MOLSCRIPT

Figure 9 Relative accuracy of comparative models. Upper left panel, comparison of homologous structures that share 40% sequence identity. Upper right panel, conformations of ileal lipid-binding protein that satisfy the NMR restraints set equally well. Lower left panel, comparison of two independently determined X-ray structures of interleukin 1(3. Lower right panel, comparison of the X-ray and NMR structures of erabutoxin. The figure was prepared using the program MOLSCRIPT [236].

Figure 10 Models of complexes between BLBP and two different fatty acids. The fatty acid ligand IS shown in the CPK representation. The small spheres in the ligand-bmdmg cavity are water molecules, (a) Model of the BLBP-oleic acid complex, in which the cavity is not filled, (b) Model of the BLBP-docosahexaenoic acid complex, m which the cavity is filled. The figure was prepared using the program MOLSCRIPT [236].

P Krauhs. MOLSCRIPT A program to produce both detailed and schematic plots of protein structure. J Appl Crystallogr 24 946-950, 1991. 

Molscript A program for displaying molecular 3D structures in both schematic and detailed representations, http //www.avatar.se/molscript/. 

Fig. 2. The structure of the Fe protein (Av2) from Azotobacter vinelandii, after Geor-giadis et al. (1). The dimeric polypeptide is depicted by a ribbon diagram and the Fe4S4 cluster and ADP by space-filling models (MOLSCRIPT (196)). The Fe4S4 cluster is at the top of the molecule, bound equally to the two identical subunits, Emd the ADP molecule spans the interface between the subunits with MoO apparently binding in place of the terminal phosphate of ATP.

Fig. 3. The tetrameric structure of the MoFe protein (Kpl) from Klebsiella pneumoniae (7). The two FeMoco clusters and the P clusters are depicted by space-filling models and the polypeptides by ribbons diagrams (MOLSCRIPT (196)). The FeMoco clusters are bound only to the a subunits, whereas the P clusters span the interface of the a and j8 subunits.

Fig. 10. The putative transition-state complex formed between the Fe protein MgADP AlFj and the MoFe protein. For simplicity only one a/3 pair of subunits of the MoFe protein is shown. The polypeptides are indicated by ribbon diagrams and the metal-sulfur clusters and MgADP AlFi" by space-filling models (MOLSCRIPT (196)). The figure indicates the spatial relationship between the metal-sulfur clusters of the two proteins in the complex.

Kraulis PJ. MOLSCRIPT A Program to Produce Both Detailed and Schematic Plots of Protein Structures. J Appl Crystallogr 1991 24 946-950. 

Fig. 4. Backscattered Raman and ROA spectra of the n-helical protein human serum albumin in H20 (top pair) and the /3-sheet protein jack bean concanavalin A in acetate buffer solution at pH 5.4, together with MOLSCRIPT diagrams (Kraulis, 1991) of their X-ray crystal structures (PDB codes lao6 and 2cna). 

Fig. 5. Backscattered Raman and ROA spectra of native (top pair) and reduced (second pair) hen lysozyme, and of native (third pair) and reduced (bottom pair) bovine ri-bonuclease A, together with MOLSCRIPT diagrams of the crystal structures (PDB codes llse and lrbx) showing the native disulfide links. The native proteins were in acetate buffer at pH 5.4 and the reduced proteins in citrate buffer at pH 2.4. The spectra were recorded at 20°C. 

The ROA spectra of native and prehbrillar amyloidogenic human lysozyme are displayed in Figure 7, together with a MOLSCRIPT diagram of the native structure. The ROA spectrum of the native protein is very similar to that of hen lysozyme (Fig. 5). However, large changes have occurred in the ROA spectrum of the prehbrillar intermediate. In particular, the positive 1340 cm-1 ROA band assigned to hydrated... 

Fig. 7. Backscattered Raman and ROA spectra of native human lysozyme in acetate buffer at pH 5.4 measured at 20°C (top pair), and of the prehbrillar intermediate in glycine buffer at pH 2.0 measured at 57°C (bottom pair), together with a MOLSCRIPT diagram of the crystal structure (PDB code ljsf) showing the tryptophans. 

Fig. 1. Cartoon of seven-residue alanine peptide in the PPII helical conformation. (A) Viewed along the long axis (B) viewed down the long axis. Figure generated using MOLSCRIPT (Kraulis, 1991). 

Fig. 4. The molecular structure, determined by solution NMR (James et al., 1997), of Syrian hamster 90-231 (SHa90-231) prion with ball-and-stick representation of the HI domain (SHal09-122 MKHMAGAAAAGAW). Note that two short /(-chains (SI, S2) nearly stack in the hydrogen-bonding direction. If the palindromic polyalanine region was also in a /(-conformation, there would be a three-stranded /(-sheet. The structural difference between PrPc and PrPSc is in the 90-145 domain. [Model drawn using MOLSCRIPT (Kraulis, 1991)].

Fig. 2. Examples of the structures of protein domains and repeats. The images were generated using Molscript (Kraulis, 1991). (A) Immunoglobulin domain (PDB identifier ltlk) (Holden et al1992), (B) A zinc finger domain with coordinated zinc ion (PDB identifienlzaa) (Pavletich and Pabo, 1991). (C) A /3-propeller domain composed of seven WD40 repeats (PDB identifier lgp2) (Wall et al., 1995), (D) An elongated domain of variant leucine-rich repeats (PDB identifienllrv) (Peters et al., 1996).

Fig. 1. Structure of the OB-fold domain. The anticodon-binding domain of the E. coli lysyl-tRNA synthetase (pdb code lkrs) is shown as a prototype of single-stranded nucleic acid-binding OB-folds. The model was drawn using the Molscript v2.1 program...

Fig. 3. The X-ray crystal structure of the oxidized state of c3itochrome cdi nitrite reductase from P. pantotrophus (drawn from PDB entry 1 qks using MolScript 98, 99)).

Fig. 1.6. The Zn binding motif of the glncocorticoid receptor in complex with DNA. Shown is the complex of the dimeric DNA-binding domain of the glncocorticoid receptor with the cognate DNA element (Luisi et al., 1991). The Zn ions are shown as spheres. The two Zn ions are clearly non-eqnivalent. While one of the Zn ions aids in the fixation of the recognition helix in the major groove, the other correctly positions a strnctnral element for the dimerization of the monomers. MOLSCRIPT drawing (Kranhs, 1991).

Fig. 1.7. Basic leudne zipper and heltx-loop-heltx motif in complex with DNA. A) The basic leucine zipper of the transcription activator GCN4 of yeast consists of two slightly curved a-hehces, which dimerize with the help of the leucine zipper motif. The sequence specific binding of DNA occurs via the basic ends of the two helices. They insert themselves into the major groove of the DNA. B) The helix-loop-helix motif of the eucaryotic transcription factor Max complexed with DNA. Molscript drawing (Kraulis 1991).

Fig. 1.9. DNA-binding via P-pleated sheets. The repressor MetJ (E. coli) com-plexed with the half-site of its operator sequence. The binding occurs via two parallel P-sheets in the major groove of the DNA. Molscript drawing (Kraulis 1991).

Fig. 1.16. Bending of DNA in the TATA box. The DNA is kinked in the complex of the TATA box binding protein (yeast) with the 8 base pair TATA box (Kim et al., 1993). The DNA is deformed in the region near the kink the minor groove, which faces the protein, is clearly widened. Molscript drawing (Kraulis, 1991).

Fig. 4.9. Structure of the RXR-T3R heterodimer in complex with DNA. Illustrated is a complex between the DNA-binding domain of the RXR-T3R heterodimer and an HRE with direct repeats of the sequence AGGTCA separated by 4 bp. The two receptor subunits contact the hexameric sequences with a recognition hehx in a manner very similar to that of the glnccocorticoid receptor (see Fig. 4.7). The Zn atoms are drawn as spheres. The figure illustrates the polarity of the binding of the two subunits. The interaction between the two snbnnits is mediated mainly via an extension of the C-terminal DNA-binding domain of the TjR. A greater or smaller distance between the two hexamers of the HRE would act contrary to the interaction between the two subunits as shown. MOLSCRIPT drawing (Kraulis, 1991).

Molscript stereo figure of the three-dimensional structure of the catalytic core of HIV-1 integrase. The two catalytically essential aspartic acid residues (D64 and D116) visible in the x-ray structure are highlighted. 

Molscript stereo figure of the structure of the nonspecific DNA-binding domain of HIV-1 integrase, in220-270, determined by heteronuclear NMR spectroscopy [28]. 

Ca trace of the ALR2 holoenzyme looking down the (( )8 barrel. The NADPH cofactor is seen bound across the carboxy-terminal end of the (3-barrel with the active nicotinamide moiety in the center. Figure produced using the MOLSCRIPT... 

Schematic stereo view of the three-dimensional structure of COMT. The ligands bound to COMT are the methyl-donating coenzyme AdoMet and the magnesium ion. Figures 5-7 and 13 were produced using the program MOLSCRIPT [50].

Functional residues of IL-1(3, identified by the site-directed mutagenesis results. Produced by Molscript [106]. 

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