Root mean square deviation structures

Example Crippen and Snow reported their success in developing a simplified potential for protein folding. In their model, single points represent amino acids. For the avian pancreatic polypeptide, the native structure is not at a potential minimum. However, a global search found that the most stable potential minimum had only a 1.8 Angstrom root-mean-square deviation from the native structure. 

In order to examine whether this sequence gave a fold similar to the template, the corresponding peptide was synthesized and its structure experimentally determined by NMR methods. The result is shown in Figure 17.15 and compared to the design target whose main chain conformation is identical to that of the Zif 268 template. The folds are remarkably similar even though there are some differences in the loop region between the two p strands. The core of the molecule, which comprises seven hydrophobic side chains, is well-ordered whereas the termini are disordered. The root mean square deviation of the main chain atoms are 2.0 A for residues 3 to 26 and 1.0 A for residues 8 to 26. 

Figure 3. A comparison of the aC backbone of PelC with PelE. The aCs which superimpose within a root-mean-square deviation of 1.5 A are shown in black and those, within 3.0 A are shown in dark gray. The remaining backbone regions are shown in light The largest structural differences occur in the loops capping one end of the parallel p as well as in those comprising the putative substrate binding groove.

Figure 2-4. Comparison of optimized and X-ray structures for the active site of RNR. The X-ray structure of R2met is superimposed on the optimized structures from active-site QM-only (left) and ONIOM2 0middle) models. The plot shows the quality of the optimizations evaluated as the root-mean-square deviations (in A) compared to the X-ray structures of RNR and MMO (right). (Adapted from Torrent et al. [24]. Reprinted with permission. Copyright 2002 Wiley Periodicals, Inc.)...

In all the studied systems addition of the surrounding protein in an ONIOM model clearly improves the calculated active-site geometries. This is clearly illustrated in Figure 2-13, which shows the root-mean-square deviation between calculated and experimental structures for four of the studied enzymes. 

From a structural point of view the OPLS results for liquids have also shown to be in accord with available experimental data, including vibrational spectroscopy and diffraction data on, for Instance, formamide, dimethylformamide, methanol, ethanol, 1-propanol, 2-methyl-2-propanol, methane, ethane and neopentane. The hydrogen bonding in alcohols, thiols and amides is well represented by the OPLS potential functions. The average root-mean-square deviation from the X-ray structures of the crystals for four cyclic hexapeptides and a cyclic pentapeptide optimized with the OPLS/AMBER model, was only 0.17 A for the atomic positions and 3% for the unit cell volumes. 

Moreover, the objective function obtained by minimizing the square of the difference between the mole fractions calculated by UNIQUAC model and the experimental data. Furthermore, he UNIQUAC structural parameters r and q were carried out from group contribution data that has been previously reported [14-15], The values of r and q used in the UNIQUAC equation are presented in table 4. The goodness of fit, between the observed and calculated mole fractions, was calculated in terms RMSD [1], The RMSD values were calculated according to the equation of percentage root mean square deviations (RMSD%) ... 

Structural biology provides a final way to define an E2 enzyme. As expected from the strong sequence conservation, the E2 core domain adopts a conserved fold. At the time this article was being prepared, twelve different E2 structures had been deposited in the Protein Data Bank. The average root-mean-square deviation of... 

The sequence conservation is reflected in a highly conserved secondary and tertiary structure that is most clearly illustrated in the three-dimensional superposition of C atoms. Ignoring the C-terminal domains of PVC and HPII, the deviation of C atoms in a superposition of HPII with PVC, BLC, PMC, and MLC results in root mean square deviations of 1.1,1.5,1.6, and 1.5 A for 525, 477, 471, and 465 eqiuvalent centers, respectively (83). In other words, there is very little difference in the tertiary structure of the subunits over almost the complete length of the protein. The large and small subunits are shown in Fig. 8 for comparison. 

In large subunit enzymes (PVC and HPII), a short segment of about 30 residues links the a-helical domain to the C-terminal domain (Fig. 8). The latter segment is a conspicuous addition to the small subunit containing about 150 residues folded into a structure that resembles flavodoxin. For example, there is a root mean square deviation of 3.0 A between flavodoxin and approximately 100 residues of the C-terminal domains of either HPII or PVC. This can be compared to the 1.8 A root mean square deviation for 134 centers between the C-terminal domains of HPII and PVC. Unlike the N-terminal end, the final C-terminal residue Ala753 is visible in the structure of HPII. The C-terminal domain contains extensive secondary structure in the form of four a-helices (al5-18) and eight fi-strands (fi9-16). Despite the obvious structural similarity to flavodoxin, there is no evidence of nucleotide binding in the domain and its function remains a mystery. 

Crane et al. first established the three-dimensional fold of NOS by solving the structure of a monomeric form of the mouse iNOS heme domain (78). This version of iNOS was missing the first 114 residues, which are known to be critical for dimer formation and activity (79). The monomer structure was soon followed by the dimeric heme domain structures of mouse iNOS (80), bovine eNOS (81), and the human isoforms of iNOS (82, 83) and eNOS (82). A comparison of eNOS and iNOS reveals that the structures are essentially the same with an overall root-mean-square deviation in backbone atoms of 1.1 A (S3). The sequence identity between human iNOS and bovine eNOS is 60% for 420 residues compared in the crystal structures (83). 

A notable feature of the HO-1 distal helix is its flexibility. The HO-1 crystal form used for solving the structure has two molecules in the asymmetric imit, which provides two independent views of the HO-1 structure. As shown in Fig. 19, a plot of the rms (root-mean-square) deviation in backbone atoms between molecules A and B in the as5un-metric imit reveals a large deviation in the distal helix as well as in the loop immediately following the distal helix. In addition, the distal... 

The rule of thumb for a successful application of molecular replacement is that the model should have a root-mean-square deviation (RMSD) on C-alpha coordinates 2.0-2.5 Angstroms with the target structure, corresponding to a sequence identity with the target of 25-35%. In practice, however, there are many more structures solved by MR in the PDB using models with sequence identity of 60% or higher than otherwise. 

One of the simplest methods is the comparison of the initial structure of the macromolecule to that throughout the trajectory via a distance measure such as the root mean square deviation (RMSD). This method is most informative for a system like a folded protein under native conditions, where the molecule is expected to spend the vast majority of the time in conformations quite similar to the crystal structure. If one computes the RMSD time series against the crystal structure, one expects to see a rapid rise due to thermal fluctuations, followed by a long plateau or fluctuations about a mean at longer timescales. If the RMSD... 

P-hydroxysteroid dehydrogenase, the root mean square deviation for the two tertiary structures is 2 A over 160 Ca carbon atoms. 

An important question is What is the relationship between percent sequence identity and similarity of tertiary structure This depends on the length of the protein the longer the protein, the lower the percent identity that implies identical structure. For a protein of 85 residues, a 25 to 30% sequence identity implies an identical three-dimensional structure. The more the percent identity of structure, the smaller the root mean square deviation of the coordinates of the two structures34 (Figure 1.21). 

Root mean square) deviation from a reference structure (what is the ligand binding mode compared with other [homologous] ligands ) ... 

Figure 2 shows the initial equilibrated intercalated state. The DNA sequence is d(GCGCACGTGCGC)2- The intercalated structure s geometry is that of the B-DNA except for the 5th to 7th base pairs (A5 to G7), which stay close to the crystal structure used for the starting conformation, with a root mean square deviation of 3.2 A for all the heavy atoms of those three basepairs. In this sequence, daunomycin is in contact with the strongest binding triplet sequence (A/T)CG [18,19]. Moreover, due to the chosen sequence of the DNA, the intercalation site is flanked by the same sequence of base-pairs in either direction, eliminating any related orientational preference of... 

The crystal structures of the E. coli DHFR-methotrexate binary complex (Bolin et al., 1982), of the Lactobacillus casei (DHFR-NADPH-methotrexate ternary complex (Filman et al., 1982), of the human DHFR-folate binary complex (Oefner et al., 1988), and of the mouse (DHFR-NADPH-trimethoprim tertiary complex (Stammers et al., 1987) have been resolved at a resolution of 2 A or better. The crystal structures of the mouse DHFR-NADPH-methotrexate (Stammers et al., 1987) and the avian DHFR—phenyltriazine (Volz et al., 1982) complexes were determined at resolutions of 2.5 and 2.9 A, respectively. Recently, the crystal structure of the E. coli DHFR—NADP + binary and DHFR-NADP+-folate tertiary complexes were resolved at resolutions of 2.4 and 2.5 A, respectively (Bystroff et al., 1990). DHFR is therefore the first dehydrogenase system for which so many structures of different complexes have been resolved. Despite less than 30% homology between the amino acid sequences of the E. coli and the L. casei enzymes, the two backbone structures are similar. When the coordinates of 142 a-carbon atoms (out of 159) of E. coli DHFR are matched to equivalent carbons of the L. casei enzyme, the root-mean-square deviation is only 1.07 A (Bolin et al., 1982). Not only are the three-dimensional structures of DHFRs from different sources similar, but, as we shall see later, the overall kinetic schemes for E. coli (Fierke et al., 1987), L. casei (Andrews et al., 1989), and mouse (Thillet et al., 1990) DHFRs have been determined and are also similar. That the structural properties of DHFRs from different sources are very similar, in spite of the considerable differences in their sequences, suggests that in the absence, so far, of structural information for ADHFR it is possible to assume, at least as a first approximation, that the a-carbon chain of the halophilic enzyme will not deviate considerably from those of the nonhalophilic ones. 

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