Protein structureProtein 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.
Protein tertiary structureProtein 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 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.
ProteinProteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity.
Protein secondary structureProtein 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.
Protein fold classIn molecular biology, protein fold classes are broad categories of protein tertiary structure topology. They describe groups of proteins that share similar amino acid and secondary structure proportions. Each class contains multiple, independent protein superfamilies (i.e. are not necessarily evolutionarily related to one another). Four large classes of protein that are generally agreed upon by the two main structure classification databases (SCOP and CATH).
Globular proteinIn biochemistry, globular proteins or spheroproteins are spherical ("globe-like") proteins and are one of the common protein types (the others being fibrous, disordered and membrane proteins). Globular proteins are somewhat water-soluble (forming colloids in water), unlike the fibrous or membrane proteins. There are multiple fold classes of globular proteins, since there are many different architectures that can fold into a roughly spherical shape. The term globin can refer more specifically to proteins including the globin fold.
Fibrous proteinIn molecular biology, fibrous proteins or scleroproteins are one of the three main classifications of protein structure (alongside globular and membrane proteins). Fibrous proteins are made up of elongated or fibrous polypeptide chains which form filamentous and sheet-like structures. These kind of protein can be distinguished from globular protein by its low solubility in water. Such proteins serve protective and structural roles by forming connective tissue, tendons, bone matrices, and muscle fiber.
Intrinsically disordered proteinsIn molecular biology, an intrinsically disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure, typically in the absence of its macromolecular interaction partners, such as other proteins or RNA. IDPs range from fully unstructured to partially structured and include random coil, molten globule-like aggregates, or flexible linkers in large multi-domain proteins. They are sometimes considered as a separate class of proteins along with globular, fibrous and membrane proteins.
Protein biosynthesisProtein biosynthesis (or protein synthesis) is a core biological process, occurring inside cells, balancing the loss of cellular proteins (via degradation or export) through the production of new proteins. Proteins perform a number of critical functions as enzymes, structural proteins or hormones. Protein synthesis is a very similar process for both prokaryotes and eukaryotes but there are some distinct differences. Protein synthesis can be divided broadly into two phases—transcription and translation.
Protein foldingProtein folding is the physical process where a protein chain is translated into its native three-dimensional structure, typically a "folded" conformation, by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA into a linear chain of amino acids.
Protein structure predictionProtein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by computational biology; and it is important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes).
Protein–protein interaction predictionProtein–protein interaction prediction is a field combining bioinformatics and structural biology in an attempt to identify and catalog physical interactions between pairs or groups of proteins. Understanding protein–protein interactions is important for the investigation of intracellular signaling pathways, modelling of protein complex structures and for gaining insights into various biochemical processes.
Molten globuleIn molecular biology, the term molten globule (MG) refers to protein states that are more or less compact (hence the "globule"), but are lacking the specific tight packing of amino acid residues which creates the solid state-like tertiary structure of completely folded proteins. It was found, for example, in cytochrome c, which conserves a native-like secondary structure content but without the tightly packed protein interior, under low pH and high salt concentration.
Protein Data BankThe Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, RCSB, and BMRB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.
Copenhagen interpretationThe Copenhagen interpretation is a collection of views about the meaning of quantum mechanics, stemming from the work of Niels Bohr, Werner Heisenberg, Max Born, and others. The term "Copenhagen interpretation" was apparently coined by Heisenberg during the 1950s to refer to ideas developed in the 1925–1927 period, glossing over his disagreements with Bohr. Consequently, there is no definitive historical statement of what the interpretation entails.
Knowledge-based systemsA knowledge-based system (KBS) is a computer program that reasons and uses a knowledge base to solve complex problems. The term is broad and refers to many different kinds of systems. The one common theme that unites all knowledge based systems is an attempt to represent knowledge explicitly and a reasoning system that allows it to derive new knowledge. Thus, a knowledge-based system has two distinguishing features: a knowledge base and an inference engine.
Many-minds interpretationThe many-minds interpretation of quantum mechanics extends the many-worlds interpretation by proposing that the distinction between worlds should be made at the level of the mind of an individual observer. The concept was first introduced in 1970 by H. Dieter Zeh as a variant of the Hugh Everett interpretation in connection with quantum decoherence, and later (in 1981) explicitly called a many or multi-consciousness interpretation. The name many-minds interpretation was first used by David Albert and Barry Loewer in 1988.
Interpretations of quantum mechanicsAn interpretation of quantum mechanics is an attempt to explain how the mathematical theory of quantum mechanics might correspond to experienced reality. Although quantum mechanics has held up to rigorous and extremely precise tests in an extraordinarily broad range of experiments, there exist a number of contending schools of thought over their interpretation. These views on interpretation differ on such fundamental questions as whether quantum mechanics is deterministic or stochastic, local or non-local, which elements of quantum mechanics can be considered real, and what the nature of measurement is, among other matters.
Protein designProtein design is the rational design of new protein molecules to design novel activity, behavior, or purpose, and to advance basic understanding of protein function. Proteins can be designed from scratch (de novo design) or by making calculated variants of a known protein structure and its sequence (termed protein redesign). Rational protein design approaches make protein-sequence predictions that will fold to specific structures.
Ensemble interpretationThe ensemble interpretation of quantum mechanics considers the quantum state description to apply only to an ensemble of similarly prepared systems, rather than supposing that it exhaustively represents an individual physical system. The advocates of the ensemble interpretation of quantum mechanics claim that it is minimalist, making the fewest physical assumptions about the meaning of the standard mathematical formalism. It proposes to take to the fullest extent the statistical interpretation of Max Born, for which he won the Nobel Prize in Physics in 1954.
