Sodium channelSodium channels are integral membrane proteins that form ion channels, conducting sodium ions (Na+) through a cell's membrane. They belong to the superfamily of cation channels. They are classified into 2 types: In excitable cells such as neurons, myocytes, and certain types of glia, sodium channels are responsible for the rising phase of action potentials. These channels go through three different states called resting, active and inactive states.
Ion channelIon channels are pore-forming membrane proteins that allow ions to pass through the channel pore. Their functions include establishing a resting membrane potential, shaping action potentials and other electrical signals by gating the flow of ions across the cell membrane, controlling the flow of ions across secretory and epithelial cells, and regulating cell volume. Ion channels are present in the membranes of all cells. Ion channels are one of the two classes of ionophoric proteins, the other being ion transporters.
ProtonA proton is a stable subatomic particle, symbol _Proton, H+, or 1H+ with a positive electric charge of +1 e (elementary charge). Its mass is slightly less than that of a neutron and 1,836 times the mass of an electron (the proton-to-electron mass ratio). Protons and neutrons, each with masses of approximately one atomic mass unit, are jointly referred to as "nucleons" (particles present in atomic nuclei). One or more protons are present in the nucleus of every atom.
Molecular dynamicsMolecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.
Voltage-gated ion channelVoltage-gated ion channels are a class of transmembrane proteins that form ion channels that are activated by changes in the electrical membrane potential near the channel. The membrane potential alters the conformation of the channel proteins, regulating their opening and closing. Cell membranes are generally impermeable to ions, thus they must diffuse through the membrane through transmembrane protein channels. They have a crucial role in excitable cells such as neuronal and muscle tissues, allowing a rapid and co-ordinated depolarization in response to triggering voltage change.
Electrochemical gradientAn electrochemical gradient is a gradient of electrochemical potential, usually for an ion that can move across a membrane. The gradient consists of two parts: The chemical gradient, or difference in solute concentration across a membrane. The electrical gradient, or difference in charge across a membrane. When there are unequal concentrations of an ion across a permeable membrane, the ion will move across the membrane from the area of higher concentration to the area of lower concentration through simple diffusion.
Potassium channelPotassium channels are the most widely distributed type of ion channel found in virtually all organisms. They form potassium-selective pores that span cell membranes. Potassium channels are found in most cell types and control a wide variety of cell functions. Potassium channels function to conduct potassium ions down their electrochemical gradient, doing so both rapidly (up to the diffusion rate of K+ ions in bulk water) and selectively (excluding, most notably, sodium despite the sub-angstrom difference in ionic radius).
Vector bundleIn mathematics, a vector bundle is a topological construction that makes precise the idea of a family of vector spaces parameterized by another space (for example could be a topological space, a manifold, or an algebraic variety): to every point of the space we associate (or "attach") a vector space in such a way that these vector spaces fit together to form another space of the same kind as (e.g. a topological space, manifold, or algebraic variety), which is then called a vector bundle over .
Fusion proteinFusion proteins or chimeric (kī-ˈmir-ik) proteins (literally, made of parts from different sources) are proteins created through the joining of two or more genes that originally coded for separate proteins. Translation of this fusion gene results in a single or multiple polypeptides with functional properties derived from each of the original proteins. Recombinant fusion proteins are created artificially by recombinant DNA technology for use in biological research or therapeutics.
Gating (electrophysiology)In electrophysiology, the term gating refers to the opening (activation) or closing (by deactivation or inactivation) of ion channels. This change in conformation is a response to changes in transmembrane voltage. When ion channels are in a 'closed' (non-conducting) state, they are impermeable to ions and do not conduct electrical current. When ion channels are in their open state, they conduct electrical current by allowing specific types of ions to pass through them, and thus, across the plasma membrane of the cell.
Proton pumpA proton pump is an integral membrane protein pump that builds up a proton gradient across a biological membrane. Proton pumps catalyze the following reaction: H+[on one side of a biological membrane] + energy H+[on the other side of the membrane] Mechanisms are based on energy-induced conformational changes of the protein structure or on the Q cycle. During evolution, proton pumps have arisen independently on multiple occasions. Thus, not only throughout nature but also within single cells, different proton pumps that are evolutionarily unrelated can be found.
Frame bundleIn mathematics, a frame bundle is a principal fiber bundle F(E) associated to any vector bundle E. The fiber of F(E) over a point x is the set of all ordered bases, or frames, for Ex. The general linear group acts naturally on F(E) via a change of basis, giving the frame bundle the structure of a principal GL(k, R)-bundle (where k is the rank of E). The frame bundle of a smooth manifold is the one associated to its tangent bundle. For this reason it is sometimes called the tangent frame bundle.
Action potentialAn action potential occurs when the membrane potential of a specific cell rapidly rises and falls. This depolarization then causes adjacent locations to similarly depolarize. Action potentials occur in several types of animal cells, called excitable cells, which include neurons, muscle cells, and in some plant cells. Certain endocrine cells such as pancreatic beta cells, and certain cells of the anterior pituitary gland are also excitable cells.
Fiber bundleIn mathematics, and particularly topology, a fiber bundle (or, in Commonwealth English: fibre bundle) is a space that is a product space, but may have a different topological structure. Specifically, the similarity between a space and a product space is defined using a continuous surjective map, that in small regions of behaves just like a projection from corresponding regions of to The map called the projection or submersion of the bundle, is regarded as part of the structure of the bundle.
Cell surface receptorCell surface receptors (membrane receptors, transmembrane receptors) are receptors that are embedded in the plasma membrane of cells. They act in cell signaling by receiving (binding to) extracellular molecules. They are specialized integral membrane proteins that allow communication between the cell and the extracellular space. The extracellular molecules may be hormones, neurotransmitters, cytokines, growth factors, cell adhesion molecules, or nutrients; they react with the receptor to induce changes in the metabolism and activity of a cell.
Molecular modellingMolecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system.
Tangent bundleIn differential geometry, the tangent bundle of a differentiable manifold is a manifold which assembles all the tangent vectors in . As a set, it is given by the disjoint union of the tangent spaces of . That is, where denotes the tangent space to at the point . So, an element of can be thought of as a pair , where is a point in and is a tangent vector to at . There is a natural projection defined by . This projection maps each element of the tangent space to the single point .
Line bundleIn mathematics, a line bundle expresses the concept of a line that varies from point to point of a space. For example, a curve in the plane having a tangent line at each point determines a varying line: the tangent bundle is a way of organising these. More formally, in algebraic topology and differential topology, a line bundle is defined as a vector bundle of rank 1. Line bundles are specified by choosing a one-dimensional vector space for each point of the space in a continuous manner.
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.
Molecular design softwareMolecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including: Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development g
