Application to protein

L. Pedersen, T. Darden, Molecular dynamics techniques and applications to proteins, in The Encyclopedia of Computational Chemistry, Vbl. 3,... 

Mian, K Sjolander and D Haussler 1994. Hidden Markov Models in Computational Biology. Applications to Protein Modelling. Journal of Molecular Biology 235 1501-1531). 

A Krogh, M Brown, IS Mian, K Sjolander, D Haussler. Hidden Markov models m computational biology Applications to protein modeling. I Mol Biol 235 1501-1531, 1994. 

Zeng, X. and Ruckenstein, E., Membrane chromatography preparation and applications to protein separations, Biotechnol. Prog., 15, 1003, 1999. 

We present a molecular theory of hydration that now makes possible a unification of these diverse views of the role of water in protein stabilization. The central element in our development is the potential distribution theorem. We discuss both its physical basis and statistical thermodynamic framework with applications to protein solution thermodynamics and protein folding in mind. To this end, we also derive an extension of the potential distribution theorem, the quasi-chemical theory, and propose its implementation to the hydration of folded and unfolded proteins. Our perspective and current optimism are justified by the understanding we have gained from successful applications of the potential distribution theorem to the hydration of simple solutes. A few examples are given to illustrate this point. 

With applications to protein solution thermodynamics in mind, we now present an alternative derivation of the potential distribution theorem. Consider a macroscopic solution consisting of the solute of interest and the solvent. We describe a macroscopic subsystem of this solution based on the grand canonical ensemble of statistical thermodynamics, accordingly specified by a temperature, a volume, and chemical potentials for all solution species including the solute of interest, which is identified with a subscript index 1. The average number of solute molecules in this subsystem is... 

B. Schmidt and D. Riesner, A fluorescence detection system for the analytical ultracentrifuge and its application to proteins, nucleic acids, viroids and viruses (in Ref. [77]). 

Simonson, T. Archontis, G. Karplus, M., Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding, J. Phys. Chem. B 1997, 101, 8349-8362... 

Fukunishi, O. Watanabe Takada, S., On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems application to protein structure prediction, J. Chem. Phys. 2002,116, 9058-9067... 

Baldus M (2007) Magnetic resonance in the solid state applications to protein folding, amyloid fibrils and membrane proteins. Eur Biophys J 36(Suppl 1) S37—48... 

Electrophoresis is for separating ions, since only ions will migrate under the influence of an electric field, negative ions to the positive electrode and positive ions to the negative electrode. Scientists have found electrophoresis especially useful in biochemistry experiments in which charged amino acid molecules and other biomolecules need to be separated. Thus, application to protein and nucleic acid analysis has been popular (see Chapter 16). 

The CE-SDS method is a size-based separation technique generally applicable to proteins from 10 to -200—300kDa. The specificity is generally tested against the formulation buffer and any other possible contaminant proteins. There is usually no interference from the formulation buffer with the assay. For samples that contain contaminant proteins with a hydrodynamic size of 10—200kDa, the method is not specific. 

Figeys, D., and Aebersold, R. (1999). Microfabricated modules for sample handling, sample concentration and flow mixing application to protein analysis by tandem mass spectrometry. /. Biomech. Eng. 121, 7—12. 

Many of the advantages that MALDI offers for peptide analysis are equally applicable to proteins. Protein analysis is similar to peptide analysis, in which ionization usually occurs through the addition of one, two, or three protons. However, since proteins are significantly bigger than peptides, ion detection is typically less efficient. Therefore, while peptides are measured at the femtomole or even attomole level with MALDI, proteins are usually measured at the high femtomole to low picomole level. 

Krogh A, Brown M, Mian IS, Sjolander K, Haussler D (1994) Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol 235 1501-1531... 

Fig. 13. Most of the kinetic models which might be applicable to protein adsorption (see Refs.70 73)) k is rate constant, subscript a and d are adsorption and desorption respectively, 1 and 2 are adsorption states — usually native and denatured...

Wong,I. andLohman,T.M. (1993) A double-filtermethodfornitrocellulose-filterbinding application to protein-nucleic acid interactions, Proc. Natl. Acad. Sci. USA 90, 5428-5432. 

Patton, W. F., Lam, L., Su, Q., Lui, M., Erdjument-Bromage, H., and Tempst, P. (1994) Metal chelates as reversible stains for detection of electroblotted proteins application to protein microsequencing and immunoblotting. Anal. Biochem. 220, 324-335. 

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