Conformational flexibility of protein

Biological activity may often be determined by compartimenta-lization, passive transport phenomena and even receptors may have sometimes a low rigidity. Recent results on conformational flexibility of proteins indicate a very wide range of flexibilities but certainly steric fit is important for the majority of receptor-effector interactions. The value of the regressional coefficient (3) in MSD and MTD-studies (3 0 6) indicates about 0.65 kcal/mol per one... 

Wilmann PG, Petersen J, Pettikiriarachchi A, Buckle AM, Smith SC, Olsen S, Perugini MA, Devenish RJ, Prescott M, Rossjohn J (2005) The 2.1 angstrom crystal structure of the far-red fluorescent protein HcRed Inherent conformational flexibility of the chromophore. J Mol Biol 349 223-237... 

To test the hypothesis that the conformational flexibility of the thermophilic enzyme is lower at room temperature than at higher temperatures, Kohen and Klinman measured, by FTIR, the time course of H/D exchange of protein N-H sites in deuterium oxide for the thermophilic alcohol dehydrogenase. Their measurements were made at the optimal host-organism temperature of 65 °C and at 25 °C, below the transition temperature. They also included yeast alcohol dehydrogenase at 25 °C, which is the optimal temperature for its own host organism. 

The conformational flexible part found in domain II of SSI is in stark contrast with other protein proteinase inhibitors, such as BPTI. In the case of BPTI, the backbone conformation is found to be nearly identical in both the free and the bovine trypsin complex.28 The conformational rigidity of protein proteinase inhibitors has been considered for a long time to be a necessary condition to inhibit their target enzymes and to protect themselves from attack by other proteinases. It is generally recognized that the substrate-like protein proteinase inhibitors, such as BPTI, STI, and Ovomucoid domain 3,... 

Inhomogeneons broadening is generally more extensive in solntions and glasses/polymers than in crystalline environments. Crystals nsnally have far better defined environments for a chromophore. Spectra of a particnlar chromophore that are measmed when this chromophore is in a crystalline environment are nsnally better resolved even when taken at ambient temperatmes. Proteins can exhibit well-defined binding sites for a chromophore. However, dne to the inherent conformational flexibility of the protein medium, there can still be a wide variation in the configmation of this nanoenvironment, as there is in a glass. 

A third region at the top of the active site showed markedly different interactions with the probes. While most differences can be attributed to interactions with the side chains of an unconserved amino acid, another area in this region is produced by different backbone carbonyl orientations. Due to the presumably lower conformational flexibility of the protein backbone compared to side chain atoms, the authors speculate that this area would be especially promising for the design of selective ligands. 

Cyclization of peptides often improves their in vivo stability and biological activity (43) it is also commonly used to reduce the conformational flexibility of peptides. So far, engineering of novel disulfide bonds has been one of the most frequently applied strategies to stabilize proteins. However, the insertion... 

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