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.
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 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.
TemperatureTemperature is a physical quantity that expresses quantitatively the perceptions of hotness and coldness. Temperature is measured with a thermometer. Thermometers are calibrated in various temperature scales that historically have relied on various reference points and thermometric substances for definition. The most common scales are the Celsius scale with the unit symbol °C (formerly called centigrade), the Fahrenheit scale (°F), and the Kelvin scale (K), the latter being used predominantly for scientific purposes.
Thermodynamic temperatureThermodynamic temperature is a quantity defined in thermodynamics as distinct from kinetic theory or statistical mechanics. Historically, thermodynamic temperature was defined by Lord Kelvin in terms of a macroscopic relation between thermodynamic work and heat transfer as defined in thermodynamics, but the kelvin was redefined by international agreement in 2019 in terms of phenomena that are now understood as manifestations of the kinetic energy of free motion of microscopic particles such as atoms, molecules, and electrons.
Negative temperatureCertain systems can achieve negative thermodynamic temperature; that is, their temperature can be expressed as a negative quantity on the Kelvin or Rankine scales. This should be distinguished from temperatures expressed as negative numbers on non-thermodynamic Celsius or Fahrenheit scales, which are nevertheless higher than absolute zero. The absolute temperature (Kelvin) scale can be understood loosely as a measure of average kinetic energy. Usually, system temperatures are positive.
Maxwell–Boltzmann distributionIn physics (in particular in statistical mechanics), the Maxwell–Boltzmann distribution, or Maxwell(ian) distribution, is a particular probability distribution named after James Clerk Maxwell and Ludwig Boltzmann. It was first defined and used for describing particle speeds in idealized gases, where the particles move freely inside a stationary container without interacting with one another, except for very brief collisions in which they exchange energy and momentum with each other or with their thermal environment.
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.
Ludwig BoltzmannLudwig Eduard Boltzmann (ˈluːtvɪç ˈbɔlt͡sman; 20 February 1844 – 5 September 1906) was an Austrian physicist and philosopher. His greatest achievements were the development of statistical mechanics, and the statistical explanation of the second law of thermodynamics. In 1877 he provided the current definition of entropy, , where Ω is the number of microstates whose energy equals the system's energy, interpreted as a measure of statistical disorder of a system. Max Planck named the constant kB the Boltzmann constant.
Protein dynamicsProteins are generally thought to adopt unique structures determined by their amino acid sequences. However, proteins are not strictly static objects, but rather populate ensembles of (sometimes similar) conformations. Transitions between these states occur on a variety of length scales (tenths of Å to nm) and time scales (ns to s), and have been linked to functionally relevant phenomena such as allosteric signaling and enzyme catalysis.
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.
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).
Implicit solvationImplicit solvation (sometimes termed continuum solvation) is a method to represent solvent as a continuous medium instead of individual “explicit” solvent molecules, most often used in molecular dynamics simulations and in other applications of molecular mechanics. The method is often applied to estimate free energy of solute-solvent interactions in structural and chemical processes, such as folding or conformational transitions of proteins, DNA, RNA, and polysaccharides, association of biological macromolecules with ligands, or transport of drugs across biological membranes.
Boltzmann distributionIn statistical mechanics and mathematics, a Boltzmann distribution (also called Gibbs distribution) is a probability distribution or probability measure that gives the probability that a system will be in a certain state as a function of that state's energy and the temperature of the system. The distribution is expressed in the form: where pi is the probability of the system being in state i, exp is the exponential function, εi is the energy of that state, and a constant kT of the distribution is the product of the Boltzmann constant k and thermodynamic temperature T.
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.
Potential energyIn physics, potential energy is the energy held by an object because of its position relative to other objects, stresses within itself, its electric charge, or other factors. The term potential energy was introduced by the 19th-century Scottish engineer and physicist William Rankine, although it has links to the ancient Greek philosopher Aristotle's concept of potentiality. Common types of potential energy include the gravitational potential energy of an object, the elastic potential energy of an extended spring, and the electric potential energy of an electric charge in an electric field.
Boltzmann constantThe Boltzmann constant (kB or k) is the proportionality factor that relates the average relative thermal energy of particles in a gas with the thermodynamic temperature of the gas. It occurs in the definitions of the kelvin and the gas constant, and in Planck's law of black-body radiation and Boltzmann's entropy formula, and is used in calculating thermal noise in resistors. The Boltzmann constant has dimensions of energy divided by temperature, the same as entropy. It is named after the Austrian scientist Ludwig Boltzmann.
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 complexA protein complex or multiprotein complex is a group of two or more associated polypeptide chains. Protein complexes are distinct from multidomain enzymes, in which multiple catalytic domains are found in a single polypeptide chain. Protein complexes are a form of quaternary structure. Proteins in a protein complex are linked by non-covalent protein–protein interactions. These complexes are a cornerstone of many (if not most) biological processes.
Chemical potentialIn thermodynamics, the chemical potential of a species is the energy that can be absorbed or released due to a change of the particle number of the given species, e.g. in a chemical reaction or phase transition. The chemical potential of a species in a mixture is defined as the rate of change of free energy of a thermodynamic system with respect to the change in the number of atoms or molecules of the species that are added to the system.
