Proteins molecular constants

Most molecular dynamics simulations, and particularly those for proteins, use constant temperature conditions. 

Vibrational spectroscopy has played a very important role in the development of potential functions for molecular mechanics studies of proteins. Force constants which appear in the energy expressions are heavily parameterized from infrared and Raman studies of small model compounds. One approach to the interpretation of vibrational spectra for biopolymers has been a harmonic analysis whereby spectra are fit by geometry and/or force constant changes. There are a number of reasons for developing other approaches. The consistent force field (CFF) type potentials used in computer simulations are meant to model the motions of the atoms over a large ranee of conformations and, implicitly temperatures, without reparameterization. It is also desirable to develop a formalism for interpreting vibrational spectra which takes into account the variation in the conformations of the chromophore and surroundings which occur due to thermal motions. 

Biirgi R, Kollman PA, van Gunsteren WF (2002) Simulating proteins at constant pH An approach combining molecular dynamics and Monte Carlo simulation. Proteins 47 469-480. 

I continue to feel that the study of the volume changes in protein reactions is sorely neglected. They may be determined by dilatometry and by the effects of pressure on protein equilibrium constants. The results complement the results of the determination of enthalpy changes as measured by calorimetry and the effects of temperature on equilibrium constants. Much useful insight at the molecular level can be obtained from a knowledge of volume changes... 

Nature has required the evolution of usefully selective hosts, and proteins (in the forms of enzymes, receptors, and antibodies) provide them. However, no individual protein molecule lasts in a cell for very long. All proteins are constantly anabolized and catabolized, with constant concentrations achieved via homeostasis. Nature never demanded permanence of its molecular recognition machinery. When we utilize biotic receptors for one-time, batch analytical applications, the receptors clearly meet the useful criterion. However, if a receptor must have an extended lifetime in a sensing device, then we propose that biotic receptors represent the easiest place in which to search instead of the right place to search. If a biotic receptor cannot reasonably be made stable enough to survive weeks of service, then it will not be useful for a sensing application no matter how avid or selective. 

Rum, G. and Herndon, W.C. (1991). Molecular Similarity Concepts. 5. Analysis of Steroid-Protein Binding Constants. J.Am.Chem.Soc., 113,9055-9060. 

Partition coefficients Metabolic rate constants Elimination rate constants Molecular weight Aqueous solubility Vapor pressure Permeability coefficients Diffusion coefficients Protein-binding constants... 

Rum G, Herndon WC. Molecular similarity concepts 5. Analysis of steroid-protein binding constants. J Am Chem Soc 1991 113 9055-9060. 

The application of the second law of thermodynamics is useful for understanding complex protein sorption phenomena (Haynes and Norde, 1994 Quiquampoix et al., 2002). It assumes that the spontaneous adsorption of a protein at constant temperature and pressure leads to a decrease in the Gibbs energy of the system. The Gibbs energy (G) depends on enthalpy [H], which is a measure of the potential energy (energy that has to be supplied to separate the molecular constituents from one another), and entropy (S), which is related to the disorder of the system. 

This leads on to a third method for molecular size measurements the use of gels of graded porosity. The principle of the technique is shown in Figure 4 it is seen that, given enough time (at least 10 kV x h) the mobility of most serum proteins becomes constant and eventually ceases as each constituent reaches a... 

Perhaps the strongest evidence in favor of the theory that the cytochrome oxidase system is composed of a single protein comes from the physicochemical studies of Takemori. Purified cytochrome oxidase appears in the ultracentrifuge as a nondispersed protein (sedimentation constant = 21.9 diffusion constant =3.58 x 10 partial specific volume = 0.72). The molecular weight of the protein was calculated on the basis of these studies and was found to equal 530,000. 

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