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Protein Topology
Protein topology is a property of protein molecule that does not change under deformation (without cutting or breaking a bond). Frameworks Two main topology frameworks have been developed and applied to protein molecules. Knot Theory Knot theory which categorises chain entanglements. The usage of knot theory is limited to a small percentage of proteins as most of them are unknot. Circuit topology Circuit topology categorises intra-chain contacts based on their arrangements. Circuit topology is a determinant of protein folding kinetics and stability. Other Uses In biology literature, the term topology is also used to refer to mutual orientation of regular secondary structures, such as alpha-helices and beta strands in protein structure For example, two adjacent interacting alpha-helices or beta-s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Anthrax Toxin Protein Key Motif
Anthrax is an infection caused by the bacterium ''Bacillus anthracis'' or ''Bacillus cereus'' biovar ''anthracis''. Infection typically occurs by contact with the skin, inhalation, or intestinal absorption. Symptom onset occurs between one day and more than two months after the infection is contracted. The skin form presents with a small blister with surrounding swelling that often turns into a painless ulcer with a black center. The inhalation form presents with fever, chest pain, and shortness of breath. The intestinal form presents with diarrhea (which may contain blood), abdominal pains, nausea, and vomiting. According to the U.S. Centers for Disease Control and Prevention, the first clinical descriptions of cutaneous anthrax were given by Maret in 1752 and Fournier in 1769. Before that, anthrax had been described only in historical accounts. The German scientist Robert Koch was the first to identify ''Bacillus anthracis'' as the bacterium that causes anthrax. Anthrax i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Knot Theory
In topology, knot theory is the study of knot (mathematics), mathematical knots. While inspired by knots which appear in daily life, such as those in shoelaces and rope, a mathematical knot differs in that the ends are joined so it cannot be undone, the simplest knot being a ring (or "unknot"). In mathematical language, a knot is an embedding of a circle in 3-dimensional Euclidean space, \mathbb^3. Two mathematical knots are equivalent if one can be transformed into the other via a deformation of \mathbb^3 upon itself (known as an ambient isotopy); these transformations correspond to manipulations of a knotted string that do not involve cutting it or passing it through itself. Knots can be described in various ways. Using different description methods, there may be more than one description of the same knot. For example, a common method of describing a knot is a planar diagram called a knot diagram, in which any knot can be drawn in many different ways. Therefore, a fundamental p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Circuit Topology
The circuit topology of a folded linear polymer refers to the arrangement of its intra-molecular contacts. Examples of linear polymers with intra-molecular contacts are nucleic acids and proteins. Proteins fold via the formation of contacts of various natures, including hydrogen bonds, disulfide bonds, and beta-beta interactions. RNA molecules fold by forming hydrogen bonds between nucleotides, forming nested or non-nested structures. Contacts in the genome are established via protein bridges including CTCF and cohesins and are measured by technologies including Chromosome conformation capture, Hi-C. Circuit topology categorises the topological arrangement of these physical contacts, that are referred to as hard contacts (or h-contacts). Furthermore, chains can fold via knotting (or the formation of "soft" contacts (s-contacts)). Circuit topology uses a similar language to categorise both "soft" and "hard" contacts, and provides a full description of a folded linear chain. In this ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Secondary Structure
Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone. Secondary structure may alternatively be defined based on the regular pattern of backbone dihedral angles in a particular region of the Ramachandran plot regardless of whether it has the correct hydrogen bonds. The concept of secondary structure was first introduced by Kaj Ulrik Linderstrøm-Lang at Stanford in 1952. Other types of biopolymers such as nucleic acids also possess characteristic secondary structures. Types ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Alpha-helices
An alpha helix (or α-helix) is a sequence of amino acids in a protein that are twisted into a coil (a helix). The alpha helix is the most common structural arrangement in the secondary structure of proteins. It is also the most extreme type of local structure, and it is the local structure that is most easily predicted from a sequence of amino acids. The alpha helix has a right-handed helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid that is four residues earlier in the protein sequence. Other names The alpha helix is also commonly called a: * Pauling–Corey–Branson α-helix (from the names of three scientists who described its structure) * 3.613-helix because there are 3.6 amino acids in one ring, with 13 atoms being involved in the ring formed by the hydrogen bond (starting with amidic hydrogen and ending with carbonyl oxygen) Discovery In the early 1930s, William Astbury showed that there were dras ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Beta Strand
The beta sheet (β-sheet, also β-pleated sheet) is a common structural motif, motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone chain, backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of peptide, polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformational isomerism, conformation. The supramolecular association of β-sheets has been implicated in the formation of the Amyloid fibril, fibrils and Amyloid plaques, protein aggregates observed in amyloidosis, Alzheimer's disease and other Proteinopathy, proteinopathies. History The first β-sheet structure was proposed by William Astbury in the 1930s. He proposed the idea of hydrogen bonding between the peptide bonds of parallel or antiparallel extended β-strands. However, Astbury did not have the necessary data on the bond geometry of the amino acids ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Structure
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, which are the monomers of the polymer. A single amino acid monomer may also be called a ''residue'', which indicates 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. 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-dimensiona ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PDBsum
PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank (PDB). Database The original version of the database was developed around 1995 by Roman Laskowski and collaborators at University College London. As of 2014, PDBsum is maintained by Laskowski and collaborators in the laboratory of Janet Thornton at the European Bioinformatics Institute (EBI). Each structure in the PDBsum database includes an image of structure (main view, Bottom view and right view), molecular components contained in the complex(structure), enzyme reaction diagram if appropriate, Gene ontology functional assignments, a 1D sequence annotated by Pfam and InterPro domain assignments, description of bound molecules and graphic showing interactions between protein and secondary structure, schematic diagrams of protein–protein interactions, analysis of clefts contained within the structure and links to external databases. The RasMol ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Membrane Topology
Topology of a transmembrane protein refers to locations of N- and C-termini of membrane-spanning polypeptide chain with respect to the inner or outer sides of the biological membrane occupied by the protein. Several databases provide experimentally determined topologies of membrane proteins. They include Uniprot, TOPDB, OPM, and ExTopoDB. There is also a database of domains located conservatively on a certain side of membranes, TOPDOM. Several computational methods were developed, with a limited success, for predicting transmembrane alpha-helices and their topology. Pioneer methods utilized the fact that membrane-spanning regions contain more hydrophobic residues than other parts of the protein, however applying different hydrophobic scales altered the prediction results. Later, several statistical methods were developed to improve the topography prediction and a special alignment method was introduced. According to the positive-inside rule, cytosolic loops near the lipid bilayer ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Folding
Protein folding is the physical process by which a protein, after Protein biosynthesis, synthesis by a ribosome as a linear chain of Amino acid, amino acids, changes from an unstable random coil into a more ordered protein tertiary structure, three-dimensional structure. This structure permits the protein to become biologically functional or active. The folding of many proteins begins even during the translation of the polypeptide chain. The amino acids interact with each other to produce a well-defined three-dimensional structure, known as the protein's native state. This structure is determined by the amino-acid sequence or primary structure. The correct three-dimensional structure is essential to function, although some parts of functional proteins Intrinsically unstructured proteins, may remain unfolded, indicating that protein dynamics are important. Failure to fold into a native structure generally produces inactive proteins, but in some instances, misfolded proteins have ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Structure
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, which are the monomers of the polymer. A single amino acid monomer may also be called a ''residue'', which indicates 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. 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-dimensiona ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
