Proteins 3-10 Stretch

Wang, T., and Ikai, A., Protein stretching III. Force-extension curves of tethered bovine carbonic anhydrase B to the silicon substrate under native, intermediate and denaturing conditions, Jpn. J. Appl. Phys., 38, 3912-3917 (1999). 

Mrcp-IOOK protein stretching curve FFT analysis... 

KD protein stretching in different solutions (Reprinted from Materials Science and Engineering A, 409, Yin J and Zhao YP, Molecular Dynamics Simulation of Barnacle Cement, 160-166, Copyright (2005), with permission from Elsevier)... 

The first term represents the forces due to the electrostatic field, the second describes forces that occur at the boundary between solute and solvent regime due to the change of dielectric constant, and the third term describes ionic forces due to the tendency of the ions in solution to move into regions of lower dielectric. Applications of the so-called PBSD method on small model systems and for the interaction of a stretch of DNA with a protein model have been discussed recently ([Elcock et al. 1997]). This simulation technique guarantees equilibrated solvent at each state of the simulation and may therefore avoid some of the problems mentioned in the previous section. Due to the smaller number of particles, the method may also speed up simulations potentially. Still, to be able to simulate long time scale protein motion, the method might ideally be combined with non-equilibrium techniques to enforce conformational transitions. 

A sequence alignment establishes the correspondences between the amino adds in th unknown protein and the template protein (or proteins) from wliich it will be built. Th three-dimensional structures of two or more related proteins are conveniently divided int structurally conserved regions (SCRs) and structurally variable regions (SVRs). Ihe structural conserved regions correspond to those stretches of maximum sequence identity or sequenc... 

Infrared spectra of fats and oils are similar regardless of their composition. The principal absorption seen is the carbonyl stretching peak which is virtually identical for all triglyceride oils. The most common appHcation of infrared spectroscopy is the determination of trans fatty acids occurring in a partially hydrogenated fat (58,59). Absorption at 965 - 975 cm is unique to the trans functionaHty. Near infrared spectroscopy has been utilized for simultaneous quantitation of fat, protein, and moisture in grain samples (60). The technique has also been reported to be useful for instmmental determination of iodine value (61). 

Eor biomolecules, such as proteins, the fastest motions are the stretching vibrations of the bonds connecting hydrogen atoms to heavy atoms (X—H stretching). The frequency of these motions is in the vicinity of 3000 cm , which means periods of about 10 fs (1 X lO s). Thus, an appropriate time step for simulating biomolecules would be At =... 

Alpha helices in proteins are found when a stretch of consecutive residues all have the 0, y angle pair approximately -60° and -50°, corresponding to the allowed region in the bottom left quadrant of the... 

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