Native conformations

In the context of protein structure, the term stability can be defined as the tendency to maintain a native conformation. Native proteins are only marginally stable the AG separating the folded and unfolded states in typical proteins under physiological conditions is in the range of only 20 to 65 kJ/mol. A given polypeptide chain... 

This effect (step 4, Table XVII) refers to the possibility that different tertiary structures of the same protein will be present during HPLC separation. The protein may exist in two conformers native and denatured. Evidence has also been presented for the existence of additional conformers for some proteins 13), e.g., partially unravelled (denatured) structures... 

AGuufoid) connotes the partitioning of a protein molecule between two conformations native and unfolded. AGujjoid measures the difference between the partial molar free energy of the macromoleeule in its unfolded or denatured state U), and its native, folded state (N). 

Milas, et al. report on zero-shear viscosity and dynamic moduli of xanthan gum(21). Concentrations 0.2 < c[r/] < 65 (c < 5 g/1) span the dilute and semidi-lute regimes. Xanthan gum has two different ordered conformations, native and... 

Conformation Native [%] Illuminated Nonpolarized light Polarized light [%] [%] ... 

The biologiccJ function of a protein or peptide is often intimately dependent upon the conformation(s) that the molecule can adopt. In contrast to most synthetic polymers where the individual molecules can adopt very different conformations, a protein usually exists in a single native state. These native states are found rmder conditions typically found in Uving cells (aqueous solvents near neutred pH at 20-40°C). Proteins can be unfolded (or denatured) using high-temperature, acidic or basic pH or certain non-aqueous solvents. However, this unfolding is often reversible cind so proteins can be folded back to their native structure in the laboratory. 

Most potential energy surfaces are extremely complex. Fiber and Karplus analyzed a 300 psec molecular dynamics trajectory of the protein myoglobin. They estimate that 2000 thermally accessible minima exist near the native protein structure. The total number of conformations is even larger. Dill derived a formula to calculate the upper bound of thermally accessible conformations in a protein. Using this formula, a protein of 150 residues (the approx-... 

Through combined effects of noncovalent forces, proteins fold into secondary stmctures, and hence a tertiary stmcture that defines the native state or conformation of a protein. The native state is then that three-dimensional arrangement of the polypeptide chain and amino acid side chains that best facihtates the biological activity of a protein, at the same time providing stmctural stabiUty. Through protein engineering subde adjustments in the stmcture of the protein can be made that can dramatically alter its function or stabiUty. 

For any given protein, the number of possible conformations that it could adopt is astronomical. Yet each protein folds into a unique stmcture totally deterrnined by its sequence. The basic assumption is that the protein is at a free energy minimum however, calometric studies have shown that a native protein is more stable than its unfolded state by only 20—80 kj/mol (5—20 kcal/mol) (5). This small difference can be accounted for by the favorable... 

A recent survey analyzed the accuracy of tliree different side chain prediction methods [134]. These methods were tested by predicting side chain conformations on nearnative protein backbones with <4 A RMSD to the native structures. The tliree methods included the packing of backbone-dependent rotamers [129], the self-consistent mean-field approach to positioning rotamers based on their van der Waals interactions [145],... 

MJ Sippl, S Weitckus. Detection of native-like models for ammo acid sequences of unknown thi ee-dimensional stiaicture in a data base of known protein conformations. Proteins 13 258-271, 1992. 

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