Chain tracing

A, B, and C, surrounded by a helices. The polypeptide chain is colored in sections from the N-terminus to facilitate following the chain tracing in the order green, blue, yellow, red and pink. The red region corresponds to the active site loop in the serpins which in ovalbumin is protruding like a handle out of the main body of the structure. (Adapted from R.W. Carrell et al.. Structure 2 257-270, 1994.)... 

There is a vast range of aqueous organic pollutants with a wide toxicity profile. Some, e.g. polychlorinated biphenyls, certain herbicides, fungicides and pesticides, and organo-mercury compounds, are persistent and may bioaccumulate in the food chain. Trace contaminants such as sodium chloride, iron and phenols (especially if chlorinated) may also impart a taste to water. Typical consent levels for industrial discharges are provided in Table 13.10. 

There are also some general rules of thumb that can be used to guess at error levels in unrefined and lower resolution structures. A first fundamental problem is to judge when there might be mistakes in the chain tracing that involve incorrect connectivity of the backbone. In a survey of 47 independent chain tracings of novel proteins which have been either confirmed or disconfirmed by further... 

Kim, Y, Grable, J. C., Love, R., Greene, P. J. and Rosenberg, J. M. (1990). Refinement of EcoRl endonuclease crystal structure a revised protein chain tracing. Science 249, 1307-1309. 

In early 1990 it became apparent that the structure of galactose oxidase from Dactylium dendroides was about to emerge. A 2.5 A multiple isomor-phous replacement (MIR) map based on area detector data from a native and three derivative crystals yielded a polypeptide chain tracing. The refined structure at 1.9 A (R = 0.179) (Ito et al., 1991) shows that galactose oxidase consists of three domains, each of which is predominandy jS... 

The 2.3 A structure of the achromobacter NIR (Godden et al., 1991) has been determined from an MIR map based on native and two derivative data sets collected on an area detector. In the crystal the tightly packed arrangement of monomers around the crystallographic threefold axis suggests that the molecule must be a trimer, rather than a dimer, as originally determined from gel filtration studies. The chain tracing substantiates this. 

The dimensions of the xylan unit cell are slightly different a = b = 1.340 nm, (fibre axis) = 0.598 nm.) Atkins and Parker T6) were able to interpret such a diffraction pattern in terms of a triple-stranded structure. Three chains, of the same polarity, intertwine about a common axis to form a triple-strand molecular rope. The individual polysaccharide chains trace out a helix with six saccharide units per turn and are related to their neighbours by azimuthal rotations of 2ir/3 and 4ir/3 respectively, with zero relative translation. A similar model for curdlan is illustrated in Figure 6. Examinations of this model shows that each chain repeats at a distance 3 x 0.582 = 1.746 nm. Thus if for any reason the precise symmetrical arrangement between chains (or with their associated water of crystallization) is disrupted, we would expect reflections to occur on layer lines which are orders of 1.746 nm. Indeed such additional reflections have been observed via patterns obtained from specimens at different relative humidity (4) offering confirmation for the triple-stranded model. 

Fig. 1. a Matrix of distances and angles corresponding to the five strands and one helix in the RT connection domain (illustrated in Fig. 1 b(i)). This is a subset of the actual matrix used in the search which consisted of 10 helices and 16 strands from the RT p51 domain, b Chain traces (produced with Molscript [80]) of (i) the RNaseH domain of RT (ii) the connection domain of RT and (iii) the la domain of actin. The helices and strands equivalenced in our study are represented as coiled ribbons and sequentially numbered arrows respectively the non-equivalent parts of the structure are shown as a smoothed C-alpha trace... 

F. Eisen me tiger, P. Algos, and R. Abagytn. A method to configure protein side-chains Doom the main-chain trace in homology modeling. A MoL Btoi. 2/3 849-860... 

Fig. 9. Chain trace of one subunit of glutathione reductase. Stereo drawing from the work of Schulz and...

Fig. 15. Chain trace of E.coli dihydrofolate reductase. Bound inhibitor (meihoirexaie) is also shown, with nitrogen (black) and oxygen (shading) atoms indicated. Stereo drawing from the work of Kraut and colleagues [68]. 

Fig, 17. Chain trace of sheep liver 6-phosphogluconatc dehydrogenase subunit based on the work of Adams and colleagues [71], The NADP + binding region is indicated. 

Fig. 18. Chain trace (centre) of a subunit of dogfish muscle lactate dehydrogenase. Diagrammatic representations (corners) show constituent parts of the structure, and their relationship to the bound coenzyme. From the work of Rossmann and colleagues [79],...

Fig. 20. Chain trace of pig heart soluble malate dehydrogenase subunit. Stereo drawing from lhe work of... 

Fig. 25. Chain trace of one subunit of horse liver alcohol dehydrogenase. Stereo drawing from the work of Branden and colleagues [117], The catalytic zinc atom is central, the structural zinc atom is at the bottom right.

Fig. 8. The main-chain trace of P2, displayed with its binding cavity containing all of the main-chain atoms of P2 as well as a shaded representation of the internal cavity, which was calculated according to the algorithm of Levitt and Banaszak (1992) using a 1-A grid. The shaded cavity represents the volume available to ligand atoms, not the total volume. See the text for details.

Figure 3, Top DOCK3 complex of compound 1 in (a) front and (b) top views. For clarity, only the a-carbon chain trace of HIVP is shown.

Interpretation of the electron density map allowed the chain tracing for most parts of the polypeptide chain. Refinement has been carried out using X-PLOR and REFMAC, and manual model rebuilding resulted in an R-factor of 22.4% for all 2a data between 10.0 and 2.8 A resolution. Using a 5% reflection test set (1,380 reflections) the free R-factor [2] value is 29.0%. 

Difference maps phased with simulated annealing refined structures often show more details of the correct chain trace [23]. However, the omission of some atoms from the computation of a difference map does not fully remove phase bias towards those atoms if... 

Once a first electron-density map is obtained, it is interpreted by the crystallographer. In the case of a MIR(AS) map, a complete model of the protein has to be fitted to the electron density. The Ca atoms are placed first (chain tracing), and subsequently the complete main chain and the side chains are built, a process which has become more and more automated in recent years, notably when high resolution data are available. In the case of molecular replacement, the search model needs to be updated to reflect the molecule present in the crystal. The model is usually of a similar protein and the changes involve the substitution of some amino acids, the introduction of insertions and deletions, the modification of some loops, and so on. 

This process is similar to the decision making crystallographers use to interpret electron density maps main-chain tracing followed by side-chain modeling. The used techniques take many of the constraints and criteria into account that a crystallographer would apply, and the created model can be refined by a crystallographer. 

For structures not determined by molecular replacement, the chemical sequence of the protein must be fit into the experimental electron density map (Figure 2.7). This is called model building or chain tracing. As one would expect, the success or failure of chain tracing is dependent upon the quality of the electron density map. Thus, map quality evaluation is very important before one attempts to trace the chain. Good (traceable) electron maps should display most of the following features. 

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