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Protein Folds
A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology). Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similarity is evident. Sequence homology can then be deduced even if not apparent (due to low sequence similarity). Superfamilies typically contain several protein families which show sequence similarity within each family. The term ''protein clan'' is commonly used for protease and glycosyl hydrolases superfamilies based on the MEROPS and CAZy classification systems. Identification Superfamilies of proteins are identified using a number of methods. Closely related members can be identified by different methods to those needed to group the most evolutionarily divergent members. Sequence similarity Historically, the similarity of different amino acid sequences has been the most common method of inferring homology. Sequence similarity is consi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Clade
In biology, a clade (), also known as a Monophyly, monophyletic group or natural group, is a group of organisms that is composed of a common ancestor and all of its descendants. Clades are the fundamental unit of cladistics, a modern approach to taxonomy adopted by most biological fields. The common ancestor may be an individual, a population, or a species (extinct or Extant taxon, extant). Clades are nested, one in another, as each branch in turn splits into smaller branches. These splits reflect evolutionary history as populations diverged and evolved independently. Clades are termed ''monophyletic'' (Greek: "one clan") groups. Over the last few decades, the cladistic approach has revolutionized biological classification and revealed surprising evolutionary relationships among organisms. Increasingly, taxonomists try to avoid naming Taxon, taxa that are not clades; that is, taxa that are not Monophyly, monophyletic. Some of the relationships between organisms that the molecul ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Histone Alignment
In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei and in most Archaeal phyla. They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn are wrapped into 30-nanometer fibers that form tightly packed chromatin. Histones prevent DNA from becoming tangled and protect it from DNA damage. In addition, histones play important roles in gene regulation and DNA replication. Without histones, unwound DNA in chromosomes would be very long. For example, each human cell has about 1.8 meters of DNA if completely stretched out; however, when wound about histones, this length is reduced to about 9 micrometers (0.09 mm) of 30 nm diameter chromatin fibers. There are five families of histones, which are designated H1/H5 (linker histones), H2, H3, and H4 (core histones). The nucleosome core is formed of two H2A-H2B dimers and a H3-H4 tetramer. The tight wrappin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tertiary Structural
Protein tertiary structure is the three-dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains and the backbone may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure. A number of these structures may bind to each other, forming a quaternary structure. History The science of the tertiary structure of proteins has progressed from one of hypothesis to one of detailed definition. Although Emil Fischer had suggested proteins were made of polypeptide chains and amino acid side chains, it was Dorothy Maud Wrinch who incorporated geometry into the prediction of protein structures. Wrinch demonstra ... [...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] |
Structural Homology Of The PA Clan
A structure is an arrangement and organization of interrelated elements in a material object or system, or the object or system so organized. Material structures include man-made objects such as buildings and machines and natural objects such as organism, biological organisms, minerals and chemical substance, chemicals. Abstract structures include data structures in computer science and musical form. Types of structure include a hierarchy (a cascade of one-to-many relationships), a Complex network, network featuring many-to-many Link (geometry), links, or a lattice (order), lattice featuring connections between components that are neighbors in space. Load-bearing Buildings, aircraft, skeletons, Ant colony, anthills, beaver dams, bridges and salt domes are all examples of Structural load, load-bearing structures. The results of construction are divided into buildings and nonbuilding structure, non-building structures, and make up the infrastructure of a human society. Built str ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Tertiary Structure
Protein tertiary structure is the three-dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains and the backbone may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure. A number of these structures may bind to each other, forming a quaternary structure. History The science of the tertiary structure of proteins has progressed from one of hypothesis to one of detailed definition. Although Emil Fischer had suggested proteins were made of polypeptide chains and amino acid side chains, it was Dorothy Maud Wrinch who incorporated geometry into the prediction of protein structures. Wrinch demonstr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural biology, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix (mathematics), matrix. Gaps are inserted between the Residue (chemistry), residues so that identical or similar characters are aligned in successive columns. Sequence alignments are also used for non-biological sequences such as calculating the Edit distance, distance cost between strings in a natural language, or to display financial data. Interpretation If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. In sequence ali ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Indel
Indel (insertion-deletion) is a molecular biology term for an insertion or deletion of bases in the genome of an organism. Indels ≥ 50 bases in length are classified as structural variants. In coding regions of the genome, unless the length of an indel is a multiple of 3, it will produce a frameshift mutation. For example, a common microindel which results in a frameshift causes Bloom syndrome in the Jewish or Japanese population. Indels can be contrasted with a point mutation. An indel inserts or deletes nucleotides from a sequence, while a point mutation is a form of substitution that ''replaces'' one of the nucleotides without changing the overall number in the DNA. Indels can also be contrasted with Tandem Base Mutations (TBM), which may result from fundamentally different mechanisms. A TBM is defined as a substitution at adjacent nucleotides (primarily substitutions at two adjacent nucleotides, but substitutions at three adjacent nucleotides have been observed). In ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Active Sites
Active may refer to: Music * ''Active'' (album), a 1992 album by Casiopea * "Active" (song), a 2024 song by Asake and Travis Scott from Asake's album ''Lungu Boy'' * Active Records, a record label Ships * ''Active'' (ship), several commercial ships by that name * HMS ''Active'', the name of various ships of the British Royal Navy * USCS ''Active'', a US Coast Survey ship in commission from 1852 to 1861 * USCGC ''Active'', the name of various ships of the US Coast Guard * USRC ''Active'', the name of various ships of the US Revenue Cutter Service * USS ''Active'', the name of various ships of the US Navy Computers and electronics * Active Enterprises, a defunct video game developer * Sky Active, the brand name for interactive features on Sky Digital available in the UK and Ireland * Active (software), software used for open publishing by Indymedia; see Independent Media Center * The "live" circuit of mains power in countries observing AS/NZS 3112 electrical s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Neutral Mutation
Neutral mutations are changes in DNA sequence that are neither beneficial nor detrimental to the ability of an organism to survive and reproduce. In population genetics, mutations in which natural selection does not affect the spread of the mutation in a species are termed neutral mutations. Neutral mutations that are inheritable and not linked to any genes under selection will be lost or will replace all other alleles of the gene. That loss or fixation of the gene proceeds based on random sampling known as genetic drift. A neutral mutation that is in linkage disequilibrium with other alleles that are under selection may proceed to loss or fixation via genetic hitchhiking and/or background selection. While many mutations in a genome may decrease an organism’s ability to survive and reproduce, also known as fitness, those mutations are selected against and are not passed on to future generations. The most commonly-observed mutations that are detectable as variation in the genet ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Conservative Mutation
A conservative replacement (also called a conservative mutation or a conservative substitution or a homologous replacement) is an amino acid replacement in a protein that changes a given amino acid to a different amino acid with similar biochemical properties (e.g. charge, hydrophobicity and size). Conversely, a radical replacement, or radical substitution, is an amino acid replacement that exchanges an initial amino acid by a final amino acid with different physicochemical properties. Description There are 20 naturally occurring amino acids, however some of these share similar characteristics. For example, leucine and isoleucine are both aliphatic, branched hydrophobes. Similarly, aspartic acid and glutamic acid are both small, negatively charged residues. Although there are many ways to classify amino acids, they are often sorted into six main classes on the basis of their structure and the general chemical characteristics of their side chains (R groups). Physicochem ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Codon Degeneracy
Degeneracy or redundancy of codons is the redundancy of the genetic code, exhibited as the multiplicity of three-base pair codon combinations that specify an amino acid. The degeneracy of the genetic code is what accounts for the existence of synonymous mutations. Background Degeneracy of the genetic code was identified by Lagerkvist. For instance, codons GAA and GAG both specify glutamic acid and exhibit redundancy; but, neither specifies any other amino acid and thus are not ambiguous or demonstrate no ambiguity. The codons encoding one amino acid may differ in any of their three positions; however, more often than not, this difference is in the second or third position. For instance, the amino acid glutamic acid is specified by GAA and GAG codons (difference in the third position); the amino acid leucine is specified by UUA, UUG, CUU, CUC, CUA, CUG codons (difference in the first or third position); and the amino acid serine is specified by UCA, UCG, UCC, UCU, AGU, AGC (differe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
