Proteins unfolding -

To facilitate conformational transitions in the before-mentioned adenylate kinase, Elamrani and co-workers scaled all atomic masses by a large factor thus allowing the use of a high effective simulation temperature of 2000K ([Elamrani et al. 1996]). To prevent protein unfolding, elements of secondary structure had to be constrained. 

Alonso D O V and V Daggett 1995. Molecular Dynamics Simulations of Protein Unfolding and Limited Refolding Characterisation of Partially Unfolded States of Ubiquitm in 60% Methanol and in Water. Journal of Molecular Biology 247 501-520. 

Finkelslain A V 1997. Can Protein Unfolding Simulate Protein Folding Protein Engineering 10 843... 

A Li, V Daggett. Characterization of the transition state of protein unfolding by use of molecular dynamics Chymotrypsm inhibitor 2. Proc Natl Acad Sci USA 91 10430-10434, 1994. 

Eigure 3.5 presents the dependence of A.S ° on temperature for chymotryp-sinogen denaturation at pH 3. A positive A.S ° indicates that the protein solution has become more disordered as the protein unfolds. Comparison of the value of 1.62 kj/mol K with the values of A.S ° in Table 3.1 shows that the present value (for chymotrypsinogen at 54.5°C) is quite large. The physical significance of the thermodynamic parameters for the unfolding of chymotrypsinogen becomes clear in the next section. 

Mechanical forces, such as shearing, shaking, and pressure, may also denature proteins [44,45], Shaking proteins may lead to inactivation owing to an increase in the area of the gas/liquid interface. At the interface, the protein unfolds and maximizes exposure of hydrophobic residues to the air. Surface denaturation may also occur at the protein/container interface and has been observed following adsorption of proteins to filter materials [46]. 

Turning now to the chapters in this volume, a variety of complementary techniques and approaches have been used to characterize peptide and protein unfolding induced by temperature, pressure, and solvent. Our goal has been to assemble these complementary views within a single volume in order to develop a more complete picture of denatured peptides and proteins. The unifying observation in common to all chapters is the detection of preferred backbone conformations in experimentally accessible unfolded states. 

Three theory papers are also included. Determinants of the Polyproline II Helix from Modeling Studies by Creamer and Campbell reexamines and extends an earlier hypothesis about Pn and its determinants. Hydration Theory for Molecular Biophysics by Paulaitis and Pratt discusses the crucial role of water in both folded and unfolded proteins. Unfolded State of Peptides by Daura et al. focuses on the unfolded state of peptides studied primarily by molecular dynamics. 

Proteins unfolded by GdmHCl or urea will have a dominant conformation, Pn- At low temperatures we find about one-third of the residues in chemically denatured proteins in the Pn-helix conformation, with two-thirds in the form of the high-temperature ensemble. Since at least one-third of the residues in this ensemble are isolated Pn residues or in Pn helices of two or three residues, the total Pn content will be 50% or greater. The Pn content of cold- and acid-denatured proteins will be substantial, probably >40%, but not as large as in chemically denatured proteins. 

Several lines of evidence indicate that oligomers of Ala in solution assume a predominantly Pn local conformation and that proteins unfolded by Gdm-HCl or urea also have a dominant conformation, Pn-Preliminary results on ubiqitin fragments and short sequences contain-ing QQQ, SSS, FFF, and VW in a series of 11-mers suggest that this is... 

That which we call a rose, by any other name would smell as sweet. The essence of the denatured state, in contrast, is rather more elusive. The difficulty stems, at least in part, from the wide variety of methods of inducing a protein to unfold. Some proteins appear to be natively unfolded that is, they remain unfolded in the cell under conditions in which they retain their biological activity (Plaxco and Gross, 1997 Wright and Dyson 1999 Dunker, 2002). Other proteins unfold only under the influence of changes in pH, high or low temperatures, or... 

Chemical denaturants, excessive heat, or low temperatures are typically not the reasons proteins unfold in the cell. Several groups have... 

The geometric properties of highly denatured states appear to be consistent with those expected for a random-coil polymer. For example, proteins unfolded at high temperatures or in high concentrations of denaturant invariably produce Kratky scattering profiles exhibiting the monotonic increase indicative of an expanded, coil-like conformation (Fig. 1) (Hagihara et al., 1998 see also Doniach et al., 1995). Consistent... 

Why is this reconciliation important After all, a 6 M GuHCl solution hardly recapitulates the physiologically milieu, and proteins unfolded under more physiologically relevant conditions are often (though not always see Hoshino et al., 1997) much more compact than expected for an excluded-volume random coil. Still, the chemically or thermally... 

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