Glossary

 
  1. 1. Analytical ultracentrifuge: An instrument that subjects samples to very high gravitational fields that cause proteins to sink to the bottom of the solutions in which they are dissolved.  Their rate of sedimentation relative to their size allows us to determine their approximate shape.

  2. 2.Dynamic NMR: the use of nuclear magnetic resonance to measure the rates and characteristics of time dependent processes such as protein folding or conformational change.  NMR is the observation of radio frequency signals coming from some nuclei in molecules placed in a large magnetic field.  These signals can be very useful in telling us about the structure and behavior of protein molecules.

  3. 3.Excluded Volume Effect: As applied to polymers like proteins, this concept is attributed to Paul Flory (Flory, Paul. (1953) Principles of Polymer Chemistry. Cornell University Press. ISBN 0-8014-0134-8).  It is based on the idea that the atoms comprising macromolecules cannot interpenetrate either other atoms on the same molecule or atoms of other molecules also found in solution.  Thus, macromolecular crowding can occur either in a highly concentrated solution of a single molecule or of a mixture of molecules, like that found in the cytoplasm of all cells.

  4. 4.Flux: The rate of conversion of reactants into products or products into reactants.  At equilibrium, the forward flux is equal to the reverse flux.  The overall flux of a multistep reaction can be calculated from the flux of the individual steps.  If the steps are parallel reactions, the fluxes are simply additive.  If the steps are sequential, then the total flux is the reciprocal of the sum of the reciprocals of the individual fluxes.  The smallest flux step (rate determining step) contributes the most to the total flux.  Flux has units of number, fraction or concentration per unit time.  To determine the predominant mechanism for two or more alternative pathways, compare the total flux through each.  It should be noted that others debate this definition of flux.

  5. 5.Intrinsically disordered protein (IDP): syn.: intrinsically unstructured protein, natively unfolded protein.  A protein whose folding equilibrium under some conditions favors the unfolded thermodynamic state (ensemble).  Note that these conditions are not necessarily physiological because it is rare that IDP’s are confirmed experimentally to be unfolded in living cells.  IDP’s are often identified on the basis of highly polar and/or low complexity sequences.

  6. 6.Ribonucleoprotein: a particle consisting of at least one protein molecule and one RNA molecule.  Many ribonucleoprotein complexes contain many protein and RNA molecules, e.g. the ribosome.