Samples of STING Millennium application:


Fig_1.

Fig_2.

 

In figure 1 we show an artistic collage of snapshots of different modules of STING Millennium session that analyzed alpha-chymotrypsin complex with turkey ovomucoid third domain (1cho.pdb); We opted to present images and features accompanied by insets (A through F, in Fig 1 and A through D, in Fig 2) and general description of menu and features that a user can find behind each inset presentation:

Inset A_Fig_1.

Central image is structure of 1cho.pdb already carrying information from actions taken during analysis. Green ribbon is enzyme: chymotrypsin chain and white one is inhibitor: ovomucoid third domain. We have prepared this image by executing following STING Millennium commands/features: differential coloring of present structural chains, ribbon presentation [see QuickLearn Action menu example]; calculation of the interface forming residues (IFR) [see Interface on example] ; calculation and display of the IFR surfaces (gold surface belongs to IFR's of the E chain and cyan surface belongs to IFR's of I chain) [see QuickLearn Build Surface and Interface example]; selection of 8 residues from the E chain sequence (white background in sequence window) and subsequent presentation in wireframe + spacefill (ws) mode in 3D with CPK coloring of atoms [see mouse marking of contiguous sequence region example]; selection of a single amino acid and coloring it in red (red background in sequence window); calculating all neighbors (from a selected residue) included within a sphere of radius of 5 Å from/to Last Heavy Atom (LHA) in a side chain of each amino acid (color coded yellow both in structure and sequence window)[see QuickLearn Search Pattern and Search Neighbors example]; color coding in blue of I chain ribbon for all amino acid residues selected by Ramachandran plot (see inset D on Fig. 1)[see QuickLearn Ramachandran example].

Inset B_Fig_1.

Sequence and control window of STING Millennium : It displays linear protein and/or DNA sequence, color coded according to hydrophobicity and charged groups [see Sequence Color Coding]. The sequence window also shows the numbering of the residues in the sequence [see Residue Numbers], gaps in the PDB sequence [see Sequence Gaps in PDB file], a chain identifier [see Sequence Chains] and ranges for secondary structure elements [see Secondary Structure Regions]. Each residue in the sequence window is "clickable", resulting in a presentation of its position in the structure window (there are 9 colors to be chosen from [Residue Color option on control panel] and 7 different display options [menu bar left from Refresh button on control panel] : Wireframe, WS =Wireframe + Spacefill, CPK, Ribbon, Backbone, Strands and Cartoon) . Blue and Red lines below the sequence are also "clickable" resulting in graphical ribbon presentation of the specified sequence region (red lines indicate helical region and blue lines indicate extended sheets region). STING Millennium Status Frame [right from STING's icon (bee) on control panel] shows the residue/nucleotide number and chain identification any time a user slides the mouse over a residues/nucleotides on the sequence window or any time a user clicks the mouse over a certain atom in the structure window. In the sequence window, background of a residue single letter code changes color accordingly to the chosen: Residue Color. Selecting residues by clicking or sliding the mouse above the sequence will cause background color to change. White background residues (VPGSWPWQ) marked in the Sequence Window are displayed in a CPK color presentation in the Structure Window. Parity and easy localization in sequence and space coordinates is fully implemented in this way. STING Millennium Action menu displays STING script commands, the purpose of which is to perform a simple structure analysis: it color codes all charged residues or differentially colors all chains, selects and displays ligand, displays ligand and water molecules in vicinity of the ligand, selects and displays ligand pockets and finally, offers "copy to clipboard" command that facilitates transfer of STING Millennium image to adequate program for image manipulation (like PhotoShop etc.). STING Millennium Windows menu offers more complex commands: Interface chain, surface, search pattern, neighbors and send script. This last one makes possible direct issuing of Rasmol/Chime commands to Structure Window and is aimed to more experienced users.

Inset C_Fig_1.

PDB Cartoon is a image of the amino acid sequence along with the secondary structure elements rendered as cartoons. In this case user has chosen to see temperature factor (provided by PDB file), which is color coded as background of single letter amino acid code. Interesting off-spin of this presentation is usable information of how good is a PDB definition of secondary structure elements: residues R-230 and V-231 of chain E, are both in the helix and in the extended sheet (also seen in sequence window annotation). PDB Cartoon can show background amino acid single letter code to represent physico chemical characteristics (rather than temperature factor as in shown inset C on fig. 1) [see also QuickLearn Pdb Cartoon example].

Inset D_Fig_1.

Ramachandran plot is displaying the main-chain dihedral angles (Phy and Psi). In this inset, we have chosen to see only "I" chain angles. In addition, we have selected (blue color dots) one of allowed regions and then map them on 3D structure window (also blue colored ribbon) by using "Sting it!" button. Most of the chosen residues are forming helical structure. Blue colored amino acids in the Structure Window are also identified by blue background (chain I) in the Sequence Window [see also QuickLearn Ramachandran Plot example].

Inset E_Fig_1.

Contacts : This inset shows fan-like virtual contact lines coming out from residue Y-11 (this numbering counts for 3 missing amino acid residues at the very N terminal) of chain I and points to an amino acid that makes a particular contact (identified by the color of the line connecting it). Information about the distance, atom partners and the type of the contact is provided on context and if a particular residue is selected with the mouse, then a zoomed image is displayed in the Structure Window representing the contacting environment in detail. The histogram along sequence of the chain I, aids in rapid localization for critical residues, having larger than average number of contacts and also, buy color differentiation, having more energy-valuable contacts (like electrostatic interaction) [see also QuickLearn Graphical Contacts example].

Inset F_Fig_1.

Interface Forming Residues Contacts: this inset demonstrates the same sequence of the chain I, but now the user can see IFR as red underlined regions. Crucial difference from the inset E, is that here, contacts are counted only between residues belonging to the different chains. One can easily spot that chosen residue L-18 of chain I, makes number of different contacts with the E chain, while it makes no contact with residues of its own I chain (see inset E on Fig. 1)[see also QuickLearn IFR Contacts example] .

Inset G_Fig_1.

Consensus Sequence: One of the STING Millennium features is a capacity to extract valuable data from HSSP database and then represent them in a variety of usable ways, such as this at inset G. Here the user can quickly grasp how diversified is a sequence for the family of protease inhibitors that have high sequence homology. In this inset, the larger the letter the larger is conservation at that particular position in sequence. However, real valuable information comes from the displayed variation of amino acids that can occupy this position. For example, position 40 is occupied by glutamic acid (in inset B on Fig. 1, one can follow this sequence region as helical VVE, which is in the last row, left side). That very same position can also be occupied by aspartic acid, but most interestingly, it also shows that some inhibitors have "accepted" a mutation that replaced negatively charged residue with positively charged one: both arginine and lysine. Exact percentages for amino acid type that occupies specific position are available interactively from this module.

On figure 2 we present exceptionally useful features of STING Millennium: display of multiple structure alignment in 3D and also sequence alignment (presented in sequence window). The sequence alignment follows in this case structural alignment. Structure can then be color coded with respect to calculated sequence entropy which consequently offers to the user a visual tool for easy identification of spots exposed to the differential selective pressure.

Inset A_Fig_2.

In this inset we show structural superposition (done by using PRISM program) of two amylase enzymes: porcine pancreatic alpha-amylase (1dhk.pdb in yellow backbone) and maltotetraose-forming exo-amylase (1jdd.pdb in magenta backbone). Although two enzymes have extensive differences if total fold is compared, there are striking similarities inside the active site. We have marked differentially two sequence regions with very good 3D overlap and which are forming respective active sites. White backbone belongs to 1dhk.pdb and blue one belongs to 1jdd.pdb. [See also QuickLearn Modes example]

Inset B_Fig_2.

Sequence window here has a crucial difference from the one presented in Fig 1.; Namely, STING Millennium here presents two sequences in such an order so that they follow structural alignment. Top sequence is the one of 1dhk.pdb and the bottom one is of the 1jdd.pdb. Differentially marked background colors are following same logistics as previously described for Fig.1. A user can easily spot conservation along the marked sequences. [See also QuickLearn Modes example]

Inset C_Fig_2.

Scorpion is a program that provided graphs for this inset. We present here residue frequency for the whole molecule (1dhk.pdb on top and 1jdd.pdb on bottom graph). This information can be transformed in cumulative frequencies for hydrophobic, polar and charged groups (one click away from demonstrated graph). Differences in frequencies are visually much easier to analyze than otherwise. [See also QuickLearn Scorpion example]

Inset D_Fig_2.

Surfaces of two superimposed molecules are presented on this inset. Such presentation visually aids in analysis of the active site (V shaped opening on the top of the figure). Golden color surface belongs to 1dhk.pdb and cyan colored one is of the 1jdd.pdb. [See also QuickLearn Build Surface example]

NOTE: before closing this session, check-out how you can add even more details to this rich structural description produced exclusively by SMS by using appropriate data parsing {active SMS links}!