|
Molten Globule
In 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. For cytochrome c and some other proteins, it has been shown that the molten globule state is a "thermodynamic state" clearly different both from the native and the denatured state, demonstrating for the first time the existence of a third equilibirum (i.e., intermediate) state. The term "molten globule" may be used to describe various types of partially-folded protein states found in slightly denaturing conditions such as low pH (generally pH = 2), mild denaturant, or high temperature. Molten globules are collapse ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Biology
Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and physical structure of biological macromolecules is known as molecular biology. Molecular biology was first described as an approach focused on the underpinnings of biological phenomena - uncovering the structures of biological molecules as well as their interactions, and how these interactions explain observations of classical biology. In 1945 the term molecular biology was used by physicist William Astbury. In 1953 Francis Crick, James Watson, Rosalind Franklin, and colleagues, working at Medical Research Council unit, Cavendish laboratory, Cambridge (now the MRC Laboratory of Molecular Biology), made a double helix model of DNA which changed the entire research scenario. They proposed the DNA structure based on previous research done by Ro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrophobic Collapse
Hydrophobic collapse is a proposed process for the production of the Protein structure, 3-D conformation adopted by Peptide, polypeptides and other molecules in polar solvents. The theory states that the nascent polypeptide forms initial Protein secondary structure, secondary structure (Alpha helix, ɑ-helices and Beta sheet, β-strands) creating localized regions of predominantly hydrophobic Amino acid, residues. The polypeptide interacts with water, thus placing Hydrophobic effect, thermodynamic pressures on these regions which then aggregate or "collapse" into a Protein tertiary structure, tertiary conformation with a hydrophobic core. Incidentally, polar residues interact favourably with water, thus the solvent-facing surface of the peptide is usually composed of predominantly Hydrophile, hydrophilic regions. Hydrophobic collapse may also reduce the affinity of conformationally flexible drugs to their protein targets by reducing the net hydrophobic contribution to binding by se ... [...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, the monomers of the polymer. A single amino acid monomer may also be called a ''residue'' indicating 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-dimensional structure. This is t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biomolecular Condensate
In biochemistry, biomolecular condensates are a class of membrane-less organelles and organelle subdomains, which carry out specialized functions within the cell. Unlike many organelles, biomolecular condensate composition is not controlled by a bounding membrane. Instead, condensates can form and maintain organization through a range of different processes, the most well-known of which is phase separation of proteins, RNA and other biopolymers into either colloidal emulsions, gels, liquid crystals, solid crystals or aggregates within cells. History Micellar theory The micellar theory of Carl Nägeli was developed from his detailed study of starch granules in 1858. Amorphous substances such as starch and cellulose were proposed to consist of building blocks, packed in a loosely crystalline array to form what he later termed “micelles”. Water could penetrate between the micelles, and new micelles could form in the interstices between old micelles. The swelling of st ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrophobic Collapse
Hydrophobic collapse is a proposed process for the production of the Protein structure, 3-D conformation adopted by Peptide, polypeptides and other molecules in polar solvents. The theory states that the nascent polypeptide forms initial Protein secondary structure, secondary structure (Alpha helix, ɑ-helices and Beta sheet, β-strands) creating localized regions of predominantly hydrophobic Amino acid, residues. The polypeptide interacts with water, thus placing Hydrophobic effect, thermodynamic pressures on these regions which then aggregate or "collapse" into a Protein tertiary structure, tertiary conformation with a hydrophobic core. Incidentally, polar residues interact favourably with water, thus the solvent-facing surface of the peptide is usually composed of predominantly Hydrophile, hydrophilic regions. Hydrophobic collapse may also reduce the affinity of conformationally flexible drugs to their protein targets by reducing the net hydrophobic contribution to binding by se ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fuzzy Complex
Fuzzy complexes are protein complexes, where structural ambiguity or multiplicity exists and is required for biological function.Fuxreiter, M. & Tompa, P. (2011) Fuzziness: Structural Disorder in Protein Complexes Austin, New York. Alteration, truncation or removal of conformationally ambiguous regions impacts the activity of the corresponding complex. Fuzzy complexes are generally formed by intrinsically disordered proteins. Structural multiplicity usually underlies functional multiplicity of protein complexes following a fuzzy logic. Distinct binding modes of the nucleosome are also regarded as a special case of fuzziness. Historical background For almost 50 years molecular biology was based on two dogmas: (i) equating biological function of the protein with a unique three-dimensional structure and (ii) assuming exquisite specificity in protein complexes. Specificity/selectivity is ensured by unambiguous set of interactions formed between the protein and its ligand (another ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Folding Funnel
The folding funnel hypothesis is a specific version of the energy landscape theory of protein folding, which assumes that a protein's native state corresponds to its free energy minimum under the solution conditions usually encountered in cells. Although energy landscapes may be "rough", with many non-native local minima in which partially folded proteins can become trapped, the folding funnel hypothesis assumes that the native state is a deep free energy minimum with steep walls, corresponding to a single well-defined tertiary structure. The term was introduced by Ken A. Dill in a 1987 article discussing the stabilities of globular proteins. The folding funnel hypothesis is closely related to the hydrophobic collapse hypothesis, under which the driving force for protein folding is the stabilization associated with the sequestration of hydrophobic amino acid side chains in the interior of the folded protein. This allows the water solvent to maximize its entropy, lowering the tot ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Intrinsically Disordered Proteins
In 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. IDPs are a very large and functionally important class of proteins and their discovery has disproved the idea that three-dimensional structures of proteins must be fixed to accomplish their biological functions. For example, IDPs have been identified to participate in weak multivalent interactions that are highly cooperative and dynamic, lending them importance in DNA regulation and in cell signaling. Many IDPs can also adopt a fixed three-dimensional structure after bi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dead-end Elimination
The dead-end elimination algorithm (DEE) is a method for optimization (mathematics), minimizing a Function (mathematics), function over a discrete set of independent variables. The basic idea is to identify "dead ends", i.e., combinations of variables that are not necessary to define a global minimum because there is always a way of replacing such combination by a better or equivalent one. Then we can refrain from searching such combinations further. Hence, dead-end elimination is a mirror image of dynamic programming, in which "good" combinations are identified and explored further. Although the method itself is general, it has been developed and applied mainly to the problems of protein structure prediction, predicting and protein design, designing the structures of proteins. It closely related to the notion of dominance in optimization also known as substitutability in a Constraint Satisfaction Problem. The original description and proof of the dead-end elimination theorem can ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Design
Protein 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. These predicted sequences can then be validated experimentally through methods such as peptide synthesis, site-directed mutagenesis, or artificial gene synthesis. Rational protein design dates back to the mid-1970s. Recently, however, there were numerous examples of successful rational design of water-soluble and even transmembrane peptides and proteins, in part due to a better understanding of different factors contributing to protein structure stability and development of better computational methods. Overview and history The goal in ration ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
De Novo Synthesis
In chemistry, ''de novo'' synthesis () refers to the synthesis of complex molecules from simple molecules such as sugars or amino acids, as opposed to recycling after partial degradation. For example, nucleotides are not needed in the diet as they can be constructed from small precursor molecules such as formate and aspartate. Methionine, on the other hand, is needed in the diet because while it can be degraded to and then regenerated from homocysteine, it cannot be synthesized ''de novo''. Nucleotide ''De novo'' pathways of nucleotides do not use free bases: adenine (abbreviated as A), guanine (G), cytosine (C), thymine (T), or uracil (U). The purine ring is built up one atom or a few atoms at a time and attached to ribose throughout the process. Pyrimidine ring is synthesized as orotate and attached to ribose phosphate and later converted to common pyrimidine nucleotides. Cholesterol Cholesterol is an essential structural component of animal cell membranes. Cholestero ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Kinetic Energy
In physics, the kinetic energy of an object is the energy that it possesses due to its motion. It is defined as the work needed to accelerate a body of a given mass from rest to its stated velocity. Having gained this energy during its acceleration, the body maintains this kinetic energy unless its speed changes. The same amount of work is done by the body when decelerating from its current speed to a state of rest. Formally, a kinetic energy is any term in a system's Lagrangian which includes a derivative with respect to time. In classical mechanics, the kinetic energy of a non-rotating object of mass ''m'' traveling at a speed ''v'' is \fracmv^2. In relativistic mechanics, this is a good approximation only when ''v'' is much less than the speed of light. The standard unit of kinetic energy is the joule, while the English unit of kinetic energy is the foot-pound. History and etymology The adjective ''kinetic'' has its roots in the Greek word κίνησις ''kinesis'', m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
