Protein chain, atomic resolution

To put the errors in comparative models into perspective, we list the differences among strucmres of the same protein that have been detennined experimentally (Fig. 9). The 1 A accuracy of main chain atom positions corresponds to X-ray structures defined at a low resolution of about 2.5 A and with an / -factor of about 25% [192], as well as to medium resolution NMR structures determined from 10 interproton distance restraints per residue [193]. Similarly, differences between the highly refined X-ray and NMR structures of the same protein also tend to be about 1 A [193]. Changes in the environment... 

Figure 18.11 Electron-density maps at different resolution show more detail at higher resolution, (a) At low resolution (5.0 A) individual groups of atoms are not resolved, and only the rodlike feature of an

Once an electron density map has become available, atoms may be fitted into the map by means of computer graphics to give an initial structural model of the protein. The quality of the electron density map and structural model may be improved through iterative structural refinement but will ultimately be limited by the resolution of the diffraction data. At low resolution, electron density maps have very few detailed features (Fig. 6), and tracing the protein chain can be rather difficult without some knowledge of the protein structure. At better than 3.0 A resolution, amino acid side chains can be recognized with the help of protein sequence information, while at better than 2.5 A resolution solvent molecules can be observed and added to the structural model with some confidence. As the resolution improves to better than 2.0 A resolution, fitting of individual atoms may be possible, and most of the... 

In all tRNAs the bases can be paired to form "clover-leaf" structures with three hairpin loops and sometimes a fourth as is indicated in Fig. 5-30.329 331 This structure can be folded into the L-shape shown in Fig. 5-31. The structure of a phenylalanine-carrying tRNA of yeast, the first tRNA whose structure was determined to atomic resolution by X-ray diffraction, is shown.170/332 334 An aspartic acid-specific tRNA from yeast,335 and an E. coli chain-initiating tRNA, which places N-formyl-methionine into the N-terminal position of proteins,336,337 have similar structures. These molecules are irregular bodies as complex in conformation as globular proteins. Numerous NMR studies show that the basic... 

Fig. 5.1 The protein chain in atomic resolution. The chain consists of quasi-planar (nearly rigid) peptide bonds -NH-CO- connected by the C atoms. Each Ca atom has additionally the CH and CR bond, where R is the aminoacid side chain (one of the twenty used by nature). The figure shows also the 4>, / angles (corresponding to a single amino acid). The conformation of the whole chain is determined by a set of , x(/, angles, where i means the z th amino acid...

At the present time, when the structure of the proton pumping protein and the membrane s surface can be gained at atomic resolution, when the dissociation of a proton can be recorded with sub-nanosecond resolution and molecular dynamics can be extended to tens of nanoseconds, it seems that a combination of these methods will be required to elucidate the mechanism of the reaction. Thus, combination of specific labeling of sites of interest by a photoacid or indicator, coupled with time-resolved measurements and molecular dynamics of the reaction, will be the next step in the research. Once these combined experiments are available, the generalization of the process, like the role of local electrostatic potential, orientation of water and the relative motion of side-chains, will be quantitated, with a subsequent improvement in the theoretical predicting power. 

Proteins are much more mobile than one would expect by looking at all the very rigid structures stored in the PDB. The development, in recent years, of new crystallization methods and the availability of increasingly intense synchrotron x-ray beams are rapidly increasing the number of structures that can be solved at real atomic resolution (better than 1.2 A). We see a large number of cases in these very high-resolution structures where atoms, side chains, residues, or even whole loops occupy multiple positions. Although this has not been really been proven, it seems a safe assumption that such alternate states are in a dynamic equilibrium. The fact that they are often seen in atomic resolution structures means that they are undoubtedly also present, but are undetectable, in all structures solved at lower resolution [36],... 

Ban et al. [26] used X-ray crystallography in a recent study to determine the crystal structure (i.e., to obtain a 2.4-A atomic resolution map) of the SOS ribosomal subunit from H. marismortui. They found that the subunit includes almost all of the entire chain of 23S rRNA (2711 out of 2923 nucleotides) and SS rRNA (aU 122 nucleotides) as well as 27 of its 31 proteins. 

Fourier synthesis, as shown by the optical analogy in Figure 4.54. A resolution of 6 A reveals the course of the polypeptide chain but few other structural details. The reason is that polypeptide chains pack together so that their centers are between 5 A and 10 A apart. Maps at higher resolution are needed to delineate groups of atoms, which lie between 2.8 A and 4.0 A apart, and individual atoms, which are between 1.0 A and 1.5 A apart. The ultimate resolution of an x-ray analysis is determined by the degree of perfection of the crystal. For proteins, this limiting resolution is usually about 2 A. 

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