Protein friction forces

Including solvent in a molecular dynamics simulation creates a frictional force that damps some motion of the solute. This affects in particular the motions of exposed side chain in proteins. 

According to these equations, for a given separation system, the main parameters involved in the separation of SDS-protein complexes are the electric force, the frictional force, and the retardation coefficient. These parameters are in turn affected by the strength of the electric field, molecular charge, analyte shape and size, polymer concentration, and temperature. 

In a polyacrylamide gel used for gel-filtration chromatography, the larger proteins can travel around the beads, thereby having a shorter path to travel and therefore eluting faster. With electrophoresis, the proteins are forced to go through the matrix, so the larger ones travel more slowly because there is more friction. 

This flickering makes possible ehanges in protein strueture that oeeur during enzyme kineties or even folding. The ever mobile water moleeules reduee the frictional forces that otherwise would retard the relevant motions of protein side-chains. This effect has been ealled the lubrieant of life . 

Debye layer on the analyte backbone, and the frictional force from the surrounding fluid. Therefore, it is not a trivial matter to determine or calculate the electrophoretic mobility of a given protein/peptide a priori from the sequence information. Also, electrophoretic mobilities of many proteins among a given proteome can be similar. Therefore, the CZE is not an ideal technique for separating a very complex protein mixture for sample preparation purposes. 

The relationship between friction force and wear is non-trivial [47]. It has been shown, for example, that a higher friction can lead to less wear in some cases [9,48]. More experiments are thus needed to clarify the effect of protein-mediated boundary lubrication for the known problem of wear. Another limitation of the present study is that the friction test was unidirectional. Multidirectional sliding is known to affect the wear rates [49]. The combination of experimental techniques presented here is thus a first step towards a more complete investigation of the molecular aspects in joint lubrication. In particular, it focuses on the relationship between protein folding, protein adsorption and boundary lubrication, as well as the significance of these effects in bio-tribological studies. 

Including solvent in a rn olecu lar dy ri arn ics sim illation creates a friction a I force that dam ps some motion of th e solti te. Tti is affects in particular th e m otion s of exposed side chain in proteins. 

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