Proteins segmental mobility

J. R. Lakowicz and G. Weber, Nanosecond segmental mobilities of tryptophan residues in proteins observed by lifetime-resolved fluorescence anisotropies, Biophys. J. 32, 591-601 (1980). 

Steady-state measurements of the fluorescence anisotropy of fluorescein derivatives form the basis of a sensitive analytical technique also used to detect and quantitate proteins [36], steroids [37-39], therapeutic drugs, and narcotics [40-42], In a different approach, the anisotropy of the fluorescein conjugate is measured as a function of the medium viscosity to determine the segmental mobility of the chains that cover the binding site [43-45],... 

In ribonuclease A 13C spin-lattice relaxation of the carbonyl and a and / carbon atoms is slower in the denaturated protein than in the native sample [177]. Apparently, the skeleton of this macromolecule becomes more flexible on denaturation, probably owing to conformational changes. However, the s carbons of lysine in the native protein exhibit relatively large T, values which change only insignificantly on denaturation [177]. This behavior is attributed to a considerable segmental mobility of the lysine side chain (Table 3.17 [177]). 

Lycksell, P.-O., and Sahlin, M., 1995, Demonstration of segmental mobility in the functionally essential carboxyl terminal part of ribonucleotide reductase protein R2 from Escherichia coli. FEBS Lett. 368 441n444. 

Another important factor for enzyme activity is temperature. In general, the reaction rate will increase with temperature (Fig. 1-14). From an Arrhenius type plot, the activation energy of the process may be calculated. With increasing temperature, however, the mobility of protein segments increases while the strength of hydro-... 

It is assumed that the limited proteolysis phenomenon derives from the fact that a specific polypeptide chain segment of the compact, folded protein substrate is exposed and flexible so that it can fit the active site of the appropriate peptidase for an efficient and selective limited hydrolysis. There is no doubt that enhanced chain flexibility or segment mobility is the key feature of the site of peptide bond hydrolysis demonstrated by a clear-cut correlation between sites of proteolytic attack and sites of enhanced chain flexibility. The present availability of automatic, efficient and sensitive techniques of protein sequencing and, particularly, the recent dramatic advances of mass spectrometry 361 in the analysis of peptides and proteins, allows a more systematic use of the limited proteolysis approach as a simple first step in the elucidation of structure-dynamics-function relationships for novel proteins which are only available in minute amounts. 

The structural analysis on KcsA was performed based on the mobility of each spin labeled side chain in the protein segments under investigation. It is worth recognizing in Pig. 4b that most of the CW RT spectra show multiple spectral components, characterized by different mobility (a few examples are highlighted by arrows). This is a very general property of the R1 side chain in proteins. The components reflect the anisotropy of the spin label reorientational motion, but their appearance could also have other causes. They could arise from a slow equilibrium between two different protein conformations or the presence of asymmetric sites in the protein. The molecular interpretation of different spectral components is cumbersome. Multifrequency EPR [17], temperature analysis of the CW spectra [27], pulse saturation recovery techniques [28], or high pressure EPR [29] can help unravel the possible origins of the spectral components. In the case of KcsA, the spin labels motional information was quantitatively extracted from the inverse central line width (A//q, mobility parameter) and was corroborated by the measure of the accessibility of the spin labeled side chains towards lipids (O2... 

The extent of segmental mobility also affects die modulated miisolropy (r ) data. The values of at low modulation frequency reflect the steady-state anisotropy and are thus lower for the proteins with higdio segmental flexibility. The transition of toward the hifdi-frequency value of ro occurs at higher frequency for proteins with greater flexibility. It is apparent from these data that the FD anisotropy data are highly sensitive to the form of the anisotropy decay and/or the dynamic properties of the proteiiis. 

Diffusion describes the random motion that transports matter from one part of a system at high concentration to another at low concentration. Mathematically, this process relates the mass-transfer rate of a substance through unit area to the concentration gradient normal to the section by a proportionality constant, D (cmVsec), also referred to as the diffusion coefficient (Crank, 1975). Factors that affect protein diffusion in polymers include properties that alter polymer chain segmental mobility (degree of crystallinity, chain stiffness, degree of cross-linking), deformations that alter the free volume, and factors that can immobilize or denature the protein (Rabek,1980). 

Rao, B., Kemple, M., and Prendergast, E, Proton nuclear magnetic resonance and fluorescence spectroscopic studies of segmental mobility in aequorin and green fluorescent protein, Photochem. Photobiol, 51, 92,1980. 

The 140-residue protein AS is able to form amyloid fibrils and as such is the main component of protein inclusions involved in Parkinson s disease. Full-length 13C/15N-labelled AS fibrils and AS reverse-labelled for two of the most abundant amino acids, K and V, were examined by homonuclear and heteronuclear 2D and 3D NMR.147 Two different types of fibrils display chemical shift differences of up to 13 ppm in the l5N dimension and up to 5 ppm for the backbone and side-chain 13C chemical shifts. Selection of regions with different mobility indicates the existence of monomers in the sample and allows the identification of mobile segments of the protein within the fibril in the presence of monomeric protein. At least 35 C-terminal residues are mobile and lack a defined secondary structure, whereas the N terminus is rigid starting from residue 22. In addition, temperature-dependent sensitivity enhancement is also noted for the AS fibrils due to both the CP efficiency and motional interference with proton decoupling.148... 

Structural domains of proteins are sometimes encoded by a single coding segment of DNA i.e., by a single exon in a split gene. Domains of this type may have served as evolutionarily mobile modules that have spread to new proteins and multiplied during evolution. For example, the immunoglobulin structural domain is found not only in antibodies but also in a variety of cell surface proteins.229 252... 

Together with proteins, phospholipids are the most important structural components of biological membranes. Since mobility of the lipid segments fa vors molecular transport through a membrane and thereby increases its permeability, a marked increase in 7] along a lipid-fatty acid chain also reflects a more efficient molecular diffusion through the lipid layer of a membrane [175]. 

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