,

Faculty of Biomedical Engineering

BME310
2023-2024

Experiment #1:
Dali Protein Structure Comparison

Name Surname
Can Mungan
Student ID
20160612031
 1. Introduction
Dali is a website that compares protein structures and evaluates how close
the provided protein structures are to one another structurally. Through analysis,
evolutionary links that are not visible through sequence comparison can be discovered.
 PDB Search: Examines a protein structure in the Protein Data Bank (PDB)
against entries.
 Pairwise comparison: Compares one protein structure under consideration to
user-specified structures.
 For a user-defined set of structures, the All Against All Comparison provides a
structural similarity dendrogram.
3D coordinates for protein structures are required as input. Get a list of
comparable structures and structural alignments as the output. A structural dendrogram
and a projection in protein structure space are also included for "all against all"
comparison.
2. Materials & Methods
We are using the DALI tool to look into protein similarities in our bioinformatics
course, with an emphasis on amidohydrolase superfamily proteins including urease,
adenosine deaminase, and phosphotriesterase.
I. Inputs
Only ATOM records are required for Dali, and the PDB format is
keyword-based. Amino acid sequences are not accepted as input by the
Dali server. PDB entries are recognized by a four-character code that
consists of a digit, three letters or digits, and a digit, such as "3ubp." On
the RCSB website, you may find PDB entries that correspond to particular
keywords. A single character serves as the chain identification for each
entry, which may contain one or more chains. To give one example, the
PDB entry "3ubp" has three chains: A, B, and C. The chain identification
and PDB code must be combined in submission forms, for example,
"3ubpC." The PDB search submission form suggests potential
continuations after the PDB code is entered.
II. Output
The amidohydrolase superfamily is used as an illustration
throughout this course. The initial observation of structural similarities
between urease, adenosine deaminase, and phosphotriesterase served
as the foundation for the amidohydrolase superfamily discovery.
 From the home page, select the "Pairwise" tab to access the
submission form for pairwise comparison.
 In the box for the initial protein structure, type 4xd3A.
  To create two input fields for second structures, press the + button
twice.
 Fill out the boxes for the second protein structures with 3ubpC and
1a4mA.
 Click "Submit."

3. Results
3D superimposition.
The chosen structures are displayed in 3D superimposition over the query structure.
The display styles are adjustable.
1. Verify the values for 3ubpC and 1a4mA on your summary page, then click "3D
Superimposition (PV)".
2. Side chains and many C-alpha traces should appear as spaghetti. Select "Cartoon"
from the radio buttons. When you uncheck "All" and select "Query" in the Show/Hide
Structures menu, a green cartoon of the query protein should appear.
3. For Query color, click "Structure conservation". In all three structures, sections in dark
blue are structurally aligned. Rotate the construction by moving the cursor in the viewer
area while holding down the left mouse button. To zoom in or out, move the cursor up or
down while holding down the middle button.
4. Change the Query color to "Sequence conservation" and select "Query" under the
Show/Hide Side Chains choices.
5. Eliminate less conserved side chains to organize the jumbled picture. Slide the ruler
to the left under "Query side chains > 0 bits" until it reads 4.15 bits. The active site's
conserved residues are now highlighted. To view labels with residue numbers for the
side chains, click on them.
6. Select Show/Hide Ligands from the menu. To view atoms' labels, click on them.
Colors on the query structure can be used to show sequence and structural
conservation. The conservation color map runs from blue (highest values) to green
(middle values), and finally red (lowest values). Colors on the query structure can be
used to show sequence and structural conservation. The conservation color map runs
from blue (highest values) to green (middle values), and finally red (lowest values).
The percentage of chosen structures that match the query structure is known as the
structure conservation ratio.
The Following Application
The knowledge gained from studying protein similarity within the amidohydrolase
superfamily might then be used to direct efforts towards protein engineering or
medication discovery, as the next application. For instance, identifying structural
similarities between these proteins may help in the development of specific medications
or in optimizing the functionality of enzymes for diverse industrial applications.
4. Discussion
Chain 1: 3ubp-C
Z-score: 14.3
RMSD: 3.3 Ångstroms
Aligned Length (lali): 213
Number of Residues (nres): 570
Percentage Identity (%id): 15%
Chain 2: 1a4m-A
Z-score: 14.2
RMSD: 3.8 Ångstroms
Aligned Length (lali): 227
Number of Residues (nres): 349
Percentage Identity (%id): 12%
In the comparison between these two chains:
Z-score: The Z-scores for the two comparisons (14.3 for 3ubp-C and 14.2 for 1a4m-A)
are both extremely high. This suggests that both structural alignments have a crucial
role.
RMSD: The average distance between the atoms of the stacked proteins is measured
by the Root Mean Square Deviation (RMSD). In general, a smaller RMSD denotes a
more precise structural alignment. Compared to 1a4m-A in this instance, 3ubp-C has a
somewhat smaller RMSD (3.3 ngstroms).
Aligned Length: The number of residues that could be structurally aligned in a protein is
represented by the aligned length. Compared to 1a4m-A, which has 227 aligned
residues, 3ubp-C has 213 aligned residues.
1a4m-A has 349 residues, whereas 3ubp-C has a total of 570 residues.
Identity as a percentage: When compared to 1a4m-A (12%), 3ubp-C has a higher
identity as a percentage (15%). The percentage of aligned residues that are the same
between the compared proteins is shown by percentage identity.
In conclusion, despite aligning fewer residues, both comparisons (3ubp-C vs. 1a4m-A)
demonstrate strong structural similarity, with 3ubp-C having a somewhat lower RMSD
and a greater % identity. Although both alignments are statistically significant, the high
Z-scores for both comparisons suggest that the proteins have a lot in common
structurally.
According to the pairwise Dali-alignment to 4xd3A, each neighbor is displayed. When a
gap is expanded, the entire sequence of the matched proteins is displayed. (If there are
numerous, unsightly, or lengthy gaps, you can hide them by unchecking the 'Expand
gaps' checkbox on the summary page.) Uppercase locations with 4xd3A are identical
architecturally. Insertions in lowercase refer to 4xd3A. The amino acid sequences of the
chosen neighbors are displayed in the first section. The secondary structural
assignments made by DSSP are displayed in the second section (helix/helix,
strand/strand, coil/coil). Each column's most prevalent amino acid type is highlighted in
color.

5. Conclusion
The Dali server offers quick and convenient access to summaries of particular
regions within structure and sequence space, making it a useful tool for structural
classification. It is easily capable of producing comparable stories for any clearly
specified structural superfamily.
6. Reference
I. http://ekhidna2.biocenter.helsinki.fi/dali/
II. https://www.rcsb.org/structure/3UBP
III. http://ekhidna2.biocenter.helsinki.fi/barcosel/tmp//Wz5uuc_6_r_//
4xd3A.html
IV. https://pubmed.ncbi.nlm.nih.gov/32006276/
V. https://link.springer.com/protocol/10.1007/978-1-0716-0270-6_3