approximately 50 amino acids is known as a protein. Proteins consist of one or more polypeptides arranged in a biologically functional way, often bound to ligands such as coenzymes and cofactors, or to another protein or other macromolecule such as DNA or RNA, or to complex macromolecular assemblies. Amino acids that have been incorporated into peptides are termed residues. A water molecule is released during formation of each amide bond.. All peptides except cyclic peptides ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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